Protein Solvent Shell Structure Provides Rapid Analysis of Hydration Dynamics
The solvation layer surrounding a protein is clearly an intrinsic part of protein structure-dynamics-function, and our understanding of how hydration dynamics influence protein function is emerging. We have recently reported simulations indicating a correlation between regional hydration dynamics an...
| Published in: | Journal of Chemical Information and Modeling |
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| Main Authors: | , , , , , |
| Format: | Text |
| Language: | English |
| Published: |
2019
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| Subjects: | |
| Online Access: | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8108405/ http://www.ncbi.nlm.nih.gov/pubmed/30865440 https://doi.org/10.1021/acs.jcim.9b00009 |
| Summary: | The solvation layer surrounding a protein is clearly an intrinsic part of protein structure-dynamics-function, and our understanding of how hydration dynamics influence protein function is emerging. We have recently reported simulations indicating a correlation between regional hydration dynamics and the structure of the solvation layer around different regions of the enzyme Candida antarctica lipase B, wherein the radial distribution function (RDF) was used to calculate pairwise entropy, providing a link between dynamics (diffusion) and thermodynamics (excess entropy) known as Rosenfeld scaling. Regions with higher RDF values/peaks in the hydration layer (the first peak, within 6 Å of the protein surface) have faster diffusion in the hydration layer. The finding thus hinted at a handle for rapid evaluation of hydration dynamics at different regions of the protein surface in molecular dynamics simulations. Such an approach may move the analysis of hydration dynamics from a specialized venture to routine analysis, enabling an informatics approach to evaluating the role of hydration dynamics in biomolecular function. This paper first confirms the correlation between diffusion coefficients and solvent shell structure (via RDF) is observed as a general relationship across a set of proteins. Second, it seeks to devise an approach for rapid analysis of hydration dynamics, determining the minimum amount of information and computational effort required to get a reliable value of hydration dynamics from structural data, based on the protein-water radial distribution function. A linear regression model using the integral of the hydration layer in the water-protein RDF was found to provide statistically-equivalent diffusion coefficients at the 95% confidence level for a set of 92 regions within 5 different proteins. In summary, RDF analysis of 10 nanoseconds of data after simulation convergence is sufficient to accurately map regions of fast and slow hydration dynamics around a protein surface. Additionally, it is ... |
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