Direct folding simulation of helical proteins using an effective polarizable bond force field

Lili Duan, Tong Zhu, Changge Ji, Qinggang Zhang, John Zhang

Research output: Contribution to journalArticle

Abstract

We report a direct folding study of seven helical proteins (2I9M, Trpcage, 1WN8, C34, N36, 2KES, 2KHK) ranging from 17 to 53 amino acids through standard molecular dynamics simulations using a recently developed polarizable force field-Effective Polarizable Bond (EPB) method. The backbone RMSDs, radius of gyrations, native contacts and native helix content are in good agreement with the experimental results. Cluster analysis has also verified that these folded structures with the highest population are in good agreement with their corresponding native structures for these proteins. In addition, the free energy landscape of seven proteins in the two dimensional space comprised of RMSD and radius of gyration proved that these folded structures are indeed of the lowest energy conformations. However, when the corresponding simulations were performed using the standard (nonpolarizable) AMBER force fields, no stable folded structures were observed for these proteins. Comparison of the simulation results based on a polarizable EPB force field and a nonpolarizable AMBER force field clearly demonstrates the importance of polarization in the folding of stable helical structures.

Original languageEnglish (US)
Pages (from-to)15273-15284
Number of pages12
JournalPhysical Chemistry Chemical Physics
Volume19
Issue number23
DOIs
StatePublished - 2017

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folding
field theory (physics)
proteins
gyration
Proteins
simulation
cluster analysis
radii
Cluster analysis
helices
Free energy
amino acids
Conformations
Molecular dynamics
free energy
Polarization
molecular dynamics
Amino Acids
Computer simulation
polarization

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

Cite this

Direct folding simulation of helical proteins using an effective polarizable bond force field. / Duan, Lili; Zhu, Tong; Ji, Changge; Zhang, Qinggang; Zhang, John.

In: Physical Chemistry Chemical Physics, Vol. 19, No. 23, 2017, p. 15273-15284.

Research output: Contribution to journalArticle

Duan, Lili ; Zhu, Tong ; Ji, Changge ; Zhang, Qinggang ; Zhang, John. / Direct folding simulation of helical proteins using an effective polarizable bond force field. In: Physical Chemistry Chemical Physics. 2017 ; Vol. 19, No. 23. pp. 15273-15284.
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