Solvent density and long-range dipole field around a DNA-binding protein studied by molecular dynamics.
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.
Higo
J
J
Biomolecular Engineering Research Institute (BERI), Suita, Osaka, Japan. higo@beri.co.jp
Kono
H
H
Nakamura
H
H
Sarai
A
A
D004268:DNA-Binding Proteins / Q000737:chemistry*; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D012097:Repressor Proteins / Q000737:chemistry*; D012997:Solvents; D014764:Viral Proteins; D054334:Viral Regulatory and Accessory Proteins; D014867:Water / Q000737:chemistry
D004268:DNA-Binding Proteins; D012097:Repressor Proteins; D012997:Solvents; D014764:Viral Proteins; D054334:Viral Regulatory and Accessory Proteins; C016649:phage repressor proteins; D014867:Water