Modeling the hydration of proteins: prediction of structural and hydrodynamic parameters from X-ray diffraction and scattering data.
The implications of protein-water 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 X-ray 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 water-shell approach CRYSOL. If the atomic coordinates are unknown, ab initio modeling approaches based on experimental scattering curves can provide model structures for hydrodynamic predictions.
Durchschlag
Helmut
H
Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, 93040 Regensburg, Germany. helmut.durchschlag@biologie.uni-regensburg.de
Zipper
Peter
P
D001665:Binding Sites; D002950:Citrate (si)-Synthase / Q000737:chemistry; D003198:Computer Simulation; D030562:Databases, Protein; D046911:Macromolecular Substances; D008292:Malate Synthase / Q000737:chemistry; D044085:Microfluidics / Q000379:methods*; D008956:Models, Chemical; D008958:Models, Molecular; D008970:Molecular Weight; D009113:Muramidase / Q000737:chemistry; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012542:Scattering, Radiation; D014783:Viscosity; D014867:Water / Q000737:chemistry*; D014961:X-Ray Diffraction / Q000379:methods*
D046911:Macromolecular Substances; D011506:Proteins; D014867:Water; D002950:Citrate (si)-Synthase; D008292:Malate Synthase; D009113:Muramidase