Probing polar solvation dynamics in proteins: A molecular dynamics simulation analysis
Probing polar solvation dynamics in proteins: A molecular dynamics simulation analysis
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DOI：
10.1021/jp065493u
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发表时间：
2007-02-15
影响因子：
3.3
通讯作者：
Karplus, Martin
中科院分区：
文献类型：
--
作者：
Golosov, Andrei A.;Karplus, Martin
在皮秒到纳秒的时间尺度上测量时间分辨斯托克斯位移已经被用来探测生物系统的极性溶剂化动力学。由于很难将测量结果分解为蛋白质和溶剂的贡献，计算机模拟有助于理解分子行为的细节。本文报道了蛋白质g的免疫球蛋白结合域B1的11个残基与溶剂的静电相互作用的模拟分析。结果表明，极性溶剂化动力学是位置依赖的和高度非均相的。测定了与蛋白质和溶剂相互作用的贡献。发现溶剂的贡献从几皮秒后可以忽略不计到数百皮秒时占主导地位不等。后者的起源被发现涉及耦合水合作用和蛋白质构象动力学。由此产生的微观图像表明，在解释时间分辨斯托克斯位移测量时，必须考虑广泛的可能性。
Measurements of time-resolved Stokes shifts on picosecond to nanosecond time scales have been used to probe the polar solvation dynamics of biological systems. Since it is difficult to decompose the measurements into protein and solvent contributions, computer simulations are useful to aid in understanding the details of the molecular behavior. Here we report the analysis of simulations of the electrostatic interactions of the rest of the protein and the solvent with 11 residues of the immunoglobulin binding domain B1 of protein G. It is shown that the polar solvation dynamics are position-dependent and highly heterogeneous. The contributions due to interactions with the protein and with the solvent are determined. The solvent contributions are found to vary from negligible after a few picoseconds to dominant on a scale of hundreds of picoseconds. The origin for the latter is found to involve coupled hydration and protein conformational dynamics. The resulting microscopic picture demonstrates that a wide range of possibilities have to be considered in the interpretation of time-resolved Stokes shift measurements.