国家自然科学基金(30970561)和山东省自然科学基金(2009ZRA14027, 2009ZRA14028)资助项目
This work was supported by grants from The National Natural Science Foundation of China (30970561) and Shandong Natural Science Foundation (2009ZRA14027, 2009ZRA14028)
采用GROMOS 43A1力场,用温度副本交换分子动力学模拟方法研究水溶液中H1小肽在4个不同温度下的结构特征.选择H1小肽的初始构象分别为α螺旋和β折叠片,完成了两组独立的36个温度副本交换的分子动力学模拟,一组从α螺旋出发的模拟用来对该小肽的结构特征进行研究,另一组从β折叠片出发的模拟用于验证构象采样的收敛性,每个副本的模拟时间为300 ns,共计模拟时间长达21.6 ?滋s.在此基础上,研究了H1小肽在温度300K、330K、350K和370K下的结构特征,分析了其主链二面角分布、天然氢键数、β转角的形成概率以及不同温度下偏好采样构象的变化特征等.模拟结果表明,在4个不同温度下,均能够采样到同β折叠片结构的C?琢原子均方根偏差最小为0.05 nm的构象类,该构象类在4个不同温度300K、330K、350K和370K下分别包含了全部构象的39%、23%、13%和11%.GROMOS 43A1力场在刻画小肽的结构方面具有一定的精度,但是在描述氢键方面仍需要加强,H1小肽在不同温度下结构特征的比较能够为分子力场的优化提供重要的帮助.
The dynamics character of H1 peptide in aqueous solution at different temperatures has been investigated through temperature replica exchange molecular dynamics (T-REMD) simulations with GROMOS 43A1 force field. The two independent T-REMD simulations were completed from initial conformations α-helix and β-sheet structures, respectively. Each replica was run for 300 ns. 36 replicas have been simulated and the total MD simulation time of all replicas was 21.6 ?滋s, the convergence of conformation sampling was verified by simulations starting from β-sheet structure. The structural character of H1 peptide at each temperature (300K, 330K, 350K and 370K) was assessed from the parameters such as the distributions of backbone dihedral angles, the number of native hydrogen bond, formation of β-turn and the favorite conformation at different temperatures. The simulations sampled conformation cluster close to β-sheet structure as demonstrate by the 0.05 nm Cα RMSD, and this cluster contains 39%, 23%, 13% and 11% conformations in total at 300K, 330K, 350K and 370K respectively. The results indicate that: GROMOS 43A1 force field has precision of the description of the conformational equilibriums, however, efforts have been made to refine the treatments of hydrogen bond, and the comparative study of H1 peptide at different temperatures can afford information for refine molecular force field.
曹赞霞,王吉华.基于温度副本交换分子动力学模拟方法研究温度致H1小肽结构变化特征[J].生物化学与生物物理进展,2010,37(3):319-325
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