Coevolution at protein complex interfaces can be detected by the complementarity trace with important impact for predictive docking Export

@article{citeulike:2856159, abstract = {10.1073/pnas.0707032105 Protein surfaces are under significant selection pressure to maintain interactions with their partners throughout evolution. Capturing how selection pressure acts at the interfaces of protein\^{a}€“protein complexes is a fundamental issue with high interest for the structural prediction of macromolecular assemblies. We tackled this issue under the assumption that, throughout evolution, mutations should minimally disrupt the physicochemical compatibility between specific clusters of interacting residues. This constraint drove the development of the so-called Surface COmplementarity Trace in Complex History score (SCOTCH), which was found to discriminate with high efficiency the structure of biological complexes. SCOTCH performances were assessed not only with respect to other evolution-based approaches, such as conservation and coevolution analyses, but also with respect to statistically based scoring methods. Validated on a set of 129 complexes of known structure exhibiting both permanent and transient intermolecular interactions, SCOTCH appears as a robust strategy to guide the prediction of protein\^{a}€“protein complex structures. Of particular interest, it also provides a basic framework to efficiently track how protein surfaces could evolve while keeping their partners in contact.}, address = {Commissariat \`{a} l'\'{E}nergie Atomique (CEA), Institut de Biologie et Technologies de Saclay, and Centre National de la Recherche Scientifique (CNRS), Gif-sur-Yvette, F-91191, France.}, author = {Madaoui, Hocine and Guerois, Rapha\~{A}«l}, citeulike-article-id = {2856159}, citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.0707032105}, citeulike-linkout-1 = {http://www.pnas.org/content/105/22/7708.abstract}, citeulike-linkout-2 = {http://www.pnas.org/content/105/22/7708.full.pdf}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/18511568}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=18511568}, doi = {10.1073/pnas.0707032105}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences}, keywords = {coevolution, complementarity, contact, correlation, docking, interaction, interface, mutation, protein}, month = {June}, number = {22}, pages = {7708--7713}, posted-at = {2009-07-01 21:08:19}, priority = {2}, title = {Coevolution at protein complex interfaces can be detected by the complementarity trace with important impact for predictive docking}, url = {http://dx.doi.org/10.1073/pnas.0707032105}, volume = {105}, year = {2008} }

TY - JOUR ID - citeulike:2856159 L3 - citeulike-article-id:2856159 N2 - 10.1073/pnas.0707032105 Protein surfaces are under significant selection pressure to maintain interactions with their partners throughout evolution. Capturing how selection pressure acts at the interfaces of protein–protein complexes is a fundamental issue with high interest for the structural prediction of macromolecular assemblies. We tackled this issue under the assumption that, throughout evolution, mutations should minimally disrupt the physicochemical compatibility between specific clusters of interacting residues. This constraint drove the development of the so-called Surface COmplementarity Trace in Complex History score (SCOTCH), which was found to discriminate with high efficiency the structure of biological complexes. SCOTCH performances were assessed not only with respect to other evolution-based approaches, such as conservation and coevolution analyses, but also with respect to statistically based scoring methods. Validated on a set of 129 complexes of known structure exhibiting both permanent and transient intermolecular interactions, SCOTCH appears as a robust strategy to guide the prediction of protein–protein complex structures. Of particular interest, it also provides a basic framework to efficiently track how protein surfaces could evolve while keeping their partners in contact. IS - 22 JF - Proceedings of the National Academy of Sciences SN - 1091-6490 AD - Commissariat à l'Énergie Atomique (CEA), Institut de Biologie et Technologies de Saclay, and Centre National de la Recherche Scientifique (CNRS), Gif-sur-Yvette, F-91191, France. EP - 7713 TI - Coevolution at protein complex interfaces can be detected by the complementarity trace with important impact for predictive docking VL - 105 SP - 7708 KW - coevolution KW - complementarity KW - contact KW - correlation KW - docking KW - interaction KW - interface KW - mutation KW - protein AU - Madaoui, Hocine AU - Guerois, Raphaël PY - 2008/06/03/ UR - http://dx.doi.org/10.1073/pnas.0707032105 ER -