Global and local Voronoi analysis of solvation shells of proteins

Abstract

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.

Adaptive resolution simulation of a biomolecule and its hydration shell: Structural and dynamical properties

“…The exact spatial extent of the perturbation is controversial 81 and may depend on which properties are being probed. Conversely, the minimum hydration level needed for correct protein function is also open to discussion 82,83 and must again depend on which protein properties are considered. In Sec.…”

Exploring volume, compressibility and hydration changes of folded proteins upon compression

“…The Voronoi-Delaunay method has been widely used in biomolecular science over the years [38][39][40][41][42][43][44] and has been described in detail elsewhere. [45][46][47] Recently, we started applying this method also to calculations of volumetric properties of biomolecular systems.…”

Computational solvation analysis of biomolecules in aqueous ionic liquid mixtures

“…Although this approach is feasible for many small solutes, it may give highly inaccurate results in case of anisotropic solutes (Zeindlhofer et al . 2017 , 2018 ) like large proteins (Neumayr et al 2010 ) due to non-symmetric excluded volume effects. Furthermore, for heterogeneous solvents with different molecular sizes, more than one shell radius would be necessary to describe a solvation shell appropriately (Haberler et al 2011 ).…”

“…This analysis can be performed for each time step during a trajectory to yield mean residence times of particular species at the surface of the biomolecule (Haberler and Steinhauser 2011 ; Haberler et al 2011 ). This shell assignment can also be applied to the radial distribution function (Neumayr et al 2010 ; Zeindlhofer et al 2018 ) as depicted in Fig. 3 .…”