Brownian dynamics simulation of electrostatically interacting proteins
Brownian dynamics simulation of electrostatically interacting proteins
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DOI：
10.1080/00268970210139868
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发表时间：
2002-09-01
影响因子：
1.7
通讯作者：
Fedotov, VD
中科院分区：
文献类型：
--
作者：
Ermakova, E;Krushelnitsky, AG;Fedotov, VD
布朗动力学模拟软件已经被开发用于研究蛋白质作为一个整体在溶液中的动力学。蛋白质被建模为球体，其中点偶极子嵌入球体中心。一组布朗动力学模拟在不同的值的偶极矩，蛋白质浓度和平移扩散系数进行研究蛋白质间的静电相互作用的动态蛋白质在溶液中的行为的影响。结果表明，这些相互作用导致蛋白质旋转减慢和复杂的非指数形状的旋转相关函数。相关函数的分析是在先前提出的基于NMR和介电谱数据的静电蛋白质间相互作用模型的框架内进行的。该模型假设，由于静电相互作用，蛋白质布朗旋转成为各向异性。这种各向异性的寿命主要由蛋白质的平移扩散控制。因此，相关函数可以分解为与周围蛋白质产生的外部电场矢量的各向异性布朗旋转和各向同性运动相对应的两个分量。
Brownian dynamics simulation software has been developed to study the dynamics of proteins as a whole in solution. The proteins were modelled as spheres with point dipoles embedded in the centre of sphere. A set of Brownian dynamics simulations at different values of the dipole moments, protein concentration and translational diffusion coefficient was performed to investigate the influence of interprotein electrostatic interactions on dynamic protein behaviour in solution. It was shown that these interactions led to the slowing down of protein rotation and a complex non-exponential shape of the rotational correlation function. Analysis of the correlation functions was performed within the frame of the model of electrostatic interprotein interactions advanced earlier on the basis of NMR and dielectric spectroscopy data. This model assumes that, due to electrostatic interactions, protein Brownian rotation becomes anisotropic. The lifetime of this anisotropy is controlled mainly by translational diffusion of proteins. Thus, the correlation function can be decomposed into two components corresponding to anisotropic Brownian rotation and an isotropic motion of an external electric field vector produced by the surrounding proteins.