Reconstructing the protein-water interface.
Using molecular dynamics simulations of fully hydrated proteins and analysis of crystal structures contained in the Protein Data Bank, we develop a transferable set of perpendicular radial distribution functions for water molecules around globular proteins. These universal functions may be used to reconstruct the unique three-dimensional solvent density distribution around every individual protein with a modest error. We discuss potential applications of this solvent treatment in protein x-ray crystallographic refinements and in theoretical modeling. We also present a fast, grid-based algorithm for construction of the perpendicular solvent density distributions.
Makarov
V A
VA
Program in Structural and Computational Biology, and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA.
Andrews
B K
BK
Pettitt
B M
BM
D000465:Algorithms; D001400:Azurin / Q000737:chemistry; D018360:Crystallography, X-Ray; D016208:Databases, Factual; D008958:Models, Molecular; D009211:Myoglobin / Q000737:chemistry; D011506:Proteins / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry; D014867:Water / Q000737:chemistry*
D009211:Myoglobin; D011506:Proteins; D012997:Solvents; D014867:Water; D001400:Azurin