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比较不同的重新加权方法在计算分子模拟中大分子构象变化的应用。

Comparison of Different Reweighting Approaches for the Calculation of Conformational Variability of Macromolecules from Molecular Simulations.

机构信息

Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.

Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy.

出版信息

Chemphyschem. 2021 Jan 7;22(1):127-138. doi: 10.1002/cphc.202000714. Epub 2020 Nov 27.

Abstract

Conformational variability and heterogeneity are crucial determinants of the function of biological macromolecules. The possibility of accessing this information experimentally suffers from severe under-determination of the problem, since there are a few experimental observables to be accounted for by a (potentially) infinite number of available conformational states. Several computational methods have been proposed over the years in order to circumvent this theoretically insurmountable obstacle. A large share of these strategies is based on reweighting an initial conformational ensemble which arises from, for example, molecular simulations of different qualities and levels of theory. In this work, we compare the outcome of three reweighting approaches based on radically different views of the conformational heterogeneity problem, namely Maximum Entropy, Maximum Parsimony and Maximum Occurrence, and we do so using the same experimental data. In this comparison we find both expected as well as unexpected similarities.

摘要

构象可变性和异质性是生物大分子功能的关键决定因素。然而,从实验上获取这些信息受到严重的欠定问题的限制,因为可用构象状态的数量(可能)是无限的,而只有少数实验可观测值需要被考虑到。多年来,已经提出了几种计算方法来规避这个理论上无法克服的障碍。这些策略中有很大一部分是基于对初始构象集合进行再加权,该集合是例如不同质量和理论水平的分子模拟的结果。在这项工作中,我们比较了三种基于构象异质性问题的不同观点的再加权方法的结果,即最大熵、最大简约和最大出现,并且我们使用相同的实验数据进行了比较。在这个比较中,我们发现了既预期又意外的相似之处。

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