Global and local Voronoi analysis of solvation shells of proteins.
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 is presented: three dimensional water and ion nuclear densities as well as the geometrical packing of water molecules are discussed. Thereby, we develop Voronoi interface surface area, the Voronoi analog of the well known solvent accessible surface area. The traditional radial distribution functions are resolved into Voronoi shells as a transient device to the new concept of shell-grained orientational order. Thus, we analyze the donor-acceptor property as well as the amount of dielectric screening. Shell dynamics is described in terms of mean residence times. In this way, a retardation factor for different shells can be derived and was compared to experimental values. All these results and properties are presented both at the global protein level as well as at the local residue level.
Neumayr
Gregor
G
Department of Computational Biological Chemistry, University of Vienna, Wien A-1090, Austria.
Rudas
Tibor
T
Steinhauser
Othmar
O
D000465:Algorithms; D064026:Calbindins; D002118:Calcium / Q000737:chemistry; D002413:Cations, Divalent; D056004:Molecular Dynamics Simulation; D010740:Phospholipases / Q000737:chemistry*; D064030:S100 Calcium Binding Protein G / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry; D055672:Static Electricity; D025801:Ubiquitin / Q000737:chemistry*; D014867:Water / Q000737:chemistry
D064026:Calbindins; D002413:Cations, Divalent; D064030:S100 Calcium Binding Protein G; D012997:Solvents; D025801:Ubiquitin; D014867:Water; D010740:Phospholipases; D002118:Calcium