Global and local Voronoi analysis of solvation shells of proteins.

@article{Neumayr2010GlobalAL,
  title={Global and local Voronoi analysis of solvation shells of proteins.},
  author={Gregor Neumayr and Tibor Rudas and Othmar Steinhauser},
  journal={The Journal of chemical physics},
  year={2010},
  volume={133 8},
  pages={
          084108
        }
}
This paper presents the structure and dynamics of hydration shells for the three proteins: ubiquitin, calbindin, and phospholipase. The raw data derived from molecular dynamics simulations are analyzed on the basis of fully atomistic Delaunay tesselations. In order to cope with the high numerical effort for the computation of these Voronoi shells, we have implemented and optimized an intrinsically periodic algorithm. Based on this highly efficient Voronoi decomposition, a variety of properties… 
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16 Citations
Background Citations
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Methods Citations
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16 Citations

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Citation Type

Decomposition of a Protein Solution into Voronoi Shells and Delaunay Layers: Calculation of the Volumetric Properties
TLDR
A simple formalism is proposed for a quantitative analysis of interatomic voids inside and outside a solute molecule in solution, based on the Voronoi-Delaunay tessellation of molecular-dynamic models of solutions.
Decomposition of a Protein Solution into Voronoi Shells and Delaunay Layers
TLDR
A simple formalism is proposed for a quantitative analysis of interatomic voids inside and outside of a molecule in solution, based on the Voronoi-Delaunay tessellation of molecular-dynamic models of solutions.
Volumetric properties of hydrated peptides: Voronoi-Delaunay analysis of molecular simulation runs.
TLDR
An astonishing coincidence is found with the predictions of a simple empirical approach, which is based on experimentally determined amino acid side chain contributions, which allows a parameter free determination of the intrinsic volume V(int) of complex solute molecules without any additional assumptions.
The geometry of protein hydration.
Based on molecular dynamics simulations of four globular proteins in dilute aqueous solution, with three different water models, we examine several, essentially geometrical, aspects of the…
Calculation of the volumetric characteristics of biomacromolecules in solution by the Voronoi-Delaunay technique.
On the influence of hydrated ionic liquids on the dynamical structure of model proteins: a computational study.
TLDR
The solvation of the protein ubiquitin in hydrated molecular ionic liquids was studied for varying water content or a diversity of ionic strengths by means of molecular dynamics simulations based on the Voronoi decomposition of space.
Convergence behaviour of solvation shells in simulated liquids.
TLDR
Findings indicate that locally defined shells should not be thought of as directly comparable to solute-centric shells or to distance, and propose a hybrid method by defining a new set of shells with boundaries at the uppermost distance of each locally derived shell.
How proteins modify water dynamics.
TLDR
The vexed issue of polarity versus topography as the primary determinant of hydration water dynamics is resolved by establishing a protein-invariant exponential dependence of the RPF on a simple confinement index.
HullRad: Fast Calculations of Folded and Disordered Protein and Nucleic Acid Hydrodynamic Properties.
The spatial range of protein hydration.
TLDR
Based on molecular dynamics simulations of four small globular proteins, an analysis of the structural and dynamic properties of the hydrogen-bonded solvent network demonstrates unequivocally that the solvent perturbation is short-ranged, with all investigated properties having exponential decay lengths of less than one hydration shell.
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