Evidence map›Paper›PMID 29780979›Full record

ArticlePhysical chemistry chemical physics : PCCP2018

Entropy connects water structure and dynamics in protein hydration layer.

Jayangika N Dahanayake, Katie R Mitchell-Koch

Abstract read
In one paragraph

Article in Physical chemistry chemical physics : PCCP, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.

0numbers the graph read from it
0cells of the map it votes in
23citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

23 citing papers in PubMed.

  1. Article
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  5. Article
  6. Ultrafast Spectroscopy Reveals Slow Water Dynamics in Biocondensates.Journal of the American Chemical Society · 2023
    Article
  7. Article
  8. Article
  9. Article
  10. Article
  11. Revisiting macromolecular hydration with HullRadSAS.European biophysics journal : EBJ · 2023
    Article
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  13. Review
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  15. Review
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

2 authors.

Jayangika N DahanayakeWichita State University, Department of Chemistry, Wichita, Kansas, USA. katie.mitchell-koch@wichita.edu.
Katie R Mitchell-Koch

Funding

Mentoring CoreP20GM103418 · NIGMS · UNIVERSITY OF KANSAS MEDICAL CENTER · PI Douglas E Wright · 2012 to 2026
$63.0M
NIGMS NIH HHS P20 GM103418
6 · The paper itself

Abstract

The enzyme Candida Antarctica lipase B (CALB) serves here as a model for understanding connections among hydration layer dynamics, solvation shell structure, and protein surface structure. The structure and dynamics of water molecules in the hydration layer were characterized for regions of the CALB surface, divided around each α-helix, β-sheet, and loop structure. Heterogeneous hydration dynamics were observed around the surface of the enzyme, in line with spectroscopic observations of other proteins. Regional differences in the structure of the biomolecular hydration layer were found to be concomitant with variations in dynamics. In particular, it was seen that regions of higher density exhibit faster water dynamics. This is analogous to the behavior of bulk water, where dynamics (diffusion coefficients) are connected to water structure (density and tetrahedrality) by excess (or pair) entropy, detailed in the Rosenfeld scaling relationship. Additionally, effects of protein surface topology and hydrophobicity on water structure and dynamics were evaluated using multiregression analysis, showing that topology has a somewhat larger effect on hydration layer structure-dynamics. Concave and hydrophobic protein surfaces favor a less dense and more tetrahedral solvation layer, akin to a more ice-like structure, with slower dynamics. Results show that pairwise entropies of local hydration layers, calculated from regional radial distribution functions, scale logarithmically with local hydration dynamics. Thus, the Rosenfeld relationship describes the heterogeneous structure-dynamics of the hydration layer around the enzyme CALB. These findings raise the question of whether this may be a general principle for understanding the structure-dynamics of biomolecular solvation.

Indexed as

EntropyMolecular Dynamics SimulationAmino AcidsAmino Acid SequenceBinding SitesFungal ProteinsHydrogen BondingHydrophobic and Hydrophilic InteractionsKineticsLipaseProtein BindingProtein ConformationSurface PropertiesWaterAmino AcidsFungal ProteinsLipaselipase B, Candida antarcticaWater

Identifiers

PMID29780979
PMCPMC6005386

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.