Reconstructing the protein-water interface

V. A. Makarov, B. K. Andrews, Bernard Pettitt

Research output: Contribution to journalArticle

59 Citations (Scopus)

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
DOIs
StatePublished - Jun 1998
Externally publishedYes

Fingerprint

Interfaces (computer)
Proteins
Water
Molecular Dynamics Simulation
Distribution functions
Molecular dynamics
Crystal structure
X-Rays
Databases
X rays
Molecules
Computer simulation

Keywords

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

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Biochemistry
  • Biophysics

Cite this

Reconstructing the protein-water interface. / Makarov, V. A.; Andrews, B. K.; Pettitt, Bernard.

In: Biopolymers, Vol. 45, No. 7, 06.1998, p. 469-478.

Research output: Contribution to journalArticle

Makarov, V. A. ; Andrews, B. K. ; Pettitt, Bernard. / Reconstructing the protein-water interface. In: Biopolymers. 1998 ; Vol. 45, No. 7. pp. 469-478.
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