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

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

Research output: Contribution to journalArticle

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 T m of ≈325 K was found to be in close agreement with experimental melting temperature, T m 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)
Pages (from-to)1-7
Number of pages7
JournalTheoretical Chemistry Accounts
Volume131
Issue number3
DOIs
StatePublished - Mar 2012

Fingerprint

folding
field theory (physics)
Thermodynamics
proteins
Conformations
Molecular dynamics
thermodynamics
replicas
Melting point
molecular dynamics
Proteins
Protein folding
melting
Electrostatics
Thermodynamic stability
Polarization
electrostatics
Computer simulation
temperature dependence
temperature

Keywords

  • Charge update
  • MFCC
  • PPC
  • Trp-cage

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry

Cite this

Folding and thermodynamic studies of Trp-cage based on polarized force field. / Mei, Ye; Wei, Caiyi; Yip, Yew Mun; Ho, Chun Ying; Zhang, John; Zhang, Dawei.

In: Theoretical Chemistry Accounts, Vol. 131, No. 3, 03.2012, p. 1-7.

Research output: Contribution to journalArticle

Mei, Ye ; Wei, Caiyi ; Yip, Yew Mun ; Ho, Chun Ying ; Zhang, John ; Zhang, Dawei. / Folding and thermodynamic studies of Trp-cage based on polarized force field. In: Theoretical Chemistry Accounts. 2012 ; Vol. 131, No. 3. pp. 1-7.
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