Author Luisa Montecchi Palazzi luisa@ebi.ac.uk psi-mi.lastac. The last accession number used in this file is stored in a separate file, It MUST be updated when this file is updated. 2006-12-22T12:25:00 $Id: psi-mi.obo,v 1.118 2007/03/14 04:38:46 girlwithglasses Exp $ PSI-MI To facilitate handling, they all have been merged in this file, though they The PSI MI schema defines short labels for controlled vocabulary terms. This file is published by the PSI MI working group see http://psidev.sourceforge.net/ are essentially independent CVs describing different aspects of molecular interactions. luisa Each of the top level terms in this file is the root term of an independent controlled vocabulary Where possible, short labels are reported as exact synonyms of a term in this file, mapping an element of the PSI Molecular Interaction XML schema. Notes: Protein complementation assay performed by dissecting a transcription factor activity (DNA binding domain and transcription activation domain) its restoration through the two hybrid proteins interaction that lead to a reporter gene expression. PMID:14755292 transcription compl transcriptional complementation assay safe DNA gel stain molecular weight estimation by sybr staining Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with sybr dyes. weight by sybr acetylated residue PMID:11125103 residue modification. sequence database Database collecting nucleic or amino acid sequences mainly derived from genomic sequence. Attribute name of annotation associated to a feature element. feature attribute name feature att name experiment database experiment database. experiment xref rfam rfam Rfam is a large collection of multiple sequence alignments and covariance models covering many common non-coding RNA families. http://www.sanger.ac.uk/Software/Rfam/ id-validation-regexp:"RF[0-9]{5}" QAC (S)-2-acetylamino-5-pentanediamic acid n-acetyl-glutamine [Q:ac] acetylglutamine acetylglutamine N-acetyl-L-glutamine residue modification. RESID:AA0045 2-amino-4-[[5-(2-amino-2-carboxylato-ethyl)-1,1,3-trimethyl-2,3-dihydroimidazol-2-yl]]but-3-enamide [H:diph] diphthamide residue modification. RESID:AA0040 2'-[3-carboxamido-3-(trimethylammonio)propyl]-histidine 2-[3-carboxamido-3-(trimethylammonio)propyl]histidine diphthamide 2'-[3-carboxamido-3-(trimethylammonio)propyl]-L-histidine HDP alpha-(aminocarbonyl)-4-(2-amino-2-carboxyethyl)-N,N,N-trimethyl-1H-imidazole-2-propanaminium 2-[(Xi)-3-carboxamido-3-(trimethylammonio)propyl]-4-((S)-2-amino-2-carboxyethyl)-1H-imidazole 2-amino-3-[[2-(3-amino-3-carbamoyl-prop-1-enyl)-1,1,3-trimethyl-2,3-dihydroimidazol-5-yl]]propanoic acid catalytic rna catalytic RNA catalytic ribonucleic acid Species of RNA that catalyses cleavage or trans-esterification of the phosphodiester link. crna This class of approaches is characterised by the use of affinity resins as tools to purify molecule of interest (baits) and their binding partners. The baits can be captured by a variety of high affinity ligands linked to a resin - for example, antibodies specific for the bait itself, antibodies for specific tags engineered to be expressed as part of the bait or other high affinity binders such as glutathione resins for GST fusion proteins, metal resins for histidine-tagged proteins. PMID:7708014 Affinity purification affinity chrom affinity chromatography technology residue modification. RESID:AA0030 4hydroxyproline HYP [P:hy_g] 4-hydroxy-L-proline 4-hydroxy-proline gpi-threonine gpi-anchor amidated threonine N-threonyl-glycosylphosphatidylinositolethanolamine RESID:AA0164 residue modification. protein array PMID:12067604 PMID:10976071 The protein array technology allows the screening of biochemical activities or binding abilities of hundreds or thousands of protein samples in parallel. After synthesis and purification by high-throughput methodologies, the proteins are printed onto the chip by using an instrument (micro-arrayer) that is capable of spotting liquid samples in a reproducible manner onto a planar support. The ordered protein array can then be probed with labelled molecules to identify proteins that bind to the bait. selenium cysteine L-selenocysteine CSE [C:sel] 3-selenylalanine selenocysteine residue modification. RESID:AA0022 genetic experimental form Descriptor of an experimental form involved in a genetic interaction methyltransferase as methyltransferase assay Measures the catalysis of the transfer of a methyl group to an acceptor molecule. array technology In this class of methodologies, the molecules to be tested are presented ordered in an array format (typically at high density) on planar supports. The characteristics and chemical nature of the planar support can vary. This format permits the simultaneous assay, in controlled conditions, of several thousand proteins/peptides/nucleic acids for different functions, for instance their ability to bind any given molecule. 10E-15 moles per liter of solution. OBSOLETE: term redundant with the schema exponent attribute of the parameter. fM fentomolar antimorph The gene function has been antagonized by a mutation in another copy of the gene. A sequence range within a protein identified as involved in an interaction. binding site Immuno blot Western blot is a procedure to identify and quantify proteins. A mixture of protein is first submitted to an electrophoresis in denaturing condition and then electro-transferred from the gel to a membrane. The membrane is then incubated with a primary antibody specific for a given protein or a specific residue modification in the sample under analysis. A secondary antibody, radiolabelled or fused to fluorophore or to a chromogenic enzyme, targets the first antibody and allows the visualisation of the protein band on the membrane. western blot Chains of amino acids joined by peptide bonds. Distinction between peptides, oligopeptides and polypeptides is arbitrarily by length; a polypeptide is perhaps more than 15 residues. polypeptide oligopeptide peptide CPS s-palmitoylcysteine [C:palm_s] s-palmitoyl-cysteine S-palmitoyl-L-cysteine 2-amino-3-(hexadecanoylthio)propanoic acid cysteine palmitate thioester (R)-2-amino-3-(hexadecanoylsulfanyl)propanoic acid RESID:AA0106 residue modification. cysteine hexadecanoate thioester range For instance when an amino acid modification is known to be in the region from 5 to 7. Displayed as '..'. Describes a sequence position known to be in a certain range, where the exact position is unclear. Reference not index in medline : Rosenberg, A., Griffin, K., Studier, W.S., McCormick, M., Berg, J., Novy, R., Mierendorf, R. inNovations, 1996, 6, 1. t7 phage display t7 phage T7 is a double stranded DNA bacteriophage with a thin-walled icosahedral capsid, ~550 Angstrom in diameter, which is decorated by 415 copies of the capsid protein, the product of gene 10. gp10 can tolerate insertions at the carboxyterminus without loosing its ability to be inserted into functional phage capsids. Both low density and high density display (albeit only with short peptides) can be achieved. http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?[libs%3d{dsmz_mutz%20ecacc_cell%20iclc%20CABI_BACT%20CIP_BACT%20CABI_YEAST%20DSMZ_PLANT_CELL}-id:${ac}]+-e search-url: id-validation-regexp:"[0-9]+|ACC\s[A-Z0-9]+|ECACC\s[A-Z0-9]+|LMBP\s[A-Z0-9]+|ICLC\s[A-Z0-9]+|CIP-[0-9]+" PMID:16381901 Ontology of cell types. http://obo.sourceforge.net/cgi-bin/detail.cgi?cell cell ontology Filter overlay assay A method in which separation depends upon the ability of one participant to bind to a filter or membrane which the other participants do not. Molecules interacting with the bound molecule will also be retain on the filter. For example, proteins expressed by different clones of an expression library are bound to a nitrocellulose membrane, by colony (bacterial library) or plaque (phage library) blotting. A labelled protein can then be used as a probe to identify clones expressing proteins that interact with the probe. Interactions occur on the nitrocellulose filters. The method is highly general and therefore widely applicable. A variety of approaches can be used to label the ligand, alternatively the ligand can be detected by a specific antibody. filter binding N6-retinylidene-L-lysine [K:retin] N6-retinal-L-lysine KRT residue modification. RESID:AA0120 N6-retinyl-lysine n6-retinal-lysine retinallysine (S)-2-amino-6-[(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)-2,4,6,8-nonatetraenylidene]aminohexanoic acid light microscopy Light visible microscopy uses environmental light to illuminate the sample and produce a magnified image of the sample. Biological function of a participant or of an interaction. function id-validation-regexp:"TIGR[0-9]+" TIGRFAMs is a collection of protein families, featuring curated multiple sequence alignments, Hidden Markov Models (HMMs) and annotation. http://www.tigr.org/TIGRFAMs TIGRFAMs tigrfams Literally, in place i.e. the protein is in its natural environment during the experiment. OBSOLETE as a full host organisms is recommended using tax id == -1 as convention to refer to 'in vitro' interaction. in situ Mass spectrometry can be used to characterise chemical modifications within peptides. One approach consists in the observation of a mass difference when a sample is treated with an enzyme that can specifically remove a peptide modification, for instance a phosphatase. The mass difference corresponds to the mass of the chemical group covalently linked to a residue. Such experiments carried out with a MALDI-TOF (Matrix-assisted laser desorption ionization time-of-flight ) do not allow the mapping of the modification site within the sequence, whereas any tandem mass spectrometer (LC MS/MS Liquid Chromatography Tandem Mass Spectrometry, nanoESI MS/MS nanoElectrospray Ionisation tandem mass spectrometry, FTMS Fourier Transform mass spectrometry) provide such information. A second approach consists of the direct mass measurement of the ionized chemical group dissociated from the residue within a tandem mass spectrometer. Both approaches need a prior enrichment of the modified peptide population in the samples with IMAC (Immobilized Metal Affinity Chromatography)or specific anti-modification antibodies. PMID for application instance:11875433 PMID:11395414 modified residue ms mass detection of residue modification S-nitrosyl-L-cysteine S-nitrosocysteine L-cysteine nitrite ester (R)-2-amino-3-nitrososulfanyl-propanoic acid nitrosylcysteine s-nitrosyl-cysteine residue modification. RESID:AA0230 Sequence variation due to insertion, deletion or substitution event. mutation method reference Reference to a related paper which more fully describes either the experimental method or one or more of the interactors used within the experiment. 2h fragment pooling This two hybrid approach involves the screening of a large number of individual proteins against a comprehensive library of randomly generated fragment as prey. The usage of degenerated fragment allows identification of the minimal protein region required for the interaction. since multiple clones that encode overlapping regions of protein are often identified, the minimal domain for interaction may be readily apparent from the initial screen. PMID for application instance:11196647 PMID:12634794 two hybrid fragment pooling approach residue modification. phosphorylated residue phosphorylated kinase homogeneous time resolved fluorescence kinase HTRF homogeneous time-resolved fluorescence PMID:14987100 Measures quenching of the nonradiative energy transfer between fluorescent long-lifetime lanthanide chelates and different acceptors. Relies on a fluorescence energy donor and acceptor being added from close proximity on the phosphorylated substrate due to the action of the kinase. kinase htrf [K:N6ac] (S)-2-amino-6-(acetylamino)hexanoic acid epsilon-acetyllysine residue modification. RESID:AA0055 n6-acetyllysine n6-acetyl-lysine KA6 N6-acetyl-L-lysine N(zeta)-acetyllysine library-used This annotation topic will be used to store information about the cDNA library. If a name is available this should be reported along with a short description of the library. hypermorph The gene function has been partially improved compared to wild-type by altering its sequence. surface patches PMID:9299343 Surface patches are built using 6 criteria: solvation potential, residue interface propensity, hydrophobicity, planarity, protrusion and accessible surface area. Protein structures having similar patches are likely to have the same interactions. [A:meth_n] N-methylalanine residue modification. RESID:AA0061 methylalanine AMT (S)-2-methylaminopropanoic acid n-methyl-alanine N-methyl-L-alanine Reference pointing to the originating database in which an interaction, or other curated information, was first described. source reference N-methylglutamine QM5 gamma-methylglutamine N(delta)-methylglutamine n5-methyl-glutamine methylglutamine [Q:meth_n5] residue modification. RESID:AA0071 N5-methyl-L-glutamine (S)-2-amino-N5-methylpentanediamic acid delivery method Method by which molecule is delivered or engineered into a cell. bind id-validation-regexp:"[0-9]+" The Biomolecular Interaction Network Database (BIND) is a collection of records documenting molecular interactions. http://www.blueprint.org/bind BIND PMID:10929120 Yellow fluorescent protein from Vibrio fischeri can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native. yellow fluorescent protein tag YFP yellow fluorescent protein yfp tag full identification by sequencing sequencing occurs during the course of the experiment. The DNA to be sequenced is used as template for the in vitro synthesis, by DNA polymerase, of a set of partial replicas, all beginning at the same place, but terminating at different points along the DNA chain. The key to this method is the use of dideoxyribonucleoside triphosphates in which the deoxyribose 3'-OH group present in normal nucleotides is missing; when such a modified nucleotide is incorporated into a DNA chain, it blocks the elongation of the chain. To determine the full sequence, the four different chain-terminating dideoxyribonucleosides are used in competition with an excess of deoxyribonucleosides in separate DNA synthesis reactions on the same DNA template. When the products of these four reactions are analysed by electrophoresis in four parallel lanes of a denaturing polyacrylamide gel, the DNA sequence can be derived. Every lane displays a family of DNA fragments of different lengths, reflecting the different sites at which a specific residue occurs in the original DNA. full dna sequence Molecule not part of or directly encoded by the genome, encompasses any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. small molecule 131i radiolabel I131 131I Molecule labelled with 131 radio isotope of iodine atoms. Role played by the participant within the experiment. experimental role attribute name Collection of topic describing the free text stored as an attribute value. CvTopic multiple parent This qualifier is used for hybrid or composite molecules with more than one crossreference to parent molecules. multiple parent reference Substrate protein pre-radiolabelled either synthetically or through the action of a kinase transferring an isotope of phosphate from a nucleotide. Substrate then exposed to phosphate under assay conditions. Substrate isolated by gel electrophoresis and loss of radiolabelling confirmed by autoradiography. in gel phosphatase in gel phosphatase assay protein footprinting Protein footprinting is a technique for identifying structural changes modulated by protein-ligand binding, and mapping protein-ligand interfaces This technique involves attaching cutting reagents randomly to amino acid residue (e.g. lysine or cysteine) on the proteins surface and then using this lysine-labelled protein to cleave polypeptide backbone of the other protein at exposed residues adjacent to its binding site. PMID:14987073 PMID:14967031 PMID:14600024 feature type Property of a subsequence that may interfere with the binding of a molecule. experimental participant identification experimental participant identification. experimental particp feature description The feature text description may include information about the feature detection method. monoclonal immunost monoclonal antibody immunostaining A monospecific antibody for the protein of interest is available, this is used to detect a specific protein within a cell or tissue sample. one hybrid yeast one-hybrid yeast one hybrid one-hybrid PMID:10589421 Protein-DNA complementation assay where a single promoter act as bait and is screened against a library of prey transcription factors. Term describing the last amino acid of a peptide chain. carboxy-terminus c-terminus c-term c-terminal position Displayed as 'c'. c-terminal coloc visual technol Techniques enabling the identification of the subcellular localisation of a protein or complex. Two different proteins show a similar distribution in the cell are said to co-localise. Obsolete since combination of Interaction Detection Method and Interaction Type. OBSOLETE. Consider using imaging techniques (MI:0428) as interaction detection method coupled with colocalisation (MI:0401) as interaction type and predetermined (MI:0396) as participant detection. colocalization/visualisation technologies secondary accession number secondary-ac Reference to the corresponding object in another database (like identity xref qualifier) but the identifier used in the external database is a secondary identifier. ONL locus name ordered locus name For instance HI0934, Rv3245c, At5g34500, YER456W. CDS number systematic gene number A name used to represent an ORF in a completely sequenced genome or chromosome. It is generally based on a prefix representing the organism and a number which usually represents the sequential ordering of genes on the chromosome. Depending on the genome sequencing center, numbers are attributed only to protein-coding genes, or also to pseudogenes, or also to tRNAs and other features. Ordered locus name ORF number PMID for application instance:10725388 PMID:9874787 In this variation of the FRET assay the donor fluorophore is replaced by a luciferase (typically Renilla luciferase). In the presence of its substrate, the luciferase catalyses a bioluminescent reaction that excites the acceptor fluorophore through a resonance energy transfer mechanism. As with FRET the energy transfer occurs only if the protein fused to the luciferase and the one fused to the acceptor fluorophore are in close proximity (10-100 Angstrom). bioluminescence resonance energy transfer bret LRET BRET The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. http://www.hprd.org/ HPRD hprd trihybrid bridge assay protein tri hybrid Two hybrid assay performed with a third protein component is co-transfected into a recombinant yeast strain together with a bait and a prey construct. Negative control show that the interaction between the bait and the prey do not occur when the third protein is not co-transfected. PMID:12935900 PMID:12761205 PMID:12052864 kon ka Association rate constant or rate of complex formation. Unit MOLE per SECOND (M-1 s-1) n-acetyl-tyrosine residue modification. RESID:AA0053 N-acetyl-L-tyrosine YAC acetyltyrosine (S)-2-acetylamino-3-(4-hydoxyphenyl)propanoic acid [Y:ac] N-acetyltyrosine nucl transformation nucleic acid transformation Transformation is the genetic alteration of a cell resulting from the introduction, uptake and expression of foreign genetic material incorporated into the cell's genome (DNA or RNA). The Rat Genome Database (RGD) curates and integrates rat genetic and genomic data. http://rgd.mcw.edu/ rgd RGD 33p radiolabel Molecule labelled with the radio isotope 33 of phosphorus atoms. P33 33P PMID:14577292 Molecule consisting of a specific sequence of amino acidic or nucleotidic monomers strung together through chemical bonds. biopolymer O3-(ADP-ribosyl)-L-serine adp-ribosylserine RESID:AA0237 residue modification. O-(ADP-ribosyl)-L-serine (S)-2-amino-3-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]oxy)-propanoic acid Formula O3-alpha-D-ribofuranosyl-L-serine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate) o-(adp-ribosyl)-serine O3-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-serine 3d-structure Comments on the 3D structure. This attribute is generally associated to an interaction. neddylated lysine PMID:111 Residue modification due to a cross-link between a lysine and a glycine from the Nedd8 protein family. palmitoylated residue palmitoylated aa residue modification. complementation PCA The function of numerous proteins or ribonucleic particles (enzymes, transcription factors, and others) can be rationally dissected into two fragments that fold autonomously but cannot complement to reconstitute the complex function, unless they are located in close proximity. In a two hybrid experiment, restoration of the activity by complementation of the two fragments when expressed as fusion with two polypeptides is taken as an evidence that the two polypeptides interact together. PMID:11495741 protein complementation assay Because of the long lifetimes of excited fluorescent molecules (nanoseconds), fluorescence can be used to monitor the rotational motion of molecules, which occurs on this timescale. This is accomplished experimentally by excitation with plane-polarized light, followed by measurement of the emission at parallel and perpendicular planes. Since rotational correlation times depend on the size of the molecule, this method can be used to measure the binding of two proteins because the observed polarization increase when a larger complex is formed. A fluorescence anisotropy experiment is normally carried out with a protein bearing a covalently added fluorescent group, which increases both the observed fluorescence lifetime of the excited state and the intensity of the fluorescent signal. Residue modification can be assessed by addition of an antibody which binds to the modified residue and alters the molecular weight of the complex. A variation of this technique has been used to show interaction of a DNA binding protein with another protein. In this case the DNA rather than protein is fluorescently labelled. PMID:12805227 fps FPS Fluorescence anisotropy fluorescence polarization spectroscopy fitc labelled Fluorescein isothiocyanate is a yellow-green coloured low molecular weight dye which couples to proteins via reaction with primary amine groups at high pH. FITC is excitable at 488nm, close to its absorption maximum at 494nm, and produces maximum fluorescence emission around 520nm. fluorescein isothiocyanate label fluorescein isothiocyanate labbeled FITC labelled enzyme Molecule doing a modification on its interacting partner. Binding will occur when this sequence range is present within a protein. sufficient binding site sufficient to bind The feature constrain free text will specificity whether a biological feature is shown to be possible (just observed) or required (experimentally demonstrated to be necessary for an interaction). feature constrain undetermined Displayed as '?'. Term describing a completely unknown or unspecified sequence position. undetermined sequence position Saturation binding experiments measure specific ligand binding at equilibrium at various concentrations of the ligand. Analysis of these data can determine receptor number and affinity. saturation binding bifc PMID:11983170 The bimolecular fluorescence complementation (BiFC) is an assay for determination of the locations of protein interactions in living cells. This approach is based on complementation between two non fluorescent fragments of the yellow fluorescent protein (YFP) when they are brought together by interactions between proteins fused to each fragment. bimolecular fluorescence complementation certain certain sequence position Position within the sequence clearly defined. omim http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=${ac} search-url: Online Mendelian Inheritance in Man (OMIM) is a catalogue of human genes and genetic disorders, with links to literature references, sequence records, maps, and related databases. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM OMIM Evidence based on the author of a paper assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences. modelled by author modeled by author inferred by author Set of terms to describe the participant experimental treatment and status. This term group in fact 4 orthologues short controlled vocabularies delivery method, expression level, molecular source, and sample process. Each participant can then be annotated with a maximum of 4 terms selected from each short list. experimental prep experimental preparation Measures the amount of radiolabel released into the medium when enzyme is added onto a film of isotope-labelled collagen. PMID:6247938 collagen film assay synthetic lethal PMID:15608217 Death phenotype observed on cells carrying combination of two independently silent mutations. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (lethal FBcv:0000351) dihydrofolate reductase reconstruction dhfr reconstruction PMID:10318894 The gene for DHFR is rationally dissected into two fragments called F[1,2] and F[3]. Two proteins or protein domains that are thought to bind to each other can then be fused to either of the two DHFR fragments. Reconstitution of enzyme activity can be monitored in vivo by cell survival in DHFR-negative cells grown in the absence of nucleotides. A fluorescence assay can also be carried out taking advantage of fMTX binding to reconstituted DHFR. The basis of this assay is that complementary fragments of DHFR, when expressed and reassembled in cells, will bind with high affinity (Kd 5 540 pM) to fMTX in a 1:1 complex. fMTX is retained in cells by this complex, whereas the unbound fMTX is actively and rapidly transported out of the cells. Survival depends only on the number of molecules of DHFR reassembled. residue modification. RESID:AA0327 glycosylarginine omega-n-glycosyl-arginine omega-N-glycosyl-L-arginine omega-N-(ADP-ribosyl)-L-arginine N(omega)-alpha-D-ribofuranosyl-L-arginine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate) N(omega)-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-arginine (S)-2-amino-5-([imino([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]amino)methyl]amino)pentanoic acid RESID:AA0168 residue modification. adp-ribosylarginine omega-n-(adp-ribosyl)-arginine PMID:16381953 PRIDE is a public repository of protein and peptide identifications for the proteomics community. http://www.ebi.ac.uk/pride/ pride PMID:8816797 Yeast strains are generated in which expression of DB-X/AD-Y or DBPX hybrid proteins is toxic under particular conditions (negative selection). Under these conditions, dissociation of an interaction should provide a selective advantage thereby facilitating detection: a few growing yeast colonies in which DB-X/AD-Y (or DBPX/binding site) fail to interact should be identified among many nongrowing colonies containing interacting DB-X/AD-Y or DBPX/binding site. reverse two hybrid living cell Molecule is observed within in a living cell. [K:meth_1] epsilon-methyllysine n6-methyl-lysine (S)-2-amino-6-methylaminohexanoic acid N6-methyl-L-lysine N(zeta)-methyllysine MLZ residue modification. methyllysine residue modification. RESID:AA0060 CPN N-(1-oxahexadecyl)-L-cysteine N-palmitoyl-L-cysteine n-palmitoylcysteine 2-hexadecanoylamino-3-mercaptopropanoic acid n-palmitoyl-cysteine [C:palm_n] (R)-2-hexadecanoylamino-3-sulfanylpropanoic acid enzymatic footprint PMID:8238889 Sites of sequence-specific DNA-protein interaction are identified by altered reactivity of an enzymatic probe to DNA bound by a protein compared to the same nucleotide sequence in naked DNA. Nucleotides in close contact with the binding protein are protected from cleavage by the enzyme. When these enzymes are administrated to intact cells, the pattern of protection from the probes identifies the location of DNA-protein interactions in vivo. enzymatic footprinting Post translational modification occurs subsequently to an interaction. resulting-ptm FlyBase http://flybase.net/cgi-bin/fbannq.html?acc=${ac} search-url: id-validation-regexp:"FBgn[0-9]{7}" flybase FlyBase is a comprehensive database for information on the genetics and molecular biology of Drosophila. http://fbserver.gen.cam.ac.uk:7081/ RESID:AA0050 Reaction, that can affect K,C,A,D,E,Q,G,I,K,M,P,S,T,Y,V residues. RESID:AA0044 RESID:AA0048 RESID:AA0051 RESID:AA0056 RESID:AA0047 RESID:AA0041 RESID:AA0042 RESID:AA0052 RESID:AA0054 RESID:AA0046 GO:0006473 RESID:AA0049 RESID:AA0043 acetylation reaction acetylation Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with comassie dye. weight by comassie molecular weight estimation by coomasie staining PMID:15833125 Single-mutant phenotype effects combine to give a double-mutant effect different from the wild type and different from single mutant effect. For instance WT < A= B < AB, B < WT = AB < A, WT < A < B < AB, B < WT < AB < A, and all additional inequalities obtained by interchanging A and B, or reversing the effect of both A and B. additive interaction additive insertion analysis In this approach, once a molecule is demonstrated to participate in an interaction, several insertion derivatives are produced and tested in the binding assay to detect the regions that are important for the interaction. ca po nuc transfect calcium phosphate nucleic acid transfection Transient introduction and expression of nucleic acid carried out by treatment with calcium phosphate. Yet to be identified interaction detection method associated with interaction data imported from a third party database. This database may have potentially different standards of curation. unspecified method (S)-2-methylamino-3-phenylpropanoic acid N-methyl-L-phenylalanine residue modification. FMT [F:meth] N-methylphenylalanine methylphenylalanine n-methyl-phenylalanine direct interaction Interaction that is proven to involve only its interactors. synthetic genetic analysis sga SGA Identification of genetic interactions by generation of an organism harbouring mutations in 2 or more genes and scoring for a phenotype, such as loss of viability, that is not observed for any of the mutations in isolation. N-acetyl-L-leucine LAC [L:ac] acetylleucine n-acetyl-leucine residue modification. light scattering Dynamic and static laser light scattering probes the size, shape, and structure of biological macromolecules or of their assemblies. A beam is focused on an optically clear cylindrical cell containing the sample. Most of the light passes directly through the sample. A small portion of the light is scattered; the scattered light intensity containing information about the scattering particle is detected at an angle (typically in the range 15-180degrees) from the direction of the incident beam. PMID:9013660 PMID:15353450 Method to identify domain-domain interactions within the same resolved structure. Domains are first projected onto a pdb structure and then the distance between all pairs of residues in different domains are calculated. When the distance between 2 residues is below the non covalent bond threshold, the corresponding pair of domains is predicted to interact. structural proximity The phenotype resulting from genetic perturbation of A has an effect on WT, but that effect is abolished by adding the suppressor B, which itself shows no single-mutant effect (for example, WT = B = AB < A); suppressive interaction suppression n-acetyl-phenylalanine residue modification. N-acetyl-L-phenylalanine FAC [F:ac] acetylphenylalanine [A:meth_n3] trimethylalanine AM3 N,N,N-trimethyl-L-alanine n,n,n-trimethyl-alanine residue modification. RESID:AA0062 (S)-1-carboxy-N,N,N-trimethylethanaminium (S)-2-(trimethylammonio)propanoic acid footprinting footprinting analysis is used to identify regions of molecules directly involved in binding other macromolecules and therefore protected from the effects of degradative enzymes. x-ray tomography X-ray Tomography is a branch of X-ray microscopy. A series of projection images are used to calculate a three dimensional reconstruction of an object. The technique has found many applications in materials science and later in biology and biomedical research. In terms of the latter, the National Center for X-ray Tomography (NCXT) is one of the principle developers of this technology, in particular for imaging whole, hydrated cells. Gene whose mutation suppress the phenotype associated to a suppressed mutation. suppressor gene (S)-2-acetylamino-3-hydroxypropanoic acid N-acetylserine N-acetyl-L-serine n-acetyl-serine acetylserine residue modification. [S:ac] SAC figure legend Text pointing to a specific paper figure legend where the experimental evidences for an interaction are shown. PMID:8248129 PMID:10436088 The protein of interest is presented on the outer membrane of Gram negative bacteria by expressing it as a fusion partner to peptide signals that direct heterologous proteins to the cell surface. For instance, a single chain Fv (scFv) antibody fragment, consisting of the variable heavy and variable light domains from two separate anti-digoxin monoclonal antibodies, was displayed on the outer membrane of Escherichia coli by fusing it to an Lpp-OmpA. Similar systems have also been developed for gram positive bacteria. Fluorescence-activated cell sorting (FACS), is used to specifically select clones displaying a protein binding to scFv-producing cells. bacterial display Isoform synonym. isoform synonym Relies on the radiolabelling of a peptide substrate immobilized on a scintillant coated SPA-bead. The kinase transfers a phosphate isotope from the nucleotide to the substrate. kinase spa kinase scintillation proximity assay Michaelis-Menten constant: concentration of substrate at which the reaction rate is equal to half the maximal rate (i.e. Km={s} when Vo=1/2Vmax). Unit Molar. Km km Xref pointing to a GO compartment term describing the end location of a migrating molecule. translocation end 3 hybrid method Group of method based on complementation assay where a third participant is shown to be necessary for the binding of a given bait prey pair. The objective of Gene Ontology (GO) is to provide controlled vocabularies for the description of the molecular function, biological process and cellular component of gene products. http://www.ebi.ac.uk/GO id-validation-regexp:"GO:[0-9]{7}" gene ontology go expression level alteration Synthesis rate of a molecule under investigation differs from its naturally occurring expression level in a cell. MFM residue modification. RESID:AA0021 [M:form] N-formyl-L-methionine 2-formylamino-4-(methylthio)butanoic acid (S)-2-formylamino-4-(methylsulfanyl)butanoic acid n-formyl-methionine formylmethionine The phenotype resulting from genetic perturbation A and the phenotype resulting from genetic perturbation B have no effect on the WT background, but the combined genetic perturbation of A and B has a phenotypic effect. synthetic synthetic interaction cy3 label The organic cyanine Cy3 emits maximally at 570 nm. PMID:11160938 In this complementation approach the bait can be any membrane protein (for example a receptor or a channel protein), the prey is cloned as a fusion protein of any cDNA from a library and the coding sequence of cytoplasmic RAS (cdc25 in yeast). If the bait and the prey interact, RAS is recruited close to the membrane and can activate cell growth. This procedure must take place in cells having a mutated RAS (Cdc25-2 yeast strain having a temperature sensitive mutation of RAS) to avoid constitutive growth activation. reverse rrs reverse ras recruitment system reverse RRS N-glycyl-glycosylphosphatidylinositolethanolamine RESID:AA0161 residue modification. gpi-anchor amidated glycine gpi-glycine methylation methylation reaction The covalent attachment of a methyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer. Irreversible reaction that can affect A,G,M,F,P,C,R,N,Q,E,H,or K residues. RESID:AA0070 RESID:AA0066 RESID:AA0073 RESID:AA0065 RESID:AA0234 RESID:AA0069 RESID:AA0067 RESID:AA0075 RESID:AA0063 RESID:AA0064 RESID:AA0074 RESID:AA0068 RESID:AA0072 RESID:AA0272 GO:0043414 RESID:AA0076 CD circular dichroism cd PMID:11578931 Circular dichroism (CD) is observed when optically active molecules absorb left and right hand circularly polarized light slightly differently. Linearly polarized light can be viewed as a superposition of two components of circularly polarized light of equal amplitude and phase but opposite handness. When this light passes through an optically active sample the two polarized components are absorbed differently. The difference in left and right handed absorbance A(l)- A(r) is the signal registered in CD spectra. This signal displays distinct features corresponding to different secondary structures present in peptides, proteins and nucleic acids. The analysis of CD spectra can therefore yield valuable information about the secondary structure of biological macromolecules and the interactions among molecules that influence their structure. residue modification. RESID:AA0354 N2-acetyl-L-arginine RAC acetylarginine [R:ac] alpha-acetylamino-delta-guanidinovaleric acid acetylarginine n2-acetyl-arginine pELISA p elisa proximity enzyme linked immunosorbent assay PMID:15155907 Method allowing efficient and precise interaction detection, along with extensive repertoires of specific binding reagents. It is based on proximity a ligation mechanism that enables sensitive high-capacity protein measurements by converting the detection of specific proteins to the analysis of DNA sequences. Proximity probes containing oligonucleotide extensions are designed to bind pairwise to target proteins and to form amplifiable tag sequences by ligation when brought in proximity. 3d-resolution Resolution of the 3D structure. This attribute is generally associated to an interaction. 2-acetylamino-3-mercaptopropanoic acid acetylcysteine n-acetyl-cysteine [C:ac] CAC residue modification. N-acetyl-L-cysteine (R)-2-acetylamino-3-sulfanylpropanoic acid N-acetylcysteine protein A linear polymer of amino acids joined by peptide bonds in a specific sequence. SO:0000358 single stranded deoxyribonucleic acid ss dna ss DNA DNA that consists of only one chain of nucleotides rather than the two base pairing strands found in DNA in the double helix form. single nonmonotonic single nonmonotonic interaction The phenotype resulting from genetic perturbation of B shows opposing effects in the WT and A backgrounds (for example, B > WT and AB< A); or, A shows opposing effects in the WT and B backgrounds, but not both. RESID:AA0034 residue modification. (R)-2-amino-3-(phosphonosulfanyl)propanoic acid phosphocysteine CPO S3-phosphocysteine [C:po] S-phosphonocysteine s-phospho-cysteine S-phospho-L-cysteine cysteine phosphate thioester Single amino acid identification along a protein sequence. protein sequence identification protein sequence Competitive binding experiments measure equilibrium binding of a single concentration of ligand at various concentrations of an unlabeled competitor. Analysis of these data gives the affinity of the receptor for the competitor. competition binding This qualifier is used when the crossreference is imported from the Gene Ontology tag definition_reference. gene ontology definition reference go-definition-ref The interaction that has a disease association. disease mutation disrupting interaction mutation disrupting Residue of a protein whose identity mutation or deletion totally disrupt an interaction. PMID for application instance:12186859 PMID:11988476 PMID:11817959 A combination of NMR and EPR. The lines in the EPR spectrum that are caused by coupling of an unpaired electron nearby nuclei change in intensity when these nuclei are excited at their NMR frequency. endor ENDOR electron nuclear double resonance The number of substrate molecules converted to product in a given unit of time, on a single enzyme molecule when the enzyme is saturated with substrate. Unit per second, or s-1. turnover number kcat methylated alanine residue modification. methionamine N-acetyl-L-methionine (S)-2-acetylamino-4-(methylsulfanyl)butanoic acid n-acetyl-methionine acetylmethionine 2-acetylamino-4-(methylthio)butanoic acid [M:ac] residue modification. acetylmethionine MAC lipid modification residue modification. adp ribosylation reaction Reaction that can affect Arg, Cys, Glu, Arg and Asn residues. RESID:AA0295 RESID:AA0231 RESID:AA0169 GO:0006471 adp ribosylation uniprot knowledge base uniprotkb search-url: http://www.ebi.uniprot.org/entry/${ac} id-validation-regexp:"[OPQ][0-9][A-Z0-9]{3}[0-9]|[OPQ][0-9][A-Z0-9]{3}[0-9]-[0-9]+|[A-Z]{3}[0-9]{5}|[OPQ][0-9][A-Z0-9]{3}[0-9]-PRO_[0-9]{10}" PMID:14681372 UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. http://www.expasy.uniprot.org/ UniProt tritium H3 3H 3h radiolabel Molecules labelled with isotope 3 of hydrogen atoms. amidation amidation reaction RESID:AA0093 RESID:AA0089 RESID:AA0085 RESID:AA0084 RESID:AA0100 RESID:AA0092 RESID:AA0088 RESID:AA0097 RESID:AA0083 RESID:AA0099 RESID:AA0082 RESID:AA0098 RESID:AA0096 RESID:AA0081 RESID:AA0095 RESID:AA0091 Irreversible reaction that can affect A,R,N,D,C,Q,E,G,H,I,L,K,M,F,P,S,T,W,Y or V residues. RESID:AA0087 RESID:AA0094 GO:0001519 RESID:AA0090 RESID:AA0086 RESID:AA0102 S-farnesyl-L-cysteined is cleaved and returns a C residue. defarnesylation defarnesylation reaction anti bait coimmunoprecipitation anti bait coip A specific antibody for the protein of interest (bait) is available, this is used to generate a high affinity resin to capture the endogenous bait present in a sample. conditional synthetic lethal cond syntetic lethal Two silent mutations show a conditional synthetic lethal phenotype when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (lethal FBcv:0000351) PMID:16338355 PMID:12120258 PMID:11896282 This method measures formation of complex by monitoring changes in the resonance angle of light impinging on a gold surface as a result of changes in the refractive index of the surface. A ligand of interest (peptide or protein) is immobilized on a dextran polymer, and a solution of interacting protein is passed over it through a cell, with a gold wall coated with this polymer. Macromolecules that interact with the immobilized ligand are retained on the polymer surface, and alter the resonance angle of impinging light as a result of the change in refractive index brought about by the increased protein mass retained on the polymer surface. Since all proteins have the same refractive index and since there is a linear correlation between resonance angle shift and protein concentration near the surface, this allows one to measure changes in protein concentration at the surface as a consequence of protein interaction. Furthermore, this can be done in real time, allowing direct measurement of both the on rate and the off rate of complex formation. Optical biosensor BIAcore(r) spr surface plasmon resonance 2h label Molecules labelled with isotope 2 of hydrogen atoms. deuterium D2 2H2 Reverse phase chromatography operates on the basis of hydrophilicity and lipophilicity. The stationary phase consists of silica based packings with n-alkyl chains covalently bound. For example, C-8 signifies an octyl chain and C-18 an octadecyl ligand in the matrix. The more hydrophobic the matrix on each ligand, the greater is the tendency of the column to retain hydrophobic moieties. Thus hydrophilic compounds elute more quickly than do hydrophobic compounds. reverse phase chromatography reverse phase chrom [E:gpe] L-glutamyl 5-glycerophosphoethanolamine (S)-2-amino-5-[2-([([2,3-dihydroxypropyl]oxy)(hydroxy)phosphoryl]oxy)ethyl]amino-5-oxopentanoic acid residue modification. RESID:AA0170 glutamyl 5-glycerylphosphorylethanolamine glycerylpo4etohamine L-glutamyl 5-glycerylphosphorylethanolamine EGE L-glutamyl 5-glycerophosphorylethanolamine ribonucleoprot compl ribonucleoprotein complex protein rna complex A macromolecular complex containing both protein and RNA molecules. GO:0030529 weight silver stain molecular weight estimation by silver staining Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with silver. disaggregation Dissociation of partners interacting via non-covalent bond. OBSOLETE because considered misleading. Techniques which depend upon the strength of the interaction between two entities. affinity techniques affinity technology This term refers to methods that aim at interfering with the activity of a specific gene by altering the gene regulatory or coding sequences. This goal can be achieved either by a classical genetic approach (random mutagenesis followed by phenotype characterization and genetic mapping) or by a reverse genetics approach where a gene of interest is modified by directed mutagenesis. genetic interference gene ontology synonym Synonym as used in Gene Ontology. go synonym Methods based on 3D structure information. structure based prediction predict from struct residue modification. hydroxylated residue search-url Search engine URL associated to Cv Database terms. siRNA micro RNA dicer RNA sirna small interfering rna Ribonucleic acid used in RNAi study. These RNA have the reverse complementary sequence of a target gene's mRNA transcript and inhibit its expression. PMID:10542148 mRNA mrna messenger rna Single-stranded RNA molecule that specifies the amino acid sequence of one or more polypeptide chains. PDBj search-url: http://pdbjs3.protein.osaka-u.ac.jp/xPSSS/DetailServlet?PDBID=${ac}&PAGEID=Summary id-validation-regexp:"[0-9][a-zA-Z0-9]{3}" pdbj PMID:12099029 PDBj(Protein Data Bank Japan) maintains the database for the protein structures with financial assistance from the Institute for Bioinformatics Research and Development of Japan Science and Technology Corporation(BIRD-JST), collaborating with the Research Collaboration for Structural Bioinformatics(RCSB) and the MSD in the European Bioinformatics Institute(MSD-EBI) in EU. All three organizations serve as deposition, data processing and distribution sites. http://www.pdbj.org/ Alternative names to describe a complex. complex-synonym Regular Expression used to check the validity of cross references' identifier. Attribute generally associated to terms in Cv Database. validation regular expression id-validation-regexp anti tag immunostaining Immunostaining assay performed when specific antibodies for the protein of interest are not available. Therefore the protein is expressed as a hybrid protein fused to a tag peptide/protein for which efficient antibodies are available. The anti tag antibody may be either monoclonal or polyclonal. anti tag immunost v5 tag The protein of interest is expressed as a fusion to the peptide GKPIPNPLLGLDST for which antibodies are commercially available. GKPIPNPLLGLDST epitope tag protease accessibility laddering pal protease access PMID:16615907 In protease accessibility laddering (PAL) tagged proteins are purified on magnetic beads in their natively folded state. While attached to the beads, proteins are probed with proteases. Proteolytic fragments are eluted and detected by immunoblotting with antibodies against the tag (e.g., Protein A, GFP, and 6xHis). alaninamide alanine amide residue modification. (S)-2-aminopropanamide alanineamide AAM [A:am] L-alanine amide residue modification. methylated residue A molecule is estimated to be expressed at lower levels than in physiological condition. under expressed level under-expressed 2-oxopyrrolidine-5-carboxylic acid 5-oxoproline pyroglutamic acid [E:pyro] 2-pyrrolidone-5-carboxylic acid residue modification. RESID:AA0031 5-oxopyrrolidine-2-carboxylic acid PCA pyroglutamic acid (S)-5-oxo-2-pyrrolidinecarboxylic acid rare isotope label Molecule can be labelled including rare isotopes among its constituent atoms that can be used to identify, localize or quantify the full molecule. rare isotope label cosedimentation Separation of a protein mixture under the influence of artificial gravity. primary-reference Used to indicate the PMID from which the experimental data is extracted. PMID:15221759 IPI provides a top level guide to the main databases that describe the proteomes of higher eukaryotic organisms. IPI effectively maintains a database of cross references between the primary data sources, provides minimally redundant yet maximally complete sets of proteins for featured species (one sequence per transcript) and maintains stable identifiers (with incremental versioning) to allow the tracking of sequences in IPI between IPI releases. IPI is updated monthly in accordance with the latest data released by the primary data sources. ipi id-validation-regexp:"IPI[0-9]+.[0-9]+|IPI[0-9]+" international protein index One of several nuclides having the same number of protons in their nuclei and hence having the same atomic number, but differing in the number of neutrons and therefore, in the mass number. isotope label A wide range of dyes have been used over the years to visualise proteins in polyacrylamide gels - Coomasie Blue and silver-staining being two classical methods. Fluorescent dyes such as Nile Red and SYPRO Orange are now increasingly used due to their superior dynamic range. Use of non-denaturing gels can allow visualisation of protein protein interactions. Several dyes can be used to specifically indicate residue modification, however this methodology will give no information as the number of residues modified or their position within the protein sequence. Examples include the use of acid fuscian or the fluorescent dansyl hydrazine to show protein glycosylation. PMID:12015990 protein staining CYGD (MIPS) MPact MIPS cygd CYGD The MIPS Comprehensive Yeast Genome Database (CYGD) aims to present information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae. In addition the data of various projects on related yeasts are used for comparative analysis. http://mips.gsf.de/proj/yeast/CYGD. http://mips.gsf.de/genre/proj/mpact n-myristoyl-glycine RESID:AA0059 residue modification. myristoylglycine N-myristoyl-glycine GMY [G:myr] SPA RIA Radio Immuno Assay SPA relies upon the fact that a beta particle emitted from a radioisotope decay can excite a fluorophore only when it is at a very short distance in water solution (few micrometers). The ligand is labelled with a radioactive atom and its potential partner is fixed to fluorophore containing beads, the emitted fluorescence proving their interaction can be measured in a scintillation counter. The scintillator measures only the amount of bound radiolabelled ligand. Competition experiment with cold competitor can be done to estimate the binding affinities (50% inhibitory concentration [IC50], cold ligand versus labelled ligand). Loss of signal can also be used to measure substrate cleavage by an enzyme, and labelled antibodies used to titrate the degree of modified residue present. PMID:3866247 spa scintillation proximity assay nucleic acid transduction Transduction is the process by which bacterial DNA is moved from one bacterium to another by a virus. nucl transduction anti tag western anti tag western blot Western blot assay performed when specific antibodies for the protein of interest are not available. Therefore the protein is expressed as a hybrid protein fused to a tag for which efficient antibodies are available.The antibody may be either monoclonal or polyclonal. A Database of Human Unidentified Gene-Encoded Large Proteins Analyzed by Kazusa Human cDNA Project. http://www.kazusa.or.jp/huge/ huge search-url: http://www.kazusa.or.jp/huge/gfpage/${ac} id-validation-regexp:"KIAA[0-9]{4}[A-Z]{0,1}" Molecule has undergone one or more purification steps to isolate it from the cellular environment. purified fluorescence-activated cell sorting facs Flow cytometry FACS Cells in suspension flow through a laser beam, the scattered light or emitted fluorescence is measured, filtered and converted to digital values. Cells can be sorted according to their properties. Using flow cytometry, any fluorescent or light scattering experiment can be carried out on entire cells. With this instrument, interactions occurring either on cell surfaces or in any other subcellular location can be studied by using suitable fluorescent labels. PMID:11988464 parameter unit Controlled vocabulary for kinetic constant units. ec50 Molar concentration of an agonist which produces 50% of the maximum possible response for that agonist. Note this measure depends on the specific agonist used and upon experimental conditions, notably temperature, pH and solution composition (e.g., salts, chelating agents and others). Thus the ec50 is a relative measure and its values can be compared only when sharing the same experimental setting. Unit Molar. EC50 Method to determine the features of the proteins involved in the interaction. feature detection method feature detection engineered Molecule has been added into system from an external source or altered within the cell. newt New EBI Web Taxonomy. http://www.ebi.ac.uk/newt search-url: http://www.ebi.ac.uk/newt/display?search=${ac} non covalent inter Interaction mediated by non-covalent, weak forces rearrangement. OBSOLETE use physical interaction (MI:0218) instead. non covalent interaction gpi-cysteine N-cysteinyl-glycosylphosphatidylinositolethanolamine gpi-anchor amidated cysteine RESID:AA0160 residue modification. IntAct http://www.ebi.ac.uk/intact/search/do/hvWelcome?searchString=${ac} search-url: id-validation-regexp:"EBI-[0-9]+" intact PMID:14681455 INTerAction datanase (IntAct) provides an open source database and toolkit for the storage, presentation and analysis of protein interactions. http://www.ebi.ac.uk/intact transactivating tag Tat tag tat tag Tag derived from the transactivating (Tat) protein of human immunodeficiency virus 1 (HIV-1) that can enter cells efficiently when added exogenously in tissue culture. The Tat tag can carry other molecules into cells, by fusion of Tat peptides (residues 1-72 or 37-72,) to any molecule under study. Tat-mediated uptake may allow the delivery of macromolecules previously thought to be impermeable to living cells. PMID:8290579 two hybrid array Two-hybrid screening can be done in a colony array format, in which each colony expresses a defined pair of proteins. Because the particular protein pair expressed in each colony is defined by its position in the array, positive signals identify interacting proteins without further characterization, thus obviating the need for DNA purification and sequencing. The interrogation of a two-hybrid colony array usually involves a mating strategy in which every DNA binding domain hybrid (the bait) is tested against all activation domain hybrids (the preys) in a grid pattern. Arrays usually use full-length open reading frames. PMID for application instance:10688190 PMID:11827624 inhibition The interaction between the proteins or the formation of a complex is disrupted by a biological molecule or by a modification of the interactors. synthetic growth defect Two silent mutations show growth defect when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective') synt growth defect guide rna Small RNA molecules that hybridize to specific mRNAs and direct their RNA editing. grna guide RNA Alexa fluorescent dye analogue to Rhodamine Red-X with an approximate excitation wavelength maximum of 568nm. PMID:10449539 alexa 568 label Xref pointing to a GO compartment term describing the start location of a migrating molecule. PMID:14681407 translocation start Evidence based on a curator assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences. modelled by curator modeled by curator inferred by curator residue modification. acetylaspartic acid acetylaspartate n-acetyl-aspartic acid N-acetyl-L-aspartic acid (S)-2-(acetylamino)butanedioic acid [D:ac] DAC nutrition synt letal Two silent mutations show a nutrition sensitive lethal phenotype when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description. conditional synthetic lethal nutrition-sensitivity PMID:10504710 The TAP method involves the fusion of the TAP tag (encoding a calmodulin binding peptide, a TEV cleavage site, and the Staphylococcus aureus Protein A) to the target protein and the introduction of the construct into the host cell or organism, maintaining the expression of the fusion protein at, or close to, its natural level. The fusion protein and associated components are recovered from cell extracts by affinity selection on an IgG matrix. After washing, the TEV protease is added to release the bound material. The eluate is incubated with calmodulin-coated beads in the presence of calcium. This second affinity step is required to remove the TEV protease as well as traces of contaminants remaining after the first affinity selection. After washing, the bound material is released with EGTA. This two steps purification steps ensures a highly selective complex purification of the tapped protein (first round of selection on the protein A, a high affinity tag) under mild condition (non denaturant pH or conditions required to remove the tag). OBSOLETE redundant term. Map to feature type: tap tagged (MI:0524) and as interaction detection method tandem affinity purification (MI:0676). tap tag coimmunoprecipitation tap tag coip fluorescence accept fluorescence acceptor Fluorophore able to absord the electromagnetic radiation at given wavelength from a specific donor fluorophore, the re-emission of its own charateristic fluorescence. (S)-2-amino-6-dimethylaminohexanoic acid [K:meth_2] epsilon-dimethyllysine N6,N6-dimethyl-L-lysine MLY n6,n6-dimethyl-lysine N(zeta)-dimethyllysine residue modification. lysine derivative Lys(y) dimethyllysine For instance this qualifier, in an interaction entry, can be associated to a cross reference to the same interaction in an other database. identical object identity Reference to the corresponding object in another database. Correspondence may be complete or partial. s35 radiolabelled S35 35S Molecule labelled with 35 radio isotope of sulfur. Proteins are often metabolically labelled, usually be growth in 35S labelled culture medium. 35s radiolabel residue modification. methylated arginine CPPs cell-penetrating peptides MTS Trojan peptides The peptides named CPPs vary greatly in size, amino acid sequence, and charge, but share the common feature that they have the ability to rapidly translocate the plasma membrane and enable delivery to the cytoplasm or nucleus. PMID:16574060 PTDs protein transduction domains membrane translocating sequences cell penetrating peptide tag omega-N,omega-N-dimethyl-L-arginine [R:meth_n7] asymmetric dimethylarginine (S)-2-amino-5-[((dimethylamino)iminomethyl)amino]pentanoic acid NG,NG-dimethylarginine RM2 dimethylarginine omega-n,omega-n-dimethyl-arginine residue modification. Name assigned to a molecule by the authors within a paper that may differ from the reference database. author assigned name feature database feature xref feature database. The interaction of two molecules is determine by their very close proximity or the overlap of their relative bands in a gel. comigration in gel electrophoresis comigration in gel conditional synthetic lethal temperature-sensitivity temprtr synt lethal Two silent mutations show a temperature sensitive lethal phenotype when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (FBcv:0000310 'temperature conditional') residue modification. gpi anchor residue Confidence classification assigned by the author of the publication to a specific interaction. author-confidence confocal microscopy A confocal is a standard epifluorescence microscope with improvement essentially coming from the rejection of out-of-focus light interference. Confocal imaging system achieves this by two strategies: a) by illuminating a single point of the specimen at any one time with a focused beam, so that illumination intensity drops off rapidly and b) by the use of blocking a pinhole aperture in a conjugate focal plane to the specimen so that light emitted away from the point in the specimen being illuminated is blocked from reaching the detector. Only the light from the single point illuminated of the specimen passing through the image pinhole is detected by a photodetector. Usually a computer is used to control the sequential scanning of the sample and to assemble the image for display onto a video screen. coimmunoprecipitation In this approach an antibody, specific for the protein of interest (bait) or any tag expressed within a fusion protein, is used to separate the bait from a protein mixture or a cell lysate and to capture its ligand simultaneously. The protein partners that bind to the bait protein retained by the resin can then be eluted and identified. coip sandwich immunoassay PMID:12454649 Antibody array where proteins retained by the arrayed antibodies are identified using a detector antibody. The detector antibody is either modified with a directly detectable label (enzyme, fluorescent molecule, isotope, etc.), or it is biotinylated for detection after subsequent probing with labeled streptavidin. N-acetyl-L-isoleucine acetylisoleucine n-acetyl-isoleucine (2S,3S)-2-acetylamino-3-methylpentanoic acid acetylisoleucine [I:ac] residue modification. IAC polyprotein fragment Subpart of a polyprotein that is naturally cleaved in vivo. polyprotein frag Indicates the sample context in which each interacting molecule is presented to its partner. sample process exp-modification Modifications of the standard experimental method described in the CV. experiment modification gal4 vp16 complementation mammalian two hybrid KISS karyoplasmic interaction ion strategy gal4 vp16 complement PMID:1387709 A chimeric protein consisting of the GAL4 DNA-binding domain (aa 1-147 of GAL4) and a transcriptional activation domain from the herpes simplex virus protein VP16 (either aa 411-490 or aa 411-455) can specifically activate transcription of a reporter gene located downstream ofGAL4 DNA binding sites and the E1B minimal promoter. Similarly, two chimeric proteins, one encoding a chimeric GAL4 protein and the other encoding a chimeric VP16 protein, can activate the reporter gene, if the domains fused to the GAL4 and VP16 sequences can complex with appropriate conformation. However, if the domains fused to the GAL4 and VP16 sequences do not interact specifically to form a + complex that reconstitutes GAL4 function, the reporter gene cannot be activated. chromatography column chromatography Used to separate and/or analyse complex mixtures. The components to be separated are distributed between two phases: a stationary phase (bed) and a mobile phase which percolates through the stationary bed. The nature of the two phases determines the separation criteria exploited by the column such as affinity, ionic charges, size or hydrophobicity of the molecules under analysis. Each type of column can be implemented with the mobile phase under atmospheric or high pressure condition. In this later case columns are designated as High Pressure Liquid Chromatography (HPLC). chromatography technology Transient introduction and expression of nucleic acid carried out by treatment with chemicals. nucleic acid transfection by treatment n transfection treat 15n label Molecules labelled with isotope 15 of nytrogen atoms. N15 15N nucleic acid SO:0000348 Linear polymers of nucleotides, linked by 3',5' phosphodiester linkages. vp16 activation domain vp16 ad Full viral protein vp16 exclusively responsible for preferential transcriptional activation of viral genes. Activation requires the formation of a complex with the host cell transcription factor. ubiquitin binding Interaction concerning ubiquitin that is covalently attached to any Lys residue of its interaction partner. OBSOLETE remap to ubiquitination reaction (MI:0220) or describe ubiquitine as a participant on the interaction using physical interaction (MI:0218) or covalent binding (MI:0195) as interaction type. Gene name. gene gene name [R:po] omega-N-phospho-L-arginine omega-n-phospho-arginine N5-[imino(phosphonoamino)methyl]-L-ornithine alpha-amino-delta-phosphonoguanidinovaleric acid (S)-2-amino-5-[imino(phosphonoamino)methyl]aminopentanoic acid RPO phosphoarginine RESID:AA0222 residue modification. feature prediction from structure feature struct pred Group of method taking advantage of 3D structure to calculate and infer the feature of interacting molecules. Entrance of molecules into cells that does not involved specific treatments but rely on natural cellular processes. passive uptake mammalian protein protein interaction trap mappit PMID:12853652 The MAPPIT(mammalian protein-protein interaction Trap) is a screening method for protein-protein interaction in mammalian cells, based on the reconstitution of a membrane STAT (signal transducers and activators of transcription) receptor. The bait protein is fused to a STAT recruitment-deficient receptor and the prey protein to a functional STAT recruitment sites. In such a configuration, a given baitprey interaction restores a STAT-dependent responses leading to the expression of a reporter gene. This system, enable to demonstrate not only protein interaction but also modification-independent and tyrosine phosphorylation- dependent interactions. Sequences can be identified in a DNA mixture by launching a PCR (Polymerase Chain Reaction) controlled by sequence specific primers. Such reaction starts only when the hybridization of the primer with a complementary sequence occurs. primer specific pcr The application of physical principles and methods to biological experiments. biophysical endogenous naturally occurring Unaltered endogenous molecule in its naturally occurring state. Example generally associated to Cv terms. example anti tag coip anti tag coimmunoprecipitation A specific antibody for the protein of interest is not available, therefore the bait protein is expressed as a hybrid protein fused to a tag peptide/protein for which efficient and specific antibodies or a specific ligand are available. neddylation Reversible reaction that create a covalent bond between a Glycine residue of an ubiquitine like NEDD8 protein and a lysine residue of the target. PMID:16127432 GO:0045116 neddylation reaction synthetic phenotype Two silent mutations show an altered phenotype when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794. gfp complementation Protein-protein interaction trap based on fusions of bait and prey protein to two dissected fragment of GFP. The system implemented in E. coli, allow screening of partners, including membrane proteins and also detect transient interaction that are stabilized by the complemented GFP. PMID:15631464 green fluorescence protein complementation assay synt growth effect synthetic growth effect Two silent mutations show altered growth effect when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective') cabri CABRI cell lines catalogue available at. http://www.cabri.org/ Western blot assay carried out using monospecific antibodies produced in the supernatant of a cell line obtained by fusing a lymphocyte B to a myeloma cell line or selected by phage display technology. monoclonal antibody western blot monoclonal western pubchem PubChem PMID:16381840 PubChem provides information on the biological activities of small molecules. http://pubchem.ncbi.nlm.nih.gov/ neural network on interface properties PMID:11874449 PMID:11455607 Neural networks are trained on the properties of residues belonging to a cluster of residues that are neighbours in space on protein surface. The predictor permits the inference of the residues that are likely to be on an interaction interface. interface predictor tap tagged Tag encoding a calmodulin binding peptide, a TEV cleavage site, and the Staphylococcus aureus Protein A fused to a target protein and the introduction of the construct into the host cell or organism, maintaining the expression of the fusion protein at, or close to, its natural level. The fusion protein and associated components are recovered from cell extracts by affinity selection on an IgG matrix. After washing, the TEV protease is added to release the bound material. The eluate is incubated with calmodulin-coated beads in the presence of calcium. This second affinity step is required to remove the TEV protease as well as traces of contaminants remaining after the first affinity selection. After washing, the bound material is released with EGTA. This tag allows two steps purification steps ensuring a highly selective purification of the tapped protein (first round of selection on the protein A, a high affinity tag) under mild condition (non denaturant pH or conditions required to remove the tag). CBP-ProtA tagged calmodulin binding peptide plus protein a tag Beta-galactosidase activity can be used to monitor the interaction of chimeric proteins. Pairs of inactive beta gal deletion mutants are capable of complementing to restore activity when fused to interacting protein partners. Critical to the success of this system is the choice of two poorly complementing mutant moieties, since strongly complementing mutants spontaneously assemble and produce functional beta-gal activity detectable in absence of any fused protein fragment. PMID:9237989 PMID:12042868 beta galactosidase beta galactosidase complementation The protein of interest is expressed as a fusion to the peptide EUKLISEED (a fragment of the Myc oncogene protein) for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem. OBSOLETE redundant term. Map to feature type: myc-tagged (MI:0522) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007). myc tag coip myc tag coimmunoprecipitation search-url: http://www.signaling-gateway.org/data/Y2H/cgi-bin/y2h_int.cgi?id=${ac} afcs AfCS Alliance for Cellular Signaling (AfCS -Nature) store yeast 2-hybrid Interaction data and expression data. Information and data are freely available to all. http://www.signaling-gateway.org alliance for cellulare signaling EcoCyc is a bioinformatics database that describes the genome and the biochemical machinery of E. coli K12 MG1655. http://ecocyc.org/ ecocyc EcoCyc source database Source database. RESID:AA0211 RESID:AA0057 GO:0018256 Reaction that can affect K or G residues. formylation reaction formylation protein kinase assay Catalysis of the transfer of a phosphate group, usually from ATP, to a protein substrate. lexa b52 complement lexa b52 complementation Yeast two-hybrid system using Escherichia coli LexA amino acids 1-202 as the DNA-binding domain (BD), E. coli B42 acidic sequence as the activation domain (AD), and two reporters, lacZ and LEU2, each containing upstream LexA binding elements. PMID:14613974 LexA B52 transcription complementation inhibitor small mol inhibitor small molecules PMID:10780927 PMID:10542155 Protein activity is inhibited by small inorganic molecules (drugs) that specifically bind to their targets. Recently this classical pharmacological approach is sometime referred to as 'chemical genetics'. OBSOLETE as such method can be described using the biological role inhibitor (MI:0586). EM5 [E:meth_o5] glutamatemethylester residue modification. 5-methyl-L-glutamate glutamic acid 5-methyl ester (S)-2-aminopentanedioic acid 5-methyl ester L-glutamic acid 5-methyl ester glutamic acid gamma-methyl ester Attribute name of annotation associated to a CV term. controlled vocabulary attribute name cv att name List of authors associated to a publication. This attribute is generally associated to an experiment. author-list protease homogeneous time resolved fluorescence Measures quenching of the nonradiative energy transfer between fluorescent long-lifetime lanthanide chelates and different acceptors. Fluorescence donor and acceptor are on the same peptide molecule and separated by the action of the protease. Protease HTRF protease htrf The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. www.pantherdb.org/ PANTHER panther Protein sample collected by in vitro translation of its mRNA taking advantage of purified translation machinery. in vitro translated protein in vitro translated The low molecular weight RNAs that specifically bind amino acids by aminoacetylation to form aminoacyl tRNA and which possess a special nucleotide triplet, the anticodon. transfer rna tRNA transfer RNA transfer ribonucleic acid trna bacterial two-hybrid adenylate cyclase complementation Adenylate cyclase is encoded by the cyaA gene and contains a catalytic domain which can be proteolytically cleaved into two complementary fragments, T25 and T18, which remain associated in the presence of calmodulin in a fully active ternary complex. In the absence of calmodulin, the mixture of the two fragments does not exhibit detectable activity, suggesting that the two fragments do not associate. When expressed in an adenylate cyclase-deficient E. coli strain (E. coli lacks calmodulin or calmodulin-related proteins), the T25 and T18 fragments fused to putative interacting proteins are brought into close association which result in cAMP synthesis. The level of reconstructed adenylate cyclase can be estimated by monitoring the expression of a cAMP dependent reporter gene. PMID:9576956 adenylate cyclase O-phosphonoserine RESID:AA0037 residue modification. 2-amino-3-hydroxypropanoic acid 3-phosphate O3-phosphoserine phosphoserine 2-amino-3-hydroxypropanoic acid 3-phosphate;O-phosphonoserine;O3-phosphoserine serine phosphate ester SPO [S:po] O-phospho-L-serine (S)-2-amino-3-(phosphonooxy)propanoic acid o-phospho-serine caution Warning about errors/ grounds for confusion. Can be associated to interaction, experiment, Cv term or any participant. antagonist Opposes the effect of a natural ligand by binding at the same receptor or alters the state of an upstream molecule to inhibit a downstream interaction. PMID:9560251 In this method the two proteins, whose interaction is under investigation, (in this case mostly membrane proteins) are fused to an terminal fragment (Nub) and to a C-terminal fragment of ubiquitin (Cub). The two fragments do not associate to form a functional ubiquitin unless the two fused membrane proteins form a complex. The association is monitored by an ingenious trick. The C-term fragment of ubiquitin is expressed as a fusion to a transcription factor that being linked to a membrane protein cannot perform its function unless it is released form the ubiquitin fusion by a specific protease. This achieved through the activity of UBP (an ubiquitin specific protease) that cleaves off the reporter protein only when a functional ubiquitin is reconstituted. ubiquitin reconstruction ub reconstruction infection Molecule introduced into a cell via an external organism, usually a virus or bacteria. poly A poly adenine poly a A sequence of adenine nucleotides that is added to the 3' end of some primary transcript messenger RNA molecules in eukaryotes during post-transcriptional processing. The added tail is believed to confer stability to the molecule. DDBJ/EMBL/GenBank Nucleotide Sequence Database Collaboration exchange new and updated data on a daily basis to achieve optimal synchronisation. http://www.ebi.ac.uk/embl/Contact/collaboration GenBank DDBJ/EMBL/GenBank ddbj/embl/genbank DDBJ id-validation-regexp:"[0-9]+|[A-Z]{1,2}[0-9]+\.[0-9]+ " http://www.ebi.ac.uk/cgi-bin/dbfetch?db=EMBLSVA&id=${ac} search-url: EMBL acetyltryptophan WAC N-acetyl-L-tryptophan [W:ac] residue modification. n-acetyl-tryptophan s-(adp-ribosyl)-cysteine S-L-cysteine alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate) S-alpha-D-ribofuranosyl-L-cysteine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate) S-(ADP-ribosyl)-L-cysteine (R)-2-amino-3-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]sulfanyl)propanoic acid residue modification. adp-ribosylcysteine A specific affinity chromatography method where a protein of interest (bait) is expressed as a fusion to an affinity tag (GST, HIS tag and others) and linked at high concentration to a support that has affinity for the tag. Purified proteins or cellular extracts are then adsorbed to the resin and the retained binding proteins are identified. Thus, in this approach, the protein that has affinity for the solid support (bait) is expressed and purified first, often in an heterologous system, and then challenged with a solution containing the candidate partner proteins. no antibodies to retain bait but other affinity stuffs. pull down a given (suppressed) mutation phenotype is reverted by a supressor gene mutation. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'mutated gene' MI:0804. suppression mutation sem Electron tomography is a general method for three-dimensional (3D) reconstruction of single, transparent objects from a series of projection images (i.e. from a tilt series) recorded with a transmission electron microscope. It offers the opportunity to obtain 3D information on structural cellular arrangements with a high resolution. PMID:12160704 electron tomography A supressed gene mutation cause of an altered phenotype that is reverted to wild type phenotype when cell also carry a suppressor gene with a specific mutation or altered expression level. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793. suppression myristoylated residue myristoylated aa residue modification. Identifier of a publication prior it pubmed indexing. digital object identifier doi id-validation-regexp:"doi:[0-9]+\.[0-9]+\/" ha tag coip The protein of interest is expressed as a fusion to the peptide YPYDVPDYA (a fragment of the influenza hemaglutinin protein) for which antibodies are commercially available. OBSOLETE redundant term. Map to feature type : ha-tagged (MI:0520) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007). ha tag coimmunoprecipitation cofactor A cofactor is a small molecule required for the catalysis of an enzyme. coenzyme protease assay Measures the enzymatic hydrolysis of a peptide bond within a peptide or protein substrate. predetermined feature predetermined featur Feature detection based on the knowledge of the molecule, before any experiment. rsa A technique used to detect genetic interactions between 2 (or more) genes in a sporulating organism by scoring a large population of haploid spores for a phenotype and correlating the phenotype with the presence of single vs double (multiple) mutations. A diploid heterozygous organism harbouring mutations in two (or more) genes is induced to sporulate. Resulting spores are meiotic segregants that are haploid and are either wild type or mutant at each locus. Spores are scored for a phenotype, such as loss of viability. spore germination RSA random-spore analysis random spore analysis confidence-mapping Description of confidence assessment method generally associated to the experiment. green fluorescent protein tag The green fluorescent protein of the bioluminescent jellyfish Aequorea victoria can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native. PMID:7491768 gfp tag green fluorescent protein GFP knock-out knock out The gene has been completely removed e.g. by genetic engineering Electron crystallography Electron cryomicroscopy PMID:11785754 Electron microscopy methods provide insights into the structure of biological macromolecules and their supramolecular assemblies. Resolution is on average around 10 Angstroms but can reach the atomic level when the samples analysed are 2D crystals. Different types of samples can be analysed by electron microscopy: crystals, single particles like viruses, macromolecular complexes or entire cells and tissue sections. Samples can be chemically fixed or vitrified by rapid freezing in liquid ethane, and then transferred into the electron microscope. Data collection consists of the recording of electron diffraction data (2D crystals) and images. Depending on the type of sample, different approaches are used to analyse and merge images and electron diffraction data. electron microscopy 3'-methyl-L-histidine N(delta)-methylhistidine residue modification. pi-methylhistidine 3'-methyl-histidine methylhistidine [H:meth_n4] pros-methylhistidine MHS 1-methylhistidine [misnomer] (S)-2-amino-3-(3-methyl-3H-imidazol-4-yl)propanoic acid deoxyribonucleic acid DNA deoxyribonucleic acid dna Polymer formed by the deoxyribose sugar group, and the nucleotides bases adenine, guanine, thymine and cytosine. SO:0000352 WormBase id-validation-regexp:"WBGene[0-9]{8}" wormbase WormBase is the central worm database that houses the gene reports, locus reports, translation reports, expression pattern data and genome browser. http://www.wormbase.org/ Three hybrid system rna tri hybrid PMID:8972875 PMID:12162957 In vivo reconstruction of specific RNA-proteins interactions. The DNA binding and transcription activator domains of GAL4 are brought together via the interaction of recombinant RNA. The first hybrid protein contains the DNA binding domain of GAL4 fused to RevM10 (a mutated RNA binding protein of HIV-1 that binds specifically to the Rev responsive element RRE of the env gene). A recombinant RNA contains the RRE sequence and a target RNA sequence X. The second hybrid protein contains the activation domain of GAL4 fused to protein Y tested for its ability to bind the target RNA X. If this interaction occurs the three hybrid reconstructs GAL4 and the transcription of a reporter gene is activated. MMDB (Molecular Modeling DataBase), is a subset of three-dimensional structures obtained from the Protein Data Bank. http://www.ncbi.nlm.nih.gov/Structure MMDB mmdb peptide-parent Describe cross link pointing to a peptide parent sequence. peptide parent sequence reference PMID:11791231 Methods based on natural language processing to detect possible interactions between proteins (direct physical interactions or indirect genetic interactions). This includes the detection of non ambiguous protein or gene names and analysis of the relation expressed in a sentence among them. predictive text mining predictive tm An altered expression is the suppressor of a phenotype. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'expression level alteration' MI:0803. suppression expression alteration suppress expression ptm post translation modification Residue covalent modifications occurring in the specific protein form involved in an interaction. deformylation reaction deformylation N6-formyl-L-lysine is cleaved and returns a K residue. dna dna pol assay dna directed dna polymerase assay Measures the catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template or primer. N-aspartyl-glycosylphosphatidylinositolethanolamine gpi-aspartate gpi-anchor amidated aspartate RESID:AA0159 residue modification. A cassette coding for a protein tag is inserted by homologous recombination onto the genomic copy of an open reading frame. The advantage of this delivery method is that the resulting engineered protein is expressed under its natural promoter control. OBSOLETE redundant term. Map to feature type : tag (MI:0507) genetic tag insertion genomic tagging mudpit multidimensional protein identification technology PMID:11231557 MudPIT is a method for rapid and large-scale protein identification by multidimensional liquid chromatography associated with tandem mass spectrometry. The chromatography step consists of strong cation exchange material back-to-back with reversed phase material inside fused silica capillaries. The peptides bound to the cation-exchange resin are freed by the gradually increasing salt concentration of the buffer and are subsequently retained by the reversed phase resin. Increasing buffers hydrophobicity progressively elute peptides from the reversed phase packing directly into the mass spectrometer. Typically this mass spectrometer will be a tandem electrospray, so peptides undergo ionization in the liquid phase, are separated in a primary mass spectrometer, analysed in the second mass spectrometer and identified. Molecules labelled with isotope 13 of carbon atoms. C13 13C 13c label phosphoshistidine phospho-histidine residue modification. RESID:AA0036 RESID:AA0035 RESID:AA0039 RESID:AA0038 RESID:AA0033 Reversible reaction that can affect D,C,H,S,T,Y,R residues. GO:0016310 phosphorylation reaction phosphorylation nucleotidyltransferase assay polymerase assay Measures the catalysis of the transfer of a free nucleotidyl group to a nucleic acid chain. The protein under study is expressed as a fusion with a labelling protein, having either fluorescence properties or an enzymatic activity that facilitates its purification, identification, localisation or quantification. fusion protein sumoylation reaction sumoylation PMID:15985640 GO:0016925 Reversible reaction that create a covalent bond between a C-terminus G of an ubiquitine like sumo protein and a K residue of the target. homogeneous pure The author states a molecule is completely pure, i.e. no other molecular species are present. tau-phosphohistidine 1'-phospho-L-histidine HPE histidine-N1'-phosphate (S)-2-amino-3-(1-phosphono-1H-imidazol-4-yl)propanoic acid 1'-phospho-histidine residue modification. histidine-N(epsilon)-phosphate histidine-3-phosphate [misnomer] 1-phosphohistidine [H:po_e] tele-phosphohistidine Stable introduction and expression of nucleic acid carried out by treatment with divalent cation. nucleic acid transformation by treatment with divalent cation n transformat cation Fluorescent microscopy uses a high intensity light to illuminate the sample. This light excites fluorescence species in the sample, which then emit light of a longer wavelength. A fluorescent microscope also produces a magnified image of the sample, but the image is based on the second light source -- the light emanating from the fluorescent species -- rather than from the light originally used to illuminate, and excite, the sample. fluorescence microscopy fluorescence imaging electron paramagnetic resonance EPR (also called ESR, Electron Spin Resonance) spectroscopy is analogous to NMR, but is based on the excitation of unpaired electrons instead of nuclei. Unpaired (single) electrons are only found in radicals and some metal ions (paramagnetic species); the EPR spectrum provides information about the environment and mobility of the paramagnetic species. The magnetic interaction of two paramagnetic centres in a protein can be used to calculate the distance between them; this allows studies of the movements and interactions of protein segments. In proteins without any intrinsic unpaired electrons it is possible to attach a radical probe (spin label). Stable nitroxide radicals can be bound to amino acid residues, in analogy with fluorescent probes. In combination with site directed mutagenesis this method is used in particular to study structure and assembly of membrane proteins, by measuring with EPR whether an amino acid is in a polar or non polar environment. epr ESR EPR lumier luminescence based mammalian interactome mapping This strategy uses Renilla luciferase enzyme (RL) fused to proteins of interest, which are then coexpressed with individual Flag-tagged partners in mammalian cells. Their interactions were determined by performing an RL enzymatic assay on immunoprecipitates using an antibody against Flag. PMID:15761153 uniparc id-validation-regexp:"UPI[A-F0-9]{10}" UniParc UniProt Archive (UniParc) is part of UniProt project. It is a non-redundant archive of protein sequences derived from many sources. http://www.ebi.ac.uk/uniparc/ Molecule whose sequence identity is derived from their molecular weight identification by weight weight identificat Description of molecules polarity on a directional interaction. biological role prosite Prosite id-validation-regexp:"PS[0-9]{5}" PROSITE is a database of protein families and domains. It consists of biologically significant sites, patterns and profiles. http://us.expasy.org/prosite/ PMID for application instance:12167034 PMID:11551470 This method permits the coupling of phenotype to genotype via the formation of a non-covalent ternary complex between mRNAs and their encoded polypeptides while they are translated in an in vitro system. As a first step a cDNA library is constructed that encodes chimeric proteins in which the natural proteins or protein domains are fused to a C-terminal tether. As a consequence when the mRNA is translated in vitro the domain can fold while the tether is still in the ribosomal tunnel. Furthermore this chimeric mRNAs lack a stop codon, thus preventing release of the mRNA and the polypeptide from the ribosome. High concentrations of magnesium and low temperature further stabilise the ternary complex. Similarly to phage display, these complexes can be used directly to select for nucleic acids encoding proteins with desired properties. ribosome display Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains. http://www.sanger.ac.uk/Software/Pfam pfam Pfam id-validation-regexp:"PF[0-9]{5}" mM 10E-3 moles per liter of solution. OBSOLETE: term redundant with the schema exponent attribute of the parameter. millimolar palmitoylation reaction RESID:AA0080 RESID:AA0079 RESID:AA0077 GO:0018318 Reversible reaction that can affect C,K,T or S residues. palmitoylation Displayed as '>'. greater-than Partially determined sequence position known to be in a location higher than a given position. pisa Protein In Situ Array is a method by which protein arrays are rapidly generated in one step directly from DNA, by cell-free protein expression and simultaneous in situ immobilisation at a surface. Individual genes or fragments are produce by PCR or RT-PCR depending on the source of genetic material using properly designed primers. The PISA is generated by cell-free protein synthesis using coupled transcription and translation to produce a double HexaHis-tagged protein, the reaction being carried out on a surface to which the protein adheres as soon as it is synthesised. PMID:11470888 protein in situ array PISA Text mining methods can be used to predict or confirm interactions by automated processing of scientific literature. Co-occurrence in the same sentence of an abstract of gene products labels are analysed to evaluate whether it represents a valid evidence of an interaction. text mining SCOP superfamily scop superfamily SUPERFAMILY is a library of profile hidden Markov models that represent all proteins of known structure. The library is based on the SCOP classification of proteins: each model corresponds to a SCOP domain. http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/ ha tag The protein of interest is expressed as a fusion to the peptide YPYDVPDYA (a fragment of the influenza hemagglutinin protein) for which antibodies are commercially available. YPYDVPDYA epitope tag Predictive algorithms that rely on the information obtained by experimental results. experimental knowledge based experimental info partial identification of protein sequence partial id prot seq partial protein sequence identification. unknown participant Any type of molecule, including complexes, that may be observed but not identified. This term should be use only at PARTICIPANT level. electrophoretic mobility shift assay Gel retardation assay band shift This method proves the interaction between a nucleic acid and a protein partner. On the same electrophoresis gel 1 lane is loaded with a radiolabeled nucleic acid of known sequence, a second lane is loaded with the same nucleic acid together with a purified protein (or a protein mixture). After the electrophoresis run and autoradiography by comparing the nucleic acid migration in the two lanes the retardation of the nucleic acid due to its interaction with a protein can be easily observed. PMID:12169687 emsa The Conserved Domain Database may be used to identify the conserved domains present in a protein sequence. http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml cdd CDD phosphatase htrf phosphatase homogeneous time resolved fluorescence Measures quenching of the nonradiative energy transfer between fluorescent long-lifetime lanthanide chelates and different acceptors. Relies on a fluorescence energy donor and acceptor being removed from close proximity on the phosphorylated substrate due to the action of the phosphatase. phosphatase HTRF homogeneous time-resolved fluorescence Attribute name of annotation associated to an interaction element. interaction att name interaction attribute name Dye coupled to a molecule allowing its identification isolation and monitoring. dye labelled dye label srpRNA signal recognition particle rna Small (300 nucleotides) stable RNAs transcribed by RNA pol III that are part of the signal-recognition particle (SRP). This particle comprises one RNA and six proteins bound to the RNA. SRP function is to assist secretory proteins sorting in the endoplasmic reticulum (ER). SRP is a cytosolic particle that transiently binds to the ER signal sequence of a nascent protein, to the large ribosomal unit, and to the SRP receptor in the ER membrane. srprna cyanine label The organic cyanine dyes emit in the red range (>550 nm), offer a number of advantages. Their emission range is such that background fluorescence is often reduced. In addition these molecules can be linked directly to specific locations in synthetically produced nucleic acids. fingerprinting peptide massfingerprinting This approach leads to protein identification by matching peptide masses, as measured by mass spectrometry, to the ones calculated from in silico fragmentation of a protein sequence database. A peptide mixture from a tryptic digest is analysed by MALDI-MS (Matrix-assisted laser desorption ionization mass spectrometry). The list of peptide masses obtained by MALDI MS is automatically compared to the calculated masses of the predicted peptide fragments for each entry in the database. High mass accuracy is very important in order to obtain a statistically significant and unambiguous match This method is best applied to completely sequenced genomes and well characterised proteomes. However, depending on the data quality, proteins that are highly homologous to already characterised proteins (greater than 80 to 90% sequence identity) can also be identified. The retrieved sequence are evaluated by mass accuracy of the peptides, matching of additional peptide masses in the MALDI spectrum after accounting for common modifications such as oxidation, acrylamidation of cysteine and missed cleavages and the use of secondary information (apparent isoelectric point and molecular weight). If any ambiguity about the identification by MALDI-MS still exists, the results must verified by an other identification method. Peptide mass fingerprint is generally carried out with a MALDI-TOF (Matrix-assisted laser desorption ionization time-of-flight ) instrument but can also be achieved ESI-TOF (Electrospray Ionisation time-of-flight) or LC-MS (Liquid Chromatography-Mass Spectrometry) mass spectrometer. PMID for application instance:11805826 PMID:11752590 PMID:10967324 Gln-Lys cross-link catalyzed by a transglutaminase. RESID:AA0124 transglutamination transglutamination reaction pathway Refers to the metabolic pathway involving an interaction or a complex. asynthetic interaction The phenotype resulting from genetic perturbation of A alone, B alone and AB combined have the same effect on the WT background. asynthetic PMID:7682645 Filamentous phages (M13, f1, fd) have been extensively used to develop and implement the technology of phage display. Repertoires of relatively short peptides of random amino acid sequences or cDNA libraries have been constructed and searched successfully. Most experiments have taken advantage of the ability to assemble phages decorated with hybrid versions of the receptor protein pIII or of the major coat protein pVIII. Both systems allow the display of foreign peptides by fusion to the amino-terminus of the capsid protein but differ in the number of peptide copies that can be displayed on each phage particle. Display libraries of very diverse protein fragments have been constructed by fusing either genomic or cDNA fragments to gene III or gene VIII. filamentous phage filamentous phage display Alexa fluorescent dye analogue to Lucifer Yellow with an approximate excitation wavelength maximum of 430 nm. alexa 430 label Connection between molecule. interaction type N6-acetyl-L-lysine or S-acetyl-L-cysteine are cleaved and return K or C residues. GO:0006476 deacetylation deacetylation reaction PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family. http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/ prints PRINTS id-validation-regexp:"PR[0-9]{6}" The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number. experimental feature url URL/Web address describing an experiment, an interaction, a Cv term or an organism. Several mutant molecules are produced by random or directed techniques and assayed for their ability to support binding. Mutants defective in binding are tested for correct folding to pinpoint the residues that are directly involved in binding. mutation analysis GO:0018347 Reversible reaction that can affect C residue. farnesylation reaction farnesylation fluorescence technology Techniques based upon the measurement of the emission of one or more photons by a molecule activated by the absorption of a quantum of electro-magnetic radiation. Typically the emission, which is characterised by a wavelength that is longer than the one of excitatory radiation, occurs within 10-8 seconds. fluorescence neutral component Molecule role in an experimental setting that does not have an embedded asymmetry. inhibitor antibodies Intracellular or extracellular expression of antibodies is used to target specific gene products in order to inactivate them. Most of the times the antibody scaffold need s to reengineered for efficient expression and solubility in the cytoplasm. OBSOLETE as such method can be described using the biological role inhibitor (MI:0586). PMID:10189716 RESID:AA0215 RESID:AA0146 RESID:AA0029 RESID:AA0028 GO:0018126 Irreversible reaction that can affect K,P,Y or R residues. hydroxylation hydroxylation reaction Two silent mutations show growth increase when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective') synthetic growth increase synt growth increase experiment description experiment descripti The experimental condition text description, should contain information about the organisms hosting the interaction. Mouse Genome Informatics (MGI) provides integrated access to data on the genetics, genomics, and biology of the laboratory mouse. http://www.informatics.jax.org/ MGD/MGI mgd/mgi id-validation-regexp:"MGI:[0-9]+" Experimental method used to identify the region of a nucleic acid involved in an interaction with a protein. One sample of a radiolabeled nucleic acid of known sequence is submitted to partial digestion. A second sample is incubated with its interacting partner and then is submitted to the same partial digestion. The two samples are then analyzed in parallel by electrophoresis on a denaturing acrylamide gel. After autoradiography the identification of the bands that correspond to fragments missing from the lane loaded with the second sample reveals the region of the nucleic acid that is protected from nuclease digestion upon binding. dna footprinting Method for temporarily permeabilising cell membranes so as to facilitate the entry of large or hydrophilic molecules (as in transfection). A brief (ca 1 msec) electric pulse is given with potential gradients of about 700V/cm. PMID:6329708 electroporation This approach uses a protein interaction network of a given organism to infer interaction in another organism using information about the interacting region. The regions or domains involved in interactions are clustered if they share sequence similarity and have common interacting partners. The resulting domain profiles are then used to screen the proteome of another organism and domain-domain interactions are inferred. Ultimately, an inferred protein interaction map is built in this second organism. PMID:11473021 domain profile pairs A stable set of interacting proteins that can be copurified and operate as a functional unit. protein complex membrane compl membrane bound complementation assay Protein complementation assay based on dissection of a membrane protein. cosedimentation through density gradient density sedimentatio Sedimentation through a density gradient measures the sedimentation rate of a mixture of proteins through either a glycerol or sucrose gradient. Two interacting proteins will sediment mostly as a complex at concentrations above the binding constant. By varying the concentration of one or both of the complex constituents and taking into account the dilution of the species during sedimentation, one can reasonably accurately estimate the binding constant. PMID:10410796 The organic cyanine Cy5 emits maximally at 670 nm. cy5 label Fluorophore which emits electromagnetic radiation of given wavelength. fluorescence donor biotinyllysine N6-[5-((3aS,4S,6aR)-hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-4-yl)-1-oxopentyl]-L-lysine N6-biotinyl-L-lysine [K:biotin] residue modification. RESID:AA0117 N6-biotinyllysine biocytin (3aS-(3aalpha,4beta,6aalpha))-N6-(5-(hexahydro-2-oxo-1H-thieno(3,4-d)imidazol-4-yl)-1-oxopentyl)-L-lysine epsilon-N-biotinyllysine (S)-2-amino-6-[5-((3aS,4S,6aR)-hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-4-yl)-1-oxopentyl]aminohexanoic acid n6-biotinyl-lysine KBT nucl delivery nucleic acid delivery Method by which nucleic acids are delivered or engineered into a cell. cyan fluorescent protein tag cyan fluorescent protein CFP The cyan fluorescent protein derived from Anthozoa reef coral can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native. cfp tag Covalent or non covalent binding of lipid group on a protein residue. GO:0006497 lipid addition Small molecules, peptides or full proteins that can be used as label as they confer some property that facilitates identification purification and monitoring to the labelled molecule. tag uM 10E-6 moles per liter of solution. OBSOLETE: term redundant with the schema exponent attribute of the parameter. micromolar o4'-phospho-tyrosine O4'-phospho-L-tyrosine (S)-2-amino-3-(4-phosphonooxyphenyl)propanoic acid residue modification. phosphotyrosine [Y:po] YPO 2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-phosphate O4-phosphotyrosine tyrosine phosphate microscopy imaging techniques Methods that provide images of molecules at various resolution depending on the technology used. MINT The Moleculer INTeraction database (MINT) is a relational database designed to store interactions between biological molecules. http://mint.bio.uniroma2.it/mint/ id-validation-regexp:"MINT_[0-9]+" mint comigration in sds page comigration in sds PMID:16732283 Method allowing the detection of strong interactions between two molecules by their very close proximity or the overlap of their relative bands in a denaturing SDS gel. adp-ribosylated adp ribosylated residue residue modification. chromatin immunoprecipitation assays PMID:12054902 Chromatin immunoprecipitation (ChIP) is a powerful approach that allows one to define the interaction of factors with specific chromosomal sites in living cells. ChIP involves treating cells or tissue briefly with formaldehyde to crosslink proteins to DNA. An antibody against a protein suspected of binding a given cis-element is then used to immunoprecipitate chromatin fragments. Polymerase chain reaction analysis of the immunoprecipitate with primers flanking the cis-element reveals whether a specific DNA sequence is recovered in an immune-specific manner and therefore whether the protein contacted the site in living cells. ch-ip PMID:11558993 FRET is a quantum mechanical process involving the radiationless transfer of energy from a donor fluorophore to an appropriately positioned acceptor fluorophore. The fluorophores are genetically fused to the protein in analysis and cotransfected. Three basic conditions must be fulfilled for FRET to occur between a donor molecule and acceptor molecule. First, the donor emission spectrum must significantly overlap the absorption spectrum of the acceptor. Second, the distance between the donor and acceptor fluorophores must fall within the range 20 to 100 Angstrom. Third, the donor and acceptor fluorophores must be in favourable orientations. fret RET FRET analysis FRET fluorescent resonance energy transfer A microarray consisting of antibodies spotted on a solid support in appropriate orientation is incubated with a biological sample (or antigen). Some proteins are captured by the antibodies in the array. Protein of forming complexes on the array are identified according to their prior labelling (tag, ELISA, biotin and others). sandwich immunoassay antigen capture assay antibody array electron donor Any molecule that is able to transfer an electron to another chemical species. Search URL to retrieve an external entry in ASCII format. Generally associated to Cv Database terms. search-url-ascii protein delivery by cationic lipid treatment Proteins are delivered into cells by treatment with cationic lipids. prot cationic lipid A protein of interest (the bait) is fused to the full-length bacteriophage lambda repressor protein (lambdacI, 237 amino acids), containing the amino terminal DNA-binding domain and the carboxylterminal dimerization domain. The corresponding target (prey) protein is fused to the N-terminal domain of the alfa-subunit of RNA polymerase (248 amino acids). The bait is tethered to the lambda operator sequence upstream of the reporter promoter through the DNA-binding domain of lambdacI. When the bait and prey interact, they recruit and stabilize the binding of RNA polymerase at the promoter and activate the transcription of the HIS3 reporter gene. Due to the tendency of both the lambda repressor protein and the N-terminal domain of the alfa-subunit of RNA polymerase to dimerize, this system might not be optimal for the analysis of proteins that self-associate unless their interaction with other protein partners depends on the oligomerization. PMID:15792953 BacterioMatch lambda repressor two hybrid lambda two hybrid small nuclear rna snrna These RNA molecules are relatively short (less than 200 nucleotides each), and there are five of them (U1, U2, U4, U5, and U6) involved in the major form of pre-mRNA splicing. Known as snRNAs (small nuclear RNAs), each is complexed with at least seven protein subunits to form a snRNP (small nuclear ribonucleoprotein). These snRNPs form the core of the spliceosome. snRNA Predicts the structure of a protein-protein complex from the unbound structures of its components. The initial approach in the majority of docking procedures is based largely on the 'rigid-body' assumption, whereby the proteins are treated as solid objects. Initial scoring of a complex is based on geometric fit or surface complementarity. This generally requires some knowledge of the binding site to limit the number of solutions. PMID for application instance:11478868 PMID:9631301 docking elongation DNA replication elongation dna strand elongation The process by which a DNA strand is synthesized from template DNA by the action of polymerases, which add nucleotides to the 3' end of the nascent DNA strand. GO:0006271 Radiolabelled nucleic acids with a known sequence are incubated with purified proteins or reproducible protein mixture (HPLC eluate fractions) and then irradiated with UV. The complex are treated with an enzyme to remove the unbound nucleic acid (Rnase A or Dnase I for example), washed and then analyzed by electrophoresis. The eventual complexes are identified by autoradiography. The proteins involved in the complex can be recognized by specific antibodies or by retrieving the original protein mixture and carrying further analysis on it. The affinity of the binding can be estimated by adding a non-labelled nucleic acid as competitor before the UV irradiation. nucleic acid uv cross-linking assay nucl ac uv crosslink alkylated cysteine Artificial residue modification enabling studies of cysteine binding status. PMID:15325307 chemical footprinting chemical footprint Sites of sequence-specific DNA-protein interaction are identified by altered reactivity of a chemical probe to DNA bound by a protein compared to the same nucleotide sequence in naked DNA. Nucleotides in close contact with the binding protein are protected from modification or cleavage by the probe. In certain case DNA-protein interactions can be indicated by enhanced modification or cleavage by the probe at particular nucleotides. When these probes are administrated to intact cells, the pattern of protection from the probes identifies the location of DNA-protein interactions in vivo. substitut analysis substitution analysis In this approach, once a molecule is demonstrated to participate in an interaction, several substitution mutants are produced and tested in the binding assay to identify the residues which identity is crucial for the interaction.