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Slow Dynamics around a Protein and Its Coupling to Solvent.

ABSTRACT: Solvent is essential for protein dynamics and function, but its role in regulating the dynamics remains debated. Here, we employ saturation transfer electron spin resonance (ST-ESR) to explore the issue and characterize the dynamics on a longer (from ?s to s) time scale than has been extensively studied. We first demonstrate the reliability of ST-ESR by showing that the dynamical changeovers revealed in the spectra agree to liquid-liquid transition (LLT) in the state diagram of the glycerol/water system. Then, we utilize ST-ESR with four different probes to systematically map out the variation in local (site-specific) dynamics around a protein surface at subfreezing temperatures (180-240 K) in 10 mol % glycerol/water mixtures. At highly exposed sites, protein and solvent dynamics are coupled, whereas they deviate from each other when temperature is greater than LLT temperature (?190 K) of the solvent. At less exposed sites, protein however exhibits a dynamic, which is distinct from the bulk solvent, throughout the temperature range studied. Dominant dynamic components are thus revealed, showing that (from low to high temperatures) the overall structural fluctuation, rotamer dynamics, and internal side-chain dynamics, in turn, dominate the temperature dependence of spin-label motions. The structural fluctuation component is relatively slow, collective, and independent of protein structural segments, which is thus inferred to a fundamental dynamic component intrinsic to protein. This study corroborates that bulk solvent plasticizes protein and facilitates rather than slaves protein dynamics.

SUBMITTER: Kuo YH

PROVIDER: S-EPMC5968437 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature

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Slow Dynamics around a Protein and Its Coupling to Solvent.

Kuo Yun-Hsuan YH Chiang Yun-Wei YW

ACS central science 20180509 5

Solvent is essential for protein dynamics and function, but its role in regulating the dynamics remains debated. Here, we employ saturation transfer electron spin resonance (ST-ESR) to explore the issue and characterize the dynamics on a longer (from μs to s) time scale than has been extensively studied. We first demonstrate the reliability of ST-ESR by showing that the dynamical changeovers revealed in the spectra agree to liquid-liquid transition (LLT) in the state diagram of the glycerol/wate ...[more]

PMID: 29806012

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Project description:The solvation layer surrounding a protein is clearly an intrinsic part of protein structure-dynamics-function, and our understanding of how the hydration dynamics influences 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 the 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 on 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 evaluate the role of hydration dynamics in biomolecular function. This paper first confirms that the correlation between regional diffusive dynamics and hydration layer structure (via water center of mass around protein side-chain atom 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 in MD simulations based on the protein-water RDF. A linear regression model using the integral of the hydration layer in the water-protein RDF was found to provide statistically equivalent apparent diffusion coefficients at the 95% confidence level for a set of 92 regions within five different proteins. In summary, RDF analysis of 10 ns of data after simulation convergence is sufficient to accurately map regions of fast and slow hydration dynamics around a protein surface. Additionally, it is anticipated that a quick look at protein-water RDFs, comparing peak heights, will be useful to provide a qualitative ranking of regions of faster and slower hydration dynamics at the protein surface for rapid analysis when investigating the role of solvent dynamics in protein function.

Dataset Information

Slow Dynamics around a Protein and Its Coupling to Solvent.

Publications

Slow Dynamics around a Protein and Its Coupling to Solvent.

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