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dc.contributor.authorDahanayake, Jayangika Niroshani
dc.contributor.authorMitchell-Koch, Katie R.
dc.date.accessioned2019-02-08T03:28:07Z
dc.date.available2019-02-08T03:28:07Z
dc.date.issued2018-07-13
dc.identifier.citationDahanayake JN and Mitchell-Koch KR (2018) How Does Solvation Layer Mobility Affect Protein Structural Dynamics? Front. Mol. Biosci. 5:65en_US
dc.identifier.issn2296-889X
dc.identifier.otherWOS:000455253600001
dc.identifier.urihttps://doi.org/10.3389/fmolb.2018.00065
dc.identifier.urihttp://hdl.handle.net/10057/15793
dc.description© 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.en_US
dc.description.abstractSalvation 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 Cane/Ida 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 alpha-helix, beta-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 tau 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/eta) 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.en_US
dc.description.sponsorshipNational Science Foundation under Grant No. CHE-1665157. This work used the Extreme Science and Engineering Discovery Environment (XSEDE) through allocation CHE170093. XSEDE is supported by National Science Foundation grant number ACI-1548562. This work is also supported by Wichita State University Department of Chemistry and Fairmount College of Liberal Arts and Sciences; the National Science Foundation under Award no. EPS-0903806 and matching support from the State of Kansas through the Kansas Board of Regents; and the National Institute of General Medical Sciences (P20 GM103418) from the National Institutes of Health.en_US
dc.language.isoen_USen_US
dc.publisherFrontiers Media S.A.en_US
dc.relation.ispartofseriesFrontiers in Molecular Biosciences;v.5
dc.subjectViscosityen_US
dc.subjectProtein dynamicsen_US
dc.subjectHydration dynamicsen_US
dc.subjectSolvation shellen_US
dc.subjectCALBen_US
dc.subjectMarkov state modelen_US
dc.subjectKramers' theoryen_US
dc.subjectNon-aqueous enzymesen_US
dc.titleHow does solvation layer mobility affect protein structural dynamics?en_US
dc.typeArticleen_US
dc.rights.holder© 2018 Dahanayake and Mitchell-Kochen_US


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