Reconstructing the protein-water interface

Vladimir A. Makarov, B. Kim Andrews, B. Montgomery Pettitt

Research output: Contribution to journalArticlepeer-review

60 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)469-478
Number of pages10
JournalBiopolymers
Volume45
Issue number7
StatePublished - Dec 1 1998
Externally publishedYes

Keywords

  • Crystal structures
  • Density distributions
  • Globular proteins
  • Hydrated proteins
  • Molecular dynamics

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Biomaterials
  • Organic Chemistry

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