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

Lirong Mou, Xiangyu Jia, Ya Gao, Yongxiu Li, John Z.H. Zhang, Ye Mei

Research output: Contribution to journalArticle

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 Cv is only 12 K higher than the experimental measurement. This study, together with our previous study, shows that AMBER032D is an accurate force field that can be used for protein folding simulations.

Original languageEnglish (US)
Article number1450026
JournalJournal of Theoretical and Computational Chemistry
Volume13
Issue number4
DOIs
StatePublished - Jun 2014

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Keywords

  • AMBER force field
  • Trp-cage
  • coupled backbone torsion
  • folding mechanism
  • melting temperature

ASJC Scopus subject areas

  • Computer Science Applications
  • Physical and Theoretical Chemistry
  • Computational Theory and Mathematics

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