Molecular mechanism and energetics of coupling between substrate binding and product release in the F1-ATPase catalytic cycle

Electric Forces and ATP Synthesis

ATP synthase is a rotary motor enzyme that drives the formation of ATP from ADP and P and uses multiple electrical forces to do this. This chapter outlines the exquisite use of these electrical forces to generate the high energy phosphates on which all our lives depend. Vacuolar ATPases and the ADP/ATP carrier also are explored.

Perspective on Integrative Simulations of Bioenergetic Domains

Bioenergetic processes in cells, such as photosynthesis or respiration, integrate many time and length scales, which makes the simulation of energy conversion with a mere single level of theory impossible. Just like the myriad of experimental techniques required to examine each level of organization, an array of overlapping computational techniques is necessary to model energy conversion. Here, a perspective is presented on recent efforts for modeling bioenergetic phenomena with a focus on molecular dynamics simulations and its variants as a primary method. An overview of the various classical, quantum mechanical, enhanced sampling, coarse-grained, Brownian dynamics, and Monte Carlo methods is presented. Example applications discussed include multiscale simulations of membrane-wide electron transport, rate kinetics of ATP turnover from electrochemical gradients, and finally, integrative modeling of the chromatophore, a photosynthetic pseudo-organelle.