1. Structural Biology and Molecular Biophysics

Cryo-EM structures reveal specialization at the myosin VI-actin interface and a mechanism of force sensitivity

  1. Pinar S Gurel
  2. Laura Y Kim
  3. Paul V Ruijgrok
  4. Tosan Omabegho
  5. Zev Bryant
  6. Gregory M Alushin  Is a corresponding author
  1. National Heart, Blood, and Lung Institute, United States
  2. Stanford University, United States
https://doi.org/10.7554/eLife.31125
Share this article
Cite this article
  1. Pinar S Gurel
  2. Laura Y Kim
  3. Paul V Ruijgrok
  4. Tosan Omabegho
  5. Zev Bryant
  6. Gregory M Alushin
(2017)
Cryo-EM structures reveal specialization at the myosin VI-actin interface and a mechanism of force sensitivity
eLife 6:e31125.
https://doi.org/10.7554/eLife.31125
  2. Download BibTeX
  3. Download .RIS

Abstract

Despite extensive scrutiny of the myosin superfamily, the lack of high-resolution structures of actin-bound states has prevented a complete description of its mechanochemical cycle and limited insight into how sequence and structural diversification of the motor domain gives rise to specialized functional properties. Here we present cryo-EM structures of the unique minus-end directed myosin VI motor domain in rigor (4.6 Å) and Mg-ADP (5.5 Å) states bound to F-actin. Comparison to the myosin IIC-F-actin rigor complex reveals an almost complete lack of conservation of residues at the actin-myosin interface despite preservation of the primary sequence regions composing it, suggesting an evolutionary path for motor specialization. Additionally, analysis of the transition from ADP to rigor provides a structural rationale for force sensitivity in this step of the mechanochemical cycle. Finally, we observe reciprocal rearrangements in actin and myosin accompanying the transition between these states, supporting a role for actin structural plasticity during force generation by myosin VI.

Data availability

The following data sets were generated

Article and author information

Author details

  1. Pinar S Gurel

    Cell Biology and Physiology Center, National Heart, Blood, and Lung Institute, Bethesda, United States
    Competing interests
    The authors declare that no competing interests exist.

  2. Laura Y Kim

    Cell Biology and Physiology Center, National Heart, Blood, and Lung Institute, Bethesda, United States
    Competing interests
    The authors declare that no competing interests exist.

  3. Paul V Ruijgrok

    Department of Bioengineering, Stanford University, Stanford, United States
    Competing interests
    The authors declare that no competing interests exist.

  4. Tosan Omabegho

    Department of Bioengineering, Stanford University, Stanford, United States
    Competing interests
    The authors declare that no competing interests exist.

  5. Zev Bryant

    Department of Bioengineering, Stanford University, Stanford, United States
    Competing interests
    The authors declare that no competing interests exist.

  6. Gregory M Alushin

    Cell Biology and Physiology Center, National Heart, Blood, and Lung Institute, Bethesda, United States
    For correspondence
    galushin@rockefeller.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7250-4484

Funding

W. M. Keck Foundation

  • Zev Bryant

Human Frontier Science Program (Long-Term Fellowship)

  • Paul V Ruijgrok

National Heart, Lung, and Blood Institute

  • Gregory M Alushin

Rockefeller University (Women & Science Fellowship)

  • Pinar S Gurel

National Institutes of Health (F32GM094420)

  • Tosan Omabegho

National Institutes of Health (1DP2 OD004690)

  • Zev Bryant

National Institutes of Health (5DP5OD017885)

  • Gregory M Alushin

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

Copyright

© 2017, Gurel 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

  • 4,382
    views
  • 722
    downloads
  • 61
    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. Pinar S Gurel
  2. Laura Y Kim
  3. Paul V Ruijgrok
  4. Tosan Omabegho
  5. Zev Bryant
  6. Gregory M Alushin
(2017)
Cryo-EM structures reveal specialization at the myosin VI-actin interface and a mechanism of force sensitivity
eLife 6:e31125.
https://doi.org/10.7554/eLife.31125

Share this article

https://doi.org/10.7554/eLife.31125

Categories and tags

Further reading

    1. Plant Biology
    2. Structural Biology and Molecular Biophysics

    Structure of the Calvin-Benson-Bassham sedoheptulose-1,7-bisphosphatase from the model microalga Chlamydomonas reinhardtii

    Théo Le Moigne, Martina Santoni ... Julien Henri
    Research Article

    The Calvin-Benson-Bassham cycle (CBBC) performs carbon fixation in photosynthetic organisms. Among the eleven enzymes that participate in the pathway, sedoheptulose-1,7-bisphosphatase (SBPase) is expressed in photo-autotrophs and catalyzes the hydrolysis of sedoheptulose-1,7-bisphosphate (SBP) to sedoheptulose-7-phosphate (S7P). SBPase, along with nine other enzymes in the CBBC, contributes to the regeneration of ribulose-1,5-bisphosphate, the carbon-fixing co-substrate used by ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). The metabolic role of SBPase is restricted to the CBBC, and a recent study revealed that the three-dimensional structure of SBPase from the moss Physcomitrium patens was found to be similar to that of fructose-1,6-bisphosphatase (FBPase), an enzyme involved in both CBBC and neoglucogenesis. In this study we report the first structure of an SBPase from a chlorophyte, the model unicellular green microalga Chlamydomonas reinhardtii. By combining experimental and computational structural analyses, we describe the topology, conformations, and quaternary structure of Chlamydomonas reinhardtii SBPase (CrSBPase). We identify active site residues and locate sites of redox- and phospho-post-translational modifications that contribute to enzymatic functions. Finally, we observe that CrSBPase adopts distinct oligomeric states that may dynamically contribute to the control of its activity.

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Allosteric inhibition of trypanosomatid pyruvate kinases by a camelid single-domain antibody

    Joar Esteban Pinto Torres, Mathieu Claes ... Yann G-J Sterckx
    Research Article

    African trypanosomes are the causative agents of neglected tropical diseases affecting both humans and livestock. Disease control is highly challenging due to an increasing number of drug treatment failures. African trypanosomes are extracellular, blood-borne parasites that mainly rely on glycolysis for their energy metabolism within the mammalian host. Trypanosomal glycolytic enzymes are therefore of interest for the development of trypanocidal drugs. Here, we report the serendipitous discovery of a camelid single-domain antibody (sdAb aka Nanobody) that selectively inhibits the enzymatic activity of trypanosomatid (but not host) pyruvate kinases through an allosteric mechanism. By combining enzyme kinetics, biophysics, structural biology, and transgenic parasite survival assays, we provide a proof-of-principle that the sdAb-mediated enzyme inhibition negatively impacts parasite fitness and growth.

    1. Structural Biology and Molecular Biophysics

    Functionally important residues from graph analysis of coevolved dynamic couplings

    Manming Xu, Sarath Chandra Dantu ... Shozeb Haider
    Research Article

    The relationship between protein dynamics and function is essential for understanding biological processes and developing effective therapeutics. Functional sites within proteins are critical for activities such as substrate binding, catalysis, and structural changes. Existing computational methods for the predictions of functional residues are trained on sequence, structural, and experimental data, but they do not explicitly model the influence of evolution on protein dynamics. This overlooked contribution is essential as it is known that evolution can fine-tune protein dynamics through compensatory mutations either to improve the proteins’ performance or diversify its function while maintaining the same structural scaffold. To model this critical contribution, we introduce DyNoPy, a computational method that combines residue coevolution analysis with molecular dynamics simulations, revealing hidden correlations between functional sites. DyNoPy constructs a graph model of residue–residue interactions, identifies communities of key residue groups, and annotates critical sites based on their roles. By leveraging the concept of coevolved dynamical couplings—residue pairs with critical dynamical interactions that have been preserved during evolution—DyNoPy offers a powerful method for predicting and analysing protein evolution and dynamics. We demonstrate the effectiveness of DyNoPy on SHV-1 and PDC-3, chromosomally encoded β-lactamases linked to antibiotic resistance, highlighting its potential to inform drug design and address pressing healthcare challenges.