How does solvation layer mobility affect protein structural dynamics?

• Published in: Frontiers in Molecular Biosciences
• Main Authors: Dahanayake, Jayangika Niroshani, Mitchell-Koch, Katie R.
• Format: Article in Journal/Newspaper
• Language: English
• Published: Frontiers Media S.A. 2018
• Subjects: Viscosity; Protein dynamics; Hydration dynamics; Solvation shell; CALB; Markov state model; Kramers' theory; Non-aqueous enzymes; Ida; Antarc*; Antarctica
• Online Access: http://hdl.handle.net/10057/15793; https://doi.org/10.3389/fmolb.2018.00065

© 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. Salvation 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 ...