CALCULATION OF STATIC AND DYNAMIC ELECTRICAL PROPERTIES OF PROTEINS

University Of Pennsylvania, Philadelphia PA

Investigators

Linked publications, trials & patents

Abstract

DESCRIPTION: (adapted from applicant?s abstract) Static and dynamical electrical properties of protein/cofactor assemblies exert a role through a variety of mechanisms, including control of protonation reactions, control of electron transfer reactions, modulation of the properties of cofactors, and modulation of ligand binding energetics. Realistic electrostatic models and associated computational tools have advanced to the point where they provide explanatory and predictive tools to examine the effects of charge distribution, the polarity and polarizability of the charge environment, the burial and stabilization of charged groups in the protein, and the screening and solvation effects of water and dissolved ions. These models will first be used to examine how each factor influences electrostatic fields inside proteins and the properties of cofactors. Second, they will be used to help understand electrical effects in the design of de novo protein/cofactor assemblies with desired new functionalities. Three specific properties will be examined. (1) The redox midpoint potential using the Poisson-Boltzmann (PB) model of electrostatics. This will address the effect of cofactor burial, environment polarity and interaction with solvent. Effects of pH on redox potential will also be considered. (2) The electron transfer reorganization energy will be computed using molecular dynamics simulations, and with a newly developed modification of PB theory. (3) The dynamic Stokes shift, S(t), using a combination of MD and PB models. S(t) depends upon fluctuations of the electrostatic field at the heme chromophore, and will provide information on the effect of protein motions on the nanosecond time scale. Calculations will be done in concert with collaborative experimental measurements to be carried out in other parts of the project.