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A hierarchy of timescales in protein dynamics is linked to enzyme catalysis

Author

Listed:
  • Katherine A. Henzler-Wildman

    (Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02454, USA)

  • Ming Lei

    (Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02454, USA)

  • Vu Thai

    (Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02454, USA)

  • S. Jordan Kerns

    (Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02454, USA)

  • Martin Karplus

    (Harvard University, Cambridge, Massachusetts 02138, USA
    Laboratoire de Chimie Biophysique, Institut de Science et d’ Ingenierie Supramoleculaires, Universite Louis Pasteur, 8 rue Gaspard Monge, F-67000 Strasbourg, France)

  • Dorothee Kern

    (Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02454, USA)

Abstract

Pico-to-nanosecond timescale atomic fluctuations in hinge regions of adenylate kinase facilitate the large-scale, slower lid motions that produce a catalytically competent state.

Suggested Citation

  • Katherine A. Henzler-Wildman & Ming Lei & Vu Thai & S. Jordan Kerns & Martin Karplus & Dorothee Kern, 2007. "A hierarchy of timescales in protein dynamics is linked to enzyme catalysis," Nature, Nature, vol. 450(7171), pages 913-916, December.
    • Handle: RePEc:nat:nature:v:450:y:2007:i:7171:d:10.1038_nature06407
    DOI: 10.1038/nature06407
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    Cited by:

    1. Rachel J. Roth Flach & Eliza Bollinger & Allan R. Reyes & Brigitte Laforest & Bethany L. Kormos & Shenping Liu & Matthew R. Reese & Luis A. Martinez Alsina & Leanne Buzon & Yuan Zhang & Bruce Bechle &, 2023. "Small molecule branched-chain ketoacid dehydrogenase kinase (BDK) inhibitors with opposing effects on BDK protein levels," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    2. Kenkre, V.M. & Spendier, K., 2022. "A theory of coalescence of signaling receptor clusters in immune cells," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 602(C).
    3. Jin Liu & Ruth Nussinov, 2009. "The Mechanism of Ubiquitination in the Cullin-RING E3 Ligase Machinery: Conformational Control of Substrate Orientation," PLOS Computational Biology, Public Library of Science, vol. 5(10), pages 1-10, October.
    4. Michael A Jamros & Leandro C Oliveira & Paul C Whitford & José N Onuchic & Joseph A Adams & Patricia A Jennings, 2012. "Substrate-Specific Reorganization of the Conformational Ensemble of CSK Implicates Novel Modes of Kinase Function," PLOS Computational Biology, Public Library of Science, vol. 8(9), pages 1-8, September.
    5. 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.
    6. Sean L Seyler & Avishek Kumar & M F Thorpe & Oliver Beckstein, 2015. "Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways," PLOS Computational Biology, Public Library of Science, vol. 11(10), pages 1-37, October.
    7. James O Wrabl & Vincent J Hilser, 2010. "Investigating Homology between Proteins using Energetic Profiles," PLOS Computational Biology, Public Library of Science, vol. 6(3), pages 1-17, March.
    8. Wojciech Potrzebowski & Jill Trewhella & Ingemar Andre, 2018. "Bayesian inference of protein conformational ensembles from limited structural data," PLOS Computational Biology, Public Library of Science, vol. 14(12), pages 1-27, December.

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