Brownian Dynamics of Cytochrome c and Cytochrome c Peroxidase Association

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Abstract
Brownian dynamics computer simulations of the diffusional association of electron transport proteins cytochrome c (cyt c) and cytochrome c peroxidase (cyt c per) were performed. A highly detailed and realistic model of the protein structures and their electrostatic interactions was used that was based on an atomic-level spatial description. Several structural features played a role in enhancing and optimizing the electron transfer efficiency of this reaction. Favorable electrostatic interactions facilitated long-lived nonspecific encounters between the proteins that allowed the severe orientational criteria for reaction to be overcome by rotational diffusion during encounters. Thus a "reduction-in-dimensionality" effect operated. The proteins achieved plausible electron transfer orientations in a multitude of electrostatically stable encounter complexes, rather than in a single dominant complex.

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