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

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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.

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Daniel A Keedy

Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States

Competing interests
No competing interests declared.
Lillian R Kenner

Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States

Competing interests
No competing interests declared.
Matthew Warkentin

Physics Department, Cornell University, Ithaca, United States

Competing interests
No competing interests declared.
Rahel A Woldeyes

Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States

Competing interests
No competing interests declared.
Jesse B Hopkins

Physics Department, Cornell University, Ithaca, United States

Competing interests
No competing interests declared.
Michael C Thompson

Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States

Competing interests
No competing interests declared.
Aaron S Brewster

Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States

Competing interests
No competing interests declared.
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.
Elizabeth L Baxter

Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States

Competing interests
No competing interests declared.
Monarin Uervirojnangkoorn

Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States

Competing interests
No competing interests declared.
Scott E McPhillips

Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States

Competing interests
No competing interests declared.
Jinhu Song

Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States

Competing interests
No competing interests declared.
Roberto Alonso-Mori

Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, United States

Competing interests
No competing interests declared.
James M Holton

Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States

Competing interests
No competing interests declared.
William I Weis

Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States

Competing interests
No competing interests declared.
Axel T Brunger

Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States

Competing interests
Axel T Brunger, Reviewing editor, eLife.
S Michael Soltis

Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States

Competing interests
No competing interests declared.
Henrik Lemke

Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, United States

Competing interests
No competing interests declared.
Ana Gonzalez

Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States

Competing interests
No competing interests declared.
Nicholas K Sauter

Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States

Competing interests
No competing interests declared.
Aina E Cohen

Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States

Competing interests
No competing interests declared.
Henry van den Bedem

Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States

Competing interests
No competing interests declared.
Robert E Thorne

Physics Department, Cornell University, Ithaca, United States

Competing interests
No competing interests declared.
James S Fraser

Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States

For correspondence
jfraser@fraserlab.com

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No competing interests declared.

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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.