中国物理B ›› 2015, Vol. 24 ›› Issue (11): 116802-116802.doi: 10.1088/1674-1056/24/11/116802
• CONDENSED MATTER: STRUCTURAL, MECHANICAL, AND THERMAL PROPERTIES • 上一篇 下一篇
姜舟婷a, 窦文辉a, 沈瑜b, 孙婷婷c, 徐鹏a
Jiang Zhou-Ting (姜舟婷)a, Dou Wen-Hui (窦文辉)a, Shen Yu (沈瑜)b, Sun Ting-Ting (孙婷婷)c, Xu Peng (徐鹏)a
摘要: 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.
中图分类号: (Polymers, organics)