Biophysical Society Thematic Meeting | Hamburg 2022

Biophysics at the Dawn of Exascale Computers

Wednesday Speaker Abstracts

MOLECULAR MECHANISMS OF TRANSPORTER MEMBRANE PROTEINS Oliver Beckstein 1,2 ; 1 Arizona State University, Physics, Tempe, AZ, USA 2 Arizona State University, Center for Biological Physics, Tempe, AZ, USA Transport of ions and small molecules across the cell membrane against electrochemical gradients is catalyzed by integral membrane proteins that use a source of free energy to drive the energetically uphill flux of the transported substrate. Secondary active transporters couple the spontaneous influx of a "driving" ion such as sodium ions or protons to the flux of the substrate. The fact that these transporters operate out of equilibrium and change their conformation between an inward-facing and outward-facing conformation in a cyclical fashion, called the alternating access mechanism, has been recognized as the general principle underlying secondary transporter function. We have been using molecular dynamics simulations (long equilibrium MD, free energy calculations, enhanced sampling for rare events, constant pH simulations) in combination with experimental techniques such as X-ray crystallography, cryo-electron microscopy, and functional measurements to better understand the mechanism of secondary active transport in a wide range of transporters such as sodium/proton antiporters, bile acid/sodium symporters, the major facilitator superfamily, nucleobase-sodium symporters, and zinc transporters. We have been following a research program to dissect key steps in the transport cycle, namely identification of binding sites of ions and substrates, delineation of the moving elements of the alternating access transition, and sampling of the transitions themselves. We employ an analytical multi-scale rate model to combine estimates of rates and free energies from simulations to arrive at a bottom-up computational estimate for the transporter turnover number as function of the external gradients. Experiments and simulations taken together allow us to understand the fundamental physiological process of ion-driven transport across the membrane at the molecular scale.

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