title: Mechanisms for Two-Step Proton Transfer Reactions in the Outward-Facing Form of MATE Transporter.
abstract: Bacterial pathogens or cancer cells can acquire multidrug resistance, which causes serious clinical problems. In cells with multidrug resistance, various drugs or antibiotics are extruded across the cell membrane by multidrug transporters. The multidrug and toxic compound extrusion (MATE) transporter is one of the five families of multidrug transporters. MATE from Pyrococcus furiosus uses H(+) to transport a substrate from the cytoplasm to the outside of a cell. Crystal structures of MATE from P. furiosus provide essential information on the relevant H(+)-binding sites (D41 and D184). Hybrid quantum mechanical/molecular mechanical simulations and continuum electrostatic calculations on the crystal structures predict that D41 is protonated in one structure (Straight) and, both D41 and D184 protonated in another (Bent). All-atom molecular dynamics simulations suggest a dynamic equilibrium between the protonation states of the two aspartic acids and that the protonation state affects hydration in the substrate binding cavity and lipid intrusion in the cleft between the N- and C-lobes. This hypothesis is examined in more detail by quantum mechanical/molecular mechanical calculations on snapshots taken from the molecular dynamics trajectories. We find the possibility of two proton transfer (PT) reactions in Straight: the 1st PT takes place between side-chains D41 and D184 through a transient formation of low-barrier hydrogen bonds and the 2nd through another H(+) from the headgroup of a lipid that intrudes into the cleft resulting in a doubly protonated (both D41 and D184) state. The 1st PT affects the local hydrogen bond network and hydration in the N-lobe cavity, which would impinge on the substrate-binding affinity. The 2nd PT would drive the conformational change from Straight to Bent. This model may be applicable to several prokaryotic H(+)-coupled MATE multidrug transporters with the relevant aspartic acids.
authors.affiliation: Theoretical Molecular Science Laboratory, RIKEN, Wako, Saitama, Japan; Interdisciplinary Theoretical Science Research Group (iTHES), RIKEN, Wako, Saitama, Japan.
authors.forename: Wataru
authors.initials: W
authors.lastname: Nishima
authors.affiliation: Theoretical Molecular Science Laboratory, RIKEN, Wako, Saitama, Japan.
authors.forename: Wataru
authors.initials: W
authors.lastname: Mizukami
authors.affiliation: Laboratory of Membrane Molecular Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan.
authors.forename: Yoshiki
authors.initials: Y
authors.lastname: Tanaka
authors.affiliation: Department of Biophysics and Biochemistry, The University of Tokyo, Tokyo, Japan.
authors.forename: Ryuichiro
authors.initials: R
authors.lastname: Ishitani
authors.affiliation: Department of Biophysics and Biochemistry, The University of Tokyo, Tokyo, Japan.
authors.forename: Osamu
authors.initials: O
authors.lastname: Nureki
authors.affiliation: Theoretical Molecular Science Laboratory, RIKEN, Wako, Saitama, Japan; Interdisciplinary Theoretical Science Research Group (iTHES), RIKEN, Wako, Saitama, Japan; Quantitative Biology Center, RIKEN, Kobe, Hyogo, Japan; Advanced Institute for Computational Science, RIKEN, Kobe, Hyogo, Japan. Electronic address: sugita@riken.jp.
authors.forename: Yuji
authors.initials: Y
authors.lastname: Sugita
mesh_terms: D019843:Archaeal Proteins / Q000737:chemistry / Q000378:metabolism*; D001665:Binding Sites; D018360:Crystallography, X-Ray; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D008055:Lipids / Q000737:chemistry; D008954:Models, Biological; D056004:Molecular Dynamics Simulation; D011522:Protons; D020027:Pyrococcus furiosus / Q000378:metabolism*
chemical_list: D019843:Archaeal Proteins; D008055:Lipids; D011522:Protons