The GB model applied to calculating pK values of titratable residues in proteins.
The GB model is
modified to permit a more accurate description of
large macromolecules. The model is tested by
computations of pK shifts for a number of titratable residues in
lysozyme, myoglobin and bacteriorhodopsin.
In general, except for some deeply buried residues of bacteriorhodopsin,
the results show reasonable agreement with both
experimental data and calculations based on numerical solution of
Poisson-Boltzmann equation. While this GB model can not be considered
a quantitative level ``replacement" for the PB model in predicting
the absolute pK values,
a very close agreement between the
two models is obtained
in an application to the prediction of
the pK shifts associated with conformational change.
The calculations based on this version of the generalized Born
approximation are much faster than finite difference solutions
of the Poisson-Boltzmann equation.
For details, see: Alexey Onufriev, D.A. Case and D. Bashford, "A Modification
of the Generalized Born Model Suitable for Macromolecules",
J. Phys. Chem 104, 3712 (2000).
E-mail: onufriev@scripps.edu