IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v15y2024i1d10.1038_s41467-024-54912-9.html
   My bibliography  Save this article

3D variability analysis reveals a hidden conformational change controlling ammonia transport in human asparagine synthetase

Author

Listed:
  • Adriana Coricello

    (Università “Magna Græcia” di Catanzaro
    Università degli Studi di Urbino “Carlo Bo”)

  • Alanya J. Nardone

    (Florida State University)

  • Antonio Lupia

    (Università “Magna Græcia” di Catanzaro
    Università degli Studi di Cagliari)

  • Carmen Gratteri

    (Università “Magna Græcia” di Catanzaro)

  • Matthijn Vos

    (Institut Pasteur)

  • Vincent Chaptal

    (University of Lyon)

  • Stefano Alcaro

    (Università “Magna Græcia” di Catanzaro
    Università “Magna Græcia” di Catanzaro)

  • Wen Zhu

    (Florida State University)

  • Yuichiro Takagi

    (Indiana University School of Medicine)

  • Nigel G. J. Richards

    (Cardiff University
    Foundation for Applied Molecular Evolution)

Abstract

Advances in X-ray crystallography and cryogenic electron microscopy (cryo-EM) offer the promise of elucidating functionally relevant conformational changes that are not easily studied by other biophysical methods. Here we show that 3D variability analysis (3DVA) of the cryo-EM map for wild-type (WT) human asparagine synthetase (ASNS) identifies a functional role for the Arg-142 side chain and test this hypothesis experimentally by characterizing the R142I variant in which Arg-142 is replaced by isoleucine. Support for Arg-142 playing a role in the intramolecular translocation of ammonia between the active site of the enzyme is provided by the glutamine-dependent synthetase activity of the R142 variant relative to WT ASNS, and MD simulations provide a possible molecular mechanism for these findings. Combining 3DVA with MD simulations is a generally applicable approach to generate testable hypotheses of how conformational changes in buried side chains might regulate function in enzymes.

Suggested Citation

  • Adriana Coricello & Alanya J. Nardone & Antonio Lupia & Carmen Gratteri & Matthijn Vos & Vincent Chaptal & Stefano Alcaro & Wen Zhu & Yuichiro Takagi & Nigel G. J. Richards, 2024. "3D variability analysis reveals a hidden conformational change controlling ammonia transport in human asparagine synthetase," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-54912-9
    DOI: 10.1038/s41467-024-54912-9
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-024-54912-9
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-024-54912-9?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Jan Philip Wurm & Sihyun Sung & Andrea Christa Kneuttinger & Enrico Hupfeld & Reinhard Sterner & Matthias Wilmanns & Remco Sprangers, 2021. "Molecular basis for the allosteric activation mechanism of the heterodimeric imidazole glycerol phosphate synthase complex," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    2. Federica Maschietto & Uriel N. Morzan & Florentina Tofoleanu & Aria Gheeraert & Apala Chaudhuri & Gregory W. Kyro & Peter Nekrasov & Bernard Brooks & J. Patrick Loria & Ivan Rivalta & Victor S. Batist, 2023. "Turning up the heat mimics allosteric signaling in imidazole-glycerol phosphate synthase," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    3. Elan Z. Eisenmesser & Oscar Millet & Wladimir Labeikovsky & Dmitry M. Korzhnev & Magnus Wolf-Watz & Daryl A. Bosco & Jack J. Skalicky & Lewis E. Kay & Dorothee Kern, 2005. "Intrinsic dynamics of an enzyme underlies catalysis," Nature, Nature, vol. 438(7064), pages 117-121, November.
    4. Hyun Joo & Zhanglin Lin & Frances H. Arnold, 1999. "Laboratory evolution of peroxide-mediated cytochrome P450 hydroxylation," Nature, Nature, vol. 399(6737), pages 670-673, June.
    5. 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.
    6. Federica Maschietto & Uriel N. Morzan & Florentina Tofoleanu & Aria Gheeraert & Apala Chaudhuri & Gregory W. Kyro & Peter Nekrasov & Bernard Brooks & J. Patrick Loria & Ivan Rivalta & Victor S. Batist, 2023. "Author Correction: Turning up the heat mimics allosteric signaling in imidazole-glycerol phosphate synthase," Nature Communications, Nature, vol. 14(1), pages 1-1, December.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    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.
    2. 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.
    3. 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.
    4. 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.
    5. Timothy R Lezon & Ivet Bahar, 2010. "Using Entropy Maximization to Understand the Determinants of Structural Dynamics beyond Native Contact Topology," PLOS Computational Biology, Public Library of Science, vol. 6(6), pages 1-12, June.
    6. Santiago Esteban-Martín & Robert Bryn Fenwick & Jörgen Ådén & Benjamin Cossins & Carlos W Bertoncini & Victor Guallar & Magnus Wolf-Watz & Xavier Salvatella, 2014. "Correlated Inter-Domain Motions in Adenylate Kinase," PLOS Computational Biology, Public Library of Science, vol. 10(7), pages 1-7, July.
    7. 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).
    8. Gregory D Friedland & Nils-Alexander Lakomek & Christian Griesinger & Jens Meiler & Tanja Kortemme, 2009. "A Correspondence Between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family," PLOS Computational Biology, Public Library of Science, vol. 5(5), pages 1-16, May.
    9. Giacomo Janson & Gilberto Valdes-Garcia & Lim Heo & Michael Feig, 2023. "Direct generation of protein conformational ensembles via machine learning," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    10. Federica Maschietto & Uriel N. Morzan & Florentina Tofoleanu & Aria Gheeraert & Apala Chaudhuri & Gregory W. Kyro & Peter Nekrasov & Bernard Brooks & J. Patrick Loria & Ivan Rivalta & Victor S. Batist, 2023. "Turning up the heat mimics allosteric signaling in imidazole-glycerol phosphate synthase," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    11. 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.
    12. Torgeir R Hvidsten & Astrid Lægreid & Andriy Kryshtafovych & Gunnar Andersson & Krzysztof Fidelis & Jan Komorowski, 2009. "A Comprehensive Analysis of the Structure-Function Relationship in Proteins Based on Local Structure Similarity," PLOS ONE, Public Library of Science, vol. 4(7), pages 1-9, July.
    13. 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.
    14. 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.
    15. 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.
    16. 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.
    17. Fabian Paul & Thomas R Weikl, 2016. "How to Distinguish Conformational Selection and Induced Fit Based on Chemical Relaxation Rates," PLOS Computational Biology, Public Library of Science, vol. 12(9), pages 1-17, September.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-54912-9. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.