Paper Citing NAMD - Abstract
Kawatsu, T.; Beratan, D.N.; Kakitani, T.
Conformationally averaged score functions for electronic propagation in proteins
JOURNAL OF PHYSICAL CHEMISTRY B, 110:5747-5757, MAR 23 2006
We explore the influence of conformational dynamics on protein-mediated electron donor-acceptor interactions. We introduce a thermally averaged score function to characterize electronic propagation from redox cofactors into the protein and solvent. The score function is explored for myoglobin at the extended-Huckel level, and the results are compared with those of simpler models. The conformationally averaged quantum results are consistent with the empirical analysis of the Pathways model. Notably, subtle effects of quantum interference among multiple coupling pathways that arise in static structures are largely averaged out when protein thermal motion is included. Propagation through bulk water near the single-protein interface decays rapidly with distance.
