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World Scientific Publishing, Journal of Theoretical and Computational Chemistry, 04(13), p. 1450026, 2014

DOI: 10.1142/s0219633614500266

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Folding simulation of Trp-cage utilizing a new AMBER compatible force field with coupled main chain torsions

Journal article published in 2014 by Lirong Mou, Xiangyu Jia ORCID, Ya Gao, Yongxiu Li, John Z. H. Zhang, Ye Mei ORCID
This paper was not found in any repository, but could be made available legally by the author.
This paper was not found in any repository, but could be made available legally by the author.

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Abstract

A newly developed AMBER compatible force field with coupled backbone torsion potential terms (AMBER032D) is utilized in a folding simulation of a mini-protein Trp-cage. Through replica exchange and direct molecular dynamics (MD) simulations, a multi-step folding mechanism with a synergetic folding of the hydrophobic core (HPC) and the α-helix in the final stage is suggested. The native structure has the lowest free energy and the melting temperature predicted from the specific heat capacity Cvis only 12 K higher than the experimental measurement. This study, together with our previous study, shows that AMBER032Dis an accurate force field that can be used for protein folding simulations.