title: Exploring biomolecular machines: energy landscape control of biological reactions.
abstract: For almost 15 years, our Pathway model has been the most powerful model in terms of predicting the tunnelling mechanism for electron transfer (ET) in biological systems, particularly proteins. Going beyond the conventional Pathway models, we have generalized our method to understand how protein dynamics modulate not only the Franck-Condon factor, but also the tunnelling matrix element. We have demonstrated that when interference among pathways modulates the electron tunnelling interactions in proteins (particularly destructive interference), dynamical effects are of critical importance. Tunnelling can be controlled by protein conformations that lie far from equilibrium-those that minimize the effect of destructive interference during tunnelling, for example. In the opposite regime, electron tunnelling is mediated by one (or a few) constructively interfering pathway tubes and dynamical effects are modest. This new mechanism for dynamical modulation of the ET rate has been able to explain and/or predict several rates that were later confirmed by experiment. However, thermal fluctuations can also affect these molecular machines in many other ways. For example, we show how global transformations, which control protein functions such as allostery, may involve large-scale motion and possibly partial unfolding during the reaction event.
authors.affiliation: Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, CA 92093, USA. jonuchic@ucsd.edu
authors.forename: José N
authors.initials: JN
authors.lastname: Onuchic
authors.forename: Chigusa
authors.initials: C
authors.lastname: Kobayashi
authors.forename: Osamu
authors.initials: O
authors.lastname: Miyashita
authors.forename: Patricia
authors.initials: P
authors.lastname: Jennings
authors.forename: Kim K
authors.initials: KK
authors.lastname: Baldridge
mesh_terms: D001400:Azurin / Q000737:chemistry; D004579:Electron Transport; D007700:Kinetics; D008956:Models, Chemical; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D013696:Temperature
chemical_list: D011506:Proteins; D001400:Azurin