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.