Quantitative Characterization of Local Protein Solvation To Predict Solvent Effects on Protein Structure
Name
Vagenende-2012-Quantitative Charact.pdf
Size
744.68 KB
Format
Adobe PDF
Checksum (MD5)
f2af12f6f8a13badf920f90d44bd1c24
Author(s)
Vagenende, Vincent
Trout, Bernhardt L.
Trout, Bernhardt L.
Date Issued
September 2012
Journal
Biophysical Journal
Publisher
Elsevier
Citation
Vagenende, Vincent, and Bernhardt L. Trout. “Quantitative Characterization of Local Protein Solvation To Predict Solvent Effects on Protein Structure.” Biophysical Journal 103, no. 6 (September 2012): 1354–1362. © 2012 Biophysical Society
Version
Final published version
Abstract
Characterization of solvent preferences of proteins is essential to the understanding of solvent effects on protein structure and stability. Although it is generally believed that solvent preferences at distinct loci of a protein surface may differ, quantitative characterization of local protein solvation has remained elusive. In this study, we show that local solvation preferences can be quantified over the entire protein surface from extended molecular dynamics simulations. By subjecting microsecond trajectories of two proteins (lysozyme and antibody fragment D1.3) in 4 M glycerol to rigorous statistical analyses, solvent preferences of individual protein residues are quantified by local preferential interaction coefficients. Local solvent preferences for glycerol vary widely from residue to residue and may change as a result of protein side-chain motions that are slower than the longest intrinsic solvation timescale of ~10 ns. Differences of local solvent preferences between distinct protein side-chain conformations predict solvent effects on local protein structure in good agreement with experiment. This study extends the application scope of preferential interaction theory and enables molecular understanding of solvent effects on protein structure through comprehensive characterization of local protein solvation.
MIT Department
Massachusetts Institute of Technology. Department of Chemical Engineering
Terms of Use
Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use.
Persistent DSpace Link
DOI of Published Version
https://doi.org/10.1016/j.bpj.2012.08.011
