David N. Beratan, Ph.D., advisor
Biological electron transfer (ET) reactions are of both fundamental and practical interests, with their importance in redox signaling, oxidative damage protection, respiratory metabolism, and bioenergetic transport. Charge hopping through aromatic amino acids and redox cofactors occurs in many biological redox systems, extending the conventional paradigms of biological ET from intermolecular, subnanometer length scale to inter-protein, nanometer, or even micrometer length scale. We developed and applied computationally accessible models to understand the mechanisms and kinetics of biological long-range electron transfer, specifically in two major systems: Geobacter bacterial nanowire and cytochrome c peroxidase - cytochrome c (CcP:Cc) protein complex.
In the study of Geobacter bacterial nanowire, two bacterial nanowire structures have been examined: type IV pili and OmcS protein assemblies. For the type IV pili bacterial nanowire, we examined the possible electron transfer mechanisms in regimes ranging from purely incoherent hopping to purely coherent transport. Our studies shown that for plausible ET parameters, electron transfer in type IV pili bacterial nanowire is predicted to be dominated by incoherent hopping between phenylalanine (Phe) and tyrosine (Tyr) residues that are 3 to 4 angstroms apart, where Phe residues in the hopping pathways may create delocalized “islands” to accelerate the ET. This mechanism could be accessible in the presence of strong oxidants, capable of oxidizing Phe and Tyr residues. We also examined the physical requirements needed to sustain biological respiration via type IV pili bacterial nanowire. We found that the hopping regimes with ET rate on the order of 10^8 s^-1 between Phe islands and Tyr residues and conductivities on the order of mS/cm can support ET fluxes that are compatible with cellular respiration rates, although sustaining this delocalization in the heterogeneous protein environment may be challenging. For the OmcS protein assemblies, we examined the temperature dependent conformational changes, and the inverse temperature dependent conductivities. Our studies shown that both reorganization energies and redox potential landscapes of the OmcS protein determine the inverse-temperature dependencies of the conductivity. In most biological reasonable ET parameter zones, conductivity increases with increasing temperatures, featuring thermally-activated redox hopping mechanisms, whereas in a strict ET parameter zone, the conductivity increases with decreasing temperatures, showing that the metallic-like characteristic in inverse-temperature dependent conductivity can be observed even in the purely incoherent hopping mechanism.
In the study of CcP:Cc protein complex, we focused on the role of tryptophan (Trp191) of CcP in supporting hole hopping charge recombination between the Cc heme and ZnPCcP Zinc porphyrin.
Experimental studies find that when Trp191 is substituted by tyrosine, phenylalanine, or redox-active aniline derivatives bound in the W191G cavity, enzymatic activity and charge recombination rates both decreases. We performed theoretical analysis on these CcP:Cc complexes and found that the ET kinetics depend strongly on the chemistry of the modified Trp site. The computed electronic couplings in the W191F and W191G species are orders of magnitude smaller than in the native protein, due largely to the absence of a hopping intermediate and the large tunneling distance. Small molecules bound in the W191G cavity are weakly coupled electronically. The couplings in W191Y are not substantially weakened compared to the native species, but the redox potential difference for tyrosine compared to tryptophan oxidation accounts for the slower rate in the W191Y mutant. Our theoretical analysis explains why only the native Trp supports rapid hole hopping in the CcP:Cc complex, where both favorable free energies and electronic couplings are essential for establishing an efficient hole hopping relay in protein-protein complexes.
Besides the main theme of biological long-range electron transfer, we have studied the hole length along DNA base pairs, using a newly developed localized orbital scaling correction (LOSC) density functional theory method. We accurately characterized the quantum delocalization of the hole wave function in double helical B-DNA and found that the hole state tends to delocalize among four guanine-cytosine (GC) base pairs and among three adenine-thymine (AT) base pairs when these adjacent bases fluctuate into degeneracy. This extend of delocalization has significant implications for assessing the role of coherent, incoherent, or flickering resonant charge transfer mechanisms in DNA.
Lastly, we reforged our inhouse cheminformatics algorithm for Chemical Space Exploration with Stochastic Search (ACSESS). In the reforged version ACSESS, the cheminformatics library OpenEye is replaced by open-source RDKit for molecular manipulations, and a serious of mutation and filtering functions were added to facilitate targeted chemical space explorations.
We applied the reforged ACSESS in exploring chemical space for potential RNA binders with restricted molecule scaffold.