We compute the autocorrelation function of the donor-acceptor tunneling matrix element ͗TDA(t)TDA ( (0)͘ is studied as a function of donor-acceptor distance, tunneling pathway structure, tunneling energy, and temperature to explore the structural and dynamical origins of non-Condon effects. For azurin, the correlation function is remarkably insensitive to tunneling pathway structure. The decay time is only slightly shorter than it is for solvent-mediated electron transfer in small organic molecules and originates, largely, from fluctuations of valence angles rather than bond lengths.correlation functions ͉ Franck-Condon breakdown ͉ dephasing ͉ coupling pathways ͉ redox reactions T he interplay among nuclear motion and electronic dynamics is the subject of increasing focus in the field of electron transfer (ET) processes (1-8). Recent research has focused on the effects of bridge nuclear motion on ET, with chemical, biological, and electronic device applications (see refs. 9-11 for reviews). Early theoretical analysis indicates that tunneling matrix element modulation by bridge dynamics can alter the free energy dependence of ET reaction rates by causing the Born-Oppenheimer (12) and FranckCondon approximations to fail (13-15). More recently, theoretical studies explored ET kinetics in systems with fluctuating donoracceptor matrix elements (16-24). Bridge motion can cause large and rapid donor-acceptor matrix element fluctuations, affecting the tunneling pathway structure and the interferences among pathways (25-37). The coupling matrix element fluctuations may have large contributions from solvent-polarization fluctuations (23), and these fluctuations facilitate electronically forbidden and gated . Finally, bridge-nuclear relaxation creates inelastic tunneling pathway channels (11,20,24,(47)(48)(49) that can change the mechanism of ET from superexchange to resonant tunneling to sequential hopping (11,(41)(42)(43)(44)(50)(51)(52)(53)(54)(55)(56)(57)(58)(59)(60)(61)(62) and can lead to breakdown of the Born-Oppenheimer approximation (63, 64).The goal of this work is to characterize tunneling matrix element fluctuations in azurin and, in particular, to examine their influence on the ET rate and on the validity of the Franck-Condon approximation. Franck-Condon breakdown can reduce the ET rate in the case of activationless ET reactions and enhance the rate for activated ET (18). ET in Ru-modified azurin is nearly activationless, and the protein is often approximated as being a rigid medium for tunneling because the tunneling pathways traverse a  sheet. In this work, we compute the effects of tunneling matrix element fluctuations on the rate as a function of distance, temperature, protein structural fluctuations, and intervening pathway structure. Further, we identify the types of motion that cause the coupling to fluctuate.The general derivation of the nonadiabatic rate expression for fluctuating donor-acceptor matrix elements cannot assume the validity of the Franck-Condon separation. As explained below, the Franck...