Influence of Simulation Box Sizes on the Stability of Lysozyme Dimers and Hexamers in a Crystallization Solution

IF 0.8 Q3 Engineering

Nanotechnologies in Russia Pub Date : 2024-09-10 DOI:10.1134/S2635167624600767

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

引用次数: 0

Abstract

The effect of the simulation box size on the stability of lysozyme dimers and hexamers formed in its solution before crystallization is studied by molecular dynamics. The behavior of these oligomers in boxes of different sizes is simulated, and their stability is assessed. It is shown that increasing the simulation box does not lead to refinement of the simulation results. The dimer stability weakly depends on the box sizes, while hexamers dissociated in all boxes considered, which is consistent with small-angle scattering data. The minimum distance between the protein and the box edge, at which the results of modeling oligomer behavior in crystallization solutions are reliable, is determined (1 nm).

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模拟盒尺寸对溶菌酶二聚体和六聚体在结晶溶液中稳定性的影响

摘要通过分子动力学研究了模拟盒大小对溶菌酶结晶前在其溶液中形成的二聚体和六聚体稳定性的影响。模拟了这些低聚物在不同大小模拟盒中的行为，并评估了它们的稳定性。结果表明，增大模拟盒并不会导致模拟结果的细化。二聚体的稳定性微弱地依赖于盒子的大小，而六聚体在所有考虑的盒子中都会解离，这与小角散射数据一致。确定了蛋白质与方框边缘之间的最小距离（1 nm），在该距离上，结晶溶液中的低聚物行为建模结果是可靠的。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Nanotechnologies in Russia NANOSCIENCE & NANOTECHNOLOGY-

CiteScore

1.20

自引率

0.00%

发文量

期刊介绍： Nanobiotechnology Reports publishes interdisciplinary research articles on fundamental aspects of the structure and properties of nanoscale objects and nanomaterials, polymeric and bioorganic molecules, and supramolecular and biohybrid complexes, as well as articles that discuss technologies for their preparation and processing, and practical implementation of products, devices, and nature-like systems based on them. The journal publishes original articles and reviews that meet the highest scientific quality standards in the following areas of science and technology studies: self-organizing structures and nanoassemblies; nanostructures, including nanotubes; functional and structural nanomaterials; polymeric, bioorganic, and hybrid nanomaterials; devices and products based on nanomaterials and nanotechnology; nanobiology and genetics, and omics technologies; nanobiomedicine and nanopharmaceutics; nanoelectronics and neuromorphic computing systems; neurocognitive systems and technologies; nanophotonics; natural science methods in a study of cultural heritage items; metrology, standardization, and monitoring in nanotechnology.