Disaccharide topology induces slowdown in local water dynamics.
Disaccharide topology induces slowdown in local water dynamics.
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二糖拓扑结构导致局部水动力学减慢。
DOI：
10.1021/jp112178c
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发表时间：
2011
期刊：
影响因子：
--
通讯作者：
R. Campen
中科院分区：
文献类型：
--
作者：
A. Vila Verde;R. Campen
在分子水平上深入了解蛋白质、脂质和核酸附近的水结构和结构动力学对于定量理解许多生物物理过程至关重要。不幸的是，理解这样的大分子周围的水合作用和水合动力学是具有挑战性的，因为需要去卷积的地形和化学异质性的影响。在这里，我们研究，通过经典的全原子模拟，水的结构和结构动力学周围的两个生物相关的溶质大到足以有显着的化学和拓扑异构性，但小到足以计算上容易处理：二糖曲二糖和海藻糖。我们发现这两种分子是强烈的两亲性（从归一化的局部密度波动量化），并诱导水的平移和旋转运动的不均匀的局部减速。详细的旋转减速的分析表明，虽然旋转机制是类似的Laage，Hynes和同事先前确定的其他水溶液系统中，观察到两个新的特点：扩大的过渡态在氢键交换（水旋转）和一个亚群的水，其中旋转是缓慢的，因为阻碍了新的接受水分子进入过渡态。这两个特点预计是通用功能的水旋转周围较大的生物分子，并一起考虑，强调在转移洞察水旋转周围的小分子大得多的两亲性溶质的困难。
Molecular level insight into water structure and structural dynamics near proteins, lipids, and nucleic acids is critical to the quantitative understanding of many biophysical processes. Unfortunately, understanding hydration and hydration dynamics around such large molecules is challenging because of the necessity of deconvoluting the effects of topography and chemical heterogeneity. Here we study, via classical all-atom simulation, the water structure and structural dynamics around two biologically relevant solutes large enough to have significant chemical and topological heterogeneity but small enough to be computationally tractable: the disaccharides kojibiose and trehalose. We find both molecules to be strongly amphiphilic (as quantified from normalized local density fluctuations) and to induce nonuniform local slowdown in water translational and rotational motions. Detailed analysis of the rotational slowdown shows that, while the rotational mechanism is similar to that previously identified in other aqueous systems by Laage, Hynes, and coworkers, two novel characteristics are observed: broadening of the transition state during hydrogen bond exchange (water rotation) and a subpopulation of water for which rotation is slowed because of hindered access of the new accepting water molecule to the transition state. Both characteristics are expected to be generic features of water rotation around larger biomolecules and, taken together, emphasize the difficulty in transferring insight into water rotation around small molecules to much larger amphiphilic solutes.
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DOI：
10.1021/jp909048f
发表时间：
2010-02-04
期刊：
The journal of physical chemistry. B
影响因子：
--
作者：
Patel AJ;Varilly P;Chandler D
通讯作者：
Chandler D
影响因子：
2.7
作者：
Crowe, JH;Crowe, LM;Tablin, F
通讯作者：
Tablin, F
影响因子：
15
作者：
Hribar, B;Southall, NT;Dill, KA
通讯作者：
Dill, KA
用超快二维红外（2D IR）振动回声光谱研究研究的盐溶液中的水动力学。
影响因子：
18.3
作者：
Fayer MD;Moilanen DE;Wong D;Rosenfeld DE;Fenn EE;Park S
通讯作者：
Park S
影响因子：
64.8
作者：
Schmidt, Daniel;Jiang, Qiu-Xing;MacKinnon, Roderick
通讯作者：
MacKinnon, Roderick