Folding and thermodynamic studies of Trp-cage based on polarized force field

Ye Mei, Caiyi Wei, Yew Mun Yip, Chun Ying Ho, John Z.H. Zhang, Dawei Zhang

Research output: Contribution to journalLetter

Abstract

Two replica exchange molecular dynamics (REMD) simulations were carried out to study the thermodynamics of a 20-residue Trp-cage folding based on a newly developed polarized protein-specific charge (PPC). Starting from a fully extended conformation, Trp-cage native conformation was successfully sampled using REMD based on a 3-step PPC update. Next, the obtained Trp-cage folded conformation was then used to calculate the PPC in which another REMD was performed to explore the thermodynamic stability of Trp-cage. The theoretical melting temperature Tm of ≈325 K was found to be in close agreement with experimental melting temperature, Tm of 315 K. This indicates that the PPC was correctly predicting the temperature dependence. The current study provides a direct proof of how electrostatic polarization affects protein folding.

Original languageEnglish (US)
Article number1168
Pages (from-to)1-7
Number of pages7
JournalTheoretical Chemistry Accounts
Volume131
Issue number3
DOIs
StatePublished - Mar 2012

Keywords

  • Charge update
  • MFCC
  • PPC
  • Trp-cage

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry

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