Solvent diffusion outside macromolecular surfaces
Solvent diffusion outside macromolecular surfaces
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DOI：
10.1103/physreve.57.791
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发表时间：
1998-01-01
影响因子：
2.4
通讯作者：
Edholm, O
中科院分区：
文献类型：
--
作者：
Lindahl, E;Edholm, O
从分子动力学模拟的蛋白质，肌红蛋白，在水溶液中的溶剂分子接近大分子表面的非均匀环境的效果进行评估。模拟分析的平均场电位从蛋白质的水分子和空间变化的平移扩散系数的溶剂分子在平行和垂直于蛋白质表面的方向。扩散系数可以从平均平方位移与时间的斜率以及从速度自相关函数的积分中获得。结果表明，由于曲线斜率随时间的变化，前一种方法产生了许多模糊性。后者，然而，经过分析校正的贡献，从代数长时间尾巴，提供了一个更可靠的替代。
The effect of the inhomogeneous environment upon solvent molecules close to a macromolecular surface is evaluated from a molecular-dynamics simulation of a protein, myoglobin, in water solution. The simulation is analyzed in terms of a mean-field potential from the protein upon the water molecules and spatially varying translational diffusion coefficients for solvent molecules in directions parallel and perpendicular to the protein surface. The diffusion coefficients can be obtained from the slope of the average-square displacements vs time, as well as from the integral of the velocity autocorrelation functions. It is shown that the former procedure gives a lot of ambiguities due to the variation of the slope of the curve with time. The latter, however, after analytic correction for the contribution from algebraic long-time tails, furnish a much more reliable alternative.