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PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
4
pubmed:dateCreated
2000-10-17
pubmed:abstractText
A simple method for predicting residues involved in protein interaction sites is proposed. In the absence of any structural report, the procedure identifies linear stretches of sequences as "receptor-binding domains" (RBDs) by analysing hydrophobicity distribution. The sequences of two databases of non-homologous interaction sites eliciting various biological activities were tested; 59-80 % were detected as RBDs. A statistical analysis of amino acid frequencies was carried out in known interaction sites and in predicted RBDs. RBDs were predicted from the 80,000 sequences of the Swissprot database. In both cases, arginine is the most frequently occurring residue. The RBD procedure can also detect residues involved in specific interaction sites such as the DNA-binding (95 % detected) and Ca-binding domains (83 % detected). We report two recent analyses; from the prediction of RBDs in sequences to the experimental demonstration of the functional activities. The examples concern a retroviral Gag protein and a penicillin-binding protein. We support that this method is a quick way to predict protein interaction sites from sequences and is helpful for guiding experiments such as site-specific mutageneses, two-hybrid systems or the synthesis of inhibitors.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
http://linkedlifedata.com/resource/pubmed/chemical/Apolipoproteins E, http://linkedlifedata.com/resource/pubmed/chemical/Arginine, http://linkedlifedata.com/resource/pubmed/chemical/Bacterial Proteins, http://linkedlifedata.com/resource/pubmed/chemical/Calcium-Binding Proteins, http://linkedlifedata.com/resource/pubmed/chemical/Carrier Proteins, http://linkedlifedata.com/resource/pubmed/chemical/Gene Products, gag, http://linkedlifedata.com/resource/pubmed/chemical/Hexosyltransferases, http://linkedlifedata.com/resource/pubmed/chemical/Muramoylpentapeptide..., http://linkedlifedata.com/resource/pubmed/chemical/Penicillin-Binding Proteins, http://linkedlifedata.com/resource/pubmed/chemical/Peptidyl Transferases, http://linkedlifedata.com/resource/pubmed/chemical/Proteins, http://linkedlifedata.com/resource/pubmed/chemical/Viral Fusion Proteins
pubmed:status
MEDLINE
pubmed:month
Sep
pubmed:issn
0022-2836
pubmed:author
pubmed:copyrightInfo
Copyright 2000 Academic Press.
pubmed:issnType
Print
pubmed:day
29
pubmed:volume
302
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
917-26
pubmed:dateRevised
2006-11-15
pubmed:meshHeading
pubmed-meshheading:10993732-Algorithms, pubmed-meshheading:10993732-Amino Acid Sequence, pubmed-meshheading:10993732-Amino Acid Substitution, pubmed-meshheading:10993732-Animals, pubmed-meshheading:10993732-Apolipoproteins E, pubmed-meshheading:10993732-Arginine, pubmed-meshheading:10993732-Bacterial Proteins, pubmed-meshheading:10993732-Binding Sites, pubmed-meshheading:10993732-Calcium-Binding Proteins, pubmed-meshheading:10993732-Carrier Proteins, pubmed-meshheading:10993732-Computational Biology, pubmed-meshheading:10993732-Databases, Factual, pubmed-meshheading:10993732-Drug Design, pubmed-meshheading:10993732-Gene Products, gag, pubmed-meshheading:10993732-Hexosyltransferases, pubmed-meshheading:10993732-Humans, pubmed-meshheading:10993732-Models, Molecular, pubmed-meshheading:10993732-Molecular Sequence Data, pubmed-meshheading:10993732-Muramoylpentapeptide Carboxypeptidase, pubmed-meshheading:10993732-Mutation, pubmed-meshheading:10993732-Penicillin-Binding Proteins, pubmed-meshheading:10993732-Peptidyl Transferases, pubmed-meshheading:10993732-Protein Binding, pubmed-meshheading:10993732-Protein Structure, Tertiary, pubmed-meshheading:10993732-Proteins, pubmed-meshheading:10993732-Sensitivity and Specificity, pubmed-meshheading:10993732-Time Factors, pubmed-meshheading:10993732-Viral Fusion Proteins
pubmed:year
2000
pubmed:articleTitle
A fast method to predict protein interaction sites from sequences.
pubmed:affiliation
Centre de Biophysique Moléculaire Numérique, Faculté Agronomique, Gembloux, 5030, Belgium. brasseur.r@fsagx.ac.be
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't