Figure 9.

Proton binding or release induces conformational change of the transmembrane domain structural repeats. (A) Substrate/proton antiport catalyzed by AcrB can be described by two coupled mechanisms. A conformational switch from L (blue) to T (yellow) is mediated by substrate binding in the DBP of the porter domain. The rearrangement of subdomain unit PN2/PC1 leads to a downward movement of linked TM2. Consequently, the TMR1–TMR2 interface rearranges and opens a periplasmic proton entry site. Protonation of residues D407 and/or D408 results in separation of the TMR1–TMR2 interaction network. A conformational change to the disengaged state results in a switch to the O-conformation (red). TM2 moves upward and the upper part of TM8 undergoes a random-coil-to-helix transition, while binding pockets in the porter domain collapse and the exit channel becomes accessible. The proton binding site opens to the cytoplasmic side. Protons are released in the cytoplasm, down the electrochemical gradient. Charged D407 and/or D408 switch the TM domain back to the engaged state. This conformational change translates back to the porter domain. Proton entry and exit are presumably mediated through a network of water molecules. (B) Close view of the proton relay comprising D407, D408, K940, and R971. These residues undergo the most dramatic conformational change during the T to O transition. In the L (blue) and T (yellow) conformations, water molecules mediate electrostatic contact between D407/D408/K940 with R971. In the O state (red), the transmembrane domain is (almost) dehydrated, greatly affecting the pK_a values of the titratable residues. (C) Insight into the structural details of the interaction of D407 in the O conformation; the H-bonding interaction of the carboxyl group of D407 with the carbonyl group of G403 is only possible if D407 is protonated. A central water molecule connects (by hydrogen bonding) the interaction partners on TM4 (D407), TM10 (K940), and TM11 (T978).