Global and local Voronoi analysis of solvation shells of proteins

Gregor Neumayr, Tibor Rudas, Othmar Steinhauser
2010 Journal of Chemical Physics  
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
more » ... s 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. Physics 133, 084108-1 084108-2 Neumayr, Rudas, and Steinhauser J. Chem. Phys. 133, 084108 ͑2010͒ 084108-3 Voronoi analysis of protein solvation shells J. Chem. Phys. 133, 084108 ͑2010͒ 084108-4 Neumayr, Rudas, and Steinhauser J. Chem. Phys. 133, 084108 ͑2010͒ 084108-5 Voronoi analysis of protein solvation shells J. Chem. Phys. 133, 084108 ͑2010͒ 084108-6 Neumayr, Rudas, and Steinhauser J. Chem. Phys. 133, 084108 ͑2010͒ 084108-7 Voronoi analysis of protein solvation shells J. Chem. Phys. 133, 084108 ͑2010͒ 084108-9 Voronoi analysis of protein solvation shells J. Chem. Phys. 133, 084108 ͑2010͒ 084108-10 Neumayr, Rudas, and Steinhauser J. Chem. Phys. 133, 084108 ͑2010͒ 084108-11 Voronoi analysis of protein solvation shells J. Chem. Phys. 133, 084108 ͑2010͒
doi:10.1063/1.3471383 pmid:20815561 fatcat:yvqjwxiakvcothvskc575ypyt4