Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography

  1. Daniel A Keedy
  2. Lillian R Kenner
  3. Matthew Warkentin
  4. Rahel A Woldeyes
  5. Jesse B Hopkins
  6. Michael C Thompson
  7. Aaron S Brewster
  8. Andrew H Van Benschoten
  9. Elizabeth L Baxter
  10. Monarin Uervirojnangkoorn
  11. Scott E McPhillips
  12. Jinhu Song
  13. Roberto Alonso-Mori
  14. James M Holton
  15. William I Weis
  16. Axel T Brunger
  17. S Michael Soltis
  18. Henrik Lemke
  19. Ana Gonzalez
  20. Nicholas K Sauter
  21. Aina E Cohen
  22. Henry van den Bedem
  23. Robert E Thorne
  24. James S Fraser  Is a corresponding author
  1. University of California, San Francisco, United States
  2. Cornell University, United States
  3. Lawrence Berkeley National Laboratory, United States
  4. SLAC National Accelerator Laboratory, United States
  5. Stanford University, United States

Abstract

Determining the interconverting conformations of dynamic proteins in atomic detail is a major challenge for structural biology. Conformational heterogeneity in the active site of the dynamic enzyme cyclophilin A (CypA) has been previously linked to its catalytic function, but the extent to which the different conformations of these residues are correlated is unclear. We monitored the temperature dependences of these alternative conformations with eight synchrotron datasets spanning 100-310 K. Multiconformer models show that many alternative conformations in CypA are populated only at 240 K and above, yet others remain populated or become populated at 180 K and below. These results point to a complex evolution of conformational heterogeneity between 180-240 K that involves both thermal deactivation and solvent-driven arrest of protein motions in the crystal. Together, our multitemperature analyses and XFEL data motivate a new generation of temperature- and time-resolved experiments to structurally characterize the dynamic underpinnings of protein function.

Article and author information

Author details

  1. Daniel A Keedy

    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
    Competing interests
    No competing interests declared.
  2. Lillian R Kenner

    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
    Competing interests
    No competing interests declared.
  3. Matthew Warkentin

    Physics Department, Cornell University, Ithaca, United States
    Competing interests
    No competing interests declared.
  4. Rahel A Woldeyes

    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
    Competing interests
    No competing interests declared.
  5. Jesse B Hopkins

    Physics Department, Cornell University, Ithaca, United States
    Competing interests
    No competing interests declared.
  6. Michael C Thompson

    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
    Competing interests
    No competing interests declared.
  7. Aaron S Brewster

    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States
    Competing interests
    No competing interests declared.
  8. Andrew H Van Benschoten

    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
    Competing interests
    No competing interests declared.
  9. Elizabeth L Baxter

    Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States
    Competing interests
    No competing interests declared.
  10. Monarin Uervirojnangkoorn

    Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States
    Competing interests
    No competing interests declared.
  11. Scott E McPhillips

    Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States
    Competing interests
    No competing interests declared.
  12. Jinhu Song

    Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States
    Competing interests
    No competing interests declared.
  13. Roberto Alonso-Mori

    Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, United States
    Competing interests
    No competing interests declared.
  14. James M Holton

    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States
    Competing interests
    No competing interests declared.
  15. William I Weis

    Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States
    Competing interests
    No competing interests declared.
  16. Axel T Brunger

    Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States
    Competing interests
    Axel T Brunger, Reviewing editor, eLife.
  17. S Michael Soltis

    Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States
    Competing interests
    No competing interests declared.
  18. Henrik Lemke

    Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, United States
    Competing interests
    No competing interests declared.
  19. Ana Gonzalez

    Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States
    Competing interests
    No competing interests declared.
  20. Nicholas K Sauter

    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States
    Competing interests
    No competing interests declared.
  21. Aina E Cohen

    Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States
    Competing interests
    No competing interests declared.
  22. Henry van den Bedem

    Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States
    Competing interests
    No competing interests declared.
  23. Robert E Thorne

    Physics Department, Cornell University, Ithaca, United States
    Competing interests
    No competing interests declared.
  24. James S Fraser

    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
    For correspondence
    jfraser@fraserlab.com
    Competing interests
    No competing interests declared.

Reviewing Editor

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

Publication history

  1. Received: March 19, 2015
  2. Accepted: September 29, 2015
  3. Accepted Manuscript published: September 30, 2015 (version 1)
  4. Version of Record published: December 23, 2015 (version 2)

Copyright

© 2015, Keedy 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.

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  1. Daniel A Keedy
  2. Lillian R Kenner
  3. Matthew Warkentin
  4. Rahel A Woldeyes
  5. Jesse B Hopkins
  6. Michael C Thompson
  7. Aaron S Brewster
  8. Andrew H Van Benschoten
  9. Elizabeth L Baxter
  10. Monarin Uervirojnangkoorn
  11. Scott E McPhillips
  12. Jinhu Song
  13. Roberto Alonso-Mori
  14. James M Holton
  15. William I Weis
  16. Axel T Brunger
  17. S Michael Soltis
  18. Henrik Lemke
  19. Ana Gonzalez
  20. Nicholas K Sauter
  21. Aina E Cohen
  22. Henry van den Bedem
  23. Robert E Thorne
  24. James S Fraser
(2015)
Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography
eLife 4:e07574.
https://doi.org/10.7554/eLife.07574

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