Author Luisa Montecchi Palazzi luisa@ebi.ac.uk psi-mi.lastac. The last accession number used in this file is stored in a separate file, It MUST be updated when this file is updated. 2006-12-22T12:25:00 $Id: psi-mi.obo,v 1.118 2007/03/14 04:38:46 girlwithglasses Exp $ PSI-MI To facilitate handling, they all have been merged in this file, though they The PSI MI schema defines short labels for controlled vocabulary terms. This file is published by the PSI MI working group see http://psidev.sourceforge.net/ are essentially independent CVs describing different aspects of molecular interactions. luisa Each of the top level terms in this file is the root term of an independent controlled vocabulary Where possible, short labels are reported as exact synonyms of a term in this file, mapping an element of the PSI Molecular Interaction XML schema. Notes: Protein complementation assay performed by dissecting a transcription factor activity (DNA binding domain and transcription activation domain) its restoration through the two hybrid proteins interaction that lead to a reporter gene expression. PMID:14755292 transcription compl transcriptional complementation assay safe DNA gel stain molecular weight estimation by sybr staining Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with sybr dyes. weight by sybr acetylated residue PMID:11125103 residue modification. sequence database Database collecting nucleic or amino acid sequences mainly derived from genomic sequence. Attribute name of annotation associated to a feature element. feature attribute name feature att name experiment database experiment database. experiment xref rfam rfam Rfam is a large collection of multiple sequence alignments and covariance models covering many common non-coding RNA families. http://www.sanger.ac.uk/Software/Rfam/ id-validation-regexp:"RF[0-9]{5}" QAC (S)-2-acetylamino-5-pentanediamic acid n-acetyl-glutamine [Q:ac] acetylglutamine acetylglutamine N-acetyl-L-glutamine residue modification. RESID:AA0045 2-amino-4-[[5-(2-amino-2-carboxylato-ethyl)-1,1,3-trimethyl-2,3-dihydroimidazol-2-yl]]but-3-enamide [H:diph] diphthamide residue modification. RESID:AA0040 2'-[3-carboxamido-3-(trimethylammonio)propyl]-histidine 2-[3-carboxamido-3-(trimethylammonio)propyl]histidine diphthamide 2'-[3-carboxamido-3-(trimethylammonio)propyl]-L-histidine HDP alpha-(aminocarbonyl)-4-(2-amino-2-carboxyethyl)-N,N,N-trimethyl-1H-imidazole-2-propanaminium 2-[(Xi)-3-carboxamido-3-(trimethylammonio)propyl]-4-((S)-2-amino-2-carboxyethyl)-1H-imidazole 2-amino-3-[[2-(3-amino-3-carbamoyl-prop-1-enyl)-1,1,3-trimethyl-2,3-dihydroimidazol-5-yl]]propanoic acid catalytic rna catalytic RNA catalytic ribonucleic acid Species of RNA that catalyses cleavage or trans-esterification of the phosphodiester link. crna This class of approaches is characterised by the use of affinity resins as tools to purify molecule of interest (baits) and their binding partners. The baits can be captured by a variety of high affinity ligands linked to a resin - for example, antibodies specific for the bait itself, antibodies for specific tags engineered to be expressed as part of the bait or other high affinity binders such as glutathione resins for GST fusion proteins, metal resins for histidine-tagged proteins. PMID:7708014 Affinity purification affinity chrom affinity chromatography technology residue modification. RESID:AA0030 4hydroxyproline HYP [P:hy_g] 4-hydroxy-L-proline 4-hydroxy-proline gpi-threonine gpi-anchor amidated threonine N-threonyl-glycosylphosphatidylinositolethanolamine RESID:AA0164 residue modification. protein array PMID:12067604 PMID:10976071 The protein array technology allows the screening of biochemical activities or binding abilities of hundreds or thousands of protein samples in parallel. After synthesis and purification by high-throughput methodologies, the proteins are printed onto the chip by using an instrument (micro-arrayer) that is capable of spotting liquid samples in a reproducible manner onto a planar support. The ordered protein array can then be probed with labelled molecules to identify proteins that bind to the bait. selenium cysteine L-selenocysteine CSE [C:sel] 3-selenylalanine selenocysteine residue modification. RESID:AA0022 genetic experimental form Descriptor of an experimental form involved in a genetic interaction methyltransferase as methyltransferase assay Measures the catalysis of the transfer of a methyl group to an acceptor molecule. array technology In this class of methodologies, the molecules to be tested are presented ordered in an array format (typically at high density) on planar supports. The characteristics and chemical nature of the planar support can vary. This format permits the simultaneous assay, in controlled conditions, of several thousand proteins/peptides/nucleic acids for different functions, for instance their ability to bind any given molecule. 10E-15 moles per liter of solution. OBSOLETE: term redundant with the schema exponent attribute of the parameter. fM fentomolar antimorph The gene function has been antagonized by a mutation in another copy of the gene. A sequence range within a protein identified as involved in an interaction. binding site Immuno blot Western blot is a procedure to identify and quantify proteins. A mixture of protein is first submitted to an electrophoresis in denaturing condition and then electro-transferred from the gel to a membrane. The membrane is then incubated with a primary antibody specific for a given protein or a specific residue modification in the sample under analysis. A secondary antibody, radiolabelled or fused to fluorophore or to a chromogenic enzyme, targets the first antibody and allows the visualisation of the protein band on the membrane. western blot Chains of amino acids joined by peptide bonds. Distinction between peptides, oligopeptides and polypeptides is arbitrarily by length; a polypeptide is perhaps more than 15 residues. polypeptide oligopeptide peptide CPS s-palmitoylcysteine [C:palm_s] s-palmitoyl-cysteine S-palmitoyl-L-cysteine 2-amino-3-(hexadecanoylthio)propanoic acid cysteine palmitate thioester (R)-2-amino-3-(hexadecanoylsulfanyl)propanoic acid RESID:AA0106 residue modification. cysteine hexadecanoate thioester range For instance when an amino acid modification is known to be in the region from 5 to 7. Displayed as '..'. Describes a sequence position known to be in a certain range, where the exact position is unclear. Reference not index in medline : Rosenberg, A., Griffin, K., Studier, W.S., McCormick, M., Berg, J., Novy, R., Mierendorf, R. inNovations, 1996, 6, 1. t7 phage display t7 phage T7 is a double stranded DNA bacteriophage with a thin-walled icosahedral capsid, ~550 Angstrom in diameter, which is decorated by 415 copies of the capsid protein, the product of gene 10. gp10 can tolerate insertions at the carboxyterminus without loosing its ability to be inserted into functional phage capsids. Both low density and high density display (albeit only with short peptides) can be achieved. http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?[libs%3d{dsmz_mutz%20ecacc_cell%20iclc%20CABI_BACT%20CIP_BACT%20CABI_YEAST%20DSMZ_PLANT_CELL}-id:${ac}]+-e search-url: id-validation-regexp:"[0-9]+|ACC\s[A-Z0-9]+|ECACC\s[A-Z0-9]+|LMBP\s[A-Z0-9]+|ICLC\s[A-Z0-9]+|CIP-[0-9]+" PMID:16381901 Ontology of cell types. http://obo.sourceforge.net/cgi-bin/detail.cgi?cell cell ontology Filter overlay assay A method in which separation depends upon the ability of one participant to bind to a filter or membrane which the other participants do not. Molecules interacting with the bound molecule will also be retain on the filter. For example, proteins expressed by different clones of an expression library are bound to a nitrocellulose membrane, by colony (bacterial library) or plaque (phage library) blotting. A labelled protein can then be used as a probe to identify clones expressing proteins that interact with the probe. Interactions occur on the nitrocellulose filters. The method is highly general and therefore widely applicable. A variety of approaches can be used to label the ligand, alternatively the ligand can be detected by a specific antibody. filter binding N6-retinylidene-L-lysine [K:retin] N6-retinal-L-lysine KRT residue modification. RESID:AA0120 N6-retinyl-lysine n6-retinal-lysine retinallysine (S)-2-amino-6-[(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)-2,4,6,8-nonatetraenylidene]aminohexanoic acid light microscopy Light visible microscopy uses environmental light to illuminate the sample and produce a magnified image of the sample. Biological function of a participant or of an interaction. function id-validation-regexp:"TIGR[0-9]+" TIGRFAMs is a collection of protein families, featuring curated multiple sequence alignments, Hidden Markov Models (HMMs) and annotation. http://www.tigr.org/TIGRFAMs TIGRFAMs tigrfams Literally, in place i.e. the protein is in its natural environment during the experiment. OBSOLETE as a full host organisms is recommended using tax id == -1 as convention to refer to 'in vitro' interaction. in situ Mass spectrometry can be used to characterise chemical modifications within peptides. One approach consists in the observation of a mass difference when a sample is treated with an enzyme that can specifically remove a peptide modification, for instance a phosphatase. The mass difference corresponds to the mass of the chemical group covalently linked to a residue. Such experiments carried out with a MALDI-TOF (Matrix-assisted laser desorption ionization time-of-flight ) do not allow the mapping of the modification site within the sequence, whereas any tandem mass spectrometer (LC MS/MS Liquid Chromatography Tandem Mass Spectrometry, nanoESI MS/MS nanoElectrospray Ionisation tandem mass spectrometry, FTMS Fourier Transform mass spectrometry) provide such information. A second approach consists of the direct mass measurement of the ionized chemical group dissociated from the residue within a tandem mass spectrometer. Both approaches need a prior enrichment of the modified peptide population in the samples with IMAC (Immobilized Metal Affinity Chromatography)or specific anti-modification antibodies. PMID for application instance:11875433 PMID:11395414 modified residue ms mass detection of residue modification S-nitrosyl-L-cysteine S-nitrosocysteine L-cysteine nitrite ester (R)-2-amino-3-nitrososulfanyl-propanoic acid nitrosylcysteine s-nitrosyl-cysteine residue modification. RESID:AA0230 Sequence variation due to insertion, deletion or substitution event. mutation method reference Reference to a related paper which more fully describes either the experimental method or one or more of the interactors used within the experiment. 2h fragment pooling This two hybrid approach involves the screening of a large number of individual proteins against a comprehensive library of randomly generated fragment as prey. The usage of degenerated fragment allows identification of the minimal protein region required for the interaction. since multiple clones that encode overlapping regions of protein are often identified, the minimal domain for interaction may be readily apparent from the initial screen. PMID for application instance:11196647 PMID:12634794 two hybrid fragment pooling approach residue modification. phosphorylated residue phosphorylated kinase homogeneous time resolved fluorescence kinase HTRF homogeneous time-resolved fluorescence PMID:14987100 Measures quenching of the nonradiative energy transfer between fluorescent long-lifetime lanthanide chelates and different acceptors. Relies on a fluorescence energy donor and acceptor being added from close proximity on the phosphorylated substrate due to the action of the kinase. kinase htrf [K:N6ac] (S)-2-amino-6-(acetylamino)hexanoic acid epsilon-acetyllysine residue modification. RESID:AA0055 n6-acetyllysine n6-acetyl-lysine KA6 N6-acetyl-L-lysine N(zeta)-acetyllysine library-used This annotation topic will be used to store information about the cDNA library. If a name is available this should be reported along with a short description of the library. hypermorph The gene function has been partially improved compared to wild-type by altering its sequence. surface patches PMID:9299343 Surface patches are built using 6 criteria: solvation potential, residue interface propensity, hydrophobicity, planarity, protrusion and accessible surface area. Protein structures having similar patches are likely to have the same interactions. [A:meth_n] N-methylalanine residue modification. RESID:AA0061 methylalanine AMT (S)-2-methylaminopropanoic acid n-methyl-alanine N-methyl-L-alanine Reference pointing to the originating database in which an interaction, or other curated information, was first described. source reference N-methylglutamine QM5 gamma-methylglutamine N(delta)-methylglutamine n5-methyl-glutamine methylglutamine [Q:meth_n5] residue modification. RESID:AA0071 N5-methyl-L-glutamine (S)-2-amino-N5-methylpentanediamic acid delivery method Method by which molecule is delivered or engineered into a cell. bind id-validation-regexp:"[0-9]+" The Biomolecular Interaction Network Database (BIND) is a collection of records documenting molecular interactions. http://www.blueprint.org/bind BIND PMID:10929120 Yellow fluorescent protein from Vibrio fischeri can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native. yellow fluorescent protein tag YFP yellow fluorescent protein yfp tag full identification by sequencing sequencing occurs during the course of the experiment. The DNA to be sequenced is used as template for the in vitro synthesis, by DNA polymerase, of a set of partial replicas, all beginning at the same place, but terminating at different points along the DNA chain. The key to this method is the use of dideoxyribonucleoside triphosphates in which the deoxyribose 3'-OH group present in normal nucleotides is missing; when such a modified nucleotide is incorporated into a DNA chain, it blocks the elongation of the chain. To determine the full sequence, the four different chain-terminating dideoxyribonucleosides are used in competition with an excess of deoxyribonucleosides in separate DNA synthesis reactions on the same DNA template. When the products of these four reactions are analysed by electrophoresis in four parallel lanes of a denaturing polyacrylamide gel, the DNA sequence can be derived. Every lane displays a family of DNA fragments of different lengths, reflecting the different sites at which a specific residue occurs in the original DNA. full dna sequence Molecule not part of or directly encoded by the genome, encompasses any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. small molecule 131i radiolabel I131 131I Molecule labelled with 131 radio isotope of iodine atoms. Role played by the participant within the experiment. experimental role attribute name Collection of topic describing the free text stored as an attribute value. CvTopic multiple parent This qualifier is used for hybrid or composite molecules with more than one crossreference to parent molecules. multiple parent reference Substrate protein pre-radiolabelled either synthetically or through the action of a kinase transferring an isotope of phosphate from a nucleotide. Substrate then exposed to phosphate under assay conditions. Substrate isolated by gel electrophoresis and loss of radiolabelling confirmed by autoradiography. in gel phosphatase in gel phosphatase assay protein footprinting Protein footprinting is a technique for identifying structural changes modulated by protein-ligand binding, and mapping protein-ligand interfaces This technique involves attaching cutting reagents randomly to amino acid residue (e.g. lysine or cysteine) on the proteins surface and then using this lysine-labelled protein to cleave polypeptide backbone of the other protein at exposed residues adjacent to its binding site. PMID:14987073 PMID:14967031 PMID:14600024 feature type Property of a subsequence that may interfere with the binding of a molecule. experimental participant identification experimental participant identification. experimental particp feature description The feature text description may include information about the feature detection method. monoclonal immunost monoclonal antibody immunostaining A monospecific antibody for the protein of interest is available, this is used to detect a specific protein within a cell or tissue sample. one hybrid yeast one-hybrid yeast one hybrid one-hybrid PMID:10589421 Protein-DNA complementation assay where a single promoter act as bait and is screened against a library of prey transcription factors. Term describing the last amino acid of a peptide chain. carboxy-terminus c-terminus c-term c-terminal position Displayed as 'c'. c-terminal coloc visual technol Techniques enabling the identification of the subcellular localisation of a protein or complex. Two different proteins show a similar distribution in the cell are said to co-localise. Obsolete since combination of Interaction Detection Method and Interaction Type. OBSOLETE. Consider using imaging techniques (MI:0428) as interaction detection method coupled with colocalisation (MI:0401) as interaction type and predetermined (MI:0396) as participant detection. colocalization/visualisation technologies secondary accession number secondary-ac Reference to the corresponding object in another database (like identity xref qualifier) but the identifier used in the external database is a secondary identifier. ONL locus name ordered locus name For instance HI0934, Rv3245c, At5g34500, YER456W. CDS number systematic gene number A name used to represent an ORF in a completely sequenced genome or chromosome. It is generally based on a prefix representing the organism and a number which usually represents the sequential ordering of genes on the chromosome. Depending on the genome sequencing center, numbers are attributed only to protein-coding genes, or also to pseudogenes, or also to tRNAs and other features. Ordered locus name ORF number PMID for application instance:10725388 PMID:9874787 In this variation of the FRET assay the donor fluorophore is replaced by a luciferase (typically Renilla luciferase). In the presence of its substrate, the luciferase catalyses a bioluminescent reaction that excites the acceptor fluorophore through a resonance energy transfer mechanism. As with FRET the energy transfer occurs only if the protein fused to the luciferase and the one fused to the acceptor fluorophore are in close proximity (10-100 Angstrom). bioluminescence resonance energy transfer bret LRET BRET The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. http://www.hprd.org/ HPRD hprd trihybrid bridge assay protein tri hybrid Two hybrid assay performed with a third protein component is co-transfected into a recombinant yeast strain together with a bait and a prey construct. Negative control show that the interaction between the bait and the prey do not occur when the third protein is not co-transfected. PMID:12935900 PMID:12761205 PMID:12052864 kon ka Association rate constant or rate of complex formation. Unit MOLE per SECOND (M-1 s-1) n-acetyl-tyrosine residue modification. RESID:AA0053 N-acetyl-L-tyrosine YAC acetyltyrosine (S)-2-acetylamino-3-(4-hydoxyphenyl)propanoic acid [Y:ac] N-acetyltyrosine nucl transformation nucleic acid transformation Transformation is the genetic alteration of a cell resulting from the introduction, uptake and expression of foreign genetic material incorporated into the cell's genome (DNA or RNA). The Rat Genome Database (RGD) curates and integrates rat genetic and genomic data. http://rgd.mcw.edu/ rgd RGD 33p radiolabel Molecule labelled with the radio isotope 33 of phosphorus atoms. P33 33P PMID:14577292 Molecule consisting of a specific sequence of amino acidic or nucleotidic monomers strung together through chemical bonds. biopolymer O3-(ADP-ribosyl)-L-serine adp-ribosylserine RESID:AA0237 residue modification. O-(ADP-ribosyl)-L-serine (S)-2-amino-3-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]oxy)-propanoic acid Formula O3-alpha-D-ribofuranosyl-L-serine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate) o-(adp-ribosyl)-serine O3-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-serine 3d-structure Comments on the 3D structure. This attribute is generally associated to an interaction. neddylated lysine PMID:111 Residue modification due to a cross-link between a lysine and a glycine from the Nedd8 protein family. palmitoylated residue palmitoylated aa residue modification. complementation PCA The function of numerous proteins or ribonucleic particles (enzymes, transcription factors, and others) can be rationally dissected into two fragments that fold autonomously but cannot complement to reconstitute the complex function, unless they are located in close proximity. In a two hybrid experiment, restoration of the activity by complementation of the two fragments when expressed as fusion with two polypeptides is taken as an evidence that the two polypeptides interact together. PMID:11495741 protein complementation assay Because of the long lifetimes of excited fluorescent molecules (nanoseconds), fluorescence can be used to monitor the rotational motion of molecules, which occurs on this timescale. This is accomplished experimentally by excitation with plane-polarized light, followed by measurement of the emission at parallel and perpendicular planes. Since rotational correlation times depend on the size of the molecule, this method can be used to measure the binding of two proteins because the observed polarization increase when a larger complex is formed. A fluorescence anisotropy experiment is normally carried out with a protein bearing a covalently added fluorescent group, which increases both the observed fluorescence lifetime of the excited state and the intensity of the fluorescent signal. Residue modification can be assessed by addition of an antibody which binds to the modified residue and alters the molecular weight of the complex. A variation of this technique has been used to show interaction of a DNA binding protein with another protein. In this case the DNA rather than protein is fluorescently labelled. PMID:12805227 fps FPS Fluorescence anisotropy fluorescence polarization spectroscopy fitc labelled Fluorescein isothiocyanate is a yellow-green coloured low molecular weight dye which couples to proteins via reaction with primary amine groups at high pH. FITC is excitable at 488nm, close to its absorption maximum at 494nm, and produces maximum fluorescence emission around 520nm. fluorescein isothiocyanate label fluorescein isothiocyanate labbeled FITC labelled enzyme Molecule doing a modification on its interacting partner. Binding will occur when this sequence range is present within a protein. sufficient binding site sufficient to bind The feature constrain free text will specificity whether a biological feature is shown to be possible (just observed) or required (experimentally demonstrated to be necessary for an interaction). feature constrain undetermined Displayed as '?'. Term describing a completely unknown or unspecified sequence position. undetermined sequence position Saturation binding experiments measure specific ligand binding at equilibrium at various concentrations of the ligand. Analysis of these data can determine receptor number and affinity. saturation binding bifc PMID:11983170 The bimolecular fluorescence complementation (BiFC) is an assay for determination of the locations of protein interactions in living cells. This approach is based on complementation between two non fluorescent fragments of the yellow fluorescent protein (YFP) when they are brought together by interactions between proteins fused to each fragment. bimolecular fluorescence complementation certain certain sequence position Position within the sequence clearly defined. omim http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=${ac} search-url: Online Mendelian Inheritance in Man (OMIM) is a catalogue of human genes and genetic disorders, with links to literature references, sequence records, maps, and related databases. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM OMIM Evidence based on the author of a paper assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences. modelled by author modeled by author inferred by author Set of terms to describe the participant experimental treatment and status. This term group in fact 4 orthologues short controlled vocabularies delivery method, expression level, molecular source, and sample process. Each participant can then be annotated with a maximum of 4 terms selected from each short list. experimental prep experimental preparation Measures the amount of radiolabel released into the medium when enzyme is added onto a film of isotope-labelled collagen. PMID:6247938 collagen film assay synthetic lethal PMID:15608217 Death phenotype observed on cells carrying combination of two independently silent mutations. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (lethal FBcv:0000351) dihydrofolate reductase reconstruction dhfr reconstruction PMID:10318894 The gene for DHFR is rationally dissected into two fragments called F[1,2] and F[3]. Two proteins or protein domains that are thought to bind to each other can then be fused to either of the two DHFR fragments. Reconstitution of enzyme activity can be monitored in vivo by cell survival in DHFR-negative cells grown in the absence of nucleotides. A fluorescence assay can also be carried out taking advantage of fMTX binding to reconstituted DHFR. The basis of this assay is that complementary fragments of DHFR, when expressed and reassembled in cells, will bind with high affinity (Kd 5 540 pM) to fMTX in a 1:1 complex. fMTX is retained in cells by this complex, whereas the unbound fMTX is actively and rapidly transported out of the cells. Survival depends only on the number of molecules of DHFR reassembled. residue modification. RESID:AA0327 glycosylarginine omega-n-glycosyl-arginine omega-N-glycosyl-L-arginine omega-N-(ADP-ribosyl)-L-arginine N(omega)-alpha-D-ribofuranosyl-L-arginine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate) N(omega)-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-arginine (S)-2-amino-5-([imino([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]amino)methyl]amino)pentanoic acid RESID:AA0168 residue modification. adp-ribosylarginine omega-n-(adp-ribosyl)-arginine PMID:16381953 PRIDE is a public repository of protein and peptide identifications for the proteomics community. http://www.ebi.ac.uk/pride/ pride PMID:8816797 Yeast strains are generated in which expression of DB-X/AD-Y or DBPX hybrid proteins is toxic under particular conditions (negative selection). Under these conditions, dissociation of an interaction should provide a selective advantage thereby facilitating detection: a few growing yeast colonies in which DB-X/AD-Y (or DBPX/binding site) fail to interact should be identified among many nongrowing colonies containing interacting DB-X/AD-Y or DBPX/binding site. reverse two hybrid living cell Molecule is observed within in a living cell. [K:meth_1] epsilon-methyllysine n6-methyl-lysine (S)-2-amino-6-methylaminohexanoic acid N6-methyl-L-lysine N(zeta)-methyllysine MLZ residue modification. methyllysine residue modification. RESID:AA0060 CPN N-(1-oxahexadecyl)-L-cysteine N-palmitoyl-L-cysteine n-palmitoylcysteine 2-hexadecanoylamino-3-mercaptopropanoic acid n-palmitoyl-cysteine [C:palm_n] (R)-2-hexadecanoylamino-3-sulfanylpropanoic acid enzymatic footprint PMID:8238889 Sites of sequence-specific DNA-protein interaction are identified by altered reactivity of an enzymatic probe to DNA bound by a protein compared to the same nucleotide sequence in naked DNA. Nucleotides in close contact with the binding protein are protected from cleavage by the enzyme. When these enzymes are administrated to intact cells, the pattern of protection from the probes identifies the location of DNA-protein interactions in vivo. enzymatic footprinting Post translational modification occurs subsequently to an interaction. resulting-ptm FlyBase http://flybase.net/cgi-bin/fbannq.html?acc=${ac} search-url: id-validation-regexp:"FBgn[0-9]{7}" flybase FlyBase is a comprehensive database for information on the genetics and molecular biology of Drosophila. http://fbserver.gen.cam.ac.uk:7081/ RESID:AA0050 Reaction, that can affect K,C,A,D,E,Q,G,I,K,M,P,S,T,Y,V residues. RESID:AA0044 RESID:AA0048 RESID:AA0051 RESID:AA0056 RESID:AA0047 RESID:AA0041 RESID:AA0042 RESID:AA0052 RESID:AA0054 RESID:AA0046 GO:0006473 RESID:AA0049 RESID:AA0043 acetylation reaction acetylation Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with comassie dye. weight by comassie molecular weight estimation by coomasie staining PMID:15833125 Single-mutant phenotype effects combine to give a double-mutant effect different from the wild type and different from single mutant effect. For instance WT < A= B < AB, B < WT = AB < A, WT < A < B < AB, B < WT < AB < A, and all additional inequalities obtained by interchanging A and B, or reversing the effect of both A and B. additive interaction additive insertion analysis In this approach, once a molecule is demonstrated to participate in an interaction, several insertion derivatives are produced and tested in the binding assay to detect the regions that are important for the interaction. ca po nuc transfect calcium phosphate nucleic acid transfection Transient introduction and expression of nucleic acid carried out by treatment with calcium phosphate. Yet to be identified interaction detection method associated with interaction data imported from a third party database. This database may have potentially different standards of curation. unspecified method (S)-2-methylamino-3-phenylpropanoic acid N-methyl-L-phenylalanine residue modification. FMT [F:meth] N-methylphenylalanine methylphenylalanine n-methyl-phenylalanine direct interaction Interaction that is proven to involve only its interactors. synthetic genetic analysis sga SGA Identification of genetic interactions by generation of an organism harbouring mutations in 2 or more genes and scoring for a phenotype, such as loss of viability, that is not observed for any of the mutations in isolation. N-acetyl-L-leucine LAC [L:ac] acetylleucine n-acetyl-leucine residue modification. light scattering Dynamic and static laser light scattering probes the size, shape, and structure of biological macromolecules or of their assemblies. A beam is focused on an optically clear cylindrical cell containing the sample. Most of the light passes directly through the sample. A small portion of the light is scattered; the scattered light intensity containing information about the scattering particle is detected at an angle (typically in the range 15-180degrees) from the direction of the incident beam. PMID:9013660 PMID:15353450 Method to identify domain-domain interactions within the same resolved structure. Domains are first projected onto a pdb structure and then the distance between all pairs of residues in different domains are calculated. When the distance between 2 residues is below the non covalent bond threshold, the corresponding pair of domains is predicted to interact. structural proximity The phenotype resulting from genetic perturbation of A has an effect on WT, but that effect is abolished by adding the suppressor B, which itself shows no single-mutant effect (for example, WT = B = AB < A); suppressive interaction suppression n-acetyl-phenylalanine residue modification. N-acetyl-L-phenylalanine FAC [F:ac] acetylphenylalanine [A:meth_n3] trimethylalanine AM3 N,N,N-trimethyl-L-alanine n,n,n-trimethyl-alanine residue modification. RESID:AA0062 (S)-1-carboxy-N,N,N-trimethylethanaminium (S)-2-(trimethylammonio)propanoic acid footprinting footprinting analysis is used to identify regions of molecules directly involved in binding other macromolecules and therefore protected from the effects of degradative enzymes. x-ray tomography X-ray Tomography is a branch of X-ray microscopy. A series of projection images are used to calculate a three dimensional reconstruction of an object. The technique has found many applications in materials science and later in biology and biomedical research. In terms of the latter, the National Center for X-ray Tomography (NCXT) is one of the principle developers of this technology, in particular for imaging whole, hydrated cells. Gene whose mutation suppress the phenotype associated to a suppressed mutation. suppressor gene (S)-2-acetylamino-3-hydroxypropanoic acid N-acetylserine N-acetyl-L-serine n-acetyl-serine acetylserine residue modification. [S:ac] SAC figure legend Text pointing to a specific paper figure legend where the experimental evidences for an interaction are shown. PMID:8248129 PMID:10436088 The protein of interest is presented on the outer membrane of Gram negative bacteria by expressing it as a fusion partner to peptide signals that direct heterologous proteins to the cell surface. For instance, a single chain Fv (scFv) antibody fragment, consisting of the variable heavy and variable light domains from two separate anti-digoxin monoclonal antibodies, was displayed on the outer membrane of Escherichia coli by fusing it to an Lpp-OmpA. Similar systems have also been developed for gram positive bacteria. Fluorescence-activated cell sorting (FACS), is used to specifically select clones displaying a protein binding to scFv-producing cells. bacterial display Isoform synonym. isoform synonym Relies on the radiolabelling of a peptide substrate immobilized on a scintillant coated SPA-bead. The kinase transfers a phosphate isotope from the nucleotide to the substrate. kinase spa kinase scintillation proximity assay Michaelis-Menten constant: concentration of substrate at which the reaction rate is equal to half the maximal rate (i.e. Km={s} when Vo=1/2Vmax). Unit Molar. Km km Xref pointing to a GO compartment term describing the end location of a migrating molecule. translocation end 3 hybrid method Group of method based on complementation assay where a third participant is shown to be necessary for the binding of a given bait prey pair. The objective of Gene Ontology (GO) is to provide controlled vocabularies for the description of the molecular function, biological process and cellular component of gene products. http://www.ebi.ac.uk/GO id-validation-regexp:"GO:[0-9]{7}" gene ontology go expression level alteration Synthesis rate of a molecule under investigation differs from its naturally occurring expression level in a cell. MFM residue modification. RESID:AA0021 [M:form] N-formyl-L-methionine 2-formylamino-4-(methylthio)butanoic acid (S)-2-formylamino-4-(methylsulfanyl)butanoic acid n-formyl-methionine formylmethionine The phenotype resulting from genetic perturbation A and the phenotype resulting from genetic perturbation B have no effect on the WT background, but the combined genetic perturbation of A and B has a phenotypic effect. synthetic synthetic interaction cy3 label The organic cyanine Cy3 emits maximally at 570 nm. PMID:11160938 In this complementation approach the bait can be any membrane protein (for example a receptor or a channel protein), the prey is cloned as a fusion protein of any cDNA from a library and the coding sequence of cytoplasmic RAS (cdc25 in yeast). If the bait and the prey interact, RAS is recruited close to the membrane and can activate cell growth. This procedure must take place in cells having a mutated RAS (Cdc25-2 yeast strain having a temperature sensitive mutation of RAS) to avoid constitutive growth activation. reverse rrs reverse ras recruitment system reverse RRS N-glycyl-glycosylphosphatidylinositolethanolamine RESID:AA0161 residue modification. gpi-anchor amidated glycine gpi-glycine methylation methylation reaction The covalent attachment of a methyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer. Irreversible reaction that can affect A,G,M,F,P,C,R,N,Q,E,H,or K residues. RESID:AA0070 RESID:AA0066 RESID:AA0073 RESID:AA0065 RESID:AA0234 RESID:AA0069 RESID:AA0067 RESID:AA0075 RESID:AA0063 RESID:AA0064 RESID:AA0074 RESID:AA0068 RESID:AA0072 RESID:AA0272 GO:0043414 RESID:AA0076 CD circular dichroism cd PMID:11578931 Circular dichroism (CD) is observed when optically active molecules absorb left and right hand circularly polarized light slightly differently. Linearly polarized light can be viewed as a superposition of two components of circularly polarized light of equal amplitude and phase but opposite handness. When this light passes through an optically active sample the two polarized components are absorbed differently. The difference in left and right handed absorbance A(l)- A(r) is the signal registered in CD spectra. This signal displays distinct features corresponding to different secondary structures present in peptides, proteins and nucleic acids. The analysis of CD spectra can therefore yield valuable information about the secondary structure of biological macromolecules and the interactions among molecules that influence their structure. residue modification. RESID:AA0354 N2-acetyl-L-arginine RAC acetylarginine [R:ac] alpha-acetylamino-delta-guanidinovaleric acid acetylarginine n2-acetyl-arginine pELISA p elisa proximity enzyme linked immunosorbent assay PMID:15155907 Method allowing efficient and precise interaction detection, along with extensive repertoires of specific binding reagents. It is based on proximity a ligation mechanism that enables sensitive high-capacity protein measurements by converting the detection of specific proteins to the analysis of DNA sequences. Proximity probes containing oligonucleotide extensions are designed to bind pairwise to target proteins and to form amplifiable tag sequences by ligation when brought in proximity. 3d-resolution Resolution of the 3D structure. This attribute is generally associated to an interaction. 2-acetylamino-3-mercaptopropanoic acid acetylcysteine n-acetyl-cysteine [C:ac] CAC residue modification. N-acetyl-L-cysteine (R)-2-acetylamino-3-sulfanylpropanoic acid N-acetylcysteine protein A linear polymer of amino acids joined by peptide bonds in a specific sequence. SO:0000358 single stranded deoxyribonucleic acid ss dna ss DNA DNA that consists of only one chain of nucleotides rather than the two base pairing strands found in DNA in the double helix form. single nonmonotonic single nonmonotonic interaction The phenotype resulting from genetic perturbation of B shows opposing effects in the WT and A backgrounds (for example, B > WT and AB< A); or, A shows opposing effects in the WT and B backgrounds, but not both. RESID:AA0034 residue modification. (R)-2-amino-3-(phosphonosulfanyl)propanoic acid phosphocysteine CPO S3-phosphocysteine [C:po] S-phosphonocysteine s-phospho-cysteine S-phospho-L-cysteine cysteine phosphate thioester Single amino acid identification along a protein sequence. protein sequence identification protein sequence Competitive binding experiments measure equilibrium binding of a single concentration of ligand at various concentrations of an unlabeled competitor. Analysis of these data gives the affinity of the receptor for the competitor. competition binding This qualifier is used when the crossreference is imported from the Gene Ontology tag definition_reference. gene ontology definition reference go-definition-ref The interaction that has a disease association. disease mutation disrupting interaction mutation disrupting Residue of a protein whose identity mutation or deletion totally disrupt an interaction. PMID for application instance:12186859 PMID:11988476 PMID:11817959 A combination of NMR and EPR. The lines in the EPR spectrum that are caused by coupling of an unpaired electron nearby nuclei change in intensity when these nuclei are excited at their NMR frequency. endor ENDOR electron nuclear double resonance The number of substrate molecules converted to product in a given unit of time, on a single enzyme molecule when the enzyme is saturated with substrate. Unit per second, or s-1. turnover number kcat methylated alanine residue modification. methionamine N-acetyl-L-methionine (S)-2-acetylamino-4-(methylsulfanyl)butanoic acid n-acetyl-methionine acetylmethionine 2-acetylamino-4-(methylthio)butanoic acid [M:ac] residue modification. acetylmethionine MAC lipid modification residue modification. adp ribosylation reaction Reaction that can affect Arg, Cys, Glu, Arg and Asn residues. RESID:AA0295 RESID:AA0231 RESID:AA0169 GO:0006471 adp ribosylation uniprot knowledge base uniprotkb search-url: http://www.ebi.uniprot.org/entry/${ac} id-validation-regexp:"[OPQ][0-9][A-Z0-9]{3}[0-9]|[OPQ][0-9][A-Z0-9]{3}[0-9]-[0-9]+|[A-Z]{3}[0-9]{5}|[OPQ][0-9][A-Z0-9]{3}[0-9]-PRO_[0-9]{10}" PMID:14681372 UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. http://www.expasy.uniprot.org/ UniProt tritium H3 3H 3h radiolabel Molecules labelled with isotope 3 of hydrogen atoms. amidation amidation reaction RESID:AA0093 RESID:AA0089 RESID:AA0085 RESID:AA0084 RESID:AA0100 RESID:AA0092 RESID:AA0088 RESID:AA0097 RESID:AA0083 RESID:AA0099 RESID:AA0082 RESID:AA0098 RESID:AA0096 RESID:AA0081 RESID:AA0095 RESID:AA0091 Irreversible reaction that can affect A,R,N,D,C,Q,E,G,H,I,L,K,M,F,P,S,T,W,Y or V residues. RESID:AA0087 RESID:AA0094 GO:0001519 RESID:AA0090 RESID:AA0086 RESID:AA0102 S-farnesyl-L-cysteined is cleaved and returns a C residue. defarnesylation defarnesylation reaction anti bait coimmunoprecipitation anti bait coip A specific antibody for the protein of interest (bait) is available, this is used to generate a high affinity resin to capture the endogenous bait present in a sample. conditional synthetic lethal cond syntetic lethal Two silent mutations show a conditional synthetic lethal phenotype when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (lethal FBcv:0000351) PMID:16338355 PMID:12120258 PMID:11896282 This method measures formation of complex by monitoring changes in the resonance angle of light impinging on a gold surface as a result of changes in the refractive index of the surface. A ligand of interest (peptide or protein) is immobilized on a dextran polymer, and a solution of interacting protein is passed over it through a cell, with a gold wall coated with this polymer. Macromolecules that interact with the immobilized ligand are retained on the polymer surface, and alter the resonance angle of impinging light as a result of the change in refractive index brought about by the increased protein mass retained on the polymer surface. Since all proteins have the same refractive index and since there is a linear correlation between resonance angle shift and protein concentration near the surface, this allows one to measure changes in protein concentration at the surface as a consequence of protein interaction. Furthermore, this can be done in real time, allowing direct measurement of both the on rate and the off rate of complex formation. Optical biosensor BIAcore(r) spr surface plasmon resonance 2h label Molecules labelled with isotope 2 of hydrogen atoms. deuterium D2 2H2 Reverse phase chromatography operates on the basis of hydrophilicity and lipophilicity. The stationary phase consists of silica based packings with n-alkyl chains covalently bound. For example, C-8 signifies an octyl chain and C-18 an octadecyl ligand in the matrix. The more hydrophobic the matrix on each ligand, the greater is the tendency of the column to retain hydrophobic moieties. Thus hydrophilic compounds elute more quickly than do hydrophobic compounds. reverse phase chromatography reverse phase chrom [E:gpe] L-glutamyl 5-glycerophosphoethanolamine (S)-2-amino-5-[2-([([2,3-dihydroxypropyl]oxy)(hydroxy)phosphoryl]oxy)ethyl]amino-5-oxopentanoic acid residue modification. RESID:AA0170 glutamyl 5-glycerylphosphorylethanolamine glycerylpo4etohamine L-glutamyl 5-glycerylphosphorylethanolamine EGE L-glutamyl 5-glycerophosphorylethanolamine ribonucleoprot compl ribonucleoprotein complex protein rna complex A macromolecular complex containing both protein and RNA molecules. GO:0030529 weight silver stain molecular weight estimation by silver staining Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with silver. disaggregation Dissociation of partners interacting via non-covalent bond. OBSOLETE because considered misleading. Techniques which depend upon the strength of the interaction between two entities. affinity techniques affinity technology This term refers to methods that aim at interfering with the activity of a specific gene by altering the gene regulatory or coding sequences. This goal can be achieved either by a classical genetic approach (random mutagenesis followed by phenotype characterization and genetic mapping) or by a reverse genetics approach where a gene of interest is modified by directed mutagenesis. genetic interference gene ontology synonym Synonym as used in Gene Ontology. go synonym Methods based on 3D structure information. structure based prediction predict from struct residue modification. hydroxylated residue search-url Search engine URL associated to Cv Database terms. siRNA micro RNA dicer RNA sirna small interfering rna Ribonucleic acid used in RNAi study. These RNA have the reverse complementary sequence of a target gene's mRNA transcript and inhibit its expression. PMID:10542148 mRNA mrna messenger rna Single-stranded RNA molecule that specifies the amino acid sequence of one or more polypeptide chains. PDBj search-url: http://pdbjs3.protein.osaka-u.ac.jp/xPSSS/DetailServlet?PDBID=${ac}&PAGEID=Summary id-validation-regexp:"[0-9][a-zA-Z0-9]{3}" pdbj PMID:12099029 PDBj(Protein Data Bank Japan) maintains the database for the protein structures with financial assistance from the Institute for Bioinformatics Research and Development of Japan Science and Technology Corporation(BIRD-JST), collaborating with the Research Collaboration for Structural Bioinformatics(RCSB) and the MSD in the European Bioinformatics Institute(MSD-EBI) in EU. All three organizations serve as deposition, data processing and distribution sites. http://www.pdbj.org/ Alternative names to describe a complex. complex-synonym Regular Expression used to check the validity of cross references' identifier. Attribute generally associated to terms in Cv Database. validation regular expression id-validation-regexp anti tag immunostaining Immunostaining assay performed when specific antibodies for the protein of interest are not available. Therefore the protein is expressed as a hybrid protein fused to a tag peptide/protein for which efficient antibodies are available. The anti tag antibody may be either monoclonal or polyclonal. anti tag immunost v5 tag The protein of interest is expressed as a fusion to the peptide GKPIPNPLLGLDST for which antibodies are commercially available. GKPIPNPLLGLDST epitope tag protease accessibility laddering pal protease access PMID:16615907 In protease accessibility laddering (PAL) tagged proteins are purified on magnetic beads in their natively folded state. While attached to the beads, proteins are probed with proteases. Proteolytic fragments are eluted and detected by immunoblotting with antibodies against the tag (e.g., Protein A, GFP, and 6xHis). alaninamide alanine amide residue modification. (S)-2-aminopropanamide alanineamide AAM [A:am] L-alanine amide residue modification. methylated residue A molecule is estimated to be expressed at lower levels than in physiological condition. under expressed level under-expressed 2-oxopyrrolidine-5-carboxylic acid 5-oxoproline pyroglutamic acid [E:pyro] 2-pyrrolidone-5-carboxylic acid residue modification. RESID:AA0031 5-oxopyrrolidine-2-carboxylic acid PCA pyroglutamic acid (S)-5-oxo-2-pyrrolidinecarboxylic acid rare isotope label Molecule can be labelled including rare isotopes among its constituent atoms that can be used to identify, localize or quantify the full molecule. rare isotope label cosedimentation Separation of a protein mixture under the influence of artificial gravity. primary-reference Used to indicate the PMID from which the experimental data is extracted. PMID:15221759 IPI provides a top level guide to the main databases that describe the proteomes of higher eukaryotic organisms. IPI effectively maintains a database of cross references between the primary data sources, provides minimally redundant yet maximally complete sets of proteins for featured species (one sequence per transcript) and maintains stable identifiers (with incremental versioning) to allow the tracking of sequences in IPI between IPI releases. IPI is updated monthly in accordance with the latest data released by the primary data sources. ipi id-validation-regexp:"IPI[0-9]+.[0-9]+|IPI[0-9]+" international protein index One of several nuclides having the same number of protons in their nuclei and hence having the same atomic number, but differing in the number of neutrons and therefore, in the mass number. isotope label A wide range of dyes have been used over the years to visualise proteins in polyacrylamide gels - Coomasie Blue and silver-staining being two classical methods. Fluorescent dyes such as Nile Red and SYPRO Orange are now increasingly used due to their superior dynamic range. Use of non-denaturing gels can allow visualisation of protein protein interactions. Several dyes can be used to specifically indicate residue modification, however this methodology will give no information as the number of residues modified or their position within the protein sequence. Examples include the use of acid fuscian or the fluorescent dansyl hydrazine to show protein glycosylation. PMID:12015990 protein staining CYGD (MIPS) MPact MIPS cygd CYGD The MIPS Comprehensive Yeast Genome Database (CYGD) aims to present information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae. In addition the data of various projects on related yeasts are used for comparative analysis. http://mips.gsf.de/proj/yeast/CYGD. http://mips.gsf.de/genre/proj/mpact n-myristoyl-glycine RESID:AA0059 residue modification. myristoylglycine N-myristoyl-glycine GMY [G:myr] SPA RIA Radio Immuno Assay SPA relies upon the fact that a beta particle emitted from a radioisotope decay can excite a fluorophore only when it is at a very short distance in water solution (few micrometers). The ligand is labelled with a radioactive atom and its potential partner is fixed to fluorophore containing beads, the emitted fluorescence proving their interaction can be measured in a scintillation counter. The scintillator measures only the amount of bound radiolabelled ligand. Competition experiment with cold competitor can be done to estimate the binding affinities (50% inhibitory concentration [IC50], cold ligand versus labelled ligand). Loss of signal can also be used to measure substrate cleavage by an enzyme, and labelled antibodies used to titrate the degree of modified residue present. PMID:3866247 spa scintillation proximity assay nucleic acid transduction Transduction is the process by which bacterial DNA is moved from one bacterium to another by a virus. nucl transduction anti tag western anti tag western blot Western blot assay performed when specific antibodies for the protein of interest are not available. Therefore the protein is expressed as a hybrid protein fused to a tag for which efficient antibodies are available.The antibody may be either monoclonal or polyclonal. A Database of Human Unidentified Gene-Encoded Large Proteins Analyzed by Kazusa Human cDNA Project. http://www.kazusa.or.jp/huge/ huge search-url: http://www.kazusa.or.jp/huge/gfpage/${ac} id-validation-regexp:"KIAA[0-9]{4}[A-Z]{0,1}" Molecule has undergone one or more purification steps to isolate it from the cellular environment. purified fluorescence-activated cell sorting facs Flow cytometry FACS Cells in suspension flow through a laser beam, the scattered light or emitted fluorescence is measured, filtered and converted to digital values. Cells can be sorted according to their properties. Using flow cytometry, any fluorescent or light scattering experiment can be carried out on entire cells. With this instrument, interactions occurring either on cell surfaces or in any other subcellular location can be studied by using suitable fluorescent labels. PMID:11988464 parameter unit Controlled vocabulary for kinetic constant units. ec50 Molar concentration of an agonist which produces 50% of the maximum possible response for that agonist. Note this measure depends on the specific agonist used and upon experimental conditions, notably temperature, pH and solution composition (e.g., salts, chelating agents and others). Thus the ec50 is a relative measure and its values can be compared only when sharing the same experimental setting. Unit Molar. EC50 Method to determine the features of the proteins involved in the interaction. feature detection method feature detection engineered Molecule has been added into system from an external source or altered within the cell. newt New EBI Web Taxonomy. http://www.ebi.ac.uk/newt search-url: http://www.ebi.ac.uk/newt/display?search=${ac} non covalent inter Interaction mediated by non-covalent, weak forces rearrangement. OBSOLETE use physical interaction (MI:0218) instead. non covalent interaction gpi-cysteine N-cysteinyl-glycosylphosphatidylinositolethanolamine gpi-anchor amidated cysteine RESID:AA0160 residue modification. IntAct http://www.ebi.ac.uk/intact/search/do/hvWelcome?searchString=${ac} search-url: id-validation-regexp:"EBI-[0-9]+" intact PMID:14681455 INTerAction datanase (IntAct) provides an open source database and toolkit for the storage, presentation and analysis of protein interactions. http://www.ebi.ac.uk/intact transactivating tag Tat tag tat tag Tag derived from the transactivating (Tat) protein of human immunodeficiency virus 1 (HIV-1) that can enter cells efficiently when added exogenously in tissue culture. The Tat tag can carry other molecules into cells, by fusion of Tat peptides (residues 1-72 or 37-72,) to any molecule under study. Tat-mediated uptake may allow the delivery of macromolecules previously thought to be impermeable to living cells. PMID:8290579 two hybrid array Two-hybrid screening can be done in a colony array format, in which each colony expresses a defined pair of proteins. Because the particular protein pair expressed in each colony is defined by its position in the array, positive signals identify interacting proteins without further characterization, thus obviating the need for DNA purification and sequencing. The interrogation of a two-hybrid colony array usually involves a mating strategy in which every DNA binding domain hybrid (the bait) is tested against all activation domain hybrids (the preys) in a grid pattern. Arrays usually use full-length open reading frames. PMID for application instance:10688190 PMID:11827624 inhibition The interaction between the proteins or the formation of a complex is disrupted by a biological molecule or by a modification of the interactors. synthetic growth defect Two silent mutations show growth defect when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective') synt growth defect guide rna Small RNA molecules that hybridize to specific mRNAs and direct their RNA editing. grna guide RNA Alexa fluorescent dye analogue to Rhodamine Red-X with an approximate excitation wavelength maximum of 568nm. PMID:10449539 alexa 568 label Xref pointing to a GO compartment term describing the start location of a migrating molecule. PMID:14681407 translocation start Evidence based on a curator assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences. modelled by curator modeled by curator inferred by curator residue modification. acetylaspartic acid acetylaspartate n-acetyl-aspartic acid N-acetyl-L-aspartic acid (S)-2-(acetylamino)butanedioic acid [D:ac] DAC nutrition synt letal Two silent mutations show a nutrition sensitive lethal phenotype when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description. conditional synthetic lethal nutrition-sensitivity PMID:10504710 The TAP method involves the fusion of the TAP tag (encoding a calmodulin binding peptide, a TEV cleavage site, and the Staphylococcus aureus Protein A) to the target protein and the introduction of the construct into the host cell or organism, maintaining the expression of the fusion protein at, or close to, its natural level. The fusion protein and associated components are recovered from cell extracts by affinity selection on an IgG matrix. After washing, the TEV protease is added to release the bound material. The eluate is incubated with calmodulin-coated beads in the presence of calcium. This second affinity step is required to remove the TEV protease as well as traces of contaminants remaining after the first affinity selection. After washing, the bound material is released with EGTA. This two steps purification steps ensures a highly selective complex purification of the tapped protein (first round of selection on the protein A, a high affinity tag) under mild condition (non denaturant pH or conditions required to remove the tag). OBSOLETE redundant term. Map to feature type: tap tagged (MI:0524) and as interaction detection method tandem affinity purification (MI:0676). tap tag coimmunoprecipitation tap tag coip fluorescence accept fluorescence acceptor Fluorophore able to absord the electromagnetic radiation at given wavelength from a specific donor fluorophore, the re-emission of its own charateristic fluorescence. (S)-2-amino-6-dimethylaminohexanoic acid [K:meth_2] epsilon-dimethyllysine N6,N6-dimethyl-L-lysine MLY n6,n6-dimethyl-lysine N(zeta)-dimethyllysine residue modification. lysine derivative Lys(y) dimethyllysine For instance this qualifier, in an interaction entry, can be associated to a cross reference to the same interaction in an other database. identical object identity Reference to the corresponding object in another database. Correspondence may be complete or partial. s35 radiolabelled S35 35S Molecule labelled with 35 radio isotope of sulfur. Proteins are often metabolically labelled, usually be growth in 35S labelled culture medium. 35s radiolabel residue modification. methylated arginine CPPs cell-penetrating peptides MTS Trojan peptides The peptides named CPPs vary greatly in size, amino acid sequence, and charge, but share the common feature that they have the ability to rapidly translocate the plasma membrane and enable delivery to the cytoplasm or nucleus. PMID:16574060 PTDs protein transduction domains membrane translocating sequences cell penetrating peptide tag omega-N,omega-N-dimethyl-L-arginine [R:meth_n7] asymmetric dimethylarginine (S)-2-amino-5-[((dimethylamino)iminomethyl)amino]pentanoic acid NG,NG-dimethylarginine RM2 dimethylarginine omega-n,omega-n-dimethyl-arginine residue modification. Name assigned to a molecule by the authors within a paper that may differ from the reference database. author assigned name feature database feature xref feature database. The interaction of two molecules is determine by their very close proximity or the overlap of their relative bands in a gel. comigration in gel electrophoresis comigration in gel conditional synthetic lethal temperature-sensitivity temprtr synt lethal Two silent mutations show a temperature sensitive lethal phenotype when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (FBcv:0000310 'temperature conditional') residue modification. gpi anchor residue Confidence classification assigned by the author of the publication to a specific interaction. author-confidence confocal microscopy A confocal is a standard epifluorescence microscope with improvement essentially coming from the rejection of out-of-focus light interference. Confocal imaging system achieves this by two strategies: a) by illuminating a single point of the specimen at any one time with a focused beam, so that illumination intensity drops off rapidly and b) by the use of blocking a pinhole aperture in a conjugate focal plane to the specimen so that light emitted away from the point in the specimen being illuminated is blocked from reaching the detector. Only the light from the single point illuminated of the specimen passing through the image pinhole is detected by a photodetector. Usually a computer is used to control the sequential scanning of the sample and to assemble the image for display onto a video screen. coimmunoprecipitation In this approach an antibody, specific for the protein of interest (bait) or any tag expressed within a fusion protein, is used to separate the bait from a protein mixture or a cell lysate and to capture its ligand simultaneously. The protein partners that bind to the bait protein retained by the resin can then be eluted and identified. coip sandwich immunoassay PMID:12454649 Antibody array where proteins retained by the arrayed antibodies are identified using a detector antibody. The detector antibody is either modified with a directly detectable label (enzyme, fluorescent molecule, isotope, etc.), or it is biotinylated for detection after subsequent probing with labeled streptavidin. N-acetyl-L-isoleucine acetylisoleucine n-acetyl-isoleucine (2S,3S)-2-acetylamino-3-methylpentanoic acid acetylisoleucine [I:ac] residue modification. IAC polyprotein fragment Subpart of a polyprotein that is naturally cleaved in vivo. polyprotein frag Indicates the sample context in which each interacting molecule is presented to its partner. sample process exp-modification Modifications of the standard experimental method described in the CV. experiment modification gal4 vp16 complementation mammalian two hybrid KISS karyoplasmic interaction ion strategy gal4 vp16 complement PMID:1387709 A chimeric protein consisting of the GAL4 DNA-binding domain (aa 1-147 of GAL4) and a transcriptional activation domain from the herpes simplex virus protein VP16 (either aa 411-490 or aa 411-455) can specifically activate transcription of a reporter gene located downstream ofGAL4 DNA binding sites and the E1B minimal promoter. Similarly, two chimeric proteins, one encoding a chimeric GAL4 protein and the other encoding a chimeric VP16 protein, can activate the reporter gene, if the domains fused to the GAL4 and VP16 sequences can complex with appropriate conformation. However, if the domains fused to the GAL4 and VP16 sequences do not interact specifically to form a + complex that reconstitutes GAL4 function, the reporter gene cannot be activated. chromatography column chromatography Used to separate and/or analyse complex mixtures. The components to be separated are distributed between two phases: a stationary phase (bed) and a mobile phase which percolates through the stationary bed. The nature of the two phases determines the separation criteria exploited by the column such as affinity, ionic charges, size or hydrophobicity of the molecules under analysis. Each type of column can be implemented with the mobile phase under atmospheric or high pressure condition. In this later case columns are designated as High Pressure Liquid Chromatography (HPLC). chromatography technology Transient introduction and expression of nucleic acid carried out by treatment with chemicals. nucleic acid transfection by treatment n transfection treat 15n label Molecules labelled with isotope 15 of nytrogen atoms. N15 15N nucleic acid SO:0000348 Linear polymers of nucleotides, linked by 3',5' phosphodiester linkages. vp16 activation domain vp16 ad Full viral protein vp16 exclusively responsible for preferential transcriptional activation of viral genes. Activation requires the formation of a complex with the host cell transcription factor. ubiquitin binding Interaction concerning ubiquitin that is covalently attached to any Lys residue of its interaction partner. OBSOLETE remap to ubiquitination reaction (MI:0220) or describe ubiquitine as a participant on the interaction using physical interaction (MI:0218) or covalent binding (MI:0195) as interaction type. Gene name. gene gene name [R:po] omega-N-phospho-L-arginine omega-n-phospho-arginine N5-[imino(phosphonoamino)methyl]-L-ornithine alpha-amino-delta-phosphonoguanidinovaleric acid (S)-2-amino-5-[imino(phosphonoamino)methyl]aminopentanoic acid RPO phosphoarginine RESID:AA0222 residue modification. feature prediction from structure feature struct pred Group of method taking advantage of 3D structure to calculate and infer the feature of interacting molecules. Entrance of molecules into cells that does not involved specific treatments but rely on natural cellular processes. passive uptake mammalian protein protein interaction trap mappit PMID:12853652 The MAPPIT(mammalian protein-protein interaction Trap) is a screening method for protein-protein interaction in mammalian cells, based on the reconstitution of a membrane STAT (signal transducers and activators of transcription) receptor. The bait protein is fused to a STAT recruitment-deficient receptor and the prey protein to a functional STAT recruitment sites. In such a configuration, a given baitprey interaction restores a STAT-dependent responses leading to the expression of a reporter gene. This system, enable to demonstrate not only protein interaction but also modification-independent and tyrosine phosphorylation- dependent interactions. Sequences can be identified in a DNA mixture by launching a PCR (Polymerase Chain Reaction) controlled by sequence specific primers. Such reaction starts only when the hybridization of the primer with a complementary sequence occurs. primer specific pcr The application of physical principles and methods to biological experiments. biophysical endogenous naturally occurring Unaltered endogenous molecule in its naturally occurring state. Example generally associated to Cv terms. example anti tag coip anti tag coimmunoprecipitation A specific antibody for the protein of interest is not available, therefore the bait protein is expressed as a hybrid protein fused to a tag peptide/protein for which efficient and specific antibodies or a specific ligand are available. neddylation Reversible reaction that create a covalent bond between a Glycine residue of an ubiquitine like NEDD8 protein and a lysine residue of the target. PMID:16127432 GO:0045116 neddylation reaction synthetic phenotype Two silent mutations show an altered phenotype when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794. gfp complementation Protein-protein interaction trap based on fusions of bait and prey protein to two dissected fragment of GFP. The system implemented in E. coli, allow screening of partners, including membrane proteins and also detect transient interaction that are stabilized by the complemented GFP. PMID:15631464 green fluorescence protein complementation assay synt growth effect synthetic growth effect Two silent mutations show altered growth effect when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective') cabri CABRI cell lines catalogue available at. http://www.cabri.org/ Western blot assay carried out using monospecific antibodies produced in the supernatant of a cell line obtained by fusing a lymphocyte B to a myeloma cell line or selected by phage display technology. monoclonal antibody western blot monoclonal western pubchem PubChem PMID:16381840 PubChem provides information on the biological activities of small molecules. http://pubchem.ncbi.nlm.nih.gov/ neural network on interface properties PMID:11874449 PMID:11455607 Neural networks are trained on the properties of residues belonging to a cluster of residues that are neighbours in space on protein surface. The predictor permits the inference of the residues that are likely to be on an interaction interface. interface predictor tap tagged Tag encoding a calmodulin binding peptide, a TEV cleavage site, and the Staphylococcus aureus Protein A fused to a target protein and the introduction of the construct into the host cell or organism, maintaining the expression of the fusion protein at, or close to, its natural level. The fusion protein and associated components are recovered from cell extracts by affinity selection on an IgG matrix. After washing, the TEV protease is added to release the bound material. The eluate is incubated with calmodulin-coated beads in the presence of calcium. This second affinity step is required to remove the TEV protease as well as traces of contaminants remaining after the first affinity selection. After washing, the bound material is released with EGTA. This tag allows two steps purification steps ensuring a highly selective purification of the tapped protein (first round of selection on the protein A, a high affinity tag) under mild condition (non denaturant pH or conditions required to remove the tag). CBP-ProtA tagged calmodulin binding peptide plus protein a tag Beta-galactosidase activity can be used to monitor the interaction of chimeric proteins. Pairs of inactive beta gal deletion mutants are capable of complementing to restore activity when fused to interacting protein partners. Critical to the success of this system is the choice of two poorly complementing mutant moieties, since strongly complementing mutants spontaneously assemble and produce functional beta-gal activity detectable in absence of any fused protein fragment. PMID:9237989 PMID:12042868 beta galactosidase beta galactosidase complementation The protein of interest is expressed as a fusion to the peptide EUKLISEED (a fragment of the Myc oncogene protein) for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem. OBSOLETE redundant term. Map to feature type: myc-tagged (MI:0522) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007). myc tag coip myc tag coimmunoprecipitation search-url: http://www.signaling-gateway.org/data/Y2H/cgi-bin/y2h_int.cgi?id=${ac} afcs AfCS Alliance for Cellular Signaling (AfCS -Nature) store yeast 2-hybrid Interaction data and expression data. Information and data are freely available to all. http://www.signaling-gateway.org alliance for cellulare signaling EcoCyc is a bioinformatics database that describes the genome and the biochemical machinery of E. coli K12 MG1655. http://ecocyc.org/ ecocyc EcoCyc source database Source database. RESID:AA0211 RESID:AA0057 GO:0018256 Reaction that can affect K or G residues. formylation reaction formylation protein kinase assay Catalysis of the transfer of a phosphate group, usually from ATP, to a protein substrate. lexa b52 complement lexa b52 complementation Yeast two-hybrid system using Escherichia coli LexA amino acids 1-202 as the DNA-binding domain (BD), E. coli B42 acidic sequence as the activation domain (AD), and two reporters, lacZ and LEU2, each containing upstream LexA binding elements. PMID:14613974 LexA B52 transcription complementation inhibitor small mol inhibitor small molecules PMID:10780927 PMID:10542155 Protein activity is inhibited by small inorganic molecules (drugs) that specifically bind to their targets. Recently this classical pharmacological approach is sometime referred to as 'chemical genetics'. OBSOLETE as such method can be described using the biological role inhibitor (MI:0586). EM5 [E:meth_o5] glutamatemethylester residue modification. 5-methyl-L-glutamate glutamic acid 5-methyl ester (S)-2-aminopentanedioic acid 5-methyl ester L-glutamic acid 5-methyl ester glutamic acid gamma-methyl ester Attribute name of annotation associated to a CV term. controlled vocabulary attribute name cv att name List of authors associated to a publication. This attribute is generally associated to an experiment. author-list protease homogeneous time resolved fluorescence Measures quenching of the nonradiative energy transfer between fluorescent long-lifetime lanthanide chelates and different acceptors. Fluorescence donor and acceptor are on the same peptide molecule and separated by the action of the protease. Protease HTRF protease htrf The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. www.pantherdb.org/ PANTHER panther Protein sample collected by in vitro translation of its mRNA taking advantage of purified translation machinery. in vitro translated protein in vitro translated The low molecular weight RNAs that specifically bind amino acids by aminoacetylation to form aminoacyl tRNA and which possess a special nucleotide triplet, the anticodon. transfer rna tRNA transfer RNA transfer ribonucleic acid trna bacterial two-hybrid adenylate cyclase complementation Adenylate cyclase is encoded by the cyaA gene and contains a catalytic domain which can be proteolytically cleaved into two complementary fragments, T25 and T18, which remain associated in the presence of calmodulin in a fully active ternary complex. In the absence of calmodulin, the mixture of the two fragments does not exhibit detectable activity, suggesting that the two fragments do not associate. When expressed in an adenylate cyclase-deficient E. coli strain (E. coli lacks calmodulin or calmodulin-related proteins), the T25 and T18 fragments fused to putative interacting proteins are brought into close association which result in cAMP synthesis. The level of reconstructed adenylate cyclase can be estimated by monitoring the expression of a cAMP dependent reporter gene. PMID:9576956 adenylate cyclase O-phosphonoserine RESID:AA0037 residue modification. 2-amino-3-hydroxypropanoic acid 3-phosphate O3-phosphoserine phosphoserine 2-amino-3-hydroxypropanoic acid 3-phosphate;O-phosphonoserine;O3-phosphoserine serine phosphate ester SPO [S:po] O-phospho-L-serine (S)-2-amino-3-(phosphonooxy)propanoic acid o-phospho-serine caution Warning about errors/ grounds for confusion. Can be associated to interaction, experiment, Cv term or any participant. antagonist Opposes the effect of a natural ligand by binding at the same receptor or alters the state of an upstream molecule to inhibit a downstream interaction. PMID:9560251 In this method the two proteins, whose interaction is under investigation, (in this case mostly membrane proteins) are fused to an terminal fragment (Nub) and to a C-terminal fragment of ubiquitin (Cub). The two fragments do not associate to form a functional ubiquitin unless the two fused membrane proteins form a complex. The association is monitored by an ingenious trick. The C-term fragment of ubiquitin is expressed as a fusion to a transcription factor that being linked to a membrane protein cannot perform its function unless it is released form the ubiquitin fusion by a specific protease. This achieved through the activity of UBP (an ubiquitin specific protease) that cleaves off the reporter protein only when a functional ubiquitin is reconstituted. ubiquitin reconstruction ub reconstruction infection Molecule introduced into a cell via an external organism, usually a virus or bacteria. poly A poly adenine poly a A sequence of adenine nucleotides that is added to the 3' end of some primary transcript messenger RNA molecules in eukaryotes during post-transcriptional processing. The added tail is believed to confer stability to the molecule. DDBJ/EMBL/GenBank Nucleotide Sequence Database Collaboration exchange new and updated data on a daily basis to achieve optimal synchronisation. http://www.ebi.ac.uk/embl/Contact/collaboration GenBank DDBJ/EMBL/GenBank ddbj/embl/genbank DDBJ id-validation-regexp:"[0-9]+|[A-Z]{1,2}[0-9]+\.[0-9]+ " http://www.ebi.ac.uk/cgi-bin/dbfetch?db=EMBLSVA&id=${ac} search-url: EMBL acetyltryptophan WAC N-acetyl-L-tryptophan [W:ac] residue modification. n-acetyl-tryptophan s-(adp-ribosyl)-cysteine S-L-cysteine alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate) S-alpha-D-ribofuranosyl-L-cysteine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate) S-(ADP-ribosyl)-L-cysteine (R)-2-amino-3-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]sulfanyl)propanoic acid residue modification. adp-ribosylcysteine A specific affinity chromatography method where a protein of interest (bait) is expressed as a fusion to an affinity tag (GST, HIS tag and others) and linked at high concentration to a support that has affinity for the tag. Purified proteins or cellular extracts are then adsorbed to the resin and the retained binding proteins are identified. Thus, in this approach, the protein that has affinity for the solid support (bait) is expressed and purified first, often in an heterologous system, and then challenged with a solution containing the candidate partner proteins. no antibodies to retain bait but other affinity stuffs. pull down a given (suppressed) mutation phenotype is reverted by a supressor gene mutation. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'mutated gene' MI:0804. suppression mutation sem Electron tomography is a general method for three-dimensional (3D) reconstruction of single, transparent objects from a series of projection images (i.e. from a tilt series) recorded with a transmission electron microscope. It offers the opportunity to obtain 3D information on structural cellular arrangements with a high resolution. PMID:12160704 electron tomography A supressed gene mutation cause of an altered phenotype that is reverted to wild type phenotype when cell also carry a suppressor gene with a specific mutation or altered expression level. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793. suppression myristoylated residue myristoylated aa residue modification. Identifier of a publication prior it pubmed indexing. digital object identifier doi id-validation-regexp:"doi:[0-9]+\.[0-9]+\/" ha tag coip The protein of interest is expressed as a fusion to the peptide YPYDVPDYA (a fragment of the influenza hemaglutinin protein) for which antibodies are commercially available. OBSOLETE redundant term. Map to feature type : ha-tagged (MI:0520) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007). ha tag coimmunoprecipitation cofactor A cofactor is a small molecule required for the catalysis of an enzyme. coenzyme protease assay Measures the enzymatic hydrolysis of a peptide bond within a peptide or protein substrate. predetermined feature predetermined featur Feature detection based on the knowledge of the molecule, before any experiment. rsa A technique used to detect genetic interactions between 2 (or more) genes in a sporulating organism by scoring a large population of haploid spores for a phenotype and correlating the phenotype with the presence of single vs double (multiple) mutations. A diploid heterozygous organism harbouring mutations in two (or more) genes is induced to sporulate. Resulting spores are meiotic segregants that are haploid and are either wild type or mutant at each locus. Spores are scored for a phenotype, such as loss of viability. spore germination RSA random-spore analysis random spore analysis confidence-mapping Description of confidence assessment method generally associated to the experiment. green fluorescent protein tag The green fluorescent protein of the bioluminescent jellyfish Aequorea victoria can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native. PMID:7491768 gfp tag green fluorescent protein GFP knock-out knock out The gene has been completely removed e.g. by genetic engineering Electron crystallography Electron cryomicroscopy PMID:11785754 Electron microscopy methods provide insights into the structure of biological macromolecules and their supramolecular assemblies. Resolution is on average around 10 Angstroms but can reach the atomic level when the samples analysed are 2D crystals. Different types of samples can be analysed by electron microscopy: crystals, single particles like viruses, macromolecular complexes or entire cells and tissue sections. Samples can be chemically fixed or vitrified by rapid freezing in liquid ethane, and then transferred into the electron microscope. Data collection consists of the recording of electron diffraction data (2D crystals) and images. Depending on the type of sample, different approaches are used to analyse and merge images and electron diffraction data. electron microscopy 3'-methyl-L-histidine N(delta)-methylhistidine residue modification. pi-methylhistidine 3'-methyl-histidine methylhistidine [H:meth_n4] pros-methylhistidine MHS 1-methylhistidine [misnomer] (S)-2-amino-3-(3-methyl-3H-imidazol-4-yl)propanoic acid deoxyribonucleic acid DNA deoxyribonucleic acid dna Polymer formed by the deoxyribose sugar group, and the nucleotides bases adenine, guanine, thymine and cytosine. SO:0000352 WormBase id-validation-regexp:"WBGene[0-9]{8}" wormbase WormBase is the central worm database that houses the gene reports, locus reports, translation reports, expression pattern data and genome browser. http://www.wormbase.org/ Three hybrid system rna tri hybrid PMID:8972875 PMID:12162957 In vivo reconstruction of specific RNA-proteins interactions. The DNA binding and transcription activator domains of GAL4 are brought together via the interaction of recombinant RNA. The first hybrid protein contains the DNA binding domain of GAL4 fused to RevM10 (a mutated RNA binding protein of HIV-1 that binds specifically to the Rev responsive element RRE of the env gene). A recombinant RNA contains the RRE sequence and a target RNA sequence X. The second hybrid protein contains the activation domain of GAL4 fused to protein Y tested for its ability to bind the target RNA X. If this interaction occurs the three hybrid reconstructs GAL4 and the transcription of a reporter gene is activated. MMDB (Molecular Modeling DataBase), is a subset of three-dimensional structures obtained from the Protein Data Bank. http://www.ncbi.nlm.nih.gov/Structure MMDB mmdb peptide-parent Describe cross link pointing to a peptide parent sequence. peptide parent sequence reference PMID:11791231 Methods based on natural language processing to detect possible interactions between proteins (direct physical interactions or indirect genetic interactions). This includes the detection of non ambiguous protein or gene names and analysis of the relation expressed in a sentence among them. predictive text mining predictive tm An altered expression is the suppressor of a phenotype. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'expression level alteration' MI:0803. suppression expression alteration suppress expression ptm post translation modification Residue covalent modifications occurring in the specific protein form involved in an interaction. deformylation reaction deformylation N6-formyl-L-lysine is cleaved and returns a K residue. dna dna pol assay dna directed dna polymerase assay Measures the catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template or primer. N-aspartyl-glycosylphosphatidylinositolethanolamine gpi-aspartate gpi-anchor amidated aspartate RESID:AA0159 residue modification. A cassette coding for a protein tag is inserted by homologous recombination onto the genomic copy of an open reading frame. The advantage of this delivery method is that the resulting engineered protein is expressed under its natural promoter control. OBSOLETE redundant term. Map to feature type : tag (MI:0507) genetic tag insertion genomic tagging mudpit multidimensional protein identification technology PMID:11231557 MudPIT is a method for rapid and large-scale protein identification by multidimensional liquid chromatography associated with tandem mass spectrometry. The chromatography step consists of strong cation exchange material back-to-back with reversed phase material inside fused silica capillaries. The peptides bound to the cation-exchange resin are freed by the gradually increasing salt concentration of the buffer and are subsequently retained by the reversed phase resin. Increasing buffers hydrophobicity progressively elute peptides from the reversed phase packing directly into the mass spectrometer. Typically this mass spectrometer will be a tandem electrospray, so peptides undergo ionization in the liquid phase, are separated in a primary mass spectrometer, analysed in the second mass spectrometer and identified. Molecules labelled with isotope 13 of carbon atoms. C13 13C 13c label phosphoshistidine phospho-histidine residue modification. RESID:AA0036 RESID:AA0035 RESID:AA0039 RESID:AA0038 RESID:AA0033 Reversible reaction that can affect D,C,H,S,T,Y,R residues. GO:0016310 phosphorylation reaction phosphorylation nucleotidyltransferase assay polymerase assay Measures the catalysis of the transfer of a free nucleotidyl group to a nucleic acid chain. The protein under study is expressed as a fusion with a labelling protein, having either fluorescence properties or an enzymatic activity that facilitates its purification, identification, localisation or quantification. fusion protein sumoylation reaction sumoylation PMID:15985640 GO:0016925 Reversible reaction that create a covalent bond between a C-terminus G of an ubiquitine like sumo protein and a K residue of the target. homogeneous pure The author states a molecule is completely pure, i.e. no other molecular species are present. tau-phosphohistidine 1'-phospho-L-histidine HPE histidine-N1'-phosphate (S)-2-amino-3-(1-phosphono-1H-imidazol-4-yl)propanoic acid 1'-phospho-histidine residue modification. histidine-N(epsilon)-phosphate histidine-3-phosphate [misnomer] 1-phosphohistidine [H:po_e] tele-phosphohistidine Stable introduction and expression of nucleic acid carried out by treatment with divalent cation. nucleic acid transformation by treatment with divalent cation n transformat cation Fluorescent microscopy uses a high intensity light to illuminate the sample. This light excites fluorescence species in the sample, which then emit light of a longer wavelength. A fluorescent microscope also produces a magnified image of the sample, but the image is based on the second light source -- the light emanating from the fluorescent species -- rather than from the light originally used to illuminate, and excite, the sample. fluorescence microscopy fluorescence imaging electron paramagnetic resonance EPR (also called ESR, Electron Spin Resonance) spectroscopy is analogous to NMR, but is based on the excitation of unpaired electrons instead of nuclei. Unpaired (single) electrons are only found in radicals and some metal ions (paramagnetic species); the EPR spectrum provides information about the environment and mobility of the paramagnetic species. The magnetic interaction of two paramagnetic centres in a protein can be used to calculate the distance between them; this allows studies of the movements and interactions of protein segments. In proteins without any intrinsic unpaired electrons it is possible to attach a radical probe (spin label). Stable nitroxide radicals can be bound to amino acid residues, in analogy with fluorescent probes. In combination with site directed mutagenesis this method is used in particular to study structure and assembly of membrane proteins, by measuring with EPR whether an amino acid is in a polar or non polar environment. epr ESR EPR lumier luminescence based mammalian interactome mapping This strategy uses Renilla luciferase enzyme (RL) fused to proteins of interest, which are then coexpressed with individual Flag-tagged partners in mammalian cells. Their interactions were determined by performing an RL enzymatic assay on immunoprecipitates using an antibody against Flag. PMID:15761153 uniparc id-validation-regexp:"UPI[A-F0-9]{10}" UniParc UniProt Archive (UniParc) is part of UniProt project. It is a non-redundant archive of protein sequences derived from many sources. http://www.ebi.ac.uk/uniparc/ Molecule whose sequence identity is derived from their molecular weight identification by weight weight identificat Description of molecules polarity on a directional interaction. biological role prosite Prosite id-validation-regexp:"PS[0-9]{5}" PROSITE is a database of protein families and domains. It consists of biologically significant sites, patterns and profiles. http://us.expasy.org/prosite/ PMID for application instance:12167034 PMID:11551470 This method permits the coupling of phenotype to genotype via the formation of a non-covalent ternary complex between mRNAs and their encoded polypeptides while they are translated in an in vitro system. As a first step a cDNA library is constructed that encodes chimeric proteins in which the natural proteins or protein domains are fused to a C-terminal tether. As a consequence when the mRNA is translated in vitro the domain can fold while the tether is still in the ribosomal tunnel. Furthermore this chimeric mRNAs lack a stop codon, thus preventing release of the mRNA and the polypeptide from the ribosome. High concentrations of magnesium and low temperature further stabilise the ternary complex. Similarly to phage display, these complexes can be used directly to select for nucleic acids encoding proteins with desired properties. ribosome display Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains. http://www.sanger.ac.uk/Software/Pfam pfam Pfam id-validation-regexp:"PF[0-9]{5}" mM 10E-3 moles per liter of solution. OBSOLETE: term redundant with the schema exponent attribute of the parameter. millimolar palmitoylation reaction RESID:AA0080 RESID:AA0079 RESID:AA0077 GO:0018318 Reversible reaction that can affect C,K,T or S residues. palmitoylation Displayed as '>'. greater-than Partially determined sequence position known to be in a location higher than a given position. pisa Protein In Situ Array is a method by which protein arrays are rapidly generated in one step directly from DNA, by cell-free protein expression and simultaneous in situ immobilisation at a surface. Individual genes or fragments are produce by PCR or RT-PCR depending on the source of genetic material using properly designed primers. The PISA is generated by cell-free protein synthesis using coupled transcription and translation to produce a double HexaHis-tagged protein, the reaction being carried out on a surface to which the protein adheres as soon as it is synthesised. PMID:11470888 protein in situ array PISA Text mining methods can be used to predict or confirm interactions by automated processing of scientific literature. Co-occurrence in the same sentence of an abstract of gene products labels are analysed to evaluate whether it represents a valid evidence of an interaction. text mining SCOP superfamily scop superfamily SUPERFAMILY is a library of profile hidden Markov models that represent all proteins of known structure. The library is based on the SCOP classification of proteins: each model corresponds to a SCOP domain. http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/ ha tag The protein of interest is expressed as a fusion to the peptide YPYDVPDYA (a fragment of the influenza hemagglutinin protein) for which antibodies are commercially available. YPYDVPDYA epitope tag Predictive algorithms that rely on the information obtained by experimental results. experimental knowledge based experimental info partial identification of protein sequence partial id prot seq partial protein sequence identification. unknown participant Any type of molecule, including complexes, that may be observed but not identified. This term should be use only at PARTICIPANT level. electrophoretic mobility shift assay Gel retardation assay band shift This method proves the interaction between a nucleic acid and a protein partner. On the same electrophoresis gel 1 lane is loaded with a radiolabeled nucleic acid of known sequence, a second lane is loaded with the same nucleic acid together with a purified protein (or a protein mixture). After the electrophoresis run and autoradiography by comparing the nucleic acid migration in the two lanes the retardation of the nucleic acid due to its interaction with a protein can be easily observed. PMID:12169687 emsa The Conserved Domain Database may be used to identify the conserved domains present in a protein sequence. http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml cdd CDD phosphatase htrf phosphatase homogeneous time resolved fluorescence Measures quenching of the nonradiative energy transfer between fluorescent long-lifetime lanthanide chelates and different acceptors. Relies on a fluorescence energy donor and acceptor being removed from close proximity on the phosphorylated substrate due to the action of the phosphatase. phosphatase HTRF homogeneous time-resolved fluorescence Attribute name of annotation associated to an interaction element. interaction att name interaction attribute name Dye coupled to a molecule allowing its identification isolation and monitoring. dye labelled dye label srpRNA signal recognition particle rna Small (300 nucleotides) stable RNAs transcribed by RNA pol III that are part of the signal-recognition particle (SRP). This particle comprises one RNA and six proteins bound to the RNA. SRP function is to assist secretory proteins sorting in the endoplasmic reticulum (ER). SRP is a cytosolic particle that transiently binds to the ER signal sequence of a nascent protein, to the large ribosomal unit, and to the SRP receptor in the ER membrane. srprna cyanine label The organic cyanine dyes emit in the red range (>550 nm), offer a number of advantages. Their emission range is such that background fluorescence is often reduced. In addition these molecules can be linked directly to specific locations in synthetically produced nucleic acids. fingerprinting peptide massfingerprinting This approach leads to protein identification by matching peptide masses, as measured by mass spectrometry, to the ones calculated from in silico fragmentation of a protein sequence database. A peptide mixture from a tryptic digest is analysed by MALDI-MS (Matrix-assisted laser desorption ionization mass spectrometry). The list of peptide masses obtained by MALDI MS is automatically compared to the calculated masses of the predicted peptide fragments for each entry in the database. High mass accuracy is very important in order to obtain a statistically significant and unambiguous match This method is best applied to completely sequenced genomes and well characterised proteomes. However, depending on the data quality, proteins that are highly homologous to already characterised proteins (greater than 80 to 90% sequence identity) can also be identified. The retrieved sequence are evaluated by mass accuracy of the peptides, matching of additional peptide masses in the MALDI spectrum after accounting for common modifications such as oxidation, acrylamidation of cysteine and missed cleavages and the use of secondary information (apparent isoelectric point and molecular weight). If any ambiguity about the identification by MALDI-MS still exists, the results must verified by an other identification method. Peptide mass fingerprint is generally carried out with a MALDI-TOF (Matrix-assisted laser desorption ionization time-of-flight ) instrument but can also be achieved ESI-TOF (Electrospray Ionisation time-of-flight) or LC-MS (Liquid Chromatography-Mass Spectrometry) mass spectrometer. PMID for application instance:11805826 PMID:11752590 PMID:10967324 Gln-Lys cross-link catalyzed by a transglutaminase. RESID:AA0124 transglutamination transglutamination reaction pathway Refers to the metabolic pathway involving an interaction or a complex. asynthetic interaction The phenotype resulting from genetic perturbation of A alone, B alone and AB combined have the same effect on the WT background. asynthetic PMID:7682645 Filamentous phages (M13, f1, fd) have been extensively used to develop and implement the technology of phage display. Repertoires of relatively short peptides of random amino acid sequences or cDNA libraries have been constructed and searched successfully. Most experiments have taken advantage of the ability to assemble phages decorated with hybrid versions of the receptor protein pIII or of the major coat protein pVIII. Both systems allow the display of foreign peptides by fusion to the amino-terminus of the capsid protein but differ in the number of peptide copies that can be displayed on each phage particle. Display libraries of very diverse protein fragments have been constructed by fusing either genomic or cDNA fragments to gene III or gene VIII. filamentous phage filamentous phage display Alexa fluorescent dye analogue to Lucifer Yellow with an approximate excitation wavelength maximum of 430 nm. alexa 430 label Connection between molecule. interaction type N6-acetyl-L-lysine or S-acetyl-L-cysteine are cleaved and return K or C residues. GO:0006476 deacetylation deacetylation reaction PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family. http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/ prints PRINTS id-validation-regexp:"PR[0-9]{6}" The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number. experimental feature url URL/Web address describing an experiment, an interaction, a Cv term or an organism. Several mutant molecules are produced by random or directed techniques and assayed for their ability to support binding. Mutants defective in binding are tested for correct folding to pinpoint the residues that are directly involved in binding. mutation analysis GO:0018347 Reversible reaction that can affect C residue. farnesylation reaction farnesylation fluorescence technology Techniques based upon the measurement of the emission of one or more photons by a molecule activated by the absorption of a quantum of electro-magnetic radiation. Typically the emission, which is characterised by a wavelength that is longer than the one of excitatory radiation, occurs within 10-8 seconds. fluorescence neutral component Molecule role in an experimental setting that does not have an embedded asymmetry. inhibitor antibodies Intracellular or extracellular expression of antibodies is used to target specific gene products in order to inactivate them. Most of the times the antibody scaffold need s to reengineered for efficient expression and solubility in the cytoplasm. OBSOLETE as such method can be described using the biological role inhibitor (MI:0586). PMID:10189716 RESID:AA0215 RESID:AA0146 RESID:AA0029 RESID:AA0028 GO:0018126 Irreversible reaction that can affect K,P,Y or R residues. hydroxylation hydroxylation reaction Two silent mutations show growth increase when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective') synthetic growth increase synt growth increase experiment description experiment descripti The experimental condition text description, should contain information about the organisms hosting the interaction. Mouse Genome Informatics (MGI) provides integrated access to data on the genetics, genomics, and biology of the laboratory mouse. http://www.informatics.jax.org/ MGD/MGI mgd/mgi id-validation-regexp:"MGI:[0-9]+" Experimental method used to identify the region of a nucleic acid involved in an interaction with a protein. One sample of a radiolabeled nucleic acid of known sequence is submitted to partial digestion. A second sample is incubated with its interacting partner and then is submitted to the same partial digestion. The two samples are then analyzed in parallel by electrophoresis on a denaturing acrylamide gel. After autoradiography the identification of the bands that correspond to fragments missing from the lane loaded with the second sample reveals the region of the nucleic acid that is protected from nuclease digestion upon binding. dna footprinting Method for temporarily permeabilising cell membranes so as to facilitate the entry of large or hydrophilic molecules (as in transfection). A brief (ca 1 msec) electric pulse is given with potential gradients of about 700V/cm. PMID:6329708 electroporation This approach uses a protein interaction network of a given organism to infer interaction in another organism using information about the interacting region. The regions or domains involved in interactions are clustered if they share sequence similarity and have common interacting partners. The resulting domain profiles are then used to screen the proteome of another organism and domain-domain interactions are inferred. Ultimately, an inferred protein interaction map is built in this second organism. PMID:11473021 domain profile pairs A stable set of interacting proteins that can be copurified and operate as a functional unit. protein complex membrane compl membrane bound complementation assay Protein complementation assay based on dissection of a membrane protein. cosedimentation through density gradient density sedimentatio Sedimentation through a density gradient measures the sedimentation rate of a mixture of proteins through either a glycerol or sucrose gradient. Two interacting proteins will sediment mostly as a complex at concentrations above the binding constant. By varying the concentration of one or both of the complex constituents and taking into account the dilution of the species during sedimentation, one can reasonably accurately estimate the binding constant. PMID:10410796 The organic cyanine Cy5 emits maximally at 670 nm. cy5 label Fluorophore which emits electromagnetic radiation of given wavelength. fluorescence donor biotinyllysine N6-[5-((3aS,4S,6aR)-hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-4-yl)-1-oxopentyl]-L-lysine N6-biotinyl-L-lysine [K:biotin] residue modification. RESID:AA0117 N6-biotinyllysine biocytin (3aS-(3aalpha,4beta,6aalpha))-N6-(5-(hexahydro-2-oxo-1H-thieno(3,4-d)imidazol-4-yl)-1-oxopentyl)-L-lysine epsilon-N-biotinyllysine (S)-2-amino-6-[5-((3aS,4S,6aR)-hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-4-yl)-1-oxopentyl]aminohexanoic acid n6-biotinyl-lysine KBT nucl delivery nucleic acid delivery Method by which nucleic acids are delivered or engineered into a cell. cyan fluorescent protein tag cyan fluorescent protein CFP The cyan fluorescent protein derived from Anthozoa reef coral can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native. cfp tag Covalent or non covalent binding of lipid group on a protein residue. GO:0006497 lipid addition Small molecules, peptides or full proteins that can be used as label as they confer some property that facilitates identification purification and monitoring to the labelled molecule. tag uM 10E-6 moles per liter of solution. OBSOLETE: term redundant with the schema exponent attribute of the parameter. micromolar o4'-phospho-tyrosine O4'-phospho-L-tyrosine (S)-2-amino-3-(4-phosphonooxyphenyl)propanoic acid residue modification. phosphotyrosine [Y:po] YPO 2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-phosphate O4-phosphotyrosine tyrosine phosphate microscopy imaging techniques Methods that provide images of molecules at various resolution depending on the technology used. MINT The Moleculer INTeraction database (MINT) is a relational database designed to store interactions between biological molecules. http://mint.bio.uniroma2.it/mint/ id-validation-regexp:"MINT_[0-9]+" mint comigration in sds page comigration in sds PMID:16732283 Method allowing the detection of strong interactions between two molecules by their very close proximity or the overlap of their relative bands in a denaturing SDS gel. adp-ribosylated adp ribosylated residue residue modification. chromatin immunoprecipitation assays PMID:12054902 Chromatin immunoprecipitation (ChIP) is a powerful approach that allows one to define the interaction of factors with specific chromosomal sites in living cells. ChIP involves treating cells or tissue briefly with formaldehyde to crosslink proteins to DNA. An antibody against a protein suspected of binding a given cis-element is then used to immunoprecipitate chromatin fragments. Polymerase chain reaction analysis of the immunoprecipitate with primers flanking the cis-element reveals whether a specific DNA sequence is recovered in an immune-specific manner and therefore whether the protein contacted the site in living cells. ch-ip PMID:11558993 FRET is a quantum mechanical process involving the radiationless transfer of energy from a donor fluorophore to an appropriately positioned acceptor fluorophore. The fluorophores are genetically fused to the protein in analysis and cotransfected. Three basic conditions must be fulfilled for FRET to occur between a donor molecule and acceptor molecule. First, the donor emission spectrum must significantly overlap the absorption spectrum of the acceptor. Second, the distance between the donor and acceptor fluorophores must fall within the range 20 to 100 Angstrom. Third, the donor and acceptor fluorophores must be in favourable orientations. fret RET FRET analysis FRET fluorescent resonance energy transfer A microarray consisting of antibodies spotted on a solid support in appropriate orientation is incubated with a biological sample (or antigen). Some proteins are captured by the antibodies in the array. Protein of forming complexes on the array are identified according to their prior labelling (tag, ELISA, biotin and others). sandwich immunoassay antigen capture assay antibody array electron donor Any molecule that is able to transfer an electron to another chemical species. Search URL to retrieve an external entry in ASCII format. Generally associated to Cv Database terms. search-url-ascii protein delivery by cationic lipid treatment Proteins are delivered into cells by treatment with cationic lipids. prot cationic lipid A protein of interest (the bait) is fused to the full-length bacteriophage lambda repressor protein (lambdacI, 237 amino acids), containing the amino terminal DNA-binding domain and the carboxylterminal dimerization domain. The corresponding target (prey) protein is fused to the N-terminal domain of the alfa-subunit of RNA polymerase (248 amino acids). The bait is tethered to the lambda operator sequence upstream of the reporter promoter through the DNA-binding domain of lambdacI. When the bait and prey interact, they recruit and stabilize the binding of RNA polymerase at the promoter and activate the transcription of the HIS3 reporter gene. Due to the tendency of both the lambda repressor protein and the N-terminal domain of the alfa-subunit of RNA polymerase to dimerize, this system might not be optimal for the analysis of proteins that self-associate unless their interaction with other protein partners depends on the oligomerization. PMID:15792953 BacterioMatch lambda repressor two hybrid lambda two hybrid small nuclear rna snrna These RNA molecules are relatively short (less than 200 nucleotides each), and there are five of them (U1, U2, U4, U5, and U6) involved in the major form of pre-mRNA splicing. Known as snRNAs (small nuclear RNAs), each is complexed with at least seven protein subunits to form a snRNP (small nuclear ribonucleoprotein). These snRNPs form the core of the spliceosome. snRNA Predicts the structure of a protein-protein complex from the unbound structures of its components. The initial approach in the majority of docking procedures is based largely on the 'rigid-body' assumption, whereby the proteins are treated as solid objects. Initial scoring of a complex is based on geometric fit or surface complementarity. This generally requires some knowledge of the binding site to limit the number of solutions. PMID for application instance:11478868 PMID:9631301 docking elongation DNA replication elongation dna strand elongation The process by which a DNA strand is synthesized from template DNA by the action of polymerases, which add nucleotides to the 3' end of the nascent DNA strand. GO:0006271 Radiolabelled nucleic acids with a known sequence are incubated with purified proteins or reproducible protein mixture (HPLC eluate fractions) and then irradiated with UV. The complex are treated with an enzyme to remove the unbound nucleic acid (Rnase A or Dnase I for example), washed and then analyzed by electrophoresis. The eventual complexes are identified by autoradiography. The proteins involved in the complex can be recognized by specific antibodies or by retrieving the original protein mixture and carrying further analysis on it. The affinity of the binding can be estimated by adding a non-labelled nucleic acid as competitor before the UV irradiation. nucleic acid uv cross-linking assay nucl ac uv crosslink alkylated cysteine Artificial residue modification enabling studies of cysteine binding status. PMID:15325307 chemical footprinting chemical footprint Sites of sequence-specific DNA-protein interaction are identified by altered reactivity of a chemical probe to DNA bound by a protein compared to the same nucleotide sequence in naked DNA. Nucleotides in close contact with the binding protein are protected from modification or cleavage by the probe. In certain case DNA-protein interactions can be indicated by enhanced modification or cleavage by the probe at particular nucleotides. When these probes are administrated to intact cells, the pattern of protection from the probes identifies the location of DNA-protein interactions in vivo. substitut analysis substitution analysis In this approach, once a molecule is demonstrated to participate in an interaction, several substitution mutants are produced and tested in the binding assay to identify the residues which identity is crucial for the interaction. Interaction leading to the formation of covalent bond within an autocatalytic molecule or between partners. covalent binding Cell has been physically or chemically broken open and molecule present in resulting mixture of cellular components. cell lysate gene3d Gene3D The Gene3D database provides a combined structural, functional and evolutionary view of the protein world. It is focused on providing structural annotation for protein sequences without structural representatives--including the complete proteome sets of over 240 different species. http://cathwww.biochem.ucl.ac.uk:8080/Gene3D/ biochemical The application of chemical principles and methods to biological experiments. electron acceptor Molecule to which and electron may be transferred from an electron donor. 32p radiolabel P32 32P Molecule labelled with the radio isotope 32 of phosphorus atoms. glycosylation glycosylation reaction The covalent attachment of a glycosyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer. Reaction that can affect Ser, Thr, Cys, Arg, and Asn residues. This reaction is known to be reversible in the case of Asn substrate. RESID:AA0155 RESID:AA0154 RESID:AA0151 RESID:AA0122 GO:0043413 aggregation Physical association among molecules. OBSOLETE since too non-specific. Consider using physical interaction (MI:0218) instead. MASMTGGQQMG epitope tag The protein of interest is expressed as a fusion to the peptide MASMTGGQQMG for which antibodies are commercially available. t7 tag ribonucleic acid SO:0000356 Polymer formed by ribose sugar group, and the bases of the nucleotides adenine, guanine, uracil and cytosine. rna RNA Interaction identifier of a database belonging to IMEx consortium. imex-primary nucl microinjection Microinjection refers to the process of using a micro needle to insert substances at a microscopic level into a single living cell. It is a simple mechanical process in which an extremely fine micro needle penetrates the cell membrane and sometimes the nuclear envelope and releases nucleic acids. nucleic acid microinjection Amino terminal (1-220) part of the Escherichia coli lexA repressor, binding to 16 base pair palindromic DNA sequences. lexa dna bd lexa dna binding domain nucl lipotransfection Lipofection (or liposome transfection) is a technique used to inject genetic material into a cell by means of liposomes which are vesicles that can easily merge with the cell membrane since they are both made of a phospholipid bilayer. nucleic acid transfection with liposome Method using an antibody coupled with some colouring agent to detect a specific protein within a cell or tissue sample. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody. immunostaining stimulator Molecule stimulating an interaction by interacting with one or more of the participants. The A genetic perturbation enhances the phenotype of the B perturbation, or vice versa (e.g. WT = A < B < AB or WT = B < A < AB). This could be conditional or additive by the above scheme. enhancement interaction enhancement gpi-asparagine N-asparaginyl-glycosylphosphatidylinositolethanolamine gpi-anchor amidated asparagine RESID:AA0158 residue modification. geranylgeranylation reaction RESID:AA0104 GO:0018348 Reversible reaction that can affect C residue. geranylgeranylation Substrate protein radio-labelled by kinase transferring an isotope of phosphate from the nucleotide. Substrate isolated by gel electrophoresis and radio-labelling confirmed by autoradiography. in-gel kinase assay in gel kinase assay 2-amino-3-oxopropionic acid L-aminomalonaldehydic acid RESID:AA0185 residue modification. L-alpha-formylglycine L-amino-malonic acid semialdehyde 3-oxoalanine L-3-oxoalanine SOX (S)-2-amino-3-oxopropanoic acid L-serinesemialdehyde [misnomer] [S:oxal] oxoalanine A molecule whose synthesis is under control of its natural gene promoter or estimated to be expressed at a similar rate. endogenous level endogenous physiological level mi Controlled vocabularies originally created for protein protein interactions, extended to other molecules interactions. molecular interaction Peptide whose sequence is experimentally identified and can lead to a full protein identification. identified peptide weight by hoechst molecular weight estimation by hoechst staining Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with Hoechst dyes. pros-phosphohistidine [H:po_d] 3-phosphohistidine histidine-1-phosphate [misnomer] HPD residue modification. (S)-2-amino-3-(3-phosphono-3H-imidazol-4-yl)propanoic acid pi-phosphohistidine 3'-phospho-histidine histidine-N(delta)-phosphate histidine-N3'-phosphate flag tag coip The protein of interest is expressed as a fusion to the peptide DYKDDDDKV for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem. OBSOLETE redundant term. Map to feature type: flag-tagged (MI:0518) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007). flag tag coimmunoprecipitation subcellular preparation Cell lysates are partially fractionated to isolate a specific subcellular fraction. subcellular prep half cystine UniMod:374 RESID:AA0025 MOD:00798 A protein modification that is effectively either one half of a cystine cross-link, or a cysteine residue with one hydrogen atom or proton removed Half of a disulfide bridge imex IMEx International Molecular Interaction Exchange. cytoplasmic compl cytoplasmic complementation assay Protein complementation assay performed by dissecting a cytoplasmic protein activity and restoring it through the two hybrid proteins interaction. contact-email E-mail address to contact the author/organisation which has produced the data. This attribute is generally associated to an experiment. glycosylated residue residue modification. isoform parent sequence reference Reference to the master sequence from which this isoform has been derived. isoform-parent two hybrid PMID:1946372 PMID:10967325 The classical two-hybrid system is a method that uses transcriptional activity as a measure of protein-protein interaction. It relies on the modular nature of many site-specific transcriptional activators (GAL 4) , which consist of a DNA-binding domain and a transcriptional activation domain. The DNA-binding domain serves to target the activator to the specific genes that will be expressed, and the activation domain contacts other proteins of the transcriptional machinery to enable transcription to occur. The two-hybrid system is based on the observation that the two domains of the activator need to be non-covalently brought together by the interaction of any two proteins. The application of this system requires the expression of two hybrid. Generally this assay is performed in yeast cell, but it can also be carried out in other organism. two-hybrid Gal4 transcription regeneration 2h 2H Information on the complex being annotated. Attribute generally associated to an interaction. complex-properties 2-(acetylamino)ethanoic acid n-acetylglycine N-acetylglycine GAC aceturic acid [G:ac] residue modification. acetylglycine biotin tag Biotin, a 244 Dalton vitamin found in tissue and blood, binds with high affinity to avidin and streptavidin protein. Since biotin is a relatively small molecule, it can be conjugated to many proteins or nucleic acids without significantly altering their biological activity. Biotinylation reagents are available for targeting a variety of specific functional groups, including primary amines, sulfhydryls, carboxyls and carbohydrates that lead to nucleotides or amino acid biotinilation. N6-myristoyl-L-lysine is cleaved and returns a K residue. RESID:AA0078 demyristoylation demyristoylation reaction ancillary Molecule required for an observed binary interaction to occur. This molecule may act as stabilizer of any of the interaction partners or may act as a bridge molecule between them but the method does not provide resolution or evidence to demonstrate its actual molecular function (i.e.Mudpit, tri hybrid etc). M Molarity is the number of moles of solute dissolved in one liter of solution. The units, therefore are moles per liter, specifically it's moles of solute per liter of solution. These units are abbreviated as M and it means moles per liter (not just moles). molar Attribute name of annotation associated to a participant element. participant attribute name participant att name The gene is mutated in some unknown manner mutated gene RESID:AA0172 residue modification. tyrosine sulfate 2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-sulfate (S)-2-amino-3-(4-sulfooxyphenyl)propanoic acid O4-sulfotyrosine sulfotyrosine o4'-sulfo-tyrosine O4'-sulfo-L-tyrosine hypomorph The gene function has been partially reduced compared to wild-type by altering its sequence e.g. a temperature sensitive mutant residue modification. n-acetyl-lysine acetyllysine crosslink cross-linking study Analysis of complexes obtained by chemical treatments that promote the formation of covalent bonds among molecules in close proximity. interactor type Molecular species involved in the interaction. participant type cross-reference type xref type refType CvXrefQualifier Qualifier to describe the type of information a cross-reference is pointing to. necessary binding site A sequence range within a protein identified as being absolutely required for an interaction. required to bind Database citation list names of databases commonly used to cross reference interaction data. database citation nitro-tyrosine nitrated tyrosine residue modification. PMID:9636206 PMID:15657065 N-alanyl-glycosylphosphatidylinositolethanolamine residue modification. RESID:AA0163 gpi-alanine gpi-anchor amidated alanine EUKLISEED epitope tag myc tag The protein of interest is expressed as a fusion to the peptide EUKLISEED (a fragment of the Myc oncogene protein) for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem. inhibited Molecule being identified as target of an inhibitor. OBSOLETE as term is deprecated to describe the target of an inhibitor that can have any other biological role. The protein is expressed and purified as a fusion to the calmoduling-binding protein. The fusion protein can be purified by affinity chromatography using a calmodulin resin. calmodulin binding protein tag cam tag Measures the catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time. rna dna pol assay rna directed dna polymerase assay partial dna sequence Genes are recognised by hybridization of a probe with a fragment of the gene sequence. partial dna sequence identification by hybridization methylatedlysine residue modification. methylated-lysine his pull down The bait protein is expressed and purified fused to an amino or carboxyterminal tail containing a variable number of histidines. The bait protein is normally attached to a metal (usually nickel) resin. OBSOLETE redundant term. Map to feature type : his-tagged (MI:0521) and Interaction detection method: pull down (MI:0096). conformational tm confirmational text mining Text mining is used to support interactions which have been determined by other methods. Measures the catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. phosphatase assay PMID:9181578 The proteins are displayed on the surface of the yeast S. cerevisiae by fusion to signal sequences for protein secretion. This method is limited by the low efficiency of the yeast display system but can take full advantage of exploiting cell sorting methods (FACS) to isolate cells that display molecules with desired binding properties. yeast display Molar concentration of an antagonist which produces 50% of the maximum possible inhibitory response for that antagonist. Note this measure depends on the specific antagonist used and upon experimental conditions, notably temperature, pH and solution composition (e.g., salts, chelating agents and others). Thus the ic50 is a relative measure and its values can be compared only when sharing the same experimental setting. Unit Molar. ic50 IC50 fcs fluorescence correlation spectroscopy PMID:10733953 FCS monitors the random motion of fluorescently labelled molecules inside a defined volume irradiated by a focused laser beam. These fluctuations provide information on the rate of diffusion or diffusion time of a particle and this is directly dependent on the particle mass. As a consequence, any increase in the mass of a biomolecule, e.g. as a result of an interaction with a second molecule, is readily detected as an increase in the diffusion time of the particle. From these results the concentration of the different molecules can be calculated as well as their binding constant. FCS alexa 532 label Alexa fluorescent dye analogue to Rhodamine 6G with an approximate excitation wavelength maximum of 532nm. 14c radiolabel C14 14C Molecule labelled with the radio isotope 14 of carbon atoms. glycosylasparagine n4-glycosyl-asparagine N4-glycosyl-L-asparagine residue modification. peptide array PMID:11167074 The peptide synthesis methods offer numerous opportunities to synthesise and subsequently screen large arrays of synthetic peptides on planar cellulose supports. Discrete spots are arranged as arrays on membrane sheets where each spot is individually accessed by manual or automated delivery of the appropriate reagent solutions. Over the past few years protein-protein recognition, peptide-metal ion interactions, peptide-nucleic acid binding, enzymatic modification of peptides experiments, have been explored using synthetic peptide arrays on planar support. unspecified role Role not specified or not applicable to the data. 10E-9 moles per liter of solution. OBSOLETE: term redundant with the schema exponent attribute of the parameter. nanomolar nM phosphotransfer phosphotransfer reaction Reaction where a phosphate is transferred between two proteins of a phosphorelay system. PMID:16712436 GO:0016926 Cleavage of the G-K bond and release of the SUMO ubiquitin like proteins. desumoylation reaction desumoylation n-acetyl-histidine N-acetyl-L-histidine HAC [H:ac] residue modification. acetylhistidine Analysis of diffraction pattern of a partially ordered sample composed of fibers oriented parallel to each other. X-ray x-ray fiber diffraction x-ray fiber diffrac Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining by autoradiography. weight autoradiogra molecular weight estimation by autoradiography Protein introduced into a cell via an external organism, usually a virus or bacteria. prot infection protein delivery by infection Analysis of a diffraction pattern generated by an isotropic sample composed of many randomly oriented crystals. x-ray powder diffrac X-ray x-ray powder diffraction spin label PMID:10966640 Paramagnetic fragment, most often a cyclic nitroxide derivative, covalently attached to a molecule of interest. The author states a molecule is only partially purified, i.e. other molecular species also known to be present. partially purified alexa 350 label Alexa fluorescent dye analogue to AMCA (7-amino-4-methylcoumarin-3-acetic acid) with an approximate excitation wavelength maximum of 350 nm. Underexpression is the suppressor of a phenotype. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'under expressed' MI:0223. suppression underexpression suppress underexpres blue native page bn-page PMID:14665681 Blue native PAGE (BN-PAGE) permits a high-resolution separation of multi-protein complexes under native conditions. Blue native (BN)-PAGE is a charge shift method, in which the electrophoretic mobility of a complex is determined by the negative charge of the bound Coomassie dye and the size and shape of the complex. Coomassie does not act as a detergent and preserves the structure of complexes. Importantly, the resolution of BN-PAGE is much higher than that of other methods such as gel filtration or sucrose-gradient ultracentrifugation. Combined with other pre-purifications or dialysis steps this method permits the analysis of multi-protein complexes of whole cellular lysates by BN-PAGE. Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker. weight by staining molecular weight estimation by staining residue modification. amidated residue Experiments performed with participants removed from the cellular environment e.g. cell extracts, isolated proteins. OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction. in vitro mass spectrometry studies of complexes PMID for application instance:12057199 PMID:12504676 Mass spectrometric approaches to the study of protein in complexes permits the identification of subunit stoichiometry and transient associations. By preserving complexes intact in the mass spectrometer, mass measurement can be used for monitoring changes in different experimental conditions, or to investigate how variations of collision energy affect their dissociation. Complexes can be transferred into the gas phase by a nanoflow ESI (Electrospray Ionisation) ionisation device. This is the method of choice for the investigation of the higher-order structure of biomolecules because it allows direct analysis of dilute aqueous solutions and the desolvation process is efficient and closer to the native-like solution environment. Mass measurements of intact macromolecular complexes is largely the domain of time of-flight (TOF) MS. This is mostly due to the high sensitivity and speed of TOF analysis, as well as the virtually unlimited m/z range. Quadrupole TOF (Q-TOF) type mass spectrometers combine a quadrupole mass filter with an orthogonal TOF analyser. These spectrometers provide supplementary structural information for ions isolated in the quadrupole and analysed in the TOF. This allows complexes well in excess of 60 kDa to be dissociated and consequently their subunit composition can be determined. ms of complexes in silico Results generated by predictive bioinformatics approaches rather than experimental data. OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction. Predictive N-acetylthreonine n-acetyl-threonine N-acetyl-L-threonine [T:ac] (2S,3R)-2-acetylamino-3-hydroxybutanoic acid residue modification. TAC acetylthreonine rna directed rna polymerase assay rna rna pol assay Measures the catalysis of the reaction: nucleoside triphosphate + RNA (n) = diphosphate + RNA (n+1); uses an RNA template. b42 ad b42 activation domain B42 is an acidic sequence of 89 residues derived from Escherichia coli acting as weak transcription activation domain. When use in two hybrid experiments, the weakness of B42 as activator increases the sensitivity of the interaction detection. gene name synonym Gene name synonym. hypusine (S,R)-2-amino-6-(4-amino-2-hydroxybutylamino)hexanoic acid [K:hypu] KHY n6-(4-amino-2-hydroxybutyl)-lysine hypusine N6-(4-amino-2-hydroxybutyl)-L-lysine residue modification. RESID:AA0116 Part of a transcription factor responsible for the activation of DNA transcription. Such tags are generally used in two hybrid experiments where they are fused to a prey polypeptide tested for its ability to interact with a bait fused to a DNA binding domain tag. activation domain activation domain tag DNase I footprinting dnase 1 footprinting Deoxyribonuclease I (DNase I) do not have high specificity for given sequences or residues, thus footprinting with DNase I permits the exact delineation of the protein-DNA binding site. Moreover DNase I, can be used for in vivo footprinting by treating intact cells with permeabilising drugs. In this latter case DNase I in vivo footprinting allow studies of the chromatin structure in genomic DNA. Attribute name of annotation associated to an experiment element. experiment attibute name experiment att name PMID:10935637 Molecule under study is fused to an enzyme, for example alkaline phosphatase, and measure of enzyme activity can be taken as indicative of presence of protein. enzyme tag Variation of the green fluorescent protein derived from the bioluminescent jellyfish Aequorea victoria, can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native. egfp tag enhanced green fluorescent protein EGFP enhanced green fluorescent protein tag This approach is used to identify the residues that are involved in an interaction. Several variants of the native protein are prepared by mutating each residue of interest to an alanine. The mutated proteins are expressed, tested for proper folding and probed in the binding assay. alanine scanning Peptide sequences or entire proteins can be displayed on phage capsids by fusion to coat proteins to generate a library of fusion phages each displaying a different peptide. Such a library can then be exploited to identify specific phages that display peptides that bind to any given bait molecule for instance an antibody. The selection is performed by a series of cycles of affinity purification known as panning. The bait protein, immobilized on a solid support (plastic, agarose, sepharose, magnetic beads and others) is soaked in the phage mixture and that phage that remains attached to the bait is amplified and carried through a further affinity purification step. Each cycle results in an approximately 1,000-fold enrichment of specific phage and after a few selection rounds (2-4), DNA sequencing of the tight-binding phage reveals only a small number of sequences. Phage display panning experiments can be carried out either on libraries of peptides of random amino acid sequence or on libraries of displaying natural peptides obtained by inserting cDNA fragments into the phage vector (cDNA libraries). Libraries have been assembled on several different phages (Fd, Lambda or T7). PMID:10975452 phage display Proteins are fractionated by PAGE (SDS-polyacrylamide gel electrophoresis), transferred to a nitrocellulose membrane and tested for the ability to bind to a protein, a peptide, or any other ligand. Cell lysates can also be fractionated before gel electrophoresis to increase the sensitivity of the method for detecting interactions with rare proteins. Denaturants are removed during the blotting procedure, which allows many proteins to recover (or partially recover) activity. However, if biological activity is not recoverable, the proteins can be fractionated by a non denaturing gel system. This variation of the method eliminates the problem of activity regeneration and allows the detection of binding when the presence of a protein complex is required for binding. The protein probe can be prepared by any one of several procedures, while fusion affinity tags greatly facilitate purification. Synthesis in E. coli with a GST fusion, epitope tag, or other affinity tag is most commonly used. The protein of interest can then be radioactively labelled, biotinylated, or used in the blotting procedure as an unlabeled probe that is detected by a specific antibody. far western blotting Affinity blotting full dna sequence autoradiography Experimental method by which radiolabel is detected by exposure to a photographic emulsion forming a pattern on the film. carboxyglutamic acid residue modification. RESID:AA0032 gamma-carboxyglutamic acid L-gamma-carboxyglutamic acid 4-carboxyglutamic acid 1-carboxyglutamic acid [misnomer] (S)-3-amino-1,1,3-propanetricarboxylic acid dna rna pol assay Measures the catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'. dna directed rna polymerase assay nucl passive uptake nucleic acid passive uptake Nucleic acid entrance into cells that does not involved specific treatments but rely on natural cellular processes. cosedimentation in solution The ultracentrifuge can be used to characterise and/or purify macromolecules in solution according to their mass and hydrodynamic properties. Sedimentation studies provide information about the molecular weight and shape of a molecule. It is also possible to measure the association state of the sample. Both the mass of a molecule and its shape, that influences the friction forces and diffusion that counterbalances gravity, determine the sedimentation speed. solution sedimentati correlated mutations PMID:11933068 Pairs of multiple alignments of orthologous sequences are used to identify potential interacting partners as proteins that show covariation of their residue identities between different species. Proteins displaying inter-protein correlated mutations during evolution are likely to be interacting proteins due to co-adapted evolution of their protein interacting interfaces. id-validation-regexp:"[0-9]+|[A-Z]{1,2}_[0-9]+|[A-Z]{1,2}_[A-Z]{1,4}[0-9]+" entrezgene/locuslink entrez gene/locuslink Entrez gene/locuslink LocusLink provides a single query interface to curated sequence and descriptive information about genetic loci. http://www.ncbi.nlm.nih.gov/LocusLink/ deacetylase radiometric assay Measures the release of radiolabelled acetic acid from pre-labeled histone. radiolabeled acetate The General Repository for Interaction Datasets (GRID) is a database of genetic and physical interactions. http://biodata.mshri.on.ca/grid grid GRID S-palmitoyl-L-cysteine, N6-palmitoyl-L-lysine, O-palmitoyl-L-threonine or O-palmitoyl-L-serine are cleaved and return C,K,T or S residues. depalmitoylation reaction depalmitoylation obsolete Deprecated terms. OBSOLETE term replaced by the default OBO class 'Obsolete'. Cross reference pointing to a Gene Ontology -'cellular process' term. gene ontology term for cellular process go process term process search-url: http://genome-www4.stanford.edu/cgi-bin/SGD/locus.pl?locus=${ac} id-validation-regexp:"S[0-9]{9}" SGD SGD is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae. http://www.yeastgenome.org/ sgd tandem affinity purification TAP tap Tandem affinity purification allows rapid purification under native conditions of complexes, even when expressed at their natural level. Prior knowledge of complex composition or function is not required. The TAP method requires fusion of the a multiple tag, either N- or C-terminally, to the target (or bait) protein of interest. The multiple tag allows two steps purification steps ensuring a highly selective complex purification. PMID:11403571 protein cleavage Covalent modification of a polypeptide occuring during its maturation or its proteolytic degradation. PMID:14744292 NMR nmr nuclear magnetic resonance PMID for application instance:12062432 PMID:12120505 NMR requires a small volume of concentrated protein solution that is placed in a strong magnetic field. Certain atomic nuclei, and in particular hydrogen, have a magnetic moment or spin; that is, they have an intrinsic magnetisation, like a bar magnet. The spin aligns along the strong magnetic field, but can be changed to a misaligned excited state in response to applied radio frequency (RF) pulses of electromagnetic radiation. When the excited hydrogen nuclei relax to their aligned state, they emit RF radiation, which can be measured and displayed as a spectrum. The nature of the emitted radiation depends on the environment of each hydrogen nucleus, and if one nucleus is excited, it will influence the absorption and emission of radiation by other nuclei that lie close to it. It is consequently possible, by an ingenious elaboration of the basic NMR technique known as two-dimensional NMR, to distinguish the signals from hydrogen nuclei in different amino acid residues and to identify and measure the small shifts in these signals that occur when these hydrogen nuclei lie close enough to interact: the size of such a shift reveals the distance between the interacting pair of hydrogen atoms. In this way NMR can give information about the distances between the parts of the protein molecule. NMR provides information about interacting atoms thereby permitting to obtain information about protein structure and protein-protein interaction. antibody mediated identification. antibody detection identification by antibody residue modification. S-glycosyl-L-cysteine glycosyl-cysteine sequence phylogeny PMID:11707606 Multiple alignments of orthologous sequences in the same species and their corresponding phylogenetic trees are built. Every phylogenetic tree is computed as a matrix of distances between all possible protein pairs. The covariation of the distance matrices reveals interacting protein pairs. sequence based phylogenetic profile Information about how the data was processed. This attribute is used mainly for large scale experiment. data-processing deglycosylation deglycosylation reaction PMID:15670854 GO:0006517 Reaction catalyzed by PNGase, a deglycosylating enzyme that promotes the hydrolysis of the beta-aspartylglycosylamine bond of aspargine-linked glycopeptides and glycoproteins. id-validation-regexp:"CHEBI:[0-9]+" ChEBI chebi A definitive, freely available database of Chemical compounds of Biological Interest (ChEBI). http://www.ebi.ac.uk/chebi/ residue modification. adpribosylasparagine n4-(adp-ribosyl)-asparagine N4-alpha-D-ribofuranosyl-L-asparagine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate) N4-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-asparagine N4-(ADP-ribosyl)-L-asparagine (S)-2-amino-4-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]amino)-4-oxobutanoic acid disulfide bond Covalent bond mediated by 2 sulfur atoms. A tandem tag consists of the concatenation of simple tags that is engineered to be cloned as a unique element onto a sequence of interest. Note that when a protein is fused to many simple tags that are inserted individually and possibly in different sequence positions these should be reported as independent features. tandem tag genetic interaction Functional relationship among genes revealed by the phenotype of cells carrying combined mutations of those genes. self Molecule that makes intramolecular interactions. copurification Approaches designed to separate cell components on the basis of their physicochemical properties. The observation that two or more proteins copurify in one or several conditions is taken as an indication that they form a molecular complex. OBSOLETE since too non-specific. Consider use of cosedimentation (MI:0027) or comigration in non denaturing gel electrophoresis (MI:0404) or affinity chromatography technologies (MI:0004) or molecular sieving (MI:0071) or for unspecific cases biochemical (MI:0401). substrate Molecule that is the target of its binding partner activity. enzyme target adp-ribosylglutamate L-isoglutamyl-poly(ADP-ribose) L-glutamyl-5-poly(ADP-ribose) (S)-2-amino-5-poly[2'-adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with 1alpha-D-ribofuranosyl]oxy-5-oxopentanoic acid glutamyl-5-poly(adp-ribose) residue modification. molecular sieving Size Exclusion Chromatography Siezing column Gel Filtration In sizing columns (gel filtration), the elution position of a protein or of a complex depends on its Stokes radius. Molecules with a radius that is smaller than the bead size are retained and retarded by the interaction with the matrix. The observation that two proteins, loaded on a sieving column, elute in a fraction(s) corresponding to a MW that is larger than the MW of either protein may be taken as an indication that the two proteins interact. Furthermore this technique provides a conceptually simple method for evaluating the affinity of the interaction. DNA that consists of two base pairing strands. The 2 nucleotide chains are held together by hydrogen bonds between base pairs of nucleotides. double stranded deoxyribonucleic acid ds dna ds DNA two hybrid pooling approach In the pooling strategy the sets of bait and prey hybrid vectors are randomly mated. The positives double hybrid clones are sequenced to identify the interacting partners. PMID for application instance:11283351 two hybrid pooling nucleic acid electroporation Electroporation, or electropermeabilization, is a significant increase in the electrical conductivity and permeability of the cell plasma membrane caused by externally applied electrical field. It is usually used in molecular biology as a way of introducing some substance inside the cell, such as loading it with a molecular probe, a drug that can change cell's function, or a piece of coding DNA. nucl electroporation interaction Previously described interaction now being used as an interactor to describe hierarchical build-up of complexes. startStatus endStatus CvFuzzyType Describes sequence positions resolution of a given participant feature. In PSI schema this CV is associated with the start and end position of a feature range. feature range status K A scale that measures an object's temperature over absolute zero, the theoretical coolest temperature where all molecular and atomic motion ceases. On the Kelvin scale, the freezing point of water is 273 (273 K = 0 o C = 32 o F). kelvin picomolar 10E-12 moles per liter of solution. OBSOLETE: term redundant with the schema exponent attribute of the parameter. pM gpm Global Proteome Machine PMID:15595733 Global Proteome Machine aim to improve the quality of analysis, make the results portable and to provide a common platform for testing and validating proteomics results. http://www.thegpm.org residue modification. other modification Rosetta Stone domain fusion PMID:10573422 The rosetta stone, or domain fusion procedure, is based on the assumption that proteins whose homologues in other organisms happen to be fused into a single protein chain are likely to interact or to be functionally related. Web resource that allows the investigation of protein interactions in the Protein Data Bank structures at the level of Pfam domains and amino acid residues. iPfam is available on the Web for browsing at. http://www.sanger.ac.uk/Software/Pfam/iPfam/ ipfam cdna library Mixed population of cDNAs (complementaryDNA) made from mRNA from a defined source, usually a specific cell type. This term should be associated only to nucleic acid interactors not to their proteins product. For instance in 2h screening use living cells (MI:0349) as sample process. PMID:6110205 pH of interaction pHint pH at which interaction was determined. go function term gene ontology term for cellular function function Cross reference pointing to a Gene Ontology -'cellular function' term. Collection of protein within the Reactome database - a knowledgebase of biological processes. http://www.reactome.org/ http://www.reactome.org/cgi-bin/search?SUBMIT=1&QUERY_CLASS=DatabaseIdentifier&QUERY=SWALL:${ac} search-url: reactome protein phospho acceptor Molecule to which a phosphate may be transferred from an phospho donor. Immunostaining assay carried out using a mixture of different antibodies that represent the immune response, normally in an experimental animal, to the protein of interest. These antibodies are used to detect the protein within a cell or tissue sample. polyclonal immunost polyclonal antibody immunostaining pep seq db peptide sequence database database storing sequences detected by peptide identification methods. component Cross reference pointing to a Gene Ontology -'cellular component' term. gene ontology term for cellular component go component term southern blot A standard procedure to identify DNA fragments containing specific gene sequences. In this procedure i) a genome is fragmented using a restriction enzyme ii) the generated fragments are separated by electrophoresis iii) the fragments are transferred to a membrane iv)the membrane is incubated with a radio labelled probe that hybridises any complementary subsequence. organism attribute name organism att name Attribute name of annotation associated to an organism element. aspartic 4-phosphoric anhydride phosphoaspartic acid residue modification. (S)-2-aminobutanedioic 4-phosphoric anhydride DPO L-aspartic 4-phosphoric anhydride phosphoaspartic acid [D:po] beta-aspartyl phosphate predetermined participant Molecule whose sequence identity is not checked and has been assumed from external or previous experimental evidence(s). predetermined Measures the rate of a phosphate transfer between two proteins phosphotransfer assa phosphotransfer assay The second is the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the cesium-133 atom. The second was originally defined as 1/86 400 mean solar day until astronomers discovered that the mean solar day is actually not constant. second sec s PSI-MI. psi-mi search-url: http://www.ebi.ac.uk/ontology-lookup/?termId=${ac} id-validation-regexp:"MI:[0-9]{4}" PSI-MI Physical interaction mediated by covalent bond rearrangement. OBSOLETE use covalent binding (MI:0195) instead. covalent interaction antisense rna This approach is based on the observation that expression of RNA that is complementary to a specific mRNA can decrease the synthesis of its gene product either by increasing the degradation of the targeted mRNA or by interfering with its translation. PMID:1340158 peptide synthesis When one of the partners participates in the interaction with a relatively short peptide fragment, it is often convenient to precisely identify the minimal region that supports the interaction by synthesising a series of overlapping peptides and by testing them in the binding assay. Synthetic peptides that are identical with peptides synthesised in vivo are useful experimental tools for such studies. Peptides are routinely synthesised in a test tube from monomeric amino acids by condensation reactions that form peptide bonds. Peptides are constructed sequentially by coupling the C-terminus of a monomeric amino acid to the N-terminus of the growing peptide. To prevent unwanted reactions involving the amino groups and carboxyl groups of the side chains during the coupling steps, a protecting (blocking) group is attached to the side chains. Without these protecting groups, branched peptides would be generated. In the last steps of synthesis, the side chain-protecting groups are removed and the peptide is cleaved from the resin on which synthesis occurs. A heterogeneous mixture of RNA molecules with a rapid turnover rate that occurs in cell nuclei during protein synthesis; it is the form of RNA synthesized in eukaryotes by RNA polymerase II, which is translated into protein. heterogeneous nuclear RNA heterogeneous nuclear ribonucleic acid heterogeneous nuclear rna hnrna radiolabelled A radiolabelled molecule has radio isotopes among its constituent atoms that can be used to identify, localize or quantify the full molecule. radiolabeled radiolabel The phenotype resulting from genetic perturbation of both A and B show opposing effects in the WT background and the background with the other mutant gene. double nonmonotonic interaction double nonmonotonic feature prediction Feature detection based on computational analysis. prerequisite-ptm Post translational modification required for an interaction to occur. Cleavage of the G-K bond and release of the NEDD8 ubiquitin like proteins. Deneddylation, which removes the NEDD8 moiety, requires the isopeptidase activity of the COP9 signalosome. GO:0000338 deneddylation deneddylation reaction classical fluorescence spectroscopy Proteins contain endogenous fluorophores such as tryptophan residue and heme or flavins groups. Protein folding and protein-protein interaction can be studied by monitoring changes in the tryptophan environment detected by changes in its intrinsic fluorescence. Changes in the fluorescence emission spectrum on complex formation can occur either due to a shift in the wavelength of maximum fluorescence emission or by a shift in fluorescence intensity caused by the mixing of two proteins. The interaction of two proteins causes a shift in the fluorescence emission spectrum relative to the sum of the individual fluorescence spectra, resulting in a difference spectrum [F (complex)-2 F (sum)], which is a measurable effect of the interaction. Loss of fluorescence signal from a substrate can be used to measure protein cleavage. fluorescence spectr knock-down knock down The gene expression has been significantly reduced compared to wild-type by introduction of an external substance, e.g. by RNA interference. protein electroporation prot electroporation Method for temporarily permeabilising cell membranes in order to facilitate the entry of a protein. MSE L-selenomethionine [M:sel] selenomethionine residue modification. Kd The equilibrium dissociation constant of a receptor/ligand or proteinA/proteinB complex. Unit Molar (generally M-1). Kd Measures the catalysis of the hydrolysis of an acetyl group or groups from a substrate molecule. deacetylase assay red fluorescent protein tag rfp tag RFP red fluorescent protein The red fluorescent protein derived from Discosoma reef coral can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native. gal4 activation domain gal4 ad Part of the yeast transcription factor GAL4 (amino acids 766-881) specifically responsible for DNA transcription activation. I125 125I 125i radiolabel Molecule labelled with 125 radio isotope of iodine atoms. omega-n-methyl-arginine residue modification. methylarginine omega-N-methyl-L-arginine NG-methylarginine; (S)-2-amino-5-[(imino(methylamino)methyl)amino]pentanoic acid GO:0018319 Reaction that can affect K or G residues. myristoylation myristoylation reaction List of tissue used as topic in UniProt RC line. http://www.expasy.org/cgi-bin/lists?tisslist.txt tissue list Participants are enzyme or substrate in a biochemical reaction. enzymatic study suppression partial A mutation is the partial suppressor of a mutant phenotype. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'knock down' MI:0789. suppression partial alteration dimethylsulphate footprinting Dimethylsulphate (DMS) is the most commonly used chemical to study DNA-protein interactions. DMS induces methylation of guanine residues so DNA interaction with protein binding to AT rich sequences or to the phosphate backbone may be not detected by DMS footprinting. However as DMS diffuses across membrane it can also be used for in vivo footprinting. The experiment involves the treatment with DMS of two DNA samples with identical sequence, one protein bound and the other naked. The two samples are treated with piperidine to induce chemical cleavage of the DMS modified guanine residues followed by digestion with restriction enzymes. Once labelled the samples are run in parallel on a gel to visualize the pattern of nested fragments sharing a common end generated by restriction enzyme(or PCR primer extension) and a variable end guanine dependent. The missing bands of the protein bound sample correspond to the guanine residues protected from modification by an interaction. dms footprinting zymography Samples run on a gelatine containing gels under non-reducing condition, gels then incubated under conditions in which the enzyme is active. Gels are stained with coomasie and gelatine-free regions of the gel taken as a measure of enzyme activity. PMID:2071592 penetrating tag Membrane shuttling peptide derived from the Drosophila homeobox protein Antennapedia: RQIKIWFQNRRMKWKK search-url: http://www.reactome.org/cgi-bin/eventbrowser?ID=${ac} Collection of functional complexes within Reactome - a knowledgebase of biological processes. http://www.reactome.org/ reactome complex Gene whose mutation phenotype is suppressed by a given suppressor mutation. suppressed gene A form of spectroscopy in which the absorption of microwave by a sample in a strong magnetic field is used to study atoms or molecules with unpaired electrons. electron resonance Comment for public view. This attribute can be associated to interaction, experiment, Cv term, an organism and any participant. comment In this approach, once a molecule is demonstrated to participate in an interaction, several deletion derivatives are produced and tested in the binding assay to identify the minimal fragment (domain) that can still support the interaction. deletion analysis mole per second Per mole per second, unit for association rate constant M-1s-1 polyclonal western polyclonal antibody western blot Western blot assay carried out using a mixture of different antibodies that represent the immune response, normally in an experimental animal, to the protein of interest. his tag coimmunoprecipitation The protein of interest is expressed as a fusion to a poly-His tail. This permits purification by chromatography over a metal column or by binding to commercially available anti poly-His antibodies. OBSOLETE redundant term. Map to feature type: his-tagged (MI:0521) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007). his tag coip The protein of interest is expressed as a fusion to a poly-His tail. This permits purification by chromatography over a metal column or by binding to commercially available anti poly-His antibodies. his tag Histidine-tag Hexa-His-tag 6-His-tag acetylglutamic acid N-acetyl-L-glutamic acid [E:ac] EAC acetylglutamate (S)-2-(acetylamino)pentanedioic acid n-acetyl-glutamic acid residue modification. Reversible reaction that create a covalent bond between a C-terminus G of ubiquitin and a K residue of the target. RESID:AA0125 PMID:11583613 GO:0016567 ubiquitination reaction ubiquitination perturbagens peptides perturbagens pep PMID:8606778 PMID:11731788 This approach is based on the expression of peptides that bind to specific target proteins thereby interfering with their activity. In a standard approach the interfering peptide is expressed by genetic fusion to a stable protein scaffold. Interfering peptides can also be introduced into cells by fusing them to proteins or peptides (homeodomains, Tat protein.) having the property of penetrating the cell membrane. The peptide-carrier fusion protein is either synthesized chemically or produced in vivo, normally in bacteria. When the purified fusion protein is added to a cell culture, it penetrates the cell membrane thereby permitting the fused peptide to interfere with its target protein. OBSOLETE as such method can be described using the biological role inhibitor (MI:0586). The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products, for a number of organisms. http://www.ncbi.nlm.nih.gov/RefSeq/ refseq id-validation-regexp:"[XNZ][A-Z]_[0-9]+|[0-9]+" Refseq Immunostaining Immunofluorescence Staining coloc immunostaining The subcellular location of a protein can be demonstrated by treating cells fixed on a microscope slide with an antibody specific for the protein of interest. A secondary antibody conjugated with a reactive enzyme (e.g. horseradish peroxidase) is then added. Following a washing step to remove the unbound secondary ligand, a chromogenic substrate (e.g. 3,3', 5,5' tetramethyl benzidine chromogen [TMB]) is converted to a soluble coloured product by the conjugated enzyme and can then be visualised by standard microscopic techniques. OBSOLETE since combination of Interaction Detection Method and Interaction Type. Consider using the Interaction Detection Method imaging techniques (MI:0428) coupled with Interaction Type colocalisation (MI:0401) and Participant detection immunostaining (MI:0402) instead. colocalization by immunostaining hotspot mutation decreasing mutation decreasing interaction Residue of a protein whose identity mutation or deletion decreases significantly interaction strength. Related object within the same database or pointing to external database. see-also Any molecule that is able to transfer an phosphate to another chemical species. phospho donor small nucleolar rna snoRNA The small nucleolar RNAs, are stable RNA contained in the nucleoli and these RNAs exist as snoRNA: protein complexes called snoRNPs (also called 'snorps'). The snoRNPs function is in the maturation of ribosomal RNA and other RNAs, by: creating two types of modified nucleotides, (2'-O-methylated nucleotides and pseudouridine), and mediating endonucleolytic cleavages of pre-rRNA. snorna alkaline phosphatase tag Protein is fused to alkaline phosphatase, and the measure of this enzyme activity can be taken as indicative of presence of protein. alk phosphatase tag mutation increasing interaction Residue of a protein whose identity mutation or deletion increases significantly interaction strength. mutation increasing Method where the internal structure of a sample is derived from the intensity distribution of the scattered monochromatic X-ray beam at very low scattering angles. saxs x ray scattering experimental form de experimental form description Free text description of all the tags and artificial process undergone by a molecule during an experiment. Reactome GKB Genome Knowledge Base reactome The Reactome project is a collaboration among Cold Spring Harbor Laboratory, The European Bioinformatics Institute, and The Gene Ontology Consortium to develop a curated resource of core pathways and reactions in human biology. http://www.reactome.org/ interaction detect Method to determine the interaction. interaction detection method Protein modifications can be identified by gel electrophoresis since any change in the mass and/or the charge of the protein can alter its mobility in PAGE. Although this method does not allow the unequivocally identification of the type of modification that has caused the shift, it is possible, by combining this approach with more direct methods, to correlate the extent of the shift to a specific modification. mobility shift complex Set of interacting molecules that can be copurified. This term and its children should be use only at PARTICIPANT level. PMID:10679368 A cross-linker is a bifunctional molecule having two reactive ends linked by a spacer, often containing a disulfide bond. Cross-linkers induce the formation of covalent bonds among proteins that are neighbours. When a reducing agent is added the disulfide bridge is cleaved, the cross-linked pairs are released and can be identified. There are various classes of cross-linkers, the most common are those having photoreactive groups that become reactive fluorophores when activated by UV light thereby resulting in photolabeling the cross-linked moieties. Photoaffinity labelling Label transfer techniques protein cross-linking with a bifunctional reagent protein crosslink Molecule experimentally treated to capture its interacting partners. bait sequence tag identification This approach leads to protein identification by combining mass measurement and short amino acid sequence information obtained by tandem mass spectrometry. This information is then used to automatically find the best match in a sequence database. A mixture of peptides derived from a protease digestion is analysed by nanoelectrospray LC-MS/MS (Liquid Chromatography Tandem Mass Spectrometer or nanoESI MS/MS) mass spectrometry. Electrospray mass spectrometry cannot be applied to dilute samples and is affected by high salt. As a consequence peptides, normally extracted from acrylamide gels by in situ proteolysis, are desalted and concentrated on a microcolumn followed by elution into a capillary used for nanoelectrospray tandem mass spectrometry. A first mass spectrum (Normal mass spectrum or Q1 mass spectrum) gives information about the masses of all the peptides. Peptides observed in the normal mass spectrum are isolated in turn and dissociated into fragments by collision with gas molecules within the mass spectrometer. Some of the fragments obtained from a peptide constitute a nested set, differing by one amino acid, and the mass difference between them allows assignment of a partial sequence. The masses of the fragments define the position of the partial sequence in the peptide. Together with the cleavage specificity of the protease used to cleave the protein, and mass information such sequence tag provides much higher search specificity to match the a database entry. The procedure is repeated with several peptides from the digest, resulting in multiple identifications of the same protein or identification of several proteins from the peptide mixture. Unknown proteins can easily be identified by using the high specificity of the peptide sequence tag for searches in most sequence databases including EST or genome databases. PMID for application instance:11805837 sequence tag toxcat toxcat tox-r dimerization assay PMID:9927659 This assay allow identification of interactions in the inner membrane of E. coli. by using a chimeric construct ToxR-TM-MBP composed of the N-terminal DNA binding/transcriptional activation domain of ToxR (a dimerization dependant transcription factor) fused to a transmembrane domain of interest (TM) and a monomeric periplasmic anchor (the maltose binding protein). Association of the two TM results in the ToxR-mediated activation of a reporter gene such as CAT (chloroamphenicol acetyltransferase activity). The level of CAT expression indicates the strength of TM association. CAT expression can then be tested and quantify by measuring CAM resistance with disk diffusion assay or CAT activity assays on cell-free extracts. In static light scattering, the average intensity of scattered light at multiple angles is measured. The data yield information on particle molecular weight, particle size and shape, and particle-particle interactions. static light scattering sls Interaction among molecules that can be direct or indirect. physical interaction aggregation experimental interac Methods based on laboratory experiments. experimental interaction detection id-validation-regexp:"[a-zA-Z]+:[a-zA-Z]+[0-9]+" KEGG kegg KEGG (Kyoto Encyclopedia of Genes and Genomes) is a knowledge base for systematic analysis of gene functions, linking genomic information with higher order functional information and also supplies information about chemical compounds, enzyme molecules and enzymatic reactions. http://www.genome.ad.jp/kegg/ RAM arginine amide arginineamide L-arginine amide (S)-2-amino-5-guanidinopentanamide argininamide [R:am] residue modification. gene product Reference of a protein object pointing to its genomic or nucleic acid sequence. Measures the catalysis of the reaction: GTP + H2O = GDP + phosphate. GTPase gtpase assay 5-dimethylaminonaphthalene-1-sulfonyl tag Dansyl is fluorescent tag. Dansyl is the acronyme of 5-dimethylaminonaphthalene-1-sulfonyl radical group reacting with any NH2 groups. dansyl tag Mixture of protein forms where N-terminus has been progressively truncated. ragged n-terminus glycosyl-serine residue modification. O3-glycosyl-L-serine O-glycosyl-L-serine N6-glycyllysine N6-glycyl-L-lysine (S)-2-amino-6-[(aminoacetyl)amino]hexanoic acid PMID:12612601 Residue modification due to a cross-link between a lysine and a glycine from the sumo (Small Ubiquitin-related MOdifier) protein. sumoylated lysine 3d-r-factors Free R-Factor and working R-Factor for the quality of the crystallographic model. This attribute is generally associated to an interaction. alexa 546 label Alexa fluorescent dye analogue to Cy3 with an approximate excitation wavelength maximum of 546nm. [C:farn] farnesylcysteine (R,E,E)-2-amino-3-(3,7,11-trimethyl-2,6,10-dodecatrienylsulfanyl)propanoic acid residue modification. s-farnesyl-cysteine S-farnesyl-L-cysteine CFN 2-amino-3-(3,7,11-trimethyl-2,6,10-dodecatrienylthio)propanoic acid prenylcysteine s-prenyl-cysteine residue modification. parameter type Parameter for enzymatic or binding kinetic studies. chip-chip PMID:11206552 PMID:11125145 The method combines a modified chromatin immunoprecipitation (ChIP) procedure, with DNA microarray analysis. Cells are fixed with formaldehyde, harvested, and disrupted by sonication. The DNA fragments cross-linked to a protein of interest are enriched by immunoprecipitation with a specific antibody. After reversal of the cross-links, the enriched DNA is amplified and labeled with a fluorescent dye (Cy5) by using a ligation-mediatedpolymerase chain reaction (LM-PCR). In parallel a sample of DNA that is not enriched by immunoprecipitation is subjected to LM-PCR in the presence of a different fluorophore (Cy3), and both immunoprecipitation (IP)-enriched and unenriched pools of labeled DNA were hybridized to a single DNA microarray containing a set of intergenic sequences. The ratio of the Cy5 to Cy3 fluorescence intensities measured at each DNA element in the microarray provided a measure of the extent of binding of the transcription factor to the corresponding genomic locus. chromatin immunoprecipitation array gene SO:0000704 interactor for genetic interaction. wwpdb wwPDB PMID:14634627 The Worldwide Protein Data Bank (wwPDB) consists of organizations that act as deposition, data processing and distribution centers for PDB data. The founding members are RCSB PDB (USA), MSD-EBI (Europe) and PDBj (Japan). The BMRB (USA) group joined the wwPDB in 2006. The mission of the wwPDB is to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community. http://www.wwpdb.org/ edman degradation In this procedure the N-terminus amino acid is cleaved from a polypeptide and identified by high-pressure liquid chromatography. The cycle is repeated on the ever-shortening polypeptide until all the residues are identified. On average only 20-30 consecutive cycles can be performed and lead to amino acid identification. Longer polypeptides or full length proteins must be cleaved by specific protease before Edman degradation and their sequences built by fragment overlapping. potassium permanganate footprinting Potassium permanganate bind to single-stranded pyrimidine residues, it is commonly used to detect promoters opening regions in vivo. KMnO4 treatment of cells, followed by treatment with piperidine, followed by either PCR and/or acrylamide gel electrophoresis allows detection of interaction between transcription factor and the DNA sequence under their control. k-mn-04 footprinting weight by bromide Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with bromide dyes. molecular weight estimation by bromide staining antibodies This annotation topic should contain information about antibodies when specific antibodies (monoclonal or polyclonal raised against specific regions of the proteins or purified in a specific manner) have been used. search-url: http://www.ebi.ac.uk/msd-srv/atlas?id=${ac} PMID:16381867 The Macromolecular Structure Database (MSD) - the European project for the collection, management and distribution of data about macromolecular structures, derived in part from the Protein Data Bank (PDB). http://www.ebi.ac.uk/msd/ msd pdb PQS e-MSD http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=${ac}&dopt=Abstract search-url: PubMed is designed to provide access to citations from biomedical literature. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi pubmed lambda phage Morphologically classified as one of the siphoviridae, lambda is a temperate bacteriophage of E.coli, with a double-stranded DNA genome. It has an icosahedral head attached to a flexible helical tail. Both the tail protein pV and the head protein pD have been used for displaying (C or N terminally) foreign peptides on the viral capsid. lambda phage display Knocked out gene is the suppressor of a phenotype. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'knock out' MI:0788. suppress knockout suppression knockout Microinjection refers to the process of using a micro needle to insert substances at a microscopic level into a single living cell. It is a simple mechanical process in which an extremely fine micro needle penetrates the cell membrane and sometimes the nuclear envelope and releases proteins. protein microinjection prot microinjection formylated residue residue modification. expression interfer This term refers to methods designed to interfere with gene expression at post-transcriptional level rather than with the gene itself. post transcriptional interference Gene pairs that show a conserved topological neighbourhood in many prokaryotic genomes are considered by this approach to encode interacting or functionally related proteins. By measuring the physical distance of any given gene pair in different genomes, interacting partners are inferred. PMID:9787636 gene neighbourhood open reading frame name A name temporarily attributed by a sequencing project to an open reading frame. This name is generally based on a cosmid numbering system. For instance MtCY277.28c, SYGP-ORF50, SpBC2F12.04, C06E1.1, CG10954. Also called Sequencing names or Contig names or Temporary ORFNames. orf name sequence cloning nucleotide sequence nucleotide sequence identification Identification of a nucleotide sequence. Depending on the experimental design, nucleotide sequence can be determined before the interaction detection while building a collection of clones or after the selection of randomly generated clones. predicted interac interaction prediction in silico methods Computational methods to predict an interaction. s-geranylgeranyl-cysteine S-geranylgeranyl-L-cysteine 2-amino-3-(3,7,11,15-tetramethyl-2,6,10,14-hexadecatetraenylthio)propanoic acid (R,E,E,E)-2-amino-3-(3,7,11,15-tetramethyl-2,6,10,14-hexadecatetraenylsulfanyl)propanoic acid CGR residue modification. geranylgeranylcys [C:ger] Bacterial conjugation is the transfer of genetic material between bacteria through cell-to-cell contact. Bacterial conjugation is often incorrectly regarded as the bacterial equivalent of sexual reproduction or mating. It is not actually sexual, as it does not involve the fusing of gametes and the creation of a zygote. It is merely the transfer of a conjugative plasmid from a donor cell to a recipient nucleic acid conjugation nucl conjugation Molecule inhibiting an interaction by interacting with one or more of its participant. inhibitor The gene function has been abolished by mutation, though the type of mutation is not known. amorph Participant isoform's comment. This attribute can be attached to interactions or participants. isoform-comment SELDI ProteinChip seldi chip proteinchip(r) on a surface-enhanced laser desorption/ionization PMID:11827829 ProteinChip(r) Array technology is a surface-enhanced laser desorption/ionization (SELDI) approach (Ciphergen Biosystems Inc. Fremont, CA, USA) for sample fractionation accomplished by retentate chromatography. Retentate chromatography is performed on ProteinChip Arrays with varying chromatographic properties (e.g. anion exchange, cation exchange, metal affinity and reverse phase). By utilising arrays with differing surface chemistries in parallel and in series, a complex mixture of proteins, as from cells or body fluids, can be resolved into subsets of proteins with common properties. Specific analytes can also be examined by using preactivated arrays to which a bait molecule (such as an antibody or biotinylated DNA) is immobilized and a solution containing the binding partner(s) is presented to the array. This array-based immunoprecipitation or protein-binding experiment has been used with good success to study DNA-binding proteins, receptor-ligand interactions, and protein complexes. Any ligand retained on a SELDI chip can directly be identified by mass spectrometry. x-ray crystallography Analysis of a diffraction pattern generated by a single crystal. X-rays have a wavelength, typically around 1 Angstrom (the diameter of a hydrogen atom). If a narrow parallel beam of X-rays is directed at a sample of a pure protein, most of the X-rays will pass straight through it. A small fraction, however, will be scattered by the atoms in the sample. If the sample is a well-ordered crystal, the scattered waves will reinforce one another at certain points and will appear as diffraction spots when the X-rays are recorded by a suitable detector. The position and intensity of each spot in the X-ray diffraction pattern contain information about the position and nature of the atoms in the crystal. The three-dimensional structure of a large molecule can be deduced from the electron-density map of its crystal. In recent years X-ray diffraction analysis has become increasingly automated, and now the slowest step is likely to be the production of suitable protein crystals. This requires high concentration of very pure protein and empirical searching for the proper crystallisation conditions. x-ray diffraction X-ray During the treatment for microscope analysis a tissue section is incubated with high-specificity antibodies coupled to heavy metals (gold). Any tissue section can then be analysed by electron microscopy to localise the target proteins within the cell. This method supports very high resolution colocalisation of different molecules in a cell. tem transmission electron microscopy dynamic light scattering In dynamic light scattering, particle diffusion in solution gives rise to fluctuations in the intensity of the scattered light on the microsecond scale. The hydrodynamic radius of the particles can be easily calculated. dls protein delivery Method by which proteins are delivered into a cell. (S)-5-amino-5-carboxy-N,N,N-trimethylpentanaminium n6,n6,n6-trimethyl-lysine [K:meth_3] N(zeta)-trimethyllysine trimethyllysine N6,N6,N6-trimethyl-L-lysine (S)-2-amino-6-(trimethylammonio)hexanoic acid epsilon-trimethyllysine residue modification. M3L FLAG-tagged FLAG DYKDDDDKV epitope tag flag tag The protein of interest is expressed as a fusion to the peptide DYKDDDDKV for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem. gst tag glutathione S-tranferase tag The protein is expressed and purified as a fusion to the glutathione S-tranferase protein. glutathione s tranferase tag ensembl PMID:15078858 Ensembl is a joint project between the EMBL-EBI and the Wellcome Trust Sanger Institute that aims at developing a system that maintains automatic annotation of large eukaryotic genomes. http://www.ebi.ac.uk/ensembl id-validation-regexp:"ENS[A-Z]+[0-9]{11}" Ensembl in vivo Experiment undertaken within a cellular environment, although this may not be the natural host of the proteins in the study. OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction. All Alexa dyes are fluorescent iodoacetamide dyes that can be conjugated with the primary amines of biomolecules. All Alexa dyes and their conjugates are more fluorescent and more photostable than the commonly used dyes. The numbers in the Alexa names indicate the approximate excitation wavelength maximum in nm). alexa label systematic evolution of ligands by exponential enrichment in vitro evolution of nucleic acids RNA and cDNA constructs with variable central sequences and a constant flanking region are collected in a complex library. The library is then screened to select either specific binding partners of a bait molecule (generally a protein) or particular enzymatic activities of the nucleic acid molecules themselves. The selected nucleic acids are amplified using the constant flanking regions to increase their abundance. Cycles of selection-amplification can be repeated to increase the specificity of the targets that, at the end, are individually identified by sequencing. PMID:11539574 selex colocalization co-occurrence of interactors in a limited subcellular location or similar distribution in various regions of a cell. gallex gallex The method is based on the repression of a reporter gene activity by two LexA DNA binding domains with different binding specificities. LexA is a transcription factor with an N-terminal DNA binding/activation domain (DBAct) and a C-terminal dimerization domain. LexA dimerization is required to repress transcription efficiently. The discovery of LexA DNA binding domains that bind to different DNA sequence enabled the development of this system. PMID:12446730 lex-a dimerization assay Method to determine the proteins involved in the interaction. participant detection participant identification method participant ident Following non-covalent binding of a purified primary ligand to a solid phase, a blocking reagent is added to prevent any non-specific binding. A specific antigen is then allowed to bind to the primary ligand. Unbound antigen is removed by washing and a secondary antibody conjugated to an enzyme (e.g. horseradish peroxidase) is added. Following a washing step to remove unbound secondary ligand, the extent to which a chromogenic substrate (e.g. 3,3', 5,5' tetramethyl benzidine chromogen [TMB]) is converted to a soluble coloured product by the conjugated enzyme in a given time is determined by spectrophotometry using a standard microplate absorbance reader. A similar type of approach can be utilized to detect enzymatic activities. The substrate, attached to a solid phase is incubated in the presence of the enzyme and the enzymatic modification is monitored by an antibody that is specific for the modified substrate (for instance a phosphorylated protein). PMID:11906746 ELISA enzyme linked immunosorbent assay elisa mass spectrometry. mass spectrometry The EMSA supershift is a EMSA experiment carried out using a third lane loaded with the radiolabeled nucleic acid, a protein mixture and an antibody for a specific protein. If an extra retardation is observed, this is due to the formation of a larger complex including the antibody. By this approach, at least one protein of the complex is directly identified. electrophoretic mobility supershift assay emsa supershift terms aiming to represent biochemical reactions referring to their resulting product modifications. enzymatic reaction Biochemical reaction Free text notes on how to contact the author organisation which has produced the data This attribute is generally associated to an experiment. contact-comment The bait protein is expressed and purified as a fusion to the glutathione S-tranferase protein. The bait protein is normally attached to a glutathione sepharose resin or alternatively to a support containing an anti-GST antibody. OBSOLETE redundant term. Map to feature type : gst-tagged (MI:0519) and Interaction detection method: pull down (MI:0096). gst pull down peptide atlas PMID:16381952 PMID:15642101 PeptideAtlas addresses these needs by identifying peptides by tandem mass spectrometry (MS/MS), statistically validating those identifications and then mapping identified sequences to the genomes of eukaryotic organisms. http://www.peptideatlas.org/ PeptideAtlas Two proteins can be localised to cell compartments, in the same experiment, if they are expressed as chimeric proteins fused to distinct proteins fluorescing at different wavelengths (Green Fluorescent Protein and Red Fluorescent Protein for example). Using a confocal microscope the two proteins can be visualized in living cells and it can be determined whether they have the same subcellular location. Fluorescence microscopy of cells expressing a GFP fusion protein can also demonstrate dynamic processes such as its translocation from one subcellular compartment to another. OBSOLETE: use imaging technique (MI:0428) and specific probe as feature of each interacting protein. coloc fluoresc probe colocalization by fluorescent probes cloning The ProDom protein domain database consists of an automatic compilation of homologous domains. http://protein.toulouse.inra.fr/prodom.html prodom ProDom id-validation-regexp:"PD[0-9]{6}" PIRSF is a classification system based on evolutionary relationship of whole proteins. http://pir.georgetown.edu/iproclass/ id-validation-regexp:"PIRSF[0-9]{5}" PIRSF pirsf The phylogenetic profile of a protein stores information about the presence and the absence of that protein in a set of genomes. By clustering identical or similar profiles, proteins with similar functions and potentially interacting are identified. PMID:10200254 phylogenetic profile ubiquitinated lysine N6-glycyllysine N6-glycyl-L-lysine KUB [K:ub] Residue modification due to a cross-link between a lysine and a glycine from the ubiquitine protein. prey Molecule experimentally identified as being captured by a given bait. experimental feature detection exp feature detect experimental feature detection. other biochemic tech Experimental methods that could not be assigned to the other large group of technologies. OBSOLETE use biochemical (MI:0401) instead. other biochemical technologies Describes the location of the experiment. OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction. experiment condition dephosphorylation reaction Phosphoresidues are cleaved and return D,C,H,S,T,Y or R residues. GO:0016311 dephosphorylation PMID:14755272 Defines whether molecule is endogenously expressed or has in any way been altered, in sequence or expression level, from its native state. For a complete description of the experimental molecule form use the orthogonal CVs expression level, delivery method, and sample process. molecular source rna interference PMID:12408823 PMID:12110901 RNA interference (RNAi) is a post-transcriptional gene silencing method reproducing a naturally occurring phenomena. RNAi is the process whereby double-stranded RNA (dsRNA) induces the sequence-specific degradation of homologous mRNA. RNAi or dsRNA-induced silencing phenomena are present in evolutionarily diverse organisms, e.g., nematodes, plants, fungi, and trypanosomes. The mechanisms by which RNAi works is initiated by a progressive cleavage of dsRNA into 21 to 23 nucleotide (nt) short interfering RNAs (siRNAs). These native siRNA duplexes are then incorporated into a protein complex called RNA-induced silencing complex (RISC). ATP-dependent unwinding of the siRNA duplex generates an active RISC complex. Guided by the antisense strand of siRNA, the active RISC complex recognizes and cleaves the corresponding mRNA. rnai search-url: http://www.ebi.ac.uk/intenz/query?cmd=Search&q=${ac}&t=exact&fields=ec id-validation-regexp:"[0-6]{1}\.[0-9]+\.[0-9]+\.[0-9]+ " IntEnz is the name for the Integrated relational Enzyme database and is the official version of the Enzyme Nomenclature. The Enzyme Nomenclature comprises recommendations of the Nomenclature Committee of the International Union of Bio chemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions. IntEnz is supported by NC-IUBMB and contains enzyme data curated and approved by this committee. The database IntEnz is available at. http://www.ebi.ac.uk/intenz PMID:14681451 intenz This method relies on the covalent coupling of mRNA to the nascent polypeptide. The mRNA (natural or artificial) is first covalently linked to a short DNA linker carrying a puromycin moiety. The mRNA mixture is then translated in vitro. When the ribosome reaches the RNA-DNA junction the ribosome stalls and the puromycin moiety enters the peptidyltransferase site of the ribosome and forms a covalent linkage to the nascent polypeptide. As a result the protein and the mRNA are covalently joined and can be isolated from the ribosome and purified. In the current protocol, a cDNA strand is then synthesised to form a less sticky RNA-DNA hybrid and these complexes are finally used for affinity selection. As in most display approaches, several selections cycles (3-6) are sufficient to enrich for mRNAs encoding ligand proteins. mrna display degeranylation reaction S-geranylgeranyl-L-cysteine is cleaved and returns a C residue. degeranylation protein passive uptake prot passive uptake Proteins entrance into cells that does not involved specific treatments but rely on natural cellular processes. Synthesis rate of a molecule under investigation described in comparison with its naturally occurring expression level in a cell. expression level predict from sequenc Computational methods based on evolutionary hypothesis, used as criteria to browse sequences and predict interacting pairs. sequence based prediction fixed cell Cells has been fixed by treatment with organic solvent, staining and inclusion in a resin for microscopic analysis. fluorescent prot tag Protein having well characterized fluorescence excitation and emission spectra used as fusion with a protein under study to facilitate its localisation or identification. fluorescent protein tag id-validation-regexp:"DIP[0-9]+[NE]" DIP The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. http://dip.doe-mbi.ucla.edu/ dip over expressed level over-expressed A molecule is estimated to be expressed at higher levels than in physiological condition. Temperature at which interaction was determined. Unit KELVIN (K) temperature of interaction Tint t interaction resid The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications. http://www.ebi.ac.uk/RESID/index.html search-url: http://srs.ebi.ac.uk/cgi-bin/wgetz?[resid-id:${ac}]+-e id-validation-regexp:"AA[0-9]{4}" translocation Xref pointing to a GO process term describing the start and end location of a migrating molecule, for instance see GO:0006611, 'protein-nucleus export'. methyltransferase radiometric assay radiolabeled methyl Measures the transfer of a radiolabelled methyl group of a donor, for example S-adenosyl-L-methionine (SAM) to a carboxyl group of an acceptor. N-methylmethionine MMT 2-methylamino-4-(methylthio)butanoic acid n-methyl-methionine N-methyl-L-methionine residue modification. methylmethionine [M:meth] (S)-2-methylamino-4-(methylsulfanyl)butanoic acid cleavage reaction Covalent bond breakage in a molecule leading to the formation of smaller molecules. cleavage Description of an activator that acts on an external cell receptor or other upstream molecule to stimulate a downstream interaction, potentially by modification of one or more of the interactors. agonist alexa 488 label Alexa fluorescent dye analogue to Oregon Green 488 with an approximate excitation wavelength maximum of 488 nm. Methods that require fully sequenced genomes either because they are based on the comparison of genome topology or on the identification of orthologous sequences in different genomes. genome prediction genome based prediction PDB The RCSB PDB provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease. http://www.pdb.org/ http://www.pdb.org/pdb/explore/explore.do?structureId=${ac} search-url: rcsb pdb mbp tag maltose binding protein tag maltose binding protein tag The protein is expressed and purified as a fusion to the glutathione maltose-binding protein (MBP). The MBP-fusion protein can be purified by affinity chromatography using an amylose resin. PMID:11731503 Protein interactions, experimentally detected in an organism, are extended to a second organism assuming that homologue proteins, in different organisms, maintain their interaction properties. Homology based interaction prediction interologs mapping The insertion of a substance into a cell through a microneedle. To extrude the substances through the very fine needle tip, either hydrostatic pressure (pressure injection) or electric currents (ionophoresis) is employed. PMID:3016916 micro-injection microinjection GO:0006379 Any process by which a pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner. mrna cleavage alexa 594 label Alexa fluorescent dye analogue to Texas Red-X with an approximate excitation wavelength maximum of 594nm. nucleic acid delivery by infection nucl infection Nucleic acid introduced into a cell via an external organism, usually a virus or bacteria.. N6-(1-oxotetradecyl)-L-lysine N(zeta)-myristoyllysine n6-myristoyl-lysine KMY epsilon-myristoyllysine [K:myr] myristoyllysine (S)-2-amino-6-(tetradecanoylamino)hexanoic acid residue modification. N6-myristoyl-L-lysine htrf homogeneous time-resolved fluorescence Methods based on the exceptionally long fluorescence lifetime characteristics of certain fluorophores, which allows the elimination of the effects of background fluorescence. Uses nonradiative energy transfer or quenching between fluorescent lanthanide chelates and different acceptors to measure reaction rates. homogeneous time resolved fluorescence less-than Displayed as '<'. Partially determined sequence position known to be in a position lower than a given position. Isothermal titration calorimetry (ITC) measures directly the energy associated with a chemical reaction triggered by the mixing of two components. A typical ITC experiment is carried out by the stepwise addition of one of the reactants (~10-6 L per injection) into the reaction cell (~1mL) containing the second reactant. The chemical reaction occurring after each injection either releases or absorbs heat (qi) proportional to the amount of ligand that binds to the protein with a characteristic binding enthalpy (DH). As modern ITC instruments operate on the heat compensation principle, the instrumental response (measured signal) is the amount of power (microcalories per second) necessary to maintain constant the temperature difference between the reaction and the reference cells. Because the amount of uncomplexed protein available progressively decreases after each successive injection, the magnitude of the peaks becomes progressively smaller until complete saturation is achieved. The difference between the concentration of bound ligand in the ith and (i-1)th injections depends on the binding constant Ka and the total ligand injected. The calculations depend on the binding model (number of substrates). Analysis of the data yields DH and DG = -RTlnKa. The entropy change is obtained by using the standard thermodynamic expression DG = DH-TDS. PMID:11785756 itc isothermal titration calorimetry ITC 3-carboxy-S-methyl-cysteine methylthioaspartate (2R,3Xi)-2-amino-3-methylsulfanylbutanedioic acid RESID:AA0232 residue modification. L-beta-methylthioaspartic acid [D:meth_b] DM2 beta-methylthioaspartic acid 3-methylthio-aspartic acid beta-methylthio-aspartic acid suppression scalable Level of over/underexpression scales the 'extend' of a phenotype. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'expression level alteration' MI:0803. gpi-serine N-seryl-glycosylphosphatidylinositolethanolamine gpi-anchor amidated serine RESID:AA0162 residue modification. IEC Stable complexes and their component proteins can be separated on the basis of their net charge by ion-exchange chromatography. If a protein has a net positive charge at pH 7, it will usually bind to a column of beads containing carboxylate groups, and can then be eluted by increasing the concentration of sodium chloride or another salt in the eluting buffer by competition of sodium ions with positively charged groups on the protein for binding to the column. Protein that have a low density of net positive charge will tend to emerge first, followed by those having a higher charge density. Positively charged complexes or proteins (cationic proteins) can be separated on negatively charged carboxymethyl-cellulose (CM-cellulose) columns. Conversely, negatively charged complexes or proteins (anionic proteins) can be separated by chromatography on positively charged diethylaminoethyl-cellulose (DEAE-cellulose) columns. ion exchange chromatography ion exchange chrom protein dna complex A stable set of interacting protein and DNA that can be copurified and operate as a functional unit. SMART id-validation-regexp:"SM[0-9]{5}" smart SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures. http://smart.embl-heidelberg.de/ ribosomal rna rRNA RNA that is transcribed from the DNA of the nucleolus and is found, together with characteristic proteins, in the ribosomes. rrna The phenotype resulting from genetic perturbation of A has an effect only in the B background, or the B mutant has an effect only in the A background. conditional interaction conditional N2-acetyllysine N2-acetyl-L-lysine n2-acetyl-lysine n2-acetyllysine (S)-2-acetylamino-6-aminohexanoic acid [K:ac] KAC residue modification. deubiquitination reaction Cleavage of the G-K bond and release of ubiquitin or ubiquitin like proteins. GO:0016579 deubiquitination Dissociation rate constant measuring the stability of a complex. Unit SECOND (s-1) kd koff beta lactamase This strategy is based on a protein fragment complementation assay (PCA) of the enzyme TEM-1 beta-lactamase. The approach includes a simple colorimetric in vitro assays using the cephalosporin nitrocefin and assays in intact cells using the fluorescent substrate CCF2/AM. The combination of in vitro colorimetric and in vivo fluorescence assays of beta-lactamase in mammalian cells permits a variety of sensitive and high-throughput large-scale applications. beta lactamase complementation residue modification. acetylalanine acetylalanine AAC N-acetyl-L-alanine [A:ac] n-acetyl-alanine (S)-2-(acetylamino)propanoic acid suppression overexpression suppress overexpress Overexpression is the suppressor of a phenotype. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'over expressed' MI:0506. Property of a subsequence that may interfere with the binding of a molecule and are supported by experimental evidences. biological feature sequence ontology The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. SO provides a common set of terms and definitions that will facilitate the exchange, analysis and management of genomic data. PMID:15892872 id-validation-regexp:"SO:[0-9]{7}" so gal4 dna bd Part of the yeast transcription factor GAL4 (amino acids 11-38) specifically responsible for DNA binding of a 17 base-pair long sequence in the upstream activating sequence of galactose-induced genes. gal4 dna binding domain stimulation Reaction occurs at a faster rate in the presence of this compound or molecule i.e. the molecule directly physically co-operates with the interaction. Reaction may not occur at all in the absence of this molecule. Descriptor of type of nomenclature used to describe interactor. CvAliasType alias type dna cleavage Covalent bond breakage of a DNA molecule leading to the formation of smaller fragements. dna binding domain Part of a transcription factor responsible for the binding of gene regulatory region prior to their transcription. Such tags are generally used in two hybrid experiments where they are fused to a bait polypeptide tested for its ability to interact with a prey fused to an activation domain tag. dna binding domain tag n-acetyl-asparagine residue modification. acetylasparagine NAC N-acetyl-L-asparagine [N:ac] r1 spin label Paramagnetic molecule (1-oxyl-2,2,5,5-tetramethylpyrroline- 3-methyl)-methanethiosulfonate. that can be covalently attached to any cysteine aminoacid producing a nitroxide side chain designated R1. genetic methods supporting genetic interactions. OBSOLETE as too unspecific use Genetic interference instead MI:0254. interpro http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=${ac} search-url: id-validation-regexp:"IPR[0-9]{6}" InterPro InterPro combines a number of databases (referred to as member databases) that use different methodologies and a varying degree of biological information on well-characterised proteins to derive protein signatures. http://www.ebi.ac.uk/interpro/ PMID:1252001 horseradish peroxidase tag hrp tag Protein is fused to horseradish peroxidase, and the measure of this enzyme activity can be taken as indicative of presence of protein. All the methods that permit the physical linking of a protein/peptide to its coding sequence. As a consequence affinity purification of the displayed peptide results in the genetic enrichment of its coding sequence. By these technologies genes encoding a peptide with desired binding properties can be selected over an excess of up to 1012 unrelated molecules. display technology Ki ki Equilibrium constant for dissociation of an inhibitor. Unit Molar. interaction xref interaction database. interaction database ms protein sequence The strategy to determine the complete amino acid sequence of a protein by mass spectrometry relies on the generation of a nested set of fragments differing by one amino acid. This permits to reveal the identity of the residue that has been removed at each degradation step by measuring the mass difference of fragments differing of one residue. Peptide fragments can be obtained by protease treatment combined with the fragmentation promoted by collision (or other methods) within a tandem mass spectrometer. This approach can be carried out with LC MS/MS (Liquid Chromatography Tandem Mass Spectrometry), nanoESI MS/MS (nanoElectrospray Ionisation tandem mass spectrometry), or FTMS (Fourier Transform mass spectrometry) instruments. PMID:10984529 de novo protein sequencing by mass spectrometry nucl transfection nucleic acid transfection Introducing DNA into eukaryotic cells, such as animal cells, is called transfection. Transfection typically involves opening transient "holes" or gates in cells to allow the entry of extracellular molecules, typically supercoiled plasmid DNA, but also siRNA, among others. Transfection differs from transformation since the DNA is not generally incorporated into the cell's genome, it is only transiently expressed. Evidence based on human assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences. inference modelled modeled glycosyl-threonine residue modification. O3-glycosyl-L-threonine O-glycosyl-L-threonine lipid cleavage Cleavage of a lipid group covalently bound to a protein residue. N-acetyl-L-proline acetylproline PAC (2S)-1-acetyl-2-pyrrolidinecarboxylic acid n-acetyl-proline [P:ac] residue modification. acetylproline 3d repertoire 3D Repertoire The aim of 3D Repertoire is to determine the structures of all amenable complexes in a cell at medium or high resolution, which will later serve to integrate in toponomic and dynamic analyses of protein complexes in a cell. Complex models, EM pictures, expression and purification protocols obtained in the project will be collected in a database connected to the PDB repository. residue modification. (S)-2-acetylamino-3-methylbutanoic acid VAC acetylvaline N-acetylvaline n-acetyl-valine N-acetyl-L-valine [V:ac] epistatic interaction The phenotype resulting from genetic perturbation of A and B have different effects (in terms of direction or magnitude) on the wild-type background and the double mutant has the same phenotype as either A or B (for example, A < WT < B = AB). epistatic Displayed as 'n'. n-terminal Term describing the first amino acid of a peptide chain. n-terminus n-term amino-terminus n-terminal position comigration by non denaturing gel electrophoresis. comigration in non denaturing gel electrophoresis comig non denat gel participant database. participant database participant xref O-phospho-L-threonine (2S,3R)-2-amino-3-phosphonooxybutanoic acid threonine phosphate ester 2-amino-3-hydroxybutanoic acid 3-phosphate TPO phosphothreonine [T:po] O3-phosphothreonine o-phospho-threonine residue modification. part of <_25i_radiolabel_MI_0848 rdf:ID="_25i_radiolabel"/> <_2p_radiolabel_MI_0236 rdf:ID="_2p_radiolabel"/> <_31i_radiolabel_MI_0234 rdf:ID="_31i_radiolabel"/> <_3c_label_MI_0379 rdf:ID="_3c_label"/> <_3p_radiolabel_MI_0237 rdf:ID="_3p_radiolabel"/> <_4c_radiolabel_MI_0235 rdf:ID="_4c_radiolabel"/> <_5n_label_MI_0380 rdf:ID="_5n_label"/> <_5s_radiolabel_MI_0371 rdf:ID="_5s_radiolabel"/> <__hydroxy_proline_MI_0149 rdf:ID="__hydroxy_proline"/> <_d_r_factors_MI_0631 rdf:ID="_d_r_factors"/> <_d_repertoire_MI_0731 rdf:ID="_d_repertoire"/> <_d_resolution_MI_0632 rdf:ID="_d_resolution"/> <_d_structure_MI_0630 rdf:ID="_d_structure"/> <_h_label_MI_0381 rdf:ID="_h_label"/> <_h_radiolabel_MI_0238 rdf:ID="_h_radiolabel"/>