Lactose permease is an integral membrane protein that uses the cell membrane's proton gradient for import of lactose. Based on extensive biochemical data and a substrate-bound crystal structure, intermediates involved in lactose/H+ co-transport have been suggested. Yet, the transport mechanism, especially the coupling of protonation states of essential residues and protein conformational changes involved in the transport, is not understood. Here we report molecular-dynamics simulations of membrane-embedded lactose permease in different protonation states, both in the presence and in the absence of lactose. The results analyzed in terms of pore diameter, salt-bridge formation, and substrate motion, strongly implicate Glu269 as one of the main proton translocation sites, whose protonation state controls several key steps of the transport process. A critical ion pair (Glu269 and Arg144) was found to keep the cytoplasmic entrance open, but via a different mechanism than the currently accepted model. After protonation of Glu269, the salt bridge between Glu269 and Arg 144 was found to break, and Arg144 to move away from Glu269, establishing a new salt bridge with Glu126; furthermore, neutralization of Glu269 and the displacement of Arg144 and consequently of water molecules from the interdomain region was seen to initiate the closing of the cytoplasmic half channel (2.6-4.0 Å reduction in diameter in the cytoplasmic constriction region in 10 ns) by allowing hydrophobic surfaces of the N- and C-domains to fuse. Charged Glu269 was found to strongly bind the lactose permeant, indicating that proton transfer from water or another residue to Glu269 is a prerequisite for unbinding of lactose from the binding pocket.
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