A global model of the protein-solvent interface.
The solvent structure and dynamics around myoglobin is investigated at the microscopic level of detail by computer simulation. We analyze a molecular dynamics trajectory in terms of solvent mobility and probability distribution. Local events, occurring in the protein-solvent interfacial region, which are often masked by other approaches are thus revealed. Specifically, the local solvent mobility is greatly enhanced for certain locations at the protein surface and in its interior. In addition, a strong correlation between the solvent mobility and density emerges on both global and local scales. We propose a simple model where the solvent distribution measured perpendicularly to the protein surface is utilized to reconstruct the simulated network of hydration within 6 A from the protein surface with a relative error of only 17%. The global precision of this solvation model matches results obtained with more complicated models usually used in refinement procedures in x-ray and neutron experiments but with far fewer parameters. The dramatically improved correspondence between observed and calculated x-ray intensities at low resolution relative to other methods both confirms the validity of the approach used in the MD (molecular dynamics) simulations and allows the results of this study to be implemented in solvent studies on real systems.
Lounnas
V
V
W. M. Keck Center for Computational Biology, University of Houston, Texas 77204-5641.
Pettitt
B M
BM
Phillips
G N
GN
D055592:Biophysical Phenomena; D001703:Biophysics; D018360:Crystallography, X-Ray; D008786:Metmyoglobin / Q000737:chemistry; D008956:Models, Chemical; D015394:Molecular Structure; D011506:Proteins / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry; D013499:Surface Properties; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
D011506:Proteins; D012997:Solvents; D014867:Water; D008786:Metmyoglobin