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Dynamic personalities of proteins

Author

Listed:
  • Katherine Henzler-Wildman

    (Howard Hughes Medical Institute, Brandeis University)

  • Dorothee Kern

    (Howard Hughes Medical Institute, Brandeis University)

Abstract

Because proteins are central to cellular function, researchers have sought to uncover the secrets of how these complex macromolecules execute such a fascinating variety of functions. Although static structures are known for many proteins, the functions of proteins are governed ultimately by their dynamic character (or 'personality'). The dream is to 'watch' proteins in action in real time at atomic resolution. This requires addition of a fourth dimension, time, to structural biology so that the positions in space and time of all atoms in a protein can be described in detail.

Suggested Citation

  • Katherine Henzler-Wildman & Dorothee Kern, 2007. "Dynamic personalities of proteins," Nature, Nature, vol. 450(7172), pages 964-972, December.
    • Handle: RePEc:nat:nature:v:450:y:2007:i:7172:d:10.1038_nature06522
    DOI: 10.1038/nature06522
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    Cited by:

    1. Maciej Majewski & Adrià Pérez & Philipp Thölke & Stefan Doerr & Nicholas E. Charron & Toni Giorgino & Brooke E. Husic & Cecilia Clementi & Frank Noé & Gianni Fabritiis, 2023. "Machine learning coarse-grained potentials of protein thermodynamics," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    2. Alistair Bailey & Andy van Hateren & Tim Elliott & Jörn M Werner, 2014. "Two Polymorphisms Facilitate Differences in Plasticity between Two Chicken Major Histocompatibility Complex Class I Proteins," PLOS ONE, Public Library of Science, vol. 9(2), pages 1-11, February.
    3. Dong Long & Rafael Brüschweiler, 2011. "In Silico Elucidation of the Recognition Dynamics of Ubiquitin," PLOS Computational Biology, Public Library of Science, vol. 7(4), pages 1-9, April.
    4. Feiyu Zhao & Tao Zhang & Xiaodi Sun & Xiyun Zhang & Letong Chen & Hejun Wang & Jinze Li & Peng Fan & Liangxue Lai & Tingting Sui & Zhanjun Li, 2023. "A strategy for Cas13 miniaturization based on the structure and AlphaFold," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    5. Yi-Ling Chen & Michael Habeck, 2017. "Data-driven coarse graining of large biomolecular structures," PLOS ONE, Public Library of Science, vol. 12(8), pages 1-17, August.
    6. Antony D. St-Jacques & Joshua M. Rodriguez & Matthew G. Eason & Scott M. Foster & Safwat T. Khan & Adam M. Damry & Natalie K. Goto & Michael C. Thompson & Roberto A. Chica, 2023. "Computational remodeling of an enzyme conformational landscape for altered substrate selectivity," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    7. Kalyan S. Chakrabarti & Simon Olsson & Supriya Pratihar & Karin Giller & Kerstin Overkamp & Ko On Lee & Vytautas Gapsys & Kyoung-Seok Ryu & Bert L. Groot & Frank Noé & Stefan Becker & Donghan Lee & Th, 2022. "A litmus test for classifying recognition mechanisms of transiently binding proteins," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    8. César Augusto F de Oliveira & Barry J Grant & Michelle Zhou & J Andrew McCammon, 2011. "Large-Scale Conformational Changes of Trypanosoma cruzi Proline Racemase Predicted by Accelerated Molecular Dynamics Simulation," PLOS Computational Biology, Public Library of Science, vol. 7(10), pages 1-7, October.
    9. Markus Götz & Anders Barth & Søren S.-R. Bohr & Richard Börner & Jixin Chen & Thorben Cordes & Dorothy A. Erie & Christian Gebhardt & Mélodie C. A. S. Hadzic & George L. Hamilton & Nikos S. Hatzakis &, 2022. "A blind benchmark of analysis tools to infer kinetic rate constants from single-molecule FRET trajectories," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    10. Tobias Linder & Bert L de Groot & Anna Stary-Weinzinger, 2013. "Probing the Energy Landscape of Activation Gating of the Bacterial Potassium Channel KcsA," PLOS Computational Biology, Public Library of Science, vol. 9(5), pages 1-9, May.
    11. Oliver F. Harder & Sarah V. Barrass & Marcel Drabbels & Ulrich J. Lorenz, 2023. "Fast viral dynamics revealed by microsecond time-resolved cryo-EM," Nature Communications, Nature, vol. 14(1), pages 1-6, December.
    12. Jochen S Hub & Bert L de Groot, 2009. "Detection of Functional Modes in Protein Dynamics," PLOS Computational Biology, Public Library of Science, vol. 5(8), pages 1-13, August.
    13. Jian-Hua Wang & Yu-Liang Tang & Zhou Gong & Rohit Jain & Fan Xiao & Yu Zhou & Dan Tan & Qiang Li & Niu Huang & Shu-Qun Liu & Keqiong Ye & Chun Tang & Meng-Qiu Dong & Xiaoguang Lei, 2022. "Characterization of protein unfolding by fast cross-linking mass spectrometry using di-ortho-phthalaldehyde cross-linkers," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    14. Eugene Klyshko & Justin Sung-Ho Kim & Lauren McGough & Victoria Valeeva & Ethan Lee & Rama Ranganathan & Sarah Rauscher, 2024. "Functional protein dynamics in a crystal," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    15. 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.
    16. Bryant Gipson & Mark Moll & Lydia E Kavraki, 2013. "SIMS: A Hybrid Method for Rapid Conformational Analysis," PLOS ONE, Public Library of Science, vol. 8(7), pages 1-12, July.
    17. Karain, Wael I., 2019. "Investigating large-amplitude protein loop motions as extreme events using recurrence interval analysis," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 520(C), pages 1-10.
    18. 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.
    19. Jonathan Schubert & Andrea Schulze & Chrisostomos Prodromou & Hannes Neuweiler, 2021. "Two-colour single-molecule photoinduced electron transfer fluorescence imaging microscopy of chaperone dynamics," Nature Communications, Nature, vol. 12(1), pages 1-12, December.

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