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NMR 弛豫参数中包含多少熵?

How Much Entropy Is Contained in NMR Relaxation Parameters?

机构信息

Center for Theoretical Chemistry, Ruhr University Bochum, D-44 780 Bochum, Germany.

Interdisciplinary Nanoscience Center and Department of Chemistry, University of Aarhus, DK-8000 Aarhus, Denmark.

出版信息

J Phys Chem B. 2022 Jan 13;126(1):54-68. doi: 10.1021/acs.jpcb.1c07786. Epub 2021 Dec 22.

Abstract

Solution-state NMR relaxation experiments are the cornerstone to study internal protein dynamics at an atomic resolution on time scales that are faster than the overall rotational tumbling time τ. Since the motions described by NMR relaxation parameters are connected to thermodynamic quantities like conformational entropies, the question arises how much of the total entropy is contained within this tumbling time. Using all-atom molecular dynamics simulations of the T4 lysozyme, we found that entropy buildup is rather fast for the backbone, such that the majority of the entropy is indeed contained in the short-time dynamics. In contrast, the contribution of the slow dynamics of side chains on time scales beyond τ on the side-chain conformational entropy is significant and should be taken into account for the extraction of accurate thermodynamic properties.

摘要

溶液态 NMR 弛豫实验是在快于整体旋转翻滚时间 τ 的时间尺度上以原子分辨率研究蛋白质内部动力学的基础。由于 NMR 弛豫参数所描述的运动与构象熵等热力学量有关,因此出现了一个问题,即在这个翻滚时间内包含多少总熵。通过对 T4 溶菌酶的全原子分子动力学模拟,我们发现骨架的熵积累相当快,以至于大部分熵确实包含在短时间动力学中。相比之下,在 τ 以外的时间尺度上,侧链的慢动力学对侧链构象熵的贡献是显著的,在提取准确的热力学性质时应将其考虑在内。

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