Modeling the hydration of proteins prediction of

Authors: Helmut Durchschlag Peter Zipper

Publish Date: 2003/04/25

Volume: 32, Issue: 5, Pages: 487-502

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Abstract

The implications of proteinwater interactions are of importance for understanding the solution behavior of proteins and for analyzing the fine structure of proteins in aqueous solution Starting from the atomic coordinates by bead modeling the scattering and hydrodynamic properties of proteins can be predicted reliably Debye modeling program HYDRO By advanced modeling techniques the hydration can be taken into account appropriately by some kind of rescaling procedures by modeling a water shell by iterative comparisons to experimental scattering curves ab initio modeling or by special hydration algorithms In the latter case the surface topography of proteins is visualized in terms of dot surface points and the normal vectors to these points are used to construct starting points for placing water molecules in definite positions on the protein envelope Bead modeling may then be used for shaping the individual atomic or amino acid residues and also for individual water molecules Among the tuning parameters the choice of the scaling factor for amino acid hydration and of the molecular volume of bound water turned out to be crucial The number and position of bound water molecules created by our hydration modeling program HYDCRYST were compared with those derived from Xray crystallography and the capability to predict hydration structural and hydrodynamic parameters hydrated volume radius of gyration translational diffusion and sedimentation coefficients was compared with the findings generated by the watershell approach CRYSOL If the atomic coordinates are unknown ab initio modeling approaches based on experimental scattering curves can provide model structures for hydrodynamic predictions

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