Functional asymmetry and electron flow in the bovine respirasome

  1. Joana S Sousa
  2. Deryck J Mills
  3. Janet Vonck
  4. Werner Kühlbrandt  Is a corresponding author
  1. Max Planck Institute of Biophysics, Germany

Abstract

Respirasomes are macromolecular assemblies of the respiratory chain complexes I, III and IV in the inner mitochondrial membrane. We determined the structure of supercomplex I1III2IV1 from bovine heart mitochondria by cryo-EM at 9 Å resolution. Most protein-protein contacts between complex I, III and IV in the membrane are mediated by supernumerary subunits. Of the two Rieske iron-sulfur cluster domains in the complex III dimer, one is resolved, indicating that this domain is immobile and unable to transfer electrons. The central position of the active complex III monomer between complex I and IV in the respirasome is optimal for accepting reduced quinone from complex I over a short diffusion distance of 11 nm, and delivering reduced cytochrome c to complex IV. The functional asymmetry of complex III provides strong evidence for directed electron flow from complex I to complex IV through the active complex III monomer in the mammalian supercomplex.

Data availability

The following data sets were generated
    1. Sousa JS
    2. Mills DJ
    3. Vonck J
    4. Kuehlbrandt W
    (2016) Cryo-EM map of bovine respirasome
    Publicly available at the EBI Protein Data Bank (accession no: EMD-4107).
    1. Sousa JS
    2. Mills DJ
    3. Vonck J
    4. Kuehlbrandt W
    (2016) Cryo-EM of bovine respirasome
    Publicly available at th EBI Protein Data Bank (accession no: EMD-4108).
    1. Sousa JS
    2. Mills DJ
    3. Vonck J
    4. Kuehlbrandt W
    (2016) Cryo-EM of bovine respirasome
    Publicly available at the EBI Protein Data Bank (accession no: EMD-4109).
    1. Sousa JS
    2. Mills DJ
    3. Vonck J
    4. Kuehlbrandt W
    (2016) cryo-EM of bovine respirasome
    Publicly available at the RCSB Protein Data Bank (accession no: 5LUF).
The following previously published data sets were used
    1. Vinothkumar KR
    2. Zhu J
    3. Hirst J
    (2014) Electron cryo-microscopy of bovine Complex I
    Publicly available at the EBI Protein Data Bank (accession no: EMD-4109).

Article and author information

Author details

  1. Joana S Sousa

    Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
    Competing interests
    No competing interests declared.
  2. Deryck J Mills

    Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
    Competing interests
    No competing interests declared.
  3. Janet Vonck

    Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5659-8863
  4. Werner Kühlbrandt

    Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
    For correspondence
    werner.kuehlbrandt@biophys.mpg.de
    Competing interests
    Werner Kühlbrandt, Reviewing editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2013-4810

Funding

Max-Planck-Gesellschaft

  • Werner Kühlbrandt

Cluster of Excellence Frankfurt

  • Werner Kühlbrandt

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Stephen C. Harrison, Harvard Medical School, United States

Version history

  1. Received: September 5, 2016
  2. Accepted: November 3, 2016
  3. Accepted Manuscript published: November 10, 2016 (version 1)
  4. Version of Record published: November 21, 2016 (version 2)

Copyright

© 2016, Sousa et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 2,696
    views
  • 620
    downloads
  • 131
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Joana S Sousa
  2. Deryck J Mills
  3. Janet Vonck
  4. Werner Kühlbrandt
(2016)
Functional asymmetry and electron flow in the bovine respirasome
eLife 5:e21290.
https://doi.org/10.7554/eLife.21290

Share this article

https://doi.org/10.7554/eLife.21290

Further reading

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics
    Damien M Rasmussen, Manny M Semonis ... Nicholas M Levinson
    Research Article

    The type II class of RAF inhibitors currently in clinical trials paradoxically activate BRAF at subsaturating concentrations. Activation is mediated by induction of BRAF dimers, but why activation rather than inhibition occurs remains unclear. Using biophysical methods tracking BRAF dimerization and conformation, we built an allosteric model of inhibitor-induced dimerization that resolves the allosteric contributions of inhibitor binding to the two active sites of the dimer, revealing key differences between type I and type II RAF inhibitors. For type II inhibitors the allosteric coupling between inhibitor binding and BRAF dimerization is distributed asymmetrically across the two dimer binding sites, with binding to the first site dominating the allostery. This asymmetry results in efficient and selective induction of dimers with one inhibited and one catalytically active subunit. Our allosteric models quantitatively account for paradoxical activation data measured for 11 RAF inhibitors. Unlike type II inhibitors, type I inhibitors lack allosteric asymmetry and do not activate BRAF homodimers. Finally, NMR data reveal that BRAF homodimers are dynamically asymmetric with only one of the subunits locked in the active αC-in state. This provides a structural mechanism for how binding of only a single αC-in inhibitor molecule can induce potent BRAF dimerization and activation.

    1. Structural Biology and Molecular Biophysics
    Nicholas James Ose, Paul Campitelli ... Sefika Banu Ozkan
    Research Article

    We integrate evolutionary predictions based on the neutral theory of molecular evolution with protein dynamics to generate mechanistic insight into the molecular adaptations of the SARS-COV-2 spike (S) protein. With this approach, we first identified candidate adaptive polymorphisms (CAPs) of the SARS-CoV-2 S protein and assessed the impact of these CAPs through dynamics analysis. Not only have we found that CAPs frequently overlap with well-known functional sites, but also, using several different dynamics-based metrics, we reveal the critical allosteric interplay between SARS-CoV-2 CAPs and the S protein binding sites with the human ACE2 (hACE2) protein. CAPs interact far differently with the hACE2 binding site residues in the open conformation of the S protein compared to the closed form. In particular, the CAP sites control the dynamics of binding residues in the open state, suggesting an allosteric control of hACE2 binding. We also explored the characteristic mutations of different SARS-CoV-2 strains to find dynamic hallmarks and potential effects of future mutations. Our analyses reveal that Delta strain-specific variants have non-additive (i.e., epistatic) interactions with CAP sites, whereas the less pathogenic Omicron strains have mostly additive mutations. Finally, our dynamics-based analysis suggests that the novel mutations observed in the Omicron strain epistatically interact with the CAP sites to help escape antibody binding.