A method to analyze multi-pathway effects on protein mediated donor-acceptor coupling interactions

Abstract

Current strategies for analyzing donor-acceptor interactions involve mapping the dominant coupling pathways or families of pathways, followed by a numerical estimate of the interaction mediated by the paths. This strategy succeeds because it properly balances the through-bond versus through-space aspects of the protein electron transfer problem. Yet, existing analytical tools do not provide general predictions of how specific protein motifs might favor or disfavor electron transfer. This issue is best addressed with methods that incorporate multiple interfering pathways and that allow the coupling to be dissected systematically into contributing factors. We present such a method that probes collective effects arising from secondary and tertiary motifs. This analysis indicates when (and why) single pathway strategies succeed or fail. Applications of this new method to model secondary structures are described.