TY - JOUR
T1 - Evaluation of the Coupled Two-Dimensional Main Chain Torsional Potential in Modeling Intrinsically Disordered Proteins
AU - Gao, Ya
AU - Zhang, Chaomin
AU - Zhang, John Z.H.
AU - Mei, Ye
N1 - Funding Information:
This work was supported by the National Natural Science Foundation of China (Grants 21503132, 21403068, and 21173082) , the National Key R&D Program (2016YFA0501700), the Shanghai Municipal Education Commission (ZZGCD15055 and 15CG59), the Zhanchi Program of Shanghai University of Engineering Science, and the Large Instruments Open Foundation of East China Normal University. We thank the Supercomputer Center of East China Normal University for CPU time support.
Publisher Copyright:
© 2017 American Chemical Society.
PY - 2017/2/27
Y1 - 2017/2/27
N2 - Intrinsically disordered proteins (IDPs) carry out crucial biological functions in essential biological processes of life. Because of the highly dynamic and conformationally heterogeneous nature of the disordered states of IDPs, molecular dynamics simulations are becoming an indispensable tool for the investigation of the conformational ensembles and dynamic properties of IDPs. Nevertheless, there is still no consensus on the most reliable force field in molecular dynamics simulations for IDPs hitherto. In this work, the recently proposed AMBER99SB2D force field is evaluated in modeling some disordered polypeptides and proteins by checking its ability to reproduce experimental NMR data. The results highlight that when the ildn side-chain corrections are included, AMBER99SB2D-ildn exhibits reliable results that agree with experiments compared with its predecessors, the AMBER14SB, AMBER99SB, AMBER99SB-ildn, and AMBER99SB2D force fields, and that decreasing the overall magnitude of protein-protein interactions in favor of protein-water interactions is a key ingredient behind the improvement.
AB - Intrinsically disordered proteins (IDPs) carry out crucial biological functions in essential biological processes of life. Because of the highly dynamic and conformationally heterogeneous nature of the disordered states of IDPs, molecular dynamics simulations are becoming an indispensable tool for the investigation of the conformational ensembles and dynamic properties of IDPs. Nevertheless, there is still no consensus on the most reliable force field in molecular dynamics simulations for IDPs hitherto. In this work, the recently proposed AMBER99SB2D force field is evaluated in modeling some disordered polypeptides and proteins by checking its ability to reproduce experimental NMR data. The results highlight that when the ildn side-chain corrections are included, AMBER99SB2D-ildn exhibits reliable results that agree with experiments compared with its predecessors, the AMBER14SB, AMBER99SB, AMBER99SB-ildn, and AMBER99SB2D force fields, and that decreasing the overall magnitude of protein-protein interactions in favor of protein-water interactions is a key ingredient behind the improvement.
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U2 - 10.1021/acs.jcim.6b00589
DO - 10.1021/acs.jcim.6b00589
M3 - Article
C2 - 28095698
AN - SCOPUS:85014230079
SN - 1549-9596
VL - 57
SP - 267
EP - 274
JO - Journal of Chemical Information and Modeling
JF - Journal of Chemical Information and Modeling
IS - 2
ER -