Dataset Information


Quantitative characterization of local protein solvation to predict solvent effects on protein structure.

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.

SUBMITTER: Vagenende V 

PROVIDER: S-EPMC3446686 | BioStudies | 2012-01-01

REPOSITORIES: biostudies

Similar Datasets

2013-01-01 | S-EPMC3656110 | BioStudies
2018-01-01 | S-EPMC6050752 | BioStudies
1000-01-01 | S-EPMC521459 | BioStudies
2018-01-01 | S-EPMC6053501 | BioStudies
2009-01-01 | S-EPMC2722364 | BioStudies
2010-01-01 | S-EPMC2943414 | BioStudies
2017-01-01 | S-EPMC7126742 | BioStudies
2011-01-01 | S-EPMC3257107 | BioStudies
2005-01-01 | S-EPMC1366563 | BioStudies
2014-01-01 | S-EPMC3958133 | BioStudies