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冷却过程中蛋白质水合水中蛋白质-水和水-水长时间弛豫——通过密度相关函数的深入观察。

Protein-Water and Water-Water Long-Time Relaxations in Protein Hydration Water upon Cooling-A Close Look through Density Correlation Functions.

机构信息

Dipartimento di Matematica e Fisica, Università degli Studi Roma Tre, Via della Vasca Navale 84, 00146 Rome, Italy.

出版信息

Molecules. 2020 Oct 7;25(19):4570. doi: 10.3390/molecules25194570.

DOI:10.3390/molecules25194570
PMID:33036320
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7583983/
Abstract

We report results on the translational dynamics of the hydration water of the lysozyme protein upon cooling obtained by means of molecular dynamics simulations. The self van Hove functions and the mean square displacements of hydration water show two different temperature activated relaxation mechanisms, determining two dynamic regimes where transient trapping of the molecules is followed by hopping phenomena to allow to the structural relaxations. The two caging and hopping regimes are different in their nature. The low-temperature hopping regime has a time scale of tenths of nanoseconds and a length scale on the order of 2-3 water shells. This is connected to the nearest-neighbours cage effect and restricted to the supercooling, it is absent at high temperature and it is the mechanism to escape from the cage also present in bulk water. The second hopping regime is active at high temperatures, on the nanoseconds time scale and over distances of nanometers. This regime is connected to water displacements driven by the protein motion and it is observed very clearly at high temperatures and for temperatures higher than the protein dynamical transition. Below this temperature, the suppression of protein fluctuations largely increases the time-scale of the protein-related hopping phenomena at least over 100 ns. These protein-related hopping phenomena permit the detection of translational motions of hydration water molecules longly persistent in the hydration shell of the protein.

摘要

我们报告了通过分子动力学模拟获得的溶菌酶蛋白质水合作用的平移动力学的冷却结果。自范霍夫函数和水合水的均方位移显示出两种不同的温度激活弛豫机制,确定了两个动态区域,其中分子的瞬时捕获随后是跳跃现象以允许结构弛豫。两个笼和跳跃区域在性质上是不同的。低温跳跃区域具有十分之纳秒的时间尺度和 2-3 个水壳的量级的长度尺度。这与最近邻笼效应有关,并且限制在过冷范围内,在高温下不存在,并且是从笼中逃脱的机制,也存在于体相水中。第二个跳跃区域在高温下活跃,在纳秒时间尺度上,并跨越纳米距离。该区域与由蛋白质运动驱动的水位移有关,在高温下以及高于蛋白质动力学转变温度时非常明显。在该温度以下,蛋白质波动的抑制至少在 100ns 以上大大增加了与蛋白质相关的跳跃现象的时间尺度。这些与蛋白质相关的跳跃现象允许检测水合水分子的平移运动,这些运动在蛋白质的水合壳中长期持续存在。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4d83/7583983/7c39c66b848c/molecules-25-04570-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4d83/7583983/6c5aed7f3027/molecules-25-04570-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4d83/7583983/cdd57eb16f76/molecules-25-04570-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4d83/7583983/0359822cc21c/molecules-25-04570-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4d83/7583983/36e4bd247313/molecules-25-04570-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4d83/7583983/6487296a7aec/molecules-25-04570-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4d83/7583983/250544e221b7/molecules-25-04570-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4d83/7583983/0a8388663824/molecules-25-04570-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4d83/7583983/7c39c66b848c/molecules-25-04570-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4d83/7583983/6c5aed7f3027/molecules-25-04570-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4d83/7583983/cdd57eb16f76/molecules-25-04570-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4d83/7583983/0359822cc21c/molecules-25-04570-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4d83/7583983/36e4bd247313/molecules-25-04570-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4d83/7583983/6487296a7aec/molecules-25-04570-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4d83/7583983/250544e221b7/molecules-25-04570-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4d83/7583983/0a8388663824/molecules-25-04570-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4d83/7583983/7c39c66b848c/molecules-25-04570-g008.jpg

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