NUMERICAL-CALCULATIONS OF ELECTROSTATIC POTENTIALS OF PROTEIN-SOLVENT SYSTEMS BY THE SELF-CONSISTENT BOUNDARY METHOD
NUMERICAL-CALCULATIONS OF ELECTROSTATIC POTENTIALS OF PROTEIN-SOLVENT SYSTEMS BY THE SELF-CONSISTENT BOUNDARY METHOD
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DOI：
10.1143/jpsj.56.1609
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发表时间：
1987-04-01
影响因子：
1.7
通讯作者：
NISHIDA, S
中科院分区：
文献类型：
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作者：
NAKAMURA, H;NISHIDA, S
用超级计算机对蛋白质-溶剂体系的宏观介电模型进行了数值计算。包含目标蛋白质分子的整个空间首先被分成许多立方体，其中一些在蛋白质内部，另一些则嵌入溶剂中。然后分别在蛋白质内部和外部数值求解泊松方程和泊松-玻尔兹曼方程。有限差分法在远离蛋白质的人工边界处，既不设势为零，也不设场为零，而是根据事先计算的场和边界内的势自一致地计算出来的。对于一些简单的模型情况，该方法与解析计算结果吻合较好。对实际的蛋白质-溶剂体系的结果与实验结果进行了定量讨论。
A macroscopic dielectric model for a protein-solvent system has been solved by a numerical calculation using a supercomputer. The whole space including a target protein molecule was first divided into lots of cubes, some of which were inside the protein and the others were embedded in the solvent. Poisson equation and Poisson-Boltzmann equation were then numerically solved inside and outside of the protein, respectively. At the artificial boundary far from the protein for the finite difference procedure, neither the potential nor the field was set to be zero, but they were calculated self-consistently from the field and the potential inside the boundary calculated beforehand. The results by this method agreed well with those by the analytical calculations for some simple model cases. The results of actual protein-solvent systems were quantitatively discussed comparing with the experiments.