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

被引：0

作者：

Kordonskaya, Yu. V. ^{[1
]}

Timofeev, V. I. ^{[1
,2
]}

Marchenkova, M. A. ^{[1
,2
]}

Pisarevsky, Yu. V. ^{[2
]}

Dyakova, Yu. A. ^{[1
]}

Kovalchuk, M. V. ^{[1
,2
]}

机构：

[1] Natl Res Ctr Kurchatov Inst, Moscow 123098, Russia

[2] Natl Res Ctr Kurchatov Inst, Shubnikov Inst Crystallog Kurchatov Complex Crysta, Moscow 119333, Russia

来源：

CRYSTALLOGRAPHY REPORTS | 2024年 / 69卷 / 05期

关键词：

MOLECULAR-DYNAMICS; PRECURSOR CLUSTER; CRYSTAL; STAGE; IDENTIFICATION; BEHAVIOR;

D O I：

10.1134/S1063774524601588

中图分类号：

O7 [晶体学];

学科分类号：

0702 ; 070205 ; 0703 ; 080501 ;

摘要：

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.

引用

页码：750 / 755

页数：6

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