Computational modeling of hole transfer in DNA-protein complexes

Hole transfer (migration of radical cation states) in nucleic acid (NA)-protein complexes has attracted considerable interest. In the presentation, we discuss the results of a computational study of electron transfer (ET) rate in radical cation states of several dimers consisting of aromatic amino acid tryptophan (Trp) and purine. Different conformations of G–Trp and A–Trp are studied. The obtained data suggest that: 1. The hole transfer rate in the complexes is very sensitive to the mutual position of monomers and can vary by several orders of magnitude. 2. Strong electronic coupling values were obtained for these systems. Surprisingly, relatively high ET rates are found in T-shaped dimers, showing that π stacking of nucleobases and aromatic amino acids is not required for feasible ET as commonly assumed. In the dimer radical cations, the excess charge is found to be confined to a single site, either a nucleobase or an amino acid. 3. It has been shown that using X-Ray structure for NA-protein complexes in computation of ET parameters may lead to unreliable estimation of electronic coupling between donor and acceptor. To get reliable results, structural fluctuations of the systems must be taken into account by averaging over many distinct conformations. In particular, significant variations of electronic coupling G-Trp are obtained in RNA-protein complex 1R9F2 when relatively small fluctuations are considere