Paper Citing NAMD - Abstract
LeBard, David N.; Martin, Daniel R.; Lin, Su; Woodbury, Neal W.; Matyushov, Dmitry V.
Protein dynamics to optimize and control bacterial photosynthesis
CHEMICAL SCIENCE, 4:4127-4136, 2013
Proteins function by sampling conformational sub-states within a given fold. How this configurational flexibility and the associated protein dynamics affect the rates of chemical reactions are open questions. The difficulty in exploring this issue arises in part from the need to identify the relevant nuclear modes affecting the reaction rate for each characteristic time-scale of the reaction. Proteins as reaction media display a hierarchy of such nuclear modes, of increasingly collective character, that produce both a broad spectrum of static fluctuations and a broad spectrum of relaxation times. In order to understand the effect of protein dynamics on reaction rates, we have chosen to study a sub-nanosecond electron transfer reaction between the bacteriopheophytin and primary quinone cofactors of the photosynthetic bacterial reaction center. We show that dynamics affects the activation barrier of the reaction through a dynamical restriction of the configurational space sampled by the protein-water solvent on the reaction time-scale. The modes which become dynamically arrested on the reaction time-scale of hundreds of picoseconds are related to elastic motions of the protein that are strongly coupled to the hydration layer of water. Several mechanistic consequences for protein electron transfer emerge from this picture. Importantly, energy parameters used to define the activation barrier of electron transfer reactions lose their direct connection to equilibrium thermodynamics and become dependent in a very direct way on the relative magnitudes of the reaction and nuclear reorganization time-scales. As a result, the energetics of protein electron transfer need to be defined on each specific reaction time-scale. This perspective offers a mechanism to optimize protein electron transfer by tuning the reaction rate to the relaxation spectrum of the reaction coordinate.
