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Transport mechanism of an electroneutral antiporter solved

April 2019. Cation-proton antiporters are membrane-embedded transport proteins involved in a wide range of essential cellular processes, from controlling pH and salt concentration to osmoregulation of the cell volume. Na+/H+ antiporters exchange sodium ions and protons on opposite sides of lipid membranes. The human antiporter NHE1 has been linked to a wide spectrum of diseases from heart failure to autism. Although its structure has not been solved yet, structural biologists from the Max Planck Institute of Biophysics in Frankfurt succeeded in solving the structure of similar antiporters from microorganisms and then teamed up with theoretical biophysicists who unravelled the transport mechanism of this type of electroneutral transporter.

Cellular transporters generally work by an alternating-access mechanism. Switching between inward-open and outward-open conformations alternatingly exposes their binding site to opposite sides of the membrane. To elucidate the transport mechanism in atomic detail, theoretical biophysicists Gerhard Hummer and Kei-ichi Okazaki from the Max Planck Institute of Biophysics performed extensive molecular dynamics simulations using structures of the archaeal Na+/H+ antiporter PaNhaP, which Werner Kühlbrandt and colleagues had previously solved. PaNhaP is a functional homologue of the human antiporter NHE1, which is an important drug target.

The team resolved the Na+ and H+ transport cycle of PaNhaP by transition-path sampling. The simulations revealed a hydrophobic gate to the extracellular side that opens and closes in response to the transporter domain motion. Weakening the gate by mutagenesis made the transporter faster, suggesting that the gate balances competing demands of fidelity and efficiency. Transition-path sampling and a committor-based reaction coordinate optimization identified the essential motions and interactions that realize conformational alternation between the two access states in transporter function. More ...


Figure: Transport cycle of PaNhaP: To shuttle ions between the inward-open (left) and outward-open conformations (right), the six-helix-bundle transporter domain (blue) translates along z, normal to the membrane, and rotates relative to the core domain (gray) around an axis in the membrane plane. Although the scheme shows the inward transport of Na+ (yellow), and the outward transport of H+ (green), both carried by the amino acid Asp159, the transport cycle is fully reversible, and its direction determined by the respective gradients of H+ and Na+ across the membrane. Coupled to the domain motion, closing of the hydrophobic gate (magenta) prevents ion leakage (Nature Communications 10, Article 1742, 2019)





Gerhard Hummer (Theoretical Biophysics Dept, gerhard.hummer@biophys.mpg.de), Werner Kühlbrandt (Structural Biology Dept, werner.kuehlbrandt@biophys.mpg.de), Kei-ichi Okazaki (Theoretical Biophysics Dept, keokazaki@ims.ac.jp), Max Planck Institute of Biophysics, Riedberg Campus, Frankfurt/Main, Germany


Kei-ichi Okazaki*, David Wöhlert, Judith Warnau, Hendrik Jung, Özkan Yildiz, Werner Kühlbrandt & Gerhard Hummer* (2019) Mechanism of the electroneutral sodium/proton antiporter PaNhaP from transition-path shooting. Nature Communications 10: 1742. http://dx.doi.org/10.1038/s41467-019-09739-0