Electrostatic effects in proteins: comparison of dielectric and charge models.
Two approaches for calculating electrostatic effects in proteins are compared and ana analysis is presented of the dependence of calculated properties on the model used to define the charge distribution. Changes in electrostatic free energy have been calculated using a screened Coulomb potential (SCP) with a distance-dependent effective dielectric permittivity to model bulk solvent effects and a finite difference approach to solve the Poisson-Boltzmann (FDPB) equation. The properties calculated include shifts in dissociation constants of ionizable groups, the effect of annihilating surface charges on the binding of metals, and shifts in redox potentials due to changes in the charge of ionizable groups. In the proteins considered the charged sites are separated by 3.5-12 A. It is shown that for the systems studied in this distance range the SCP yields calculated values which are at least as accurate as those obtained from solution of the FDPB equation. In addition, in the distance range 3-5 A the SCP gives substantially better results than the FDPB equation. Possible sources of this difference between the two methods are discussed. Shifts in binding constants and redox potentials were calculated with several standard charge sets, and the resulting values show a variation of 20-40% between the 'best' and 'worst' cases. From this study it is concluded that in most applications, changes in electrostatic free energies can be calculated economically and reliably using an SCP approach with a single functional form of the screening function.
Mehler
E L
EL
Department of Structural Biology, University of Basel, Switzerland.
Solmajer
T
T
D001426:Bacterial Proteins; D064026:Calbindins; D003574:Cytochrome c Group / Q000737:chemistry; D008432:Mathematical Computing; D008956:Models, Chemical; D010084:Oxidation-Reduction; D016012:Poisson Distribution; D011506:Proteins / Q000737:chemistry*; D011522:Protons; D064030:S100 Calcium Binding Protein G / Q000737:chemistry; D012984:Software
D001426:Bacterial Proteins; D064026:Calbindins; D003574:Cytochrome c Group; D011506:Proteins; D011522:Protons; D064030:S100 Calcium Binding Protein G; C017167:cytochrome C(551)