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      How Does Solvation Layer Mobility Affect Protein Structural Dynamics?

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          Abstract

          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 τ 2 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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          Most cited references 79

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          Canonical sampling through velocity-rescaling

          We present a new molecular dynamics algorithm for sampling the canonical distribution. In this approach the velocities of all the particles are rescaled by a properly chosen random factor. The algorithm is formally justified and it is shown that, in spite of its stochastic nature, a quantity can still be defined that remains constant during the evolution. In numerical applications this quantity can be used to measure the accuracy of the sampling. We illustrate the properties of this new method on Lennard-Jones and TIP4P water models in the solid and liquid phases. Its performance is excellent and largely independent on the thermostat parameter also with regard to the dynamic properties.
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            The stable states picture of chemical reactions. II. Rate constants for condensed and gas phase reaction models

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              Hydrogen-bond kinetics in liquid water

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                Author and article information

                Contributors
                Journal
                Front Mol Biosci
                Front Mol Biosci
                Front. Mol. Biosci.
                Frontiers in Molecular Biosciences
                Frontiers Media S.A.
                2296-889X
                13 July 2018
                2018
                : 5
                Affiliations
                Department of Chemistry, Wichita State University , Wichita, KS, United States
                Author notes

                Edited by: David Douglas Boehr, Pennsylvania State University, United States

                Reviewed by: Wei Yang, State College of Florida, Manatee–Sarasota, United States; Pratul K. Agarwal, Oak Ridge National Laboratory (DOE), United States; Donald Hamelberg, Georgia State University, United States

                *Correspondence: Katie R. Mitchell-Koch katie.mitchell-koch@ 123456wichita.edu

                This article was submitted to Structural Biology, a section of the journal Frontiers in Molecular Biosciences

                Article
                10.3389/fmolb.2018.00065
                6053501
                Copyright © 2018 Dahanayake and Mitchell-Koch.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                Page count
                Figures: 10, Tables: 6, Equations: 10, References: 94, Pages: 20, Words: 12906
                Funding
                Funded by: American Chemical Society Petroleum Research Fund 10.13039/100006770
                Award ID: 55975-DN16
                Funded by: National Science Foundation 10.13039/100000057
                Award ID: CHE-1665157
                Award ID: EPS-0903806
                Award ID: ACI-1548562
                Funded by: National Institute of General Medical Sciences 10.13039/100000057
                Award ID: P20 GM103418
                Categories
                Molecular Biosciences
                Hypothesis and Theory

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