Direct folding simulation of alpha-helices and beta-hairpins based on a single all-atom force field with an implicit solvation model

@article{citeulike:3467108, abstract = {Recently, we have shown that a modified energy model based on the param99 force field with the generalized Born (GB) solvation model produces reliable free energy landscapes of mini-proteins with a betabetaalpha motif (BBA5, 1FSD, and 1PSV), with the native structures of the mini-proteins located in their lowest free energy minimum states. One of the main features in the modified energy model is a significant improvement for more balanced treatments of alpha and beta strands in proteins. In this study, using the replica exchange molecular dynamics (REMD) simulation method with this new force field, we have carried out extensive ab initio folding studies of several well-known peptides with alpha or beta strands (C-peptide, EK-peptide, le0q, and gbl). Starting from fully extended conformations as the initial conditions, all of the native-like structures of the target peptides were successfully identified by REMD, with reasonable representations of free energy surfaces. The present simulation results with the modified energy model are consistent with experiments, demonstrating an extended applicability of the energy model to folding studies of a variety of alpha-helices, beta-strands, and alpha/beta proteins. Proteins 2007. {\copyright} 2006 Wiley-Liss, Inc.}, address = {Department of Applied Chemistry, Sejong University, Seoul 143-747, Korea; Department of Chemistry, Pusan National University, Busan 609-735, Korea}, author = {Jang, Soonmin and Kim, Eunae and Pak, Youngshang}, citeulike-article-id = {3467108}, doi = {10.1002/prot.21173}, journal = {Proteins: Structure, Function, and Bioinformatics}, keywords = {protein\_folding}, number = {1}, pages = {53--60}, posted-at = {2008-10-30 23:56:07}, priority = {2}, title = {Direct folding simulation of alpha-helices and beta-hairpins based on a single all-atom force field with an implicit solvation model}, url = {http://dx.doi.org/10.1002/prot.21173}, volume = {66}, year = {2007} }

TY - JOUR ID - citeulike:3467108 L3 - citeulike-article-id:3467108 N2 - Recently, we have shown that a modified energy model based on the param99 force field with the generalized Born (GB) solvation model produces reliable free energy landscapes of mini-proteins with a betabetaalpha motif (BBA5, 1FSD, and 1PSV), with the native structures of the mini-proteins located in their lowest free energy minimum states. One of the main features in the modified energy model is a significant improvement for more balanced treatments of alpha and beta strands in proteins. In this study, using the replica exchange molecular dynamics (REMD) simulation method with this new force field, we have carried out extensive ab initio folding studies of several well-known peptides with alpha or beta strands (C-peptide, EK-peptide, le0q, and gbl). Starting from fully extended conformations as the initial conditions, all of the native-like structures of the target peptides were successfully identified by REMD, with reasonable representations of free energy surfaces. The present simulation results with the modified energy model are consistent with experiments, demonstrating an extended applicability of the energy model to folding studies of a variety of alpha-helices, beta-strands, and alpha/beta proteins. Proteins 2007. © 2006 Wiley-Liss, Inc. IS - 1 JF - Proteins: Structure, Function, and Bioinformatics AD - Department of Applied Chemistry, Sejong University, Seoul 143-747, Korea; Department of Chemistry, Pusan National University, Busan 609-735, Korea EP - 60 TI - Direct folding simulation of alpha-helices and beta-hairpins based on a single all-atom force field with an implicit solvation model VL - 66 SP - 53 KW - protein_folding AU - Jang, Soonmin AU - Kim, Eunae AU - Pak, Youngshang PY - 2007/// UR - http://dx.doi.org/10.1002/prot.21173 ER -