蛋白质静电的耗散电弹性网络模型
Dissipative electro-elastic network model of protein electrostatics
摘要：
本文提出了一个耗散电弹性网络模型（DENM）来描述蛋白质活性位点静电涨落的动力学和统计特性。该模型结合了谐波网络的残留珠与过阻尼动力学的正常模式的网络特征在于由两个摩擦系数。通过蛋白质力场的原子电荷将静电分量引入模型。网络的静电波动的整体效果是通过在活性位点的静电势和电场的频率依赖性响应函数记录的。我们还考虑了网络中单个残基的位移动态和残基对之间的距离动态。该模型进行了测试对损失谱的残留位移和静电势和电场在血红素的铁从全原子分子动力学模拟三水合球状蛋白。
英文摘要：
We propose a dissipative electro-elastic network model (DENM) to describe the dynamics and statistics of electrostatic fluctuations at active sites of proteins. The model combines the harmonic network of residue beads with overdamped dynamics of the normal modes of the network characterized by two friction coefficients. The electrostatic component is introduced to the model through atomic charges of the protein force field. The overall effect of the electrostatic fluctuations of the network is recorded through the frequency-dependent response functions of the electrostatic potential and electric field at the active site. We also consider the dynamics of displacements of individual residues in the network and the dynamics of distances between pairs of residues. The model is tested against loss spectra of residue displacements and the electrostatic potential and electric field at the heme's iron from all-atom molecular dynamics simulations of three hydrated globular proteins.
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