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 language | English (US) |
---|---|
Pages (from-to) | 469-478 |
Number of pages | 10 |
Journal | Biopolymers |
Volume | 45 |
Issue number | 7 |
DOIs | |
State | Published - 1998 |
Externally published | Yes |
Keywords
- Crystal structures
- Density distributions
- Globular proteins
- Hydrated proteins
- Molecular dynamics
ASJC Scopus subject areas
- Biophysics
- Biochemistry
- Biomaterials
- Organic Chemistry