Mechanisms for Two-Step Proton Transfer Reactions in the Outward-Facing Form of MATE Transporter

Wataru Nishima, Wataru Mizukami, Yoshiki Tanaka, Ryuichiro Ishitani, Osamu Nureki, Yuji Sugita

    Research output: Contribution to journalArticle

    11 Citations (Scopus)

    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.

    Original languageEnglish
    Pages (from-to)1346-1354
    Number of pages9
    JournalBiophysical Journal
    Volume110
    Issue number6
    DOIs
    Publication statusPublished - Mar 29 2016

    Fingerprint

    Poisons
    Protons
    Pyrococcus furiosus
    Multiple Drug Resistance
    Molecular Dynamics Simulation
    Aspartic Acid
    Hydrogen
    Lipids
    Membrane Transport Proteins
    Static Electricity
    Cytoplasm
    Binding Sites
    Cell Membrane
    Anti-Bacterial Agents
    Pharmaceutical Preparations
    Neoplasms

    All Science Journal Classification (ASJC) codes

    • Biophysics

    Cite this

    Nishima, W., Mizukami, W., Tanaka, Y., Ishitani, R., Nureki, O., & Sugita, Y. (2016). Mechanisms for Two-Step Proton Transfer Reactions in the Outward-Facing Form of MATE Transporter. Biophysical Journal, 110(6), 1346-1354. https://doi.org/10.1016/j.bpj.2016.01.027

    Mechanisms for Two-Step Proton Transfer Reactions in the Outward-Facing Form of MATE Transporter. / Nishima, Wataru; Mizukami, Wataru; Tanaka, Yoshiki; Ishitani, Ryuichiro; Nureki, Osamu; Sugita, Yuji.

    In: Biophysical Journal, Vol. 110, No. 6, 29.03.2016, p. 1346-1354.

    Research output: Contribution to journalArticle

    Nishima, W, Mizukami, W, Tanaka, Y, Ishitani, R, Nureki, O & Sugita, Y 2016, 'Mechanisms for Two-Step Proton Transfer Reactions in the Outward-Facing Form of MATE Transporter', Biophysical Journal, vol. 110, no. 6, pp. 1346-1354. https://doi.org/10.1016/j.bpj.2016.01.027
    Nishima, Wataru ; Mizukami, Wataru ; Tanaka, Yoshiki ; Ishitani, Ryuichiro ; Nureki, Osamu ; Sugita, Yuji. / Mechanisms for Two-Step Proton Transfer Reactions in the Outward-Facing Form of MATE Transporter. In: Biophysical Journal. 2016 ; Vol. 110, No. 6. pp. 1346-1354.
    @article{f97a9b3724854a77bd8604ea4b3fe906,
    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.",
    author = "Wataru Nishima and Wataru Mizukami and Yoshiki Tanaka and Ryuichiro Ishitani and Osamu Nureki and Yuji Sugita",
    year = "2016",
    month = "3",
    day = "29",
    doi = "10.1016/j.bpj.2016.01.027",
    language = "English",
    volume = "110",
    pages = "1346--1354",
    journal = "Biophysical Journal",
    issn = "0006-3495",
    publisher = "Biophysical Society",
    number = "6",

    }

    TY - JOUR

    T1 - Mechanisms for Two-Step Proton Transfer Reactions in the Outward-Facing Form of MATE Transporter

    AU - Nishima, Wataru

    AU - Mizukami, Wataru

    AU - Tanaka, Yoshiki

    AU - Ishitani, Ryuichiro

    AU - Nureki, Osamu

    AU - Sugita, Yuji

    PY - 2016/3/29

    Y1 - 2016/3/29

    N2 - 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.

    AB - 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.

    UR - http://www.scopus.com/inward/record.url?scp=84964257929&partnerID=8YFLogxK

    UR - http://www.scopus.com/inward/citedby.url?scp=84964257929&partnerID=8YFLogxK

    U2 - 10.1016/j.bpj.2016.01.027

    DO - 10.1016/j.bpj.2016.01.027

    M3 - Article

    C2 - 27028644

    AN - SCOPUS:84964257929

    VL - 110

    SP - 1346

    EP - 1354

    JO - Biophysical Journal

    JF - Biophysical Journal

    SN - 0006-3495

    IS - 6

    ER -