Brownian dynamics simulations of biomolecular diffusional association processes

IF 16.8 2区 化学 Q1 CHEMISTRY, MULTIDISCIPLINARY
Abraham Mu?iz-Chicharro, Lane W. Votapka, Rommie E. Amaro, Rebecca C. Wade
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引用次数: 1

Abstract

Brownian dynamics (BD) is a computational method to simulate molecular diffusion processes. Although the BD method has been developed over several decades and is well established, new methodological developments are improving its accuracy, widening its scope, and increasing its application. In biological applications, BD is used to investigate the diffusive behavior of molecules subject to forces due to intermolecular interactions or interactions with material surfaces. BD can be used to compute rate constants for diffusional association, generate structures of encounter complexes for molecular binding partners, and examine the transport properties of geometrically complex molecules. Often, a series of simulations is performed, for example, for different protein mutants or environmental conditions, so that the effects of the changes on diffusional properties can be estimated. While biomolecules are commonly described at atomic resolution and internal molecular motions are typically neglected, coarse-graining and the treatment of conformational flexibility are increasingly employed. Software packages for BD simulations of biomolecules are growing in capabilities, with several new packages providing novel features that expand the range of questions that can be addressed. These advances, when used in concert with experiment or other simulation methods, such as molecular dynamics, open new opportunities for application to biochemical and biological systems. Here, we review some of the latest developments in the theory, methods, software, and applications of BD simulations to study biomolecular diffusional association processes and provide a perspective on their future use and application to outstanding challenges in biology, bioengineering, and biomedicine.

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生物分子扩散结合过程的布朗动力学模拟
布朗动力学(BD)是一种模拟分子扩散过程的计算方法。虽然BD方法已经发展了几十年,并且已经建立良好,但新的方法发展正在提高其准确性,扩大其范围,并增加其应用。在生物学应用中,BD用于研究分子在分子间相互作用或与材料表面相互作用下的扩散行为。BD可用于计算扩散缔合的速率常数,生成分子结合伙伴的相遇配合物结构,以及检查几何复杂分子的输运性质。通常,对不同的蛋白质突变体或环境条件进行一系列模拟,以便可以估计这些变化对扩散特性的影响。虽然生物分子通常以原子分辨率描述,而内部分子运动通常被忽视,但粗粒化和构象柔韧性的处理越来越多地被采用。用于生物分子BD模拟的软件包的功能正在增长,有几个新软件包提供了新的功能,扩展了可以解决的问题的范围。这些进步,当与实验或其他模拟方法(如分子动力学)协同使用时,为生物化学和生物系统的应用开辟了新的机会。本文综述了生物分子扩散结合过程模拟在理论、方法、软件和应用方面的最新进展,并展望了生物分子扩散结合过程模拟在生物学、生物工程和生物医学领域的应用前景。本文分类如下:
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来源期刊
Wiley Interdisciplinary Reviews: Computational Molecular Science
Wiley Interdisciplinary Reviews: Computational Molecular Science CHEMISTRY, MULTIDISCIPLINARY-MATHEMATICAL & COMPUTATIONAL BIOLOGY
CiteScore
28.90
自引率
1.80%
发文量
52
审稿时长
6-12 weeks
期刊介绍: Computational molecular sciences harness the power of rigorous chemical and physical theories, employing computer-based modeling, specialized hardware, software development, algorithm design, and database management to explore and illuminate every facet of molecular sciences. These interdisciplinary approaches form a bridge between chemistry, biology, and materials sciences, establishing connections with adjacent application-driven fields in both chemistry and biology. WIREs Computational Molecular Science stands as a platform to comprehensively review and spotlight research from these dynamic and interconnected fields.
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