How Does Solvation Layer Mobility Affect Protein Structural Dynamics?
How Does Solvation Layer Mobility Affect Protein Structural Dynamics?
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DOI：
10.3389/fmolb.2018.00065
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发表时间：
2018
影响因子：
5
通讯作者：
Mitchell-Koch KR
中科院分区：
文献类型：
--
作者：
Dahanayake JN;Mitchell-Koch KR
溶剂化是蛋白质结构动力学的关键。光谱研究表明蛋白质和溶剂动力学之间的关系，和血红素蛋白质在水溶液中的气体结合率以前观察到溶液粘度成反比。在这项工作中，溶剂相容的酶Candida anastritica脂肪酶B，在水和有机溶剂中的功能，采用分子动力学模拟建模。除了水之外，还获得了在乙腈、环己烷、正丁醇和叔丁醇中的酶的数据。蛋白质动力学和溶剂化壳动力学的特征是区域性的：对于每个α-螺旋，β-折叠，环或连接器区域。溶剂流动性和蛋白质的灵活性之间的相关性。那么，局部粘度能解释蛋白质结构动力学和溶剂化层动力学之间的关系吗？Halle和Davidovic对描述蛋白质（在溶液中翻滚）的整体流体动力学的数据进行了令人信服的分析，该分析符合一个模型，其中蛋白质的界面粘度高于本体水的粘度，这是由于水合层中的水动力学延迟（以NMR τ 2重定向时间测量）。大量的实验表明，蛋白质和溶剂化层的动力学之间的耦合，在特定地点的测量。我们的数据提供了溶剂壳动力学的空间分辨表征，显示了在水溶液和有机溶剂中区域溶剂化层动力学和蛋白质动力学之间的相关性。在几个蛋白质区域和相当不同的溶剂集合中考虑了蛋白质柔性和逆溶剂粘度（1/η）之间的相关性。可以看出，当考虑局部溶剂壳动力学时，相关性始终较高，而不是体积粘度。蛋白质的灵活性被认为是最好的相关性与当地的界面粘度或流动性的有机溶剂在一个区域的溶剂化层相对于相同区域周围的水合动力学的比率。结果提供了深入了解水溶性蛋白质的功能，同时也提出了一个框架，用于解释和预测酶在非水溶剂中的结构动力学，溶剂化层内的溶剂的流动性的基础上。我们建议，Kramers的理论可以在未来的工作中使用的模型蛋白质构象转变在不同的溶剂中，通过将本地粘度的影响。
Solvation is critical for protein structural dynamics. Spectroscopic studies have indicated relationships between protein and solvent dynamics, and rates of gas binding to heme proteins in aqueous solution were previously observed to depend inversely on solution viscosity. In this work, the solvent-compatible enzyme Candida antarctica lipase B, which functions in aqueous and organic solvents, was modeled using molecular dynamics simulations. Data was obtained for the enzyme in acetonitrile, cyclohexane, n-butanol, and tert-butanol, in addition to water. Protein dynamics and solvation shell dynamics are characterized regionally: for each α-helix, β-sheet, and loop or connector region. Correlations are seen between solvent mobility and protein flexibility. So, does local viscosity explain the relationship between protein structural dynamics and solvation layer dynamics? Halle and Davidovic presented a cogent analysis of data describing the global hydrodynamics of a protein (tumbling in solution) that fits a model in which the protein's interfacial viscosity is higher than that of bulk water's, due to retarded water dynamics in the hydration layer (measured in NMR τ2 reorientation times). Numerous experiments have shown coupling between protein and solvation layer dynamics in site-specific measurements. Our data provides spatially-resolved characterization of solvent shell dynamics, showing correlations between regional solvation layer dynamics and protein dynamics in both aqueous and organic solvents. Correlations between protein flexibility and inverse solvent viscosity (1/η) are considered across several protein regions and for a rather disparate collection of solvents. It is seen that the correlation is consistently higher when local solvent shell dynamics are considered, rather than bulk viscosity. Protein flexibility is seen to correlate best with either the local interfacial viscosity or the ratio of the mobility of an organic solvent in a regional solvation layer relative to hydration dynamics around the same region. Results provide insight into the function of aqueous proteins, while also suggesting a framework for interpreting and predicting enzyme structural dynamics in non-aqueous solvents, based on the mobility of solvents within the solvation layer. We suggest that Kramers' theory may be used in future work to model protein conformational transitions in different solvents by incorporating local viscosity effects.
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DOI：
10.1073/pnas.1410144111
发表时间：
2014-12-16
影响因子：
11.1
作者：
Dielmann-Gessner, Jessica;Grossman, Moran;Sagi, Irit
通讯作者：
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影响因子：
2.7
作者：
Duarte, DR;Castillo, E;López-Munguía, A
通讯作者：
López-Munguía, A
影响因子：
3.4
作者：
Denisov, VP;Halle, B
通讯作者：
Halle, B
影响因子：
2.9
作者：
BEECE, D;EISENSTEIN, L;YUE, KT
通讯作者：
YUE, KT
DOI：
10.1073/pnas.212637899
发表时间：
2002-12-10
影响因子：
11.1
作者：
Fenimore, PW;Frauenfelder, H;Parak, FG
通讯作者：
Parak, FG