Tunneling matrix element in Ru-modified blue copper proteins: Pruning the protein in search of electron transfer pathways

We investigate with semi-empirical extended Huckel theory calculations the tunneling matrix element for electron transfer in three ruthenium-modified blue copper azurin molecules from the bacterium Pseudomonas aeruginosa which have been recently synthesized and studied experimentally by Gray and co-workers. All of the atoms in the protein can be included in the calculations with the method of transition amplitudes that has been developed recently. Our particular focus here, however, is to develop procedures that create a truncated protein much smaller than the initial 2000 atom one, the aim being to retain only those amino acids that are important to the electron tunneling mechanism. Such a procedure, which we refer to as 'pruning', is useful, first because it reduces the size of the problem, perhaps allowing for more accurate techniques to be used on the truncated protein, and second because it allows for the identification of the regions in the protein in which the tunneling election is localized. The pruning procedures enable us to reduce the number of atoms required in an extended Huckel theory analysis of the tunneling mechanism by approximately a factor of 10 over that in the original protein.