Int. J. Mol. Sci. 2012, 13(11), 14451-14469; doi:10.3390/ijms131114451
Article

A Generic Force Field for Protein Coarse-Grained Molecular Dynamics Simulation

1 State Key Laboratory of Structural Analysis for Industrial Equipment, Department of Engineering Mechanics, Dalian University of Technology, Dalian 116023, China 2 Faculty of Chemical, Environmental and Biological Science and Technology, Dalian University of Technology, Dalian 116023, China 3 School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
* Author to whom correspondence should be addressed.
Received: 3 September 2012; in revised form: 26 October 2012 / Accepted: 26 October 2012 / Published: 8 November 2012
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
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Abstract: Coarse-grained (CG) force fields have become promising tools for studies of protein behavior, but the balance of speed and accuracy is still a challenge in the research of protein coarse graining methodology. In this work, 20 CG beads have been designed based on the structures of amino acid residues, with which an amino acid can be represented by one or two beads, and a CG solvent model with five water molecules was adopted to ensure the consistence with the protein CG beads. The internal interactions in protein were classified according to the types of the interacting CG beads, and adequate potential functions were chosen and systematically parameterized to fit the energy distributions. The proposed CG force field has been tested on eight proteins, and each protein was simulated for 1000 ns. Even without any extra structure knowledge of the simulated proteins, the Cα root mean square deviations (RMSDs) with respect to their experimental structures are close to those of relatively short time all atom molecular dynamics simulations. However, our coarse grained force field will require further refinement to improve agreement with and persistence of native-like structures. In addition, the root mean square fluctuations (RMSFs) relative to the average structures derived from the simulations show that the conformational fluctuations of the proteins can be sampled.
Keywords: coarse-grained; force field; molecular dynamics; protein

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MDPI and ACS Style

Gu, J.; Bai, F.; Li, H.; Wang, X. A Generic Force Field for Protein Coarse-Grained Molecular Dynamics Simulation. Int. J. Mol. Sci. 2012, 13, 14451-14469.

AMA Style

Gu J, Bai F, Li H, Wang X. A Generic Force Field for Protein Coarse-Grained Molecular Dynamics Simulation. International Journal of Molecular Sciences. 2012; 13(11):14451-14469.

Chicago/Turabian Style

Gu, Junfeng; Bai, Fang; Li, Honglin; Wang, Xicheng. 2012. "A Generic Force Field for Protein Coarse-Grained Molecular Dynamics Simulation." Int. J. Mol. Sci. 13, no. 11: 14451-14469.

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