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

Abstract

We report 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 simulation 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 experimental results. Cluster analysis 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 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 polarizable EPB force field and nonpolariable AMBER force field clearly demonstrates the importance of polarization in the folding of stable helical structures.

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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, Accepted Manuscript
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    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, Accepted Manuscript , DOI: 10.1039/C7CP02101A

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