Jump to main content
Jump to site search

Issue 23, 2017
Previous Article Next Article

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

Author affiliations

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.

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

Back to tab navigation

Supplementary files

Publication details

The article was received on 31 Mar 2017, accepted on 16 May 2017 and first published on 16 May 2017


Article type: Paper
DOI: 10.1039/C7CP02101A
Citation: Phys. Chem. Chem. Phys., 2017,19, 15273-15284
  •   Request permissions

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

    L. Duan, T. Zhu, C. Ji, Q. Zhang and J. Z. H. Zhang, Phys. Chem. Chem. Phys., 2017, 19, 15273
    DOI: 10.1039/C7CP02101A

Search articles by author

Spotlight

Advertisements