Zx. Xiang et al., CALCULATION OF SOLVATION ENERGY WITH A COMBINATION OF THE BOUNDARY-ELEMENT METHOD AND PDLD MODEL, Journal of physical chemistry, 98(48), 1994, pp. 12782-12788
A general formalism for a computational stimulation of the biomolecula
r functions at a microscopic level has been developed. This method was
achieved by a combination of the boundary element method and PDLD mod
el in the case of nonzero ionic strength. Calculations with our method
have been performed both on a simple model and on realistic problems.
The latter concerns the solvation energies of foul residues in bovine
pancreatic trypsin inhibitor (BPTI) and the pK-shift of His-64 of mut
ant subtilisin BPN'. We focus our analysis on evaluating the influence
of the parameter such as polarizability, charge, ionic strength, solv
ent screening, etc.,on the total solvation energies. Our calculation c
onfirms that bulk solvent screening effects on protein induced dipoles
can be simply ignored, introducing a relative error less than 5%, whi
le the polarization of protein induced dipoles on the solvent accounts
for up to -10 kcal/mol and must be considered, and that the change of
solvation energies is not sensitive to the parameters of charge, pola
rizability, and ionic strength. Moreover, it is found that the effects
of protein induced dipoles that are more than 9 Angstrom away from th
e sites of interest can be ignored and that all atom partial charges s
hould be considered.