Premium
Solvent density and long‐range dipole field around a DNA‐binding protein studied by molecular dynamics
Author(s) -
Higo Junichi,
Kono Hidetoshi,
Nakamura Haruki,
Sarai Akinori
Publication year - 2000
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/(sici)1097-0134(20000801)40:2<193::aid-prot30>3.0.co;2-0
Subject(s) - dipole , chemistry , solvent , chemical physics , molecular dynamics , poisson–boltzmann equation , crystallography , hydrogen bond , protonation , computational chemistry , ion , molecule , organic chemistry
The distribution and orientation of solvent around a DNA‐binding protein, 434 Cro, were investigated by molecular dynamics simulations with a periodic‐boundary condition. The protein was treated in two states: charged and neutral. The computed high‐density sites of the solvent around the protein correlated well with the experimentally determined crystal‐water sites, in both the charged and neutral states. A local density map, introduced to investigate the solvent density around the highly mobile regions of the protein, showed a hydration shell around hydrophobic sidechains and hydrogen‐bondable sites around hydrophilic sidechains, and also showed that the solvent density is sensitive to the slight concaves of the sidechain surface. The long‐range solvent‐dipole field was observed around the protein, where the pattern of the dipole ordering was considerably different between the charged and neutral states. A local solvent‐dipole field was introduced, and the pattern of the dipole ordering was different between the hydrophobic and hydrophilic sidechains. The dipole field from the charged state provided a higher correlation to the electrostatic field obtained from the Poisson‐Boltzmann's equation than that from the neutral state, although the correlation become weak quickly for the both states with increasing the protein‐solvent distance. Proteins 2000;40:193–206. © 2000 Wiley‐Liss, Inc.