Data_Sheet_1_How Does Solvation Layer Mobility Affect Protein Structural Dynamics?.docx

• Main Authors: Jayangika N. Dahanayake, Katie R. Mitchell-Koch
• Format: Dataset
• Language: unknown
• Published: 2018
• Subjects: Biochemistry; Molecular Biology; Structural Biology; Enzymes; Protein Trafficking; Proteomics and Intermolecular Interactions (excl. Medical Proteomics); Receptors and Membrane Biology; Signal Transduction; Structural Biology (incl. Macromolecular Modelling); Synthetic Biology; viscosity; protein dynamics; hydration dynamics; solvation shell; CALB; Markov state model; Kramers' theory; non-aqueous enzymes; Antarc*; Antarctica
• Online Access: https://doi.org/10.3389/fmolb.2018.00065.s001; https://figshare.com/articles/Data_Sheet_1_How_Does_Solvation_Layer_Mobility_Affect_Protein_Structural_Dynamics_docx/6814076

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 ...