Dear colleagues,
the following abstract may be of some interest as for water solvent models.
The paper deals with molecular dynamics, however.
Best regards
Ivan Torshin.
UI - 89362454
AU - Brooks CL 3d
AU - Karplus M
TI - Solvent effects on protein motion and protein effects on solvent
motion. Dynamics of the active site region of lysozyme.
LA - Eng
MH - Animal
MH - Binding Sites
MH - Kinetics
MH - Models, Molecular
MH - Muramidase/*metabolism
MH - Proteins/*metabolism
MH - Solvents/*metabolism
MH - Support, U.S. Gov't, P.H.S.
MH - Thermodynamics
RN - EC 3.2.1.17 (Muramidase)
RN - 0 (Solvents)
PT - JOURNAL ARTICLE
DA - 19891005
DP - 1989 Jul 5
IS - 0022-2836
TA - J Mol Biol
PG - 159-81
SB - M
SB - X
CY - ENGLAND
IP - 1
VI - 208
JC - J6V
AA - Author
EM - 198912
AB - The stochastic boundary molecular dynamics methodology is applied to
the active site of the enzyme lysozyme. A comparison is made of in
vacuo dynamics results from the stochastic boundary method and a full
conventional molecular dynamics simulation of lysozyme. Excellent
agreement between the two approaches is obtained. The influence of
solvent on the residues in the active site region is explored and it is
shown that both the structure and dynamics are affected. Of particular
importance for the structure of the protein is the solvation of polar
residues and the stabilization of like-charged ion pairs. The magnitude
of the fluctuations is only slightly altered by the solvent; the
overall increase in the root-mean-square fluctuations, relative to the
vacuum run, is 11%. The solvent effect on dynamical properties is found
not to be simply related to the solvent viscosity. Both the solvent
exposure and dynamic aspects of protein-solvent interactions, including
the relative time scales of the motions, are shown to play a role. The
effects of the protein on solvent dynamics and structure are also
observed to be significant. The solvent molecules around atoms in
charged, polar and apolar side-chains show markedly different diffusion
coefficients as well as exhibiting different solvation structures. One
key example is the water around apolar groups, which is much less
mobile than bulk water, or water solvating polar groups.
AD - Department of Chemistry, Harvard University, Cambridge, MA 02138.
PMID- 0002769750
CU - 1991
SO - J Mol Biol 1989 Jul 5;208(1):159-81
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