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

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

  • 4,362
    views
  • 722
    downloads
  • 60
    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

Further reading

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics
    Yi-Hsuan Lin, Tae Hun Kim ... Hue Sun Chan
    Research Article

    Liquid-liquid phase separation (LLPS) involving intrinsically disordered protein regions (IDRs) is a major physical mechanism for biological membraneless compartmentalization. The multifaceted electrostatic effects in these biomolecular condensates are exemplified here by experimental and theoretical investigations of the different salt- and ATP-dependent LLPSs of an IDR of messenger RNA-regulating protein Caprin1 and its phosphorylated variant pY-Caprin1, exhibiting, for example, reentrant behaviors in some instances but not others. Experimental data are rationalized by physical modeling using analytical theory, molecular dynamics, and polymer field-theoretic simulations, indicating that interchain ion bridges enhance LLPS of polyelectrolytes such as Caprin1 and the high valency of ATP-magnesium is a significant factor for its colocalization with the condensed phases, as similar trends are observed for other IDRs. The electrostatic nature of these features complements ATP’s involvement in π-related interactions and as an amphiphilic hydrotrope, underscoring a general role of biomolecular condensates in modulating ion concentrations and its functional ramifications.

    1. Structural Biology and Molecular Biophysics
    Kingsley Y Wu, Ta I Hung, Chia-en A Chang
    Research Article

    PROteolysis TArgeting Chimeras (PROTACs) are small molecules that induce target protein degradation via the ubiquitin-proteasome system. PROTACs recruit the target protein and E3 ligase; a critical first step is forming a ternary complex. However, while the formation of a ternary complex is crucial, it may not always guarantee successful protein degradation. The dynamics of the PROTAC-induced degradation complex play a key role in ubiquitination and subsequent degradation. In this study, we computationally modelled protein complex structures and dynamics associated with a series of PROTACs featuring different linkers to investigate why these PROTACs, all of which formed ternary complexes with Cereblon (CRBN) E3 ligase and the target protein bromodomain-containing protein 4 (BRD4BD1), exhibited varying degrees of degradation potency. We constructed the degradation machinery complexes with Culling-Ring Ligase 4A (CRL4A) E3 ligase scaffolds. Through atomistic molecular dynamics simulations, we illustrated how PROTAC-dependent protein dynamics facilitating the arrangement of surface lysine residues of BRD4BD1 into the catalytic pocket of E2/ubiquitin cascade for ubiquitination. Despite featuring identical warheads in this PROTAC series, the linkers were found to affect the residue-interaction networks, and thus governing the essential motions of the entire degradation machine for ubiquitination. These findings offer a structural dynamic perspective on ligand-induced protein degradation, providing insights to guide future PROTAC design endeavors.