Reconstructing the protein–water interface

✍ Scribed by Vladimir A. Makarov; B. Kim Andrews; B. Montgomery Pettitt

• Book ID: 101240773
• Publisher: Wiley (John Wiley & Sons)
• Year: 1998
• Tongue: English
• Weight: 472 KB
• Volume: 45
• Category: Article
• ISSN: 0006-3525
• DOI: 10.1002/(sici)1097-0282(199806)45:7<469::aid-bip1>3.0.co;2-m

✦ Synopsis

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.