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分子模拟中拥挤环境的建模

Modeling Crowded Environment in Molecular Simulations.

作者信息

Ostrowska Natalia, Feig Michael, Trylska Joanna

机构信息

Centre of New Technologies, University of Warsaw, Warsaw, Poland.

College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Warsaw, Poland.

出版信息

Front Mol Biosci. 2019 Sep 11;6:86. doi: 10.3389/fmolb.2019.00086. eCollection 2019.

Abstract

Biomolecules perform their various functions in living cells, namely in an environment that is crowded by many macromolecules. Thus, simulating the dynamics and interactions of biomolecules should take into account not only water and ions but also other binding partners, metabolites, lipids and macromolecules found in cells. In the last decade, research on how to model macromolecular crowders around proteins in order to simulate their dynamics in models of cellular environments has gained a lot of attention. In this mini-review we focus on the models of crowding agents that have been used in computer modeling studies of proteins and peptides, especially via molecular dynamics simulations.

摘要

生物分子在活细胞中发挥其各种功能,也就是说,它们处于一个被许多大分子挤满的环境中。因此,模拟生物分子的动力学和相互作用不仅应考虑水和离子,还应考虑细胞中发现的其他结合伴侣、代谢物、脂质和大分子。在过去十年中,关于如何在蛋白质周围对大分子拥挤物进行建模以在细胞环境模型中模拟其动力学的研究受到了广泛关注。在本综述中,我们重点关注在蛋白质和肽的计算机建模研究中,特别是通过分子动力学模拟所使用的拥挤剂模型。

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