MARTINI 粗粒度力场在模拟结晶溶液中蛋白质低聚物中的适用性

IF 0.6 4区材料科学 Q4 CRYSTALLOGRAPHY Crystallography Reports Pub Date : 2024-11-14 DOI:10.1134/S1063774524601588

Yu. V. Kordonskaya, V. I. Timofeev, M. A. Marchenkova, Yu. V. Pisarevsky, Yu. A. Dyakova, M. V. Kovalchuk

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引用次数: 0

摘要

利用 MARTINI 粗粒度力场模拟了两种溶菌酶八聚体在结晶条件下的分子动力学。对所得结果和用 Amber99sb-ildn 全原子力场模拟相同八聚体的模拟数据进行比较分析后发现，在两种力场中，八聚体 A 比八聚体 B 更稳定。因此，使用两种力场对八聚体进行分子动力学模拟的结果是一致的。尽管蛋白质在不同力场中的行为存在一些差异，但这些差异并不影响使用 MARTINI 所获得数据的有效性。这证实了 MARTINI 力场适用于研究蛋白质的结晶溶液。

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Applicability of the MARTINI Coarse-Grained Force Field for Simulations of Protein Oligomers in Crystallization Solution

The molecular dynamics of two types of lysozyme octamers was simulated under crystallization conditions with the MARTINI coarse-grained force field. A comparative analysis of the obtained results and the simulation data for the same octamers modelled with the Amber99sb-ildn all-atom force field showed that octamer A is more stable compared to octamer B in both force fields. Therefore, the results of molecular dynamics simulations of octamers using both force fields are consistent with each other. Despite some differences in the behavior of the protein in different force fields, they do not affect the validity of the data obtained using MARTINI. This confirms the applicability of the MARTINI force field for studying crystallization solutions of proteins.

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来源期刊

Crystallography Reports 化学-晶体学

CiteScore

1.10

自引率

28.60%

发文量

审稿时长

4-8 weeks

期刊介绍： Crystallography Reports is a journal that publishes original articles short communications, and reviews on various aspects of crystallography: diffraction and scattering of X-rays, electrons, and neutrons, determination of crystal structure of inorganic and organic substances, including proteins and other biological substances; UV-VIS and IR spectroscopy; growth, imperfect structure and physical properties of crystals; thin films, liquid crystals, nanomaterials, partially disordered systems, and the methods of studies.