Reconstructing the protein-water interface

Biopolymers. 1998 Jun;45(7):469-78. doi: 10.1002/(SICI)1097-0282(199806)45:7<469::AID-BIP1>3.0.CO;2-M.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Algorithms
  • Azurin / chemistry
  • Crystallography, X-Ray
  • Databases, Factual
  • Models, Molecular
  • Myoglobin / chemistry
  • Proteins / chemistry*
  • Solvents / chemistry
  • Water / chemistry*

Substances

  • Myoglobin
  • Proteins
  • Solvents
  • Water
  • Azurin