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Slow conformational exchange and overall rocking motion in ubiquitin protein crystals

Author

Listed:
  • Vilius Kurauskas

    (Université Grenoble Alpes
    CEA, Institut de Biologie Structurale
    CNRS, Institut de Biologie Structurale)

  • Sergei A. Izmailov

    (St. Petersburg State University)

  • Olga N. Rogacheva

    (St. Petersburg State University)

  • Audrey Hessel

    (Université Grenoble Alpes
    CEA, Institut de Biologie Structurale
    CNRS, Institut de Biologie Structurale)

  • Isabel Ayala

    (Université Grenoble Alpes
    CEA, Institut de Biologie Structurale
    CNRS, Institut de Biologie Structurale)

  • Joyce Woodhouse

    (Université Grenoble Alpes
    CEA, Institut de Biologie Structurale
    CNRS, Institut de Biologie Structurale)

  • Anastasya Shilova

    (European Synchrotron Radiation Facility)

  • Yi Xue

    (Purdue University)

  • Tairan Yuwen

    (Purdue University)

  • Nicolas Coquelle

    (Université Grenoble Alpes
    CEA, Institut de Biologie Structurale
    CNRS, Institut de Biologie Structurale)

  • Jacques-Philippe Colletier

    (Université Grenoble Alpes
    CEA, Institut de Biologie Structurale
    CNRS, Institut de Biologie Structurale)

  • Nikolai R. Skrynnikov

    (St. Petersburg State University
    Purdue University)

  • Paul Schanda

    (Université Grenoble Alpes
    CEA, Institut de Biologie Structurale
    CNRS, Institut de Biologie Structurale)

Abstract

Proteins perform their functions in solution but their structures are most frequently studied inside crystals. Here we probe how the crystal packing alters microsecond dynamics, using solid-state NMR measurements and multi-microsecond MD simulations of different crystal forms of ubiquitin. In particular, near-rotary-resonance relaxation dispersion (NERRD) experiments probe angular backbone motion, while Bloch–McConnell relaxation dispersion data report on fluctuations of the local electronic environment. These experiments and simulations reveal that the packing of the protein can significantly alter the thermodynamics and kinetics of local conformational exchange. Moreover, we report small-amplitude reorientational motion of protein molecules in the crystal lattice with an ~3–5° amplitude on a tens-of-microseconds time scale in one of the crystals, but not in others. An intriguing possibility arises that overall motion is to some extent coupled to local dynamics. Our study highlights the importance of considering the packing when analyzing dynamics of crystalline proteins.

Suggested Citation

  • Vilius Kurauskas & Sergei A. Izmailov & Olga N. Rogacheva & Audrey Hessel & Isabel Ayala & Joyce Woodhouse & Anastasya Shilova & Yi Xue & Tairan Yuwen & Nicolas Coquelle & Jacques-Philippe Colletier &, 2017. "Slow conformational exchange and overall rocking motion in ubiquitin protein crystals," Nature Communications, Nature, vol. 8(1), pages 1-12, December.
  • Handle: RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_s41467-017-00165-8
    DOI: 10.1038/s41467-017-00165-8
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    Cited by:

    1. Diego F. Gauto & Pavel Macek & Duccio Malinverni & Hugo Fraga & Matteo Paloni & Iva Sučec & Audrey Hessel & Juan Pablo Bustamante & Alessandro Barducci & Paul Schanda, 2022. "Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR," Nature Communications, Nature, vol. 13(1), pages 1-13, December.

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