Notes: To facilitate handling, they all have been merged in this file, though they $Id: psi-mi.obo,v 1.118 2007/03/14 04:38:46 girlwithglasses Exp $ psi-mi.lastac. The last accession number used in this file is stored in a separate file, The PSI MI schema defines short labels for controlled vocabulary terms. Where possible, short labels are reported as exact synonyms of a term in this file, This file is published by the PSI MI working group see http://psidev.sourceforge.net/ luisa 2006-12-22T12:25:00 It MUST be updated when this file is updated. Author Luisa Montecchi Palazzi luisa@ebi.ac.uk mapping an element of the PSI Molecular Interaction XML schema. PSI-MI Each of the top level terms in this file is the root term of an independent controlled vocabulary are essentially independent CVs describing different aspects of molecular interactions. interaction detection method interaction detect PMID:14755292 Method to determine the interaction. neddylation GO:0045116 PMID:16127432 Reversible reaction that create a covalent bond between a Glycine residue of an ubiquitine like NEDD8 protein and a lysine residue of the target. neddylation reaction uniprot knowledge base 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/ 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}" http://www.ebi.uniprot.org/entry/${ac} search-url: UniProt uniprotkb nanomolar 10E-9 moles per liter of solution. OBSOLETE: term redundant with the schema exponent attribute of the parameter. nM ki Ki Equilibrium constant for dissociation of an inhibitor. Unit Molar. 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. nucleic acid transfection with liposome 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. nucl lipotransfection predicted interac Computational methods to predict an interaction. interaction prediction in silico methods Dye coupled to a molecule allowing its identification isolation and monitoring. PMID:14577292 dye label dye labelled PMID:11827624 PMID for application instance:10688190 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. two hybrid array neutral component Molecule role in an experimental setting that does not have an embedded asymmetry. deneddylation reaction 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 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/ rfam id-validation-regexp:"RF[0-9]{5}" rfam additive interaction additive 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. display technology 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. n-acetyl-aspartic acid [D:ac] PMID:11125103 RESID:AA0042 residue modification. acetylaspartate acetylaspartic acid DAC N-acetyl-L-aspartic acid (S)-2-(acetylamino)butanedioic acid Molecule inhibiting an interaction by interacting with one or more of its participant. inhibitor complex-properties Information on the complex being annotated. Attribute generally associated to an interaction. cleavage reaction Covalent bond breakage in a molecule leading to the formation of smaller molecules. cleavage phospho donor Any molecule that is able to transfer an phosphate to another chemical species. systematic evolution of ligands by exponential enrichment selex 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 AAC acetylalanine n-acetyl-alanine [A:ac] acetylalanine N-acetyl-L-alanine (S)-2-(acetylamino)propanoic acid RESID:AA0041 residue modification. 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') PMID:15608217 bridge assay trihybrid 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:12052864 PMID:12761205 PMID:12935900 protein tri hybrid undetermined Term describing a completely unknown or unspecified sequence position. undetermined sequence position Displayed as '?'. (R)-2-amino-3-nitrososulfanyl-propanoic acid L-cysteine nitrite ester S-nitrosocysteine S-nitrosyl-L-cysteine residue modification. RESID:AA0230 nitrosylcysteine s-nitrosyl-cysteine Deprecated terms. OBSOLETE term replaced by the default OBO class 'Obsolete'. obsolete 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 Temperature at which interaction was determined. Unit KELVIN (K) temperature of interaction t interaction Tint deacetylation GO:0006476 RESID:AA0055 RESID:AA0056 N6-acetyl-L-lysine or S-acetyl-L-cysteine are cleaved and return K or C residues. deacetylation reaction weight by comassie molecular weight estimation by coomasie 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 comassie dye. phosphotransfer assay phosphotransfer assa Measures the rate of a phosphate transfer between two proteins suppressor gene Gene whose mutation suppress the phenotype associated to a suppressed mutation. kd koff Dissociation rate constant measuring the stability of a complex. Unit SECOND (s-1) RESID:AA0124 Gln-Lys cross-link catalyzed by a transglutaminase. transglutamination reaction transglutamination lex-a dimerization assay gallex PMID:12446730 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. gallex PMID:10410796 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. density sedimentatio cosedimentation through density gradient sufficient to bind sufficient binding site Binding will occur when this sequence range is present within a protein. prenylcysteine s-prenyl-cysteine residue modification. mrna cleavage Any process by which a pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner. GO:0006379 PMID:14681407 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). PMID:10504710 tap tag coimmunoprecipitation tap tag coip id-validation-regexp:"[XNZ][A-Z]_[0-9]+|[0-9]+" 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 refseq 13C C13 13c label Molecules labelled with isotope 13 of carbon atoms. 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. PMID:7708014 coip Residue modification due to a cross-link between a lysine and a glycine from the Nedd8 protein family. PMID:111 neddylated lysine mammalian protein protein interaction trap mappit 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. PMID:12853652 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. The gene expression has been significantly reduced compared to wild-type by introduction of an external substance, e.g. by RNA interference. knock down knock-down v5 tag The protein of interest is expressed as a fusion to the peptide GKPIPNPLLGLDST for which antibodies are commercially available. GKPIPNPLLGLDST epitope tag nucl conjugation 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 second 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. s sec 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. weight silver stain PMID:14681451 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 id-validation-regexp:"[0-6]{1}\.[0-9]+\.[0-9]+\.[0-9]+ " http://www.ebi.ac.uk/intenz/query?cmd=Search&q=${ac}&t=exact&fields=ec search-url: intenz acetylisoleucine IAC N-acetyl-L-isoleucine acetylisoleucine (2S,3S)-2-acetylamino-3-methylpentanoic acid [I:ac] n-acetyl-isoleucine residue modification. RESID:AA0047 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 antibody array PMID:12454649 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). antigen capture assay sandwich immunoassay protease assay Measures the enzymatic hydrolysis of a peptide bond within a peptide or protein substrate. isoform-comment Participant isoform's comment. This attribute can be attached to interactions or participants. methyltransferase assay methyltransferase as Measures the catalysis of the transfer of a methyl group to an acceptor molecule. formylated residue residue modification. mutated gene The gene is mutated in some unknown manner n-methyl-methionine methylmethionine (S)-2-methylamino-4-(methylsulfanyl)butanoic acid N-methyl-L-methionine N-methylmethionine [M:meth] MMT residue modification. RESID:AA0064 2-methylamino-4-(methylthio)butanoic acid n6-(4-amino-2-hydroxybutyl)-lysine N6-(4-amino-2-hydroxybutyl)-L-lysine KHY [K:hypu] (S,R)-2-amino-6-(4-amino-2-hydroxybutylamino)hexanoic acid residue modification. RESID:AA0116 hypusine hypusine proteinchip(r) on a surface-enhanced laser desorption/ionization SELDI ProteinChip 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. PMID:11827829 seldi chip Cell has been physically or chemically broken open and molecule present in resulting mixture of cellular components. cell lysate 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. N-acetyl-L-cysteine residue modification. RESID:AA0043 CAC n-acetyl-cysteine (R)-2-acetylamino-3-sulfanylpropanoic acid [C:ac] N-acetylcysteine 2-acetylamino-3-mercaptopropanoic acid acetylcysteine fluorescence microscopy 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 imaging tap tagged CBP-ProtA tagged calmodulin binding peptide plus protein a tag 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). anti bait coip anti bait coimmunoprecipitation 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. comment Comment for public view. This attribute can be associated to interaction, experiment, Cv term, an organism and any participant. 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 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 Synonym as used in Gene Ontology. go synonym gene ontology synonym SO:0000704 interactor for genetic interaction. gene 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 mint 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. single nonmonotonic single nonmonotonic interaction ELISA 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 enzyme linked immunosorbent assay elisa 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. For instance HI0934, Rv3245c, At5g34500, YER456W. Ordered locus name ordered locus name CDS number ORF number locus name ONL systematic gene number 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. blue native page id-validation-regexp:"[0-9]+|[A-Z]{1,2}[0-9]+\.[0-9]+ " DDBJ EMBL 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 DDBJ/EMBL/GenBank ddbj/embl/genbank search-url: http://www.ebi.ac.uk/cgi-bin/dbfetch?db=EMBLSVA&id=${ac} GenBank 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. PMID:3016916 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. micro-injection microinjection 33P P33 Molecule labelled with the radio isotope 33 of phosphorus atoms. 33p radiolabel alias type Descriptor of type of nomenclature used to describe interactor. CvAliasType beta lactamase beta lactamase complementation 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. PMID:12042868 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. PMID:14613974 b42 activation domain b42 ad 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. anti tag coip anti tag coimmunoprecipitation The interaction between the proteins or the formation of a complex is disrupted by a biological molecule or by a modification of the interactors. inhibition 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 two hybrid fragment pooling approach 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:12634794 PMID for application instance:11196647 partial identification of protein sequence partial protein sequence identification. partial id prot seq residue modification. selenomethionine [M:sel] L-selenomethionine MSE 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. yfp tag yellow fluorescent protein YFP yellow fluorescent protein tag DNA that consists of two base pairing strands. The 2 nucleotide chains are held together by hydrogen bonds between base pairs of nucleotides. ds DNA ds dna double stranded deoxyribonucleic acid Any type of molecule, including complexes, that may be observed but not identified. This term should be use only at PARTICIPANT level. unknown participant (S)-2-amino-6-dimethylaminohexanoic acid RESID:AA0075 residue modification. dimethyllysine n6,n6-dimethyl-lysine N(zeta)-dimethyllysine epsilon-dimethyllysine MLY N6,N6-dimethyl-L-lysine [K:meth_2] lysine derivative Lys(y) orf 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. open reading frame name interaction type Connection between molecule. 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. IEC ion exchange chromatography ion exchange chrom lexa dna binding domain Amino terminal (1-220) part of the Escherichia coli lexA repressor, binding to 16 base pair palindromic DNA sequences. lexa dna bd kinase 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 added from close proximity on the phosphorylated substrate due to the action of the kinase. PMID:14987100 kinase htrf homogeneous time-resolved fluorescence kinase HTRF RESID:AA0168 residue modification. (S)-2-amino-5-([imino([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]amino)methyl]amino)pentanoic acid N(omega)-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-arginine N(omega)-alpha-D-ribofuranosyl-L-arginine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate) omega-N-(ADP-ribosyl)-L-arginine omega-n-(adp-ribosyl)-arginine adp-ribosylarginine experiment modification exp-modification Modifications of the standard experimental method described in the CV. 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. 3 hybrid method competition binding 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. experimental knowledge based experimental info Predictive algorithms that rely on the information obtained by experimental results. gpi anchor residue residue modification. IMEx International Molecular Interaction Exchange. imex 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 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. prot microinjection protein microinjection ms protein sequence de novo protein sequencing by mass spectrometry PMID:10984529 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. Artificial residue modification enabling studies of cysteine binding status. PMID:15325307 alkylated cysteine methylated alanine residue modification. RESID:AA0061 RESID:AA0062 gamma-carboxyglutamic acid residue modification. RESID:AA0032 (S)-3-amino-1,1,3-propanetricarboxylic acid 1-carboxyglutamic acid [misnomer] 4-carboxyglutamic acid L-gamma-carboxyglutamic acid carboxyglutamic acid ipi 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. international protein index id-validation-regexp:"IPI[0-9]+.[0-9]+|IPI[0-9]+" less-than Partially determined sequence position known to be in a position lower than a given position. Displayed as '<'. 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. FITC labelled fluorescein isothiocyanate labbeled fluorescein isothiocyanate label fitc labelled SO:0000352 Polymer formed by the deoxyribose sugar group, and the nucleotides bases adenine, guanine, thymine and cytosine. deoxyribonucleic acid dna deoxyribonucleic acid DNA SO:0000356 Polymer formed by ribose sugar group, and the bases of the nucleotides adenine, guanine, uracil and cytosine. RNA rna ribonucleic acid covalent binding Interaction leading to the formation of covalent bond within an autocatalytic molecule or between partners. 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. nucleotide sequence identification nucleotide sequence sequence cloning 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. PMID:9013660 dls dynamic light scattering fluorescent resonance energy transfer 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. PMID:11558993 fret FRET FRET analysis RET gpi-serine gpi-anchor amidated serine residue modification. RESID:AA0162 N-seryl-glycosylphosphatidylinositolethanolamine Computational methods based on evolutionary hypothesis, used as criteria to browse sequences and predict interacting pairs. sequence based prediction predict from sequenc disease The interaction that has a disease association. predetermined feature Feature detection based on the knowledge of the molecule, before any experiment. predetermined featur 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 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. southern blot Transduction is the process by which bacterial DNA is moved from one bacterium to another by a virus. nucleic acid transduction nucl transduction Synthesis rate of a molecule under investigation differs from its naturally occurring expression level in a cell. expression level alteration necessary binding site A sequence range within a protein identified as being absolutely required for an interaction. required to bind 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. kcat turnover number A sequence range within a protein identified as involved in an interaction. binding site Reversible reaction that can affect C residue. GO:0018347 RESID:AA0102 farnesylation reaction farnesylation PMID:10449539 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 Description of confidence assessment method generally associated to the experiment. confidence-mapping 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 radiolabeled methyl methyltransferase radiometric assay 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. PMID:10189716 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). inhibitor antibodies 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 RESID:AA0068 RESID:AA0069 residue modification. methylated arginine gene neighbourhood 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 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 E-mail address to contact the author/organisation which has produced the data. This attribute is generally associated to an experiment. contact-email experimental interac experimental interaction detection Methods based on laboratory experiments. protein delivery by cationic lipid treatment prot cationic lipid Proteins are delivered into cells by treatment with cationic lipids. Irreversible reaction that can affect K,P,Y or R residues. GO:0018126 RESID:AA0028 RESID:AA0029 RESID:AA0030 RESID:AA0146 RESID:AA0215 hydroxylation reaction hydroxylation 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 interaction synthetic Fluorophore able to absord the electromagnetic radiation at given wavelength from a specific donor fluorophore, the re-emission of its own charateristic fluorescence. fluorescence acceptor fluorescence accept e-MSD PQS msd pdb id-validation-regexp:"[0-9][a-zA-Z0-9]{3}" search-url: http://www.ebi.ac.uk/msd-srv/atlas?id=${ac} 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/ PMID:16381867 Paramagnetic fragment, most often a cyclic nitroxide derivative, covalently attached to a molecule of interest. PMID:10966640 spin label static light scattering sls 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. heterogeneous nuclear rna heterogeneous nuclear ribonucleic acid heterogeneous nuclear RNA hnrna 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. 1-methylhistidine [misnomer] RESID:AA0073 residue modification. [H:meth_n4] (S)-2-amino-3-(3-methyl-3H-imidazol-4-yl)propanoic acid N(delta)-methylhistidine MHS 3'-methyl-L-histidine 3'-methyl-histidine methylhistidine pros-methylhistidine pi-methylhistidine RESID:AA0049 residue modification. acetylmethionine (S)-2-acetylamino-4-(methylsulfanyl)butanoic acid n-acetyl-methionine MAC 2-acetylamino-4-(methylthio)butanoic acid acetylmethionine methionamine N-acetyl-L-methionine [M:ac] his tag 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. 6-His-tag Hexa-His-tag Histidine-tag RESID:AA0161 residue modification. gpi-anchor amidated glycine gpi-glycine N-glycyl-glycosylphosphatidylinositolethanolamine kinase scintillation proximity assay kinase spa 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. 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 N6-formyl-L-lysine is cleaved and returns a K residue. RESID:AA0211 deformylation deformylation reaction participant identification method participant ident Method to determine the proteins involved in the interaction. participant detection id-validation-regexp:"PD[0-9]{6}" prodom ProDom The ProDom protein domain database consists of an automatic compilation of homologous domains. http://protein.toulouse.inra.fr/prodom.html 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. PMID:11791231 predictive text mining predictive tm immunostaining 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. feature type Property of a subsequence that may interfere with the binding of a molecule. 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 The protein is expressed and purified as a fusion to the glutathione S-tranferase protein. glutathione s tranferase tag glutathione S-tranferase tag gst tag dms 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. PMID:8238889 dimethylsulphate footprinting PMID:7491768 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. green fluorescent protein tag GFP green fluorescent protein gfp tag Sequence variation due to insertion, deletion or substitution event. mutation RESID:AA0035 residue modification. histidine-N1'-phosphate 1'-phospho-histidine tau-phosphohistidine 1-phosphohistidine (S)-2-amino-3-(1-phosphono-1H-imidazol-4-yl)propanoic acid tele-phosphohistidine HPE 1'-phospho-L-histidine histidine-3-phosphate [misnomer] histidine-N(epsilon)-phosphate [H:po_e] Protein complementation assay based on dissection of a membrane protein. membrane bound complementation assay membrane compl experiment descripti experiment description The experimental condition text description, should contain information about the organisms hosting the interaction. dihydrofolate reductase reconstruction dhfr reconstruction 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. PMID:10318894 GO:0006471 RESID:AA0169 RESID:AA0231 RESID:AA0237 RESID:AA0295 Reaction that can affect Arg, Cys, Glu, Arg and Asn residues. adp ribosylation reaction adp ribosylation protein sequence Single amino acid identification along a protein sequence. protein sequence identification p elisa proximity enzyme linked immunosorbent assay pELISA 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. Resolution of the 3D structure. This attribute is generally associated to an interaction. 3d-resolution 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 alexa 546 label Alexa fluorescent dye analogue to Cy3 with an approximate excitation wavelength maximum of 546nm. caution Warning about errors/ grounds for confusion. Can be associated to interaction, experiment, Cv term or any participant. deubiquitination reaction GO:0016579 PMID:11583613 RESID:AA0125 Cleavage of the G-K bond and release of ubiquitin or ubiquitin like proteins. deubiquitination biopolymer Molecule consisting of a specific sequence of amino acidic or nucleotidic monomers strung together through chemical bonds. id-validation-regexp:"MGI:[0-9]+" MGD/MGI 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 Fluorophore which emits electromagnetic radiation of given wavelength. fluorescence donor id-validation-regexp:"PR[0-9]{6}" PRINTS prints 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/ weight by hoechst 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. molecular weight estimation by hoechst staining smart 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/ id-validation-regexp:"SM[0-9]{5}" Any molecule that is able to transfer an electron to another chemical species. electron donor emsa supershift 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. PMID:12169687 electrophoretic mobility supershift assay hotspot mutation decreasing interaction Residue of a protein whose identity mutation or deletion decreases significantly interaction strength. mutation decreasing under expressed level A molecule is estimated to be expressed at lower levels than in physiological condition. under-expressed PROSITE is a database of protein families and domains. It consists of biologically significant sites, patterns and profiles. http://us.expasy.org/prosite/ id-validation-regexp:"PS[0-9]{5}" prosite Prosite 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. synthetic phenotype 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. dnase 1 footprinting DNase I footprinting N2-acetyllysine N2-acetyl-L-lysine [K:ac] KAC (S)-2-acetylamino-6-aminohexanoic acid n2-acetyllysine residue modification. RESID:AA0048 n2-acetyl-lysine isothermal titration calorimetry itc ITC PMID:11785756 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. myristoylated residue myristoylated aa residue modification. 10E-15 moles per liter of solution. OBSOLETE: term redundant with the schema exponent attribute of the parameter. fM fentomolar cdna library PMID:6110205 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. pirsf 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 Post translational modification required for an interaction to occur. prerequisite-ptm antibody detection antibody mediated identification. identification by antibody List of authors associated to a publication. This attribute is generally associated to an experiment. author-list 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. PMID:11495741 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. PCA complementation protein complementation assay n-acetyl-lysine residue modification. acetyllysine n6-methyl-lysine epsilon-methyllysine residue modification. N(zeta)-methyllysine N6-methyl-L-lysine methyllysine (S)-2-amino-6-methylaminohexanoic acid [K:meth_1] MLZ MMDB 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 id-validation-regexp:"[0-9]+" n2-acetyl-arginine alpha-acetylamino-delta-guanidinovaleric acid [R:ac] N2-acetyl-L-arginine acetylarginine acetylarginine residue modification. RESID:AA0354 RAC Cross reference pointing to a Gene Ontology -'cellular component' term. gene ontology term for cellular component component go component term N-aspartyl-glycosylphosphatidylinositolethanolamine gpi-aspartate gpi-anchor amidated aspartate residue modification. RESID:AA0159 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 N-methyl-L-alanine methylalanine AMT (S)-2-methylaminopropanoic acid n-methyl-alanine [A:meth_n] residue modification. N-methylalanine Association rate constant or rate of complex formation. Unit MOLE per SECOND (M-1 s-1) ka kon 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. 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 glycosyl-threonine residue modification. RESID:AA0155 O-glycosyl-L-threonine O3-glycosyl-L-threonine imex-primary Interaction identifier of a database belonging to IMEx consortium. alexa 568 label Alexa fluorescent dye analogue to Rhodamine Red-X with an approximate excitation wavelength maximum of 568nm. SGD is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae. http://www.yeastgenome.org/ id-validation-regexp:"S[0-9]{9}" search-url: http://genome-www4.stanford.edu/cgi-bin/SGD/locus.pl?locus=${ac} sgd SGD Interaction that is proven to involve only its interactors. direct interaction 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. Affinity purification affinity chrom affinity chromatography technology see-also Related object within the same database or pointing to external database. 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 sequence phylogeny maltose binding protein tag mbp 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. maltose binding protein tag 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 MOD:00798 RESID:AA0025 UniMod:374 half cystine Half of a disulfide bridge 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. inferred by curator modeled by curator modelled by curator rna tri hybrid Three hybrid system 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. PMID:12162957 PMID:8972875 interaction database interaction database. interaction xref myc tag coip myc tag coimmunoprecipitation 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). aggregation Physical association among molecules. OBSOLETE since too non-specific. Consider using physical interaction (MI:0218) instead. enhancement enhancement interaction 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. interaction Previously described interaction now being used as an interactor to describe hierarchical build-up of complexes. residue modification. RESID:AA0120 N6-retinal-L-lysine n6-retinal-lysine [K:retin] N6-retinyl-lysine N6-retinylidene-L-lysine retinallysine KRT (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 Text pointing to a specific paper figure legend where the experimental evidences for an interaction are shown. figure legend 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]+" search-url: 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 tissue list List of tissue used as topic in UniProt RC line. http://www.expasy.org/cgi-bin/lists?tisslist.txt inhibitor small molecules inhibitor small mol PMID:10542155 PMID:10780927 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). radiolabelled A radiolabelled molecule has radio isotopes among its constituent atoms that can be used to identify, localize or quantify the full molecule. radiolabel radiolabeled Molecule experimentally treated to capture its interacting partners. bait 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 amidated residue residue modification. antisense rna PMID:1340158 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:11731788 PMID:8606778 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). perturbagens peptides perturbagens pep (2S,3R)-2-acetylamino-3-hydroxybutanoic acid [T:ac] acetylthreonine n-acetyl-threonine N-acetylthreonine RESID:AA0052 residue modification. TAC N-acetyl-L-threonine X-ray Analysis of diffraction pattern of a partially ordered sample composed of fibers oriented parallel to each other. x-ray fiber diffraction x-ray fiber diffrac sirna dicer RNA micro RNA siRNA small interfering rna PMID:10542148 Ribonucleic acid used in RNAi study. These RNA have the reverse complementary sequence of a target gene's mRNA transcript and inhibit its expression. cross-linking study crosslink Analysis of complexes obtained by chemical treatments that promote the formation of covalent bonds among molecules in close proximity. Predictive 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. LocusLink provides a single query interface to curated sequence and descriptive information about genetic loci. http://www.ncbi.nlm.nih.gov/LocusLink/ Entrez gene/locuslink entrezgene/locuslink id-validation-regexp:"[0-9]+|[A-Z]{1,2}_[0-9]+|[A-Z]{1,2}_[A-Z]{1,4}[0-9]+" entrez gene/locuslink Nucleic acid introduced into a cell via an external organism, usually a virus or bacteria.. nucleic acid delivery by infection nucl infection 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 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 gene product Reference of a protein object pointing to its genomic or nucleic acid sequence. gpi-threonine RESID:AA0164 residue modification. N-threonyl-glycosylphosphatidylinositolethanolamine gpi-anchor amidated threonine residue modification. RESID:AA0036 phosphoshistidine phospho-histidine in vitro translated protein Protein sample collected by in vitro translation of its mRNA taking advantage of purified translation machinery. in vitro translated Set of interacting molecules that can be copurified. This term and its children should be use only at PARTICIPANT level. complex xref type CvXrefQualifier refType cross-reference type Qualifier to describe the type of information a cross-reference is pointing to. 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. PMID:10935637 enzyme tag Cells has been fixed by treatment with organic solvent, staining and inclusion in a resin for microscopic analysis. fixed cell 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') conditional synthetic lethal temperature-sensitivity temprtr synt lethal footprinting analysis is used to identify regions of molecules directly involved in binding other macromolecules and therefore protected from the effects of degradative enzymes. footprinting A macromolecular complex containing both protein and RNA molecules. GO:0030529 protein rna complex ribonucleoprot compl ribonucleoprotein complex anti tag western blot anti tag western 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. 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. PMID:9299343 surface patches residue modification. RESID:AA0051 N-acetyl-L-serine n-acetyl-serine acetylserine N-acetylserine SAC (S)-2-acetylamino-3-hydroxypropanoic acid [S:ac] feature prediction Feature detection based on computational analysis. Km km 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. URL/Web address describing an experiment, an interaction, a Cv term or an organism. url 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. oligopeptide polypeptide peptide PubChem provides information on the biological activities of small molecules. http://pubchem.ncbi.nlm.nih.gov/ PMID:16381840 pubchem PubChem 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 id-validation-regexp:"EBI-[0-9]+" search-url: http://www.ebi.ac.uk/intact/search/do/hvWelcome?searchString=${ac} 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 PMID:14681455 IntAct intact [G:myr] GMY N-myristoyl-glycine n-myristoyl-glycine myristoylglycine RESID:AA0059 residue modification. 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 fluorescence-activated cell sorting facs FACS Flow cytometry O3-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-serine (S)-2-amino-3-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]oxy)-propanoic acid Formula O3-(ADP-ribosyl)-L-serine adp-ribosylserine o-(adp-ribosyl)-serine O3-alpha-D-ribofuranosyl-L-serine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate) residue modification. O-(ADP-ribosyl)-L-serine affinity technology affinity techniques Techniques which depend upon the strength of the interaction between two entities. unspecified method 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. 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 genome based prediction genome prediction 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. monoclonal western monoclonal antibody western blot 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. mudpit multidimensional protein identification technology 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. PMID:11231557 organism att name organism attribute name Attribute name of annotation associated to an organism element. mutation increasing interaction mutation increasing Residue of a protein whose identity mutation or deletion increases significantly interaction strength. 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 Filter overlay assay 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. protein cross-linking with a bifunctional reagent Label transfer techniques Photoaffinity labelling protein crosslink 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. Molecule whose sequence identity is not checked and has been assumed from external or previous experimental evidence(s). predetermined predetermined participant [R:po] alpha-amino-delta-phosphonoguanidinovaleric acid RESID:AA0222 residue modification. (S)-2-amino-5-[imino(phosphonoamino)methyl]aminopentanoic acid omega-N-phospho-L-arginine RPO phosphoarginine omega-n-phospho-arginine N5-[imino(phosphonoamino)methyl]-L-ornithine acetylation reaction RESID:AA0053 RESID:AA0046 GO:0006473 RESID:AA0045 Reaction, that can affect K,C,A,D,E,Q,G,I,K,M,P,S,T,Y,V residues. RESID:AA0044 RESID:AA0050 RESID:AA0054 acetylation id-validation-regexp:"WBGene[0-9]{8}" 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/ wormbase WormBase colocalization by fluorescent probes cloning 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 hypomorph The gene function has been partially reduced compared to wild-type by altering its sequence e.g. a temperature sensitive mutant transcription compl transcriptional complementation assay 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. Molecule labelled with the radio isotope 32 of phosphorus atoms. 32p radiolabel 32P P32 bacterial display 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. PMID:10436088 PMID:8248129 S-farnesyl-L-cysteined is cleaved and returns a C residue. defarnesylation defarnesylation reaction 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 residue modification. phosphorylated phosphorylated residue gfp complementation PMID:15631464 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. green fluorescence protein complementation assay panther 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 The author states a molecule is completely pure, i.e. no other molecular species are present. homogeneous pure polyprotein fragment polyprotein frag Subpart of a polyprotein that is naturally cleaved in vivo. http://www.signaling-gateway.org/data/Y2H/cgi-bin/y2h_int.cgi?id=${ac} search-url: AfCS alliance for cellulare signaling 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 afcs 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. confocal microscopy [S:oxal] L-3-oxoalanine L-amino-malonic acid semialdehyde oxoalanine L-serinesemialdehyde [misnomer] (S)-2-amino-3-oxopropanoic acid 2-amino-3-oxopropionic acid 3-oxoalanine L-alpha-formylglycine L-aminomalonaldehydic acid RESID:AA0185 residue modification. SOX pH at which interaction was determined. pH of interaction pHint protein kinase assay Catalysis of the transfer of a phosphate group, usually from ATP, to a protein substrate. synthetic lethal 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) 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. flag tag DYKDDDDKV epitope tag FLAG FLAG-tagged 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. vp16 activation domain N6-acetyl-L-lysine n6-acetyllysine residue modification. (S)-2-amino-6-(acetylamino)hexanoic acid epsilon-acetyllysine N(zeta)-acetyllysine n6-acetyl-lysine [K:N6ac] KA6 [C:po] s-phospho-cysteine S3-phosphocysteine (R)-2-amino-3-(phosphonosulfanyl)propanoic acid S-phospho-L-cysteine CPO phosphocysteine S-phosphonocysteine cysteine phosphate thioester RESID:AA0034 residue modification. 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 alexa 488 label Alexa fluorescent dye analogue to Oregon Green 488 with an approximate excitation wavelength maximum of 488 nm. 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. [F:ac] FAC N-acetyl-L-phenylalanine residue modification. acetylphenylalanine n-acetyl-phenylalanine Molecule has undergone one or more purification steps to isolate it from the cellular environment. purified Kd Kd The equilibrium dissociation constant of a receptor/ligand or proteinA/proteinB complex. Unit Molar (generally M-1). ss dna single stranded deoxyribonucleic acid DNA that consists of only one chain of nucleotides rather than the two base pairing strands found in DNA in the double helix form. ss DNA contact-comment Free text notes on how to contact the author organisation which has produced the data This attribute is generally associated to an experiment. Entrance of molecules into cells that does not involved specific treatments but rely on natural cellular processes. passive uptake agonist 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. PubMed is designed to provide access to citations from biomedical literature. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi pubmed search-url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=${ac}&dopt=Abstract phosphatase assay Measures the catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Position within the sequence clearly defined. certain sequence position certain 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. PMID:11578931 circular dichroism cd CD [E:ac] n-acetyl-glutamic acid N-acetyl-L-glutamic acid EAC acetylglutamate (S)-2-(acetylamino)pentanedioic acid acetylglutamic acid residue modification. 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. suppression scalable PMID:11473021 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. domain profile pairs activation domain 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 tag Molecules labelled with isotope 15 of nytrogen atoms. 15N N15 15n label 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 glycosylasparagine RESID:AA0151 residue modification. n4-glycosyl-asparagine N4-glycosyl-L-asparagine 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. zymography PMID:2071592 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. rna interference PMID:12110901 PMID:12408823 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 calcium phosphate nucleic acid transfection ca po nuc transfect Transient introduction and expression of nucleic acid carried out by treatment with calcium phosphate. Protein complementation assay performed by dissecting a cytoplasmic protein activity and restoring it through the two hybrid proteins interaction. cytoplasmic complementation assay cytoplasmic compl Partially determined sequence position known to be in a location higher than a given position. greater-than Displayed as '>'. electron microscopy 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 cryomicroscopy Electron crystallography 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. PMID:14755272 molecular source 131I I131 131i radiolabel Molecule labelled with 131 radio isotope of iodine atoms. myristoylation reaction GO:0018319 RESID:AA0078 Reaction that can affect K or G residues. myristoylation Attribute name of annotation associated to an experiment element. experiment att name experiment attibute name Molecule labelled with 35 radio isotope of sulfur. Proteins are often metabolically labelled, usually be growth in 35S labelled culture medium. 35s radiolabel 35S S35 s35 radiolabelled nucleic acid electroporation nucl 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. Example generally associated to Cv terms. example http://www.ebi.ac.uk/newt/display?search=${ac} search-url: New EBI Web Taxonomy. http://www.ebi.ac.uk/newt newt mass detection of residue modification 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:11395414 PMID for application instance:11875433 modified residue ms 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. grid The General Repository for Interaction Datasets (GRID) is a database of genetic and physical interactions. http://biodata.mshri.on.ca/grid GRID 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 phospho acceptor Molecule to which a phosphate may be transferred from an phospho donor. 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 X-ray x-ray diffraction 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 crystallography comigration in non denaturing gel electrophoresis comigration by non denaturing gel electrophoresis. comig non denat gel emsa 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. band shift Gel retardation assay electrophoretic mobility shift assay CvTopic attribute name Collection of topic describing the free text stored as an attribute value. mrna display PMID:11551470 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. random spore analysis random-spore analysis RSA spore germination 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. rsa alk phosphatase tag Protein is fused to alkaline phosphatase, and the measure of this enzyme activity can be taken as indicative of presence of protein. alkaline phosphatase tag 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. library-used palmitoylation reaction palmitoylation GO:0018318 RESID:AA0060 RESID:AA0077 RESID:AA0079 RESID:AA0080 RESID:AA0106 Reversible reaction that can affect C,K,T or S residues. 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 CvFuzzyType endStatus startStatus 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 [R:meth_n7] dimethylarginine (S)-2-amino-5-[((dimethylamino)iminomethyl)amino]pentanoic acid omega-n,omega-n-dimethyl-arginine omega-N,omega-N-dimethyl-L-arginine NG,NG-dimethylarginine asymmetric dimethylarginine residue modification. RM2 lexa b52 complementation LexA B52 transcription complementation lexa b52 complement 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. 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:10967324 PMID:11752590 PMID for application instance:11805826 fingerprinting peptide massfingerprinting 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. PMID:9927659 tox-r dimerization assay toxcat toxcat translocation end Xref pointing to a GO compartment term describing the end location of a migrating molecule. conformational tm Text mining is used to support interactions which have been determined by other methods. confirmational text mining 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/ scop superfamily 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. classical fluorescence spectroscopy fluorescence spectr Cell lysates are partially fractionated to isolate a specific subcellular fraction. subcellular preparation subcellular prep 2'-[3-carboxamido-3-(trimethylammonio)propyl]-histidine 2-[(Xi)-3-carboxamido-3-(trimethylammonio)propyl]-4-((S)-2-amino-2-carboxyethyl)-1H-imidazole 2'-[3-carboxamido-3-(trimethylammonio)propyl]-L-histidine 2-amino-3-[[2-(3-amino-3-carbamoyl-prop-1-enyl)-1,1,3-trimethyl-2,3-dihydroimidazol-5-yl]]propanoic acid diphthamide 2-amino-4-[[5-(2-amino-2-carboxylato-ethyl)-1,1,3-trimethyl-2,3-dihydroimidazol-2-yl]]but-3-enamide HDP residue modification. RESID:AA0040 2-[3-carboxamido-3-(trimethylammonio)propyl]histidine [H:diph] diphthamide alpha-(aminocarbonyl)-4-(2-amino-2-carboxyethyl)-N,N,N-trimethyl-1H-imidazole-2-propanaminium N-acetylglycine [G:ac] residue modification. n-acetylglycine GAC aceturic acid acetylglycine 2-(acetylamino)ethanoic acid 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. 3d repertoire suppress overexpress suppression overexpression 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. 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 id-validation-regexp:"AA[0-9]{4}" search-url: http://srs.ebi.ac.uk/cgi-bin/wgetz?[resid-id:${ac}]+-e PDB The RCSB PDB provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease. http://www.pdb.org/ PMID:14634627 rcsb pdb search-url: http://www.pdb.org/pdb/explore/explore.do?structureId=${ac} participant database participant xref participant database. uM 10E-6 moles per liter of solution. OBSOLETE: term redundant with the schema exponent attribute of the parameter. micromolar feature xref feature database. feature database Method by which proteins are delivered into a cell. protein delivery hprd HPRD 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/ predict from struct Methods based on 3D structure information. structure based prediction (R,E,E,E)-2-amino-3-(3,7,11,15-tetramethyl-2,6,10,14-hexadecatetraenylsulfanyl)propanoic acid s-geranylgeranyl-cysteine geranylgeranylcys 2-amino-3-(3,7,11,15-tetramethyl-2,6,10,14-hexadecatetraenylthio)propanoic acid [C:ger] S-geranylgeranyl-L-cysteine residue modification. RESID:AA0104 CGR formylmethionine RESID:AA0021 residue modification. (S)-2-formylamino-4-(methylsulfanyl)butanoic acid n-formyl-methionine MFM N-formyl-L-methionine 2-formylamino-4-(methylthio)butanoic acid [M:form] Name assigned to a molecule by the authors within a paper that may differ from the reference database. author assigned name N(zeta)-myristoyllysine myristoyllysine (S)-2-amino-6-(tetradecanoylamino)hexanoic acid residue modification. [K:myr] KMY N6-myristoyl-L-lysine N6-(1-oxotetradecyl)-L-lysine epsilon-myristoyllysine n6-myristoyl-lysine protease htrf Protease HTRF 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 homogeneous time resolved fluorescence search-url-ascii Search URL to retrieve an external entry in ASCII format. Generally associated to Cv Database terms. acetylhistidine n-acetyl-histidine [H:ac] HAC N-acetyl-L-histidine residue modification. n-palmitoyl-cysteine N-(1-oxahexadecyl)-L-cysteine [C:palm_n] n-palmitoylcysteine 2-hexadecanoylamino-3-mercaptopropanoic acid CPN residue modification. N-palmitoyl-L-cysteine (R)-2-hexadecanoylamino-3-sulfanylpropanoic acid 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 identification by sequencing full dna sequence database citation Database citation list names of databases commonly used to cross reference interaction data. Biological function of a participant or of an interaction. function PMID:9631301 PMID for application instance:11478868 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. docking Role not specified or not applicable to the data. unspecified role Unaltered endogenous molecule in its naturally occurring state. naturally occurring endogenous This qualifier is used when the crossreference is imported from the Gene Ontology tag definition_reference. gene ontology definition reference go-definition-ref 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. synthetic genetic analysis [L:ac] LAC N-acetyl-L-leucine acetylleucine residue modification. n-acetyl-leucine column chromatography 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 QAC (S)-2-acetylamino-5-pentanediamic acid acetylglutamine [Q:ac] n-acetyl-glutamine N-acetyl-L-glutamine acetylglutamine residue modification. Mixture of protein forms where N-terminus has been progressively truncated. ragged n-terminus deletion analysis 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. transfer ribonucleic acid transfer RNA tRNA trna 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 suppression 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. (2S)-1-acetyl-2-pyrrolidinecarboxylic acid acetylproline residue modification. PAC [P:ac] n-acetyl-proline acetylproline N-acetyl-L-proline