论文部分内容阅读
研究自组装小肽RADA16-1的稳定构象具有一定挑战性,为了解决这个问题,分别利用经典分子动力学(MD)模拟方法和温度副本交换分子动力学(REMD)模拟方法进行对比研究.采用CHARMM力场参数,研究小肽RADA16-1在生理温度310 K左右的稳定构象.其中利用REMD完成26 ns时长水溶性小肽RADA16-1的模拟,利用MD完成3次160 ns时长小肽的模拟.之后,对比分析了RADA16-1小肽能量、氢键、回转半径(RGYR)和溶剂可及表面积(SASA)的变化特征.通过模拟结果的对比,发现REMD计算较MD计算能够使用更少的计算量搜索到相对明确的稳定构象信息,从而通过对能量、氢键、RGYR和SASA的结果分析,确定疏水作用和氢键相互作用共同稳定小肽的空间构象.
To study the stable conformation of self-assembling small peptide RADA16-1, we use classical molecular dynamics (MD) simulation method and temperature replica exchange molecular dynamics (REMD) simulation method to compare with each other.Using CHARMM Force field parameters to study the stable conformation of the small peptide RADA16-1 at a physiological temperature of about 310 K. The simulation of RADA16-1, a water-soluble small peptide with a length of 26 ns, was completed by REMD. Afterwards, the characteristics of energy, hydrogen bond, radius of gyration (RGYR) and solvent accessible surface area (SASA) of RADA16-1 were comparatively analyzed.Comparison of simulation results showed that REMD calculation could use less calculation than MD calculation Quantitative search of relatively stable and stable conformation information, through the energy, hydrogen bonds, RGYR and SASA results to determine the hydrophobic interaction and hydrogen bonding interactions together to stabilize the spatial conformation of small peptides.