Kinesin motility driven by subdomain dynamics

  1. Wonmuk Hwang  Is a corresponding author
  2. Matthew Lang  Is a corresponding author
  3. Martin Karplus  Is a corresponding author
  1. Texas A&M University, United States
  2. Vanderbilt University, United States
  3. Harvard University, United States

Abstract

The microtubule (MT)-associated motor protein kinesin utilizes its conserved ATPase head to achieve diverse motility characteristics. Despite considerable knowledge about how its ATPase activity and MT binding are coupled to the motility cycle, the atomic mechanism of the core events remain to be found. To obtain insights into the mechanism, we performed 38.5 microseconds of all-atom molecular dynamics simulations of kinesin-MT complexes in different nucleotide states. Local subdomain dynamics were found to be essential for nucleotide processing. Catalytic water molecules are dynamically organized by the switch domains of the nucleotide binding pocket while ATP is torsionally strained. Hydrolysis products are 'pulled' by switch-I, and a new ATP is "captured" by a concerted motion of the α0/L5/switch-I trio. The dynamic and wet kinesin-MT interface is tuned for rapid interactions while maintaining specificity. The resulting mechanism provides the flexibility necessary for walking in the crowded cellular environment.

Article and author information

Author details

  1. Wonmuk Hwang

    Department of Biomedical Engineering, Texas A&M University, College Station, United States
    For correspondence
    hwm@tamu.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7514-3186
  2. Matthew Lang

    Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, United States
    For correspondence
    matt.lang@vanderbilt.edu
    Competing interests
    The authors declare that no competing interests exist.
  3. Martin Karplus

    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
    For correspondence
    marci@tammy.harvard.edu
    Competing interests
    The authors declare that no competing interests exist.

Funding

National Institutes of Health (R01GM087677)

  • Wonmuk Hwang
  • Matthew Lang

PIttsburgh Supercomputing Center (Anton Supercomputer)

  • Wonmuk Hwang
  • Martin Karplus

Texas A&M Supercomputing Facility

  • Wonmuk Hwang

Texas Advanced Computing Center

  • Wonmuk Hwang

CHARMM Development Project

  • Martin Karplus

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

Reviewing Editor

  1. Antoine M van Oijen, University of Wollongong, Australia

Publication history

  1. Received: May 24, 2017
  2. Accepted: November 3, 2017
  3. Accepted Manuscript published: November 7, 2017 (version 1)
  4. Version of Record published: December 6, 2017 (version 2)

Copyright

© 2017, Hwang 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

  • 2,731
    Page views
  • 445
    Downloads
  • 28
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, Scopus, PubMed Central.

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. Wonmuk Hwang
  2. Matthew Lang
  3. Martin Karplus
(2017)
Kinesin motility driven by subdomain dynamics
eLife 6:e28948.
https://doi.org/10.7554/eLife.28948

Further reading

    1. Structural Biology and Molecular Biophysics
    Zeyu Shen, Bowen Jia ... Mingjie Zhang
    Research Article

    Formation of membraneless organelles or biological condensates via phase separation and related processes hugely expands the cellular organelle repertoire. Biological condensates are dense and viscoelastic soft matters instead of canonical dilute solutions. To date, numerous different biological condensates have been discovered; but mechanistic understanding of biological condensates remains scarce. In this study, we developed an adaptive single molecule imaging method that allows simultaneous tracking of individual molecules and their motion trajectories in both condensed and dilute phases of various biological condensates. The method enables quantitative measurements of concentrations, phase boundary, motion behavior and speed of molecules in both condensed and dilute phases as well as the scale and speed of molecular exchanges between the two phases. Notably, molecules in the condensed phase do not undergo uniform Brownian motion, but instead constantly switch between a (class of) confined state(s) and a random diffusion-like motion state. Transient confinement is consistent with strong interactions associated with large molecular networks (i.e., percolation) in the condensed phase. In this way, molecules in biological condensates behave distinctly different from those in dilute solutions. The methods and findings described herein should be generally applicable for deciphering the molecular mechanisms underlying the assembly, dynamics and consequently functional implications of biological condensates.

    1. Structural Biology and Molecular Biophysics
    Seoyoon Kim, Daehyo Lee ... Duyoung Min
    Tools and Resources

    Single-molecule tweezers, such as magnetic tweezers, are powerful tools for probing nm-scale structural changes in single membrane proteins under force. However, the weak molecular tethers used for the membrane protein studies have limited the observation of long-time, repetitive molecular transitions due to force-induced bond breakage. The prolonged observation of numerous transitions is critical in reliable characterizations of structural states, kinetics, and energy barrier properties. Here, we present a robust single-molecule tweezer method that uses dibenzocyclooctyne (DBCO) cycloaddition and traptavidin binding, enabling the estimation of the folding 'speed limit' of helical membrane proteins. This method is >100 times more stable than a conventional linkage system regarding the lifetime, allowing for the survival for ~12 h at 50 pN and ~1000 pulling cycle experiments. By using this method, we were able to observe numerous structural transitions of a designer single-chained transmembrane (TM) homodimer for 9 h at 12 pN, and reveal its folding pathway including the hidden dynamics of helix-coil transitions. We characterized the energy barrier heights and folding times for the transitions using a model-independent deconvolution method and the hidden Markov modeling (HMM) analysis, respectively. The Kramers rate framework yields a considerably low speed limit of 21 ms for a helical hairpin formation in lipid bilayers, compared to μs scale for soluble protein folding. This large discrepancy is likely due to the highly viscous nature of lipid membranes, retarding the helix-helix interactions. Our results offer a more valid guideline for relating the kinetics and free energies of membrane protein folding.