Abstract

The 10-nanosecond simulation of a lysozyme dimer, which is a fragment of the tetragonal lysozyme crystal structure, has been carried out by the molecular dynamics method at different simulation box sizes and precipitant concentrations in a solution. The dimer stability has been estimated by calculating the root-mean-square fluctuations of protein atoms. It is shown that the box size does not significantly affect the mobility of protein atoms on a relatively short trajectory, while the effect of the precipitant concentration on this trajectory is noticeable.

中文翻译：

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模拟盒大小和沉淀剂浓度对四方溶菌酶二聚体行为的影响

摘要

溶菌酶二聚体的10纳秒模拟是四方溶菌酶晶体结构的一部分，已通过分子动力学方法在不同的模拟盒尺寸和溶液中的沉淀剂浓度下进行了模拟。通过计算蛋白质原子的均方根波动来估算二聚体稳定性。结果表明，盒子的尺寸在相对较短的轨迹上不会显着影响蛋白质原子的迁移率，而沉淀剂浓度对该轨迹的影响却很明显。