Electron transfer (ET) plays a key role in various biological processes, including protection against oxidative stress, magneto-reception in migratory birds, and DNA repair. Recent analysis by Gray and Winkler showed that approximately one third of the structurally characterized proteins contain chains of Trp and Tyr residues, which can potentially serve for electron/hole transfer. Identification of electron transfer channels involving aromatic residues side-chains, is therefore, is a key step for understanding ET involved in various biological processes. To this end we introduce eMap, a web application that is aimed at automatic identification and visualization of ET channels based on the protein's crystal structure using graph theory. The model can be viewed as a coarse-grained adaptation of Beratan's pathway model, which only accounts for the through-space tunneling between aromatic residues side chains. Side chains of Tryptophan (Trp) and Tyrosine (Tyr) residues and non-protein aromatic residues are, therefore, modeled as vertices in a weighted graph, where the the edge weights are distances between centers of mass. Shortest path algorithms are used to compute the most efficient pathways from a specified donor to the surface of the protein, or to a specified acceptor. Pathways are visualized side by-side in the two-dimensional aromatic residue network, and highlighted in the three-dimensional protein structure. The details of the implementation as well as several benchmark calculations will be discussed.

eMap: A web application for mapping and visualizing electron/hole transfer channels in proteins

256th National Meeting (2018)

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