自组装小肽RADA16-1的构象研究

A numerical study of the conformation of self-assembling peptide RADA16-1

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.

It is a challenge to study the stable conformation of RADA16-1, an important self-assembling peptide. Here, we utilized classical molecular dynamics （MD） and temperature replica exchange molecular dynamics （REMD） simulation methods to investigate its stable conformation and compare the results of these two theoretical approaches. The stable conformation of RADA16-1 peptide was explored at the physiological temperature around 310 K with CHARMM force field. The REMD simulation ran for 26 ns, and the MD simulation completed three independent runs which were 160 ns respectively for the water-soluble RADA16-1 peptide. Then we compared the differences in energy, the number of hydrogen bonds, radius of gyration （RGYR） and solvent accessible surface area （SASA） of RADA16-1 peptide from MD and REMD calculations. From the comparison, we found the REMD calculation could search and achieve the relatively stable conformation information with less amount of computation cost than the MD calculation. Additionally, by the analysis of energy, hydrogen bonds, RGYR and SASA, the stable spatial conformation of RADA16-1 peptide could be determined under the combined effects from the hydrophobic and hydrogen bond interactions.