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Microscopic rotary mechanism of ion translocation in the Fo complex of ATP synthases

Nature Chemical Biology volume 6, pages 891–899 (2010)Cite this article

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Abstract

The microscopic mechanism of coupled c-ring rotation and ion translocation in F1Fo-ATP synthases is unknown. Here we present conclusive evidence supporting the notion that the ability of c-rings to rotate within the Fo complex derives from the interplay between the ion-binding sites and their nonhomogenous microenvironment. This evidence rests on three atomic structures of the c15 rotor from crystals grown at low pH, soaked at high pH and, after N,N′-dicyclohexylcarbodiimide (DCCD) modification, resolved at 1.8, 3.0 and 2.2 Å, respectively. Alongside a quantitative DCCD-labeling assay and free-energy molecular dynamics calculations, these data demonstrate how the thermodynamic stability of the so-called proton-locked state is maximized by the lipid membrane. By contrast, a hydrophilic environment at the a-subunit–c-ring interface appears to unlock the binding-site conformation and promotes proton exchange with the surrounding solution. Rotation thus occurs as c-subunits stochastically alternate between these environments, directionally biased by the electrochemical transmembrane gradient.

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Figure 1: Environmental control of the conformation and proton affinity of the c-subunit binding sites.
Figure 2: Crystal structures of the S. platensis c15 ring at low and high pH.
Figure 4: Simulation of the structural effect of an artifactual deprotonation of Glu62 in a lipid-membrane environment.
Figure 3: pH dependence of DCCD labeling of the S. platensis c15 ring.
Figure 5: Structure of the S. platensis c15 ring with the bound inhibitor DCCD at 2.2-Å resolution.
Figure 6: Microscopic model of proton translocation and coupled rotation in the Fo complex from S. platensis.

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Acknowledgements

The authors thank the staff of the Swiss Light Source (PXII) and the European Synchrotron Radiation Facility (ID23-1 and ID23-2) for their assistance at the beamlines. We also thank R.H. Fillingame (University of Wisconsin) for providing unpublished data and discussions on water accessibility of the a-c interface, K.M. Pos for helpful discussions on DCCD labeling and H. Michel for his comments on this work. T.M., Ö.Y. and D.P. wish to express their gratitude to W. Kühlbrandt for his exceptional scientific support. This work was funded in part by the Cluster of Excellence “Macromolecular Complexes” (DFG Project EXC 115) (to J.D.F.-G. and T.M.), the DFG Collaborative Research Center (S.F.B.) 807 (to T.M.) and a EUROCORES project (EuroSYNBIO) of the European Science Foundation (to T.M). Experimental and computational resources were provided in part by the EU ESFRI INSTRUCT program, the BMBF Membrane Protein Core Center and the Jülich Supercomputing Centre.

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  1. José D Faraldo-Gómez and Thomas Meier: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany

    Denys Pogoryelov, Özkan Yildiz & Thomas Meier

  2. Theoretical Molecular Biophysics Group, Max Planck Institute of Biophysics, Frankfurt am Main, Germany

    Alexander Krah & José D Faraldo-Gómez

  3. Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany

    Julian D Langer

  4. Cluster of Excellence Macromolecular Complexes, Frankfurt am Main, Germany

    José D Faraldo-Gómez & Thomas Meier

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  1. Denys Pogoryelov
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Contributions

D.P. conceived, designed and performed most of the experiments, analyzed the data and wrote parts of the manuscript. A.K. and J.D.F.-G. performed computer simulations and analyzed the data. J.D.L. performed the mass spectrometry experiments and MS data analysis. Ö.Y. helped to collect and analyze crystallographic data and contributed analysis tools. J.D.F.-G. and T.M. directed the project, conceived, designed and performed experiments, analyzed the data and wrote the paper.

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Correspondence to José D Faraldo-Gómez or Thomas Meier.

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Pogoryelov, D., Krah, A., Langer, J. et al. Microscopic rotary mechanism of ion translocation in the Fo complex of ATP synthases. Nat Chem Biol 6, 891–899 (2010). https://doi.org/10.1038/nchembio.457

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