Folding helical proteins in explicit solvent using dihedral-biased tempering.

Proceedings of the National Academy of Sciences of the United States of America
Cheng Zhang, Jianpeng Ma

Abstract

Using a single-trajectory-based tempering method with a high-temperature dihedral bias, we repeatedly folded four helical proteins [α(3)D (PDB ID: 2A3D, 73 residues), α(3)W (1LQ7, 67 residues), Fap1-NR(α) (2KUB, 81 residues) and S-836 (2JUA, 102 residues)] and some of the mutants in explicit solvent within several microseconds. The lowest root-mean-square deviations of backbone atoms from the experimentally determined structures were 1.9, 1.4, 1.0, and 2.1 Å, respectively. Cluster analyses of folding trajectories showed the native conformation usually occupied the most populated cluster. The simulation protocol can be applied to large-scale simulations of other helical proteins on commonly accessible computing platforms.

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Citations

Feb 7, 2013·Journal of Biomolecular Structure & Dynamics·B Montgomery Pettitt
Aug 3, 2014·The Journal of Chemical Physics·Tianwu ZangJianpeng Ma
Feb 22, 2013·Proteins·Abhijeet Kapoor, Alex Travesset
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Feb 3, 2018·The Journal of Chemical Physics·Wenhui Xi, Ulrich H E Hansmann
Aug 24, 2018·The Journal of Chemical Physics·Tianwu ZangJianpeng Ma
Feb 19, 2015·The Journal of Physical Chemistry. B·Qiang Shao
Nov 10, 2017·Journal of Chemical Theory and Computation·Qiang Shao, Weiliang Zhu
Aug 25, 2018·The Journal of Physical Chemistry. B·Yong WangKresten Lindorff-Larsen

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