Complementarity of Structure Ensembles in Protein-Protein Binding Export

@article{Gruenberg2004, abstract = {Protein-protein association is often accompanied by changes in receptor and ligand structure. This interplay between protein flexibility and protein-protein recognition is currently the largest obstacle both to our understanding of and to the reliable prediction of protein complexes. We performed two sets of molecular dynamics simulations for the unbound receptor and ligand structures of 17 protein complexes and applied shape-driven rigid body docking to all combinations of representative snapshots. The crossdocking of structure ensembles increased the likelihood of finding near-native solutions. The free ensembles appeared to contain multiple complementary conformations. These were in general not related to the bound structure. We suggest that protein-protein binding follows a three-step mechanism of diffusion, free conformer selection, and refolding. This model combines previously conflicting ideas and is in better agreement with the current data on interaction forces, time scales, and kinetics.}, author = {Gruenberg, Raik and Leckner, Johan and Nilges, Michael}, citeulike-article-id = {445907}, citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.str.2004.09.014}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/15576027}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=15576027}, citeulike-linkout-3 = {http://www.sciencedirect.com/science/article/B6VSR-4DYV1YN-7/2/59492aef638de7bd0546d77e16d88fe0}, doi = {10.1016/j.str.2004.09.014}, journal = {Structure}, keywords = {40061085, ensambles, ensembles, estructuras, structure}, month = {December}, number = {12}, pages = {2125--2136}, posted-at = {2007-05-11 21:22:45}, priority = {2}, title = {Complementarity of Structure Ensembles in Protein-Protein Binding}, url = {http://dx.doi.org/10.1016/j.str.2004.09.014}, volume = {12}, year = {2004} }

TY - JOUR ID - Gruenberg2004 L3 - citeulike-article-id:445907 N2 - Protein-protein association is often accompanied by changes in receptor and ligand structure. This interplay between protein flexibility and protein-protein recognition is currently the largest obstacle both to our understanding of and to the reliable prediction of protein complexes. We performed two sets of molecular dynamics simulations for the unbound receptor and ligand structures of 17 protein complexes and applied shape-driven rigid body docking to all combinations of representative snapshots. The crossdocking of structure ensembles increased the likelihood of finding near-native solutions. The free ensembles appeared to contain multiple complementary conformations. These were in general not related to the bound structure. We suggest that protein-protein binding follows a three-step mechanism of diffusion, free conformer selection, and refolding. This model combines previously conflicting ideas and is in better agreement with the current data on interaction forces, time scales, and kinetics. IS - 12 JF - Structure EP - 2136 TI - Complementarity of Structure Ensembles in Protein-Protein Binding VL - 12 SP - 2125 KW - 40061085 KW - ensambles KW - ensembles KW - estructuras KW - structure AU - Gruenberg, Raik AU - Leckner, Johan AU - Nilges, Michael PY - 2004/12// UR - http://dx.doi.org/10.1016/j.str.2004.09.014 ER -