Uptake Dynamics in the LacY Membrane Protein Transporter

Abstract

Membrane protein transporters govern important cellular processes and are therefore central to human health. To accomplish transport, these proteins rearrange their structures to alternatively expose an internal binding site to either side of the membrane. Recent advances in protein structural determination methods have resulted in a steadily increasing number of high-resolution structures of membrane transporters trapped in different intermediate states. However, to understand the underlying transport mechanism, the molecular details of uptake and release need to be determined. We have used specialized simulation hardware to simulate uptake of galactoside sugar into the Lactose permease (LacY) of Escherichia coli. The extended brute-force simulation revealed large-scale structural rearrangements, lipid and amino acid interactions, and hydration associated with sugar uptake. The free energy landscape of sugar entry was determined by parallel bias-exchange metadynamics simulations and identified a global free energy minimum that coincided with the crystallographic binding site and also a local free energy minimum in the larger periplasmic cavity of LacY. Together, our observations show a putative molecular mechanism for sugar uptake in this prototype membrane transporter.