Simultaneous prediction of protein folding and docking at high resolution Export

@article{citeulike:6097327, abstract = {10.1073/pnas.0904407106 Interleaved dimers and higher order symmetric oligomers are ubiquitous in biology but present a challenge to de novo structure prediction methodology: The structure adopted by a monomer can be stabilized largely by interactions with other monomers and hence not the lowest energy state of a single chain. Building on the Rosetta framework, we present a general method to simultaneously model the folding and docking of multiple-chain interleaved homo-oligomers. For more than a third of the cases in a benchmark set of interleaved homo-oligomers, the method generates near-native models of large \^{I}±-helical bundles, interlocking \^{I}² sandwiches, and interleaved \^{I}±/\^{I}² motifs with an accuracy high enough for molecular replacement based phasing. With the incorporation of NMR chemical shift information, accurate models can be obtained consistently for symmetric complexes with as many as 192 total amino acids; a blind prediction was within 1 \~{A}… rmsd of the traditionally determined NMR structure, and fit independently collected RDC data equally well. Together, these results show that the Rosetta \^{a}€œfold-and-dock\^{a}€ protocol can produce models of homo-oligomeric complexes with near-atomic-level accuracy and should be useful for crystallographic phasing and the rapid determination of the structures of multimers with limited NMR information.}, author = {Das, Rhiju and Andr\~{A}{\copyright}, Ingemar and Shen, Yang and Wu, Yibing and Lemak, Alexander and Bansal, Sonal and Arrowsmith, Cheryl H. and Szyperski, Thomas and Baker, David}, citeulike-article-id = {6097327}, citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.0904407106}, citeulike-linkout-1 = {http://www.pnas.org/content/106/45/18978.abstract}, citeulike-linkout-2 = {http://www.pnas.org/content/106/45/18978.full.pdf}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/19864631}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=19864631}, day = {10}, doi = {10.1073/pnas.0904407106}, journal = {Proceedings of the National Academy of Sciences}, keywords = {folding, prediction, protein}, month = {November}, number = {45}, pages = {18978--18983}, posted-at = {2009-11-11 10:39:19}, priority = {2}, title = {Simultaneous prediction of protein folding and docking at high resolution}, url = {http://dx.doi.org/10.1073/pnas.0904407106}, volume = {106}, year = {2009} }

TY - JOUR ID - citeulike:6097327 L3 - citeulike-article-id:6097327 N2 - 10.1073/pnas.0904407106 Interleaved dimers and higher order symmetric oligomers are ubiquitous in biology but present a challenge to de novo structure prediction methodology: The structure adopted by a monomer can be stabilized largely by interactions with other monomers and hence not the lowest energy state of a single chain. Building on the Rosetta framework, we present a general method to simultaneously model the folding and docking of multiple-chain interleaved homo-oligomers. For more than a third of the cases in a benchmark set of interleaved homo-oligomers, the method generates near-native models of large α-helical bundles, interlocking β sandwiches, and interleaved α/β motifs with an accuracy high enough for molecular replacement based phasing. With the incorporation of NMR chemical shift information, accurate models can be obtained consistently for symmetric complexes with as many as 192 total amino acids; a blind prediction was within 1 Å rmsd of the traditionally determined NMR structure, and fit independently collected RDC data equally well. Together, these results show that the Rosetta “fold-and-dock” protocol can produce models of homo-oligomeric complexes with near-atomic-level accuracy and should be useful for crystallographic phasing and the rapid determination of the structures of multimers with limited NMR information. IS - 45 JF - Proceedings of the National Academy of Sciences EP - 18983 TI - Simultaneous prediction of protein folding and docking at high resolution VL - 106 SP - 18978 KW - folding KW - prediction KW - protein AU - Das, Rhiju AU - André, Ingemar AU - Shen, Yang AU - Wu, Yibing AU - Lemak, Alexander AU - Bansal, Sonal AU - Arrowsmith, Cheryl AU - Szyperski, Thomas AU - Baker, David PY - 2009/11/10/ UR - http://dx.doi.org/10.1073/pnas.0904407106 ER -