Sugar binding and protein conformational changes in lactose permease

¹ University of Illinois at Urbana-Champaign

^* To whom correspondence should be addressed. E-mail: emad{at}ks.uiuc.edu.

Submitted on March 28, 2006
Revised on May 28, 2006
Accepted on 25 August 2006

	Abstract

Lactose permease (LacY) 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 certain residues and protein conformational changes involved in the transport, is not understood. Here we report MD simulations of membrane embedded LacY 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, however, via a different mechanism from the currently accepted model. After protonation of Glu269, the salt bridge between Glu269 and Arg144 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.

Key Words: hydration, membrane proteins, molecular dynamics, proton transfer, salt bridge, transporter

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