THE EFFECTS OF SOLVENT ON THE CONFORMATION AND THE COLLECTIVE MOTIONS OF PROTEIN - NORMAL MODE ANALYSIS AND MOLECULAR-DYNAMICS SIMULATIONS OF MELITTIN IN WATER AND IN VACUUM
THE EFFECTS OF SOLVENT ON THE CONFORMATION AND THE COLLECTIVE MOTIONS OF PROTEIN - NORMAL MODE ANALYSIS AND MOLECULAR-DYNAMICS SIMULATIONS OF MELITTIN IN WATER AND IN VACUUM
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DOI：
10.1016/0301-0104(91)87082-7
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发表时间：
1991-12-15
期刊：
影响因子：
2.3
通讯作者：
GO, N
中科院分区：
文献类型：
--
作者：
KITAO, A;HIRATA, F;GO, N
通过计算机模拟研究了溶剂对蛋白质构象和动力学的影响。动力学的研究主要集中在蛋白质分子的集体运动。对蜂毒的主要成分蜂毒素进行了三种类型的模拟：正态分析、真空分子动力学和水中分子动力学。为了确定集体运动主，进行了分量分析和正态模态分析。波动幅度较大的主分量与低频正态模态有很好的对应关系。分子动力学模拟的轨迹被投影到主轴上。从投影运动中计算出时间相关函数。结果表明，频率小于几乎等于50 cm-1的极低频模态在水中出现过阻尼，其松弛时间约为振荡运动周期的两倍。利用由水中分子动力学轨迹计算得到的速度相关函数确定的摩擦系数矩阵，进行了有效的朗之万模式分析。该分析较好地再现了水中的模拟结果。发现溶剂水的存在也会影响势能表面的形状，使其产生许多局部极小值，中间有低能势垒，其包线由真空中的表面给出。最小值间的跃迁使水中蛋白质的构象动力学具有另一种扩散特性，这种特性已经存在于最小值内的集体运动中。
The effects of solvent on the conformation and dynamics of protein is studied by computer simulation. The dynamics is studied by focusing mainly on collective motions of the protein molecule. Three types of simulation, normal mode analysis, molecular dynamics in vacuum, and molecular dynamics in water are applied to melittin, the major component of bee venom. To define collective motions principal, component analysis as well as normal mode analysis has been carried out. The principal components with large fluctuation amplitudes have a very good correspondence with the low-frequency normal modes. Trajectories of the molecular dynamics simulation are projected onto the principal axes. From the projected motions time correlation functions are calculated. The results indicate that the very-low-frequency modes, whose frequencies are less than almost-equal-to 50 cm-1, are overdamping in water with relaxation times roughly twice as long as the period of the oscillatory motion. Effective Langevin mode analysis is carried out by using the friction coefficient matrix determined from the velocity correlation function calculated from the molecular dynamics trajectory in water. This analysis reproduces the results of the simulation in water reasonably well. The presence of the solvent water is found also to affect the shape of the potential energy surface in such a way that it produces many local minima with low-energy barriers in between, the envelope of which is given by the surface in vacuum. Inter-minimum transitions endow the conformational dynamics of proteins in water another diffusive character, which already exists in the intra-minimum collective motions.