Simulation of the thermodynamics of folding and unfolding of the Trp-cage mini-protein TC5b using different combinations of force fields and solvation models

Lili Duan, Ye Mei, Yongle Li, Qinggang Zhang, Dawei Zhang, John Zhang

Research output: Contribution to journalArticle

Abstract

Molecular dynamics simulations based on AMBER force fields (ff96 and ff03) and generalized Born models (igb1 and igb5) have been carried out in order to study folding/unfolding of the Trp-cage mini-protein TC5b. The thermodynamic properties of TC5b were found to be sensitive to the specific version of the solvation model and force field employed. When the ff96/igb5 combination was used, the predicted melting temperature from unfolding simulations was in good agreement with the experimental value of 315 K, but the folding simulation did not converge. The most stable thermodynamic profile in both folding and unfolding simulations was obtained when the ff03/igb5 combination was employed, and the predicted melting temperature was about 345 K, showing over-stabilization of the protein. Simulations using the igb1 version in combination with ff96 or ff03 were difficult to converge within the simulation time limit (50 ns).

Original languageEnglish (US)
Pages (from-to)196-201
Number of pages6
JournalScience China Chemistry
Volume53
Issue number1
DOIs
StatePublished - Jan 2010

Fingerprint

Solvation
Melting point
Thermodynamics
Molecular dynamics
Proteins
Thermodynamic properties
Stabilization
Computer simulation

Keywords

  • Folding and unfolding
  • Implicit solvation
  • Melting curve
  • Replica-exchange
  • TC5b
  • Trp-cage

ASJC Scopus subject areas

  • Chemistry(all)

Cite this

Simulation of the thermodynamics of folding and unfolding of the Trp-cage mini-protein TC5b using different combinations of force fields and solvation models. / Duan, Lili; Mei, Ye; Li, Yongle; Zhang, Qinggang; Zhang, Dawei; Zhang, John.

In: Science China Chemistry, Vol. 53, No. 1, 01.2010, p. 196-201.

Research output: Contribution to journalArticle

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AU - Zhang, Dawei

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