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 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 - 2014

Fingerprint

Torsional stress
folding
field theory (physics)
Specific heat
torsion
Protein folding
Free energy
Melting point
Molecular dynamics
simulation
specific heat
proteins
Proteins
Computer simulation
replicas
helices
free energy
melting
molecular dynamics
temperature

Keywords

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

ASJC Scopus subject areas

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

Cite this

Folding simulation of Trp-cage utilizing a new AMBER compatible force field with coupled main chain torsions. / Mou, Lirong; Jia, Xiangyu; Gao, Ya; Li, Yongxiu; Zhang, John; Mei, Ye.

In: Journal of Theoretical and Computational Chemistry, Vol. 13, No. 4, 1450026, 2014.

Research output: Contribution to journalArticle

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AU - Mei, Ye

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