Residual occurrence and energy property of proteins in HNP model

doi:10.1088/1674-1056/24/11/116802

Abstract Four categories of globular proteins, including all-α, all-β, α +β, and α/β types, are simplified as the off-lattice HNP model involving the secondary-structural information of each protein. The propensity of three types of residues, i.e., H, N, and P to form a secondary structure is investigated based on 146 protein samples. We find that P residues are easy to form α -helices, whereas H residues have a higher tendency to construct β-sheets. The statistical analysis also indicates that the occurrence of P residues is invariably higher than that of H residues, which is independent of protein category. Changes in bond-and non-bonded potential energies of all protein samples under a wide temperature range are presented by coarse-grained molecular dynamics (MD) simulation. The simulation results clearly show a linear relationship between the bond-stretching/bending potential energy and the reduced temperature. The bond-torsional and non-bonded potential energies show distinct transitions with temperature. The bond-torsional energy increases to the maximum and then decreases with the increase of temperature, which is opposite to the change in non-bonded potential energy. The transition temperature of non-bonded potential energy is independent of the protein category, while that of bond-torsional energy is closely related to the protein secondary structure, i.e., α -helix or β-sheet. The quantitatively bonded-and semi-quantitatively non-bonded potential energy of 24 α +β and 23 α/β protein samples are successfully predicted according to the statistical results obtained from MD simulations.

Keywords: HNP model molecular dynamics simulation residue hydrophobicity

Received: 04 May 2015
Revised: 03 July 2015
Accepted manuscript online:

PACS:

68.35.bm

(Polymers, organics)

Fund: Project supported by the National Natural Science Foundation of China (Grant Nos. 21204078, 11304282, and 11202201) and the Natural Science Foundation of Zhejiang Province, China (Grant No. LY12B04003).

Corresponding Authors: Jiang Zhou-Ting
E-mail: z.jiang@cjlu.edu.cn

Cite this article:

Jiang Zhou-Ting (姜舟婷), Dou Wen-Hui (窦文辉), Shen Yu (沈瑜), Sun Ting-Ting (孙婷婷), Xu Peng (徐鹏) Residual occurrence and energy property of proteins in HNP model 2015 Chin. Phys. B 24 116802

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