摘要
简要阐述分子动力学模拟的原理及步骤,介绍研究溶菌酶的一般方法和优缺点。在Ubuntu操作系统环境下,利用Gromacs软件和其自带的Gromos96力场,通过分子动力学模拟(MD)鸡蛋清溶菌酶晶体(chicken egg-whitelysozyme,HEWL)溶液,考察真空、水溶液和加入NaCl 3种不同环境条件对溶菌酶晶体构象动力学行为的影响,发现无论从均方根位移(rmsd)、回旋半径、还是从B因子值的轨迹图分析,HEWL在水溶液特别是加入抗衡离子(Na^+,Cl^-)的水溶液的环境下的结构更稳定、合理,与(protein data bank)数据库的真实情况相符。原因是Cl^-与溶菌酶晶体在界面处发生了吸附现象,局部形成溶菌酶-Cl^-复合物,抑制了蛋白-水合物中水分子在相邻水合位置间的跳跃,从而使单晶体在离子液态中更加稳定。模拟结果表明,在pH值6.5,等电位点13.1,总电荷7.999 6的体系下,影响HEWL的吸附位点为123号残基(色氨酸),对从分子水平上解释HEWL晶体的动力学吸附行为具有重要指导意义。
In this paper, the concept of molecular dynamics simulation, the basic condition and the processes of the simulation were briefly introduced. The development research approach and the current status in Lysozyme protein were also introduced. This simulation used to research the solution of HEWL by gromos96 force field and MD in ubuntu system, especially the dynamic behavior and function of principal protein residues in vacuo, water and water with the counter ions were considered respectively. It showed that the molecular dynamics of HEWL in the water with the counter ions was closest to the experiment from the trajectory of rmsd, radius of gyrate, the B factor. The result was that chloride ions were combined with HEWL molecules, and restrain the ＂jump＂ between one hydration site and the other, so the structure was steady. The data of the MD result showed that the adsorption interact on 123 residue （tryptophan） of HEWL, and it was important for the further researching on adsorption dynamics.
出处
《计算机与应用化学》
CAS
CSCD
北大核心
2010年第2期173-178,共6页
Computers and Applied Chemistry
关键词
分子动力学模拟
动力学行为
计算机模拟
溶菌酶
环境条件
molecular dynamics simulation, dynamics behavior, computer simulation, lysozyme, condition of circumstance
