IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v13y2022i1d10.1038_s41467-022-29416-z.html
   My bibliography  Save this article

Structure-based design of stabilized recombinant influenza neuraminidase tetramers

Author

Listed:
  • Daniel Ellis

    (University of Washington
    University of Washington
    University of Washington
    Icosavax Inc.)

  • Julia Lederhofer

    (National Institutes of Health)

  • Oliver J. Acton

    (University of Washington)

  • Yaroslav Tsybovsky

    (Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute)

  • Sally Kephart

    (University of Washington)

  • Christina Yap

    (National Institutes of Health)

  • Rebecca A. Gillespie

    (National Institutes of Health)

  • Adrian Creanga

    (National Institutes of Health)

  • Audrey Olshefsky

    (University of Washington
    University of Washington)

  • Tyler Stephens

    (Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute)

  • Deleah Pettie

    (University of Washington
    University of Washington)

  • Michael Murphy

    (University of Washington
    University of Washington)

  • Claire Sydeman

    (University of Washington
    University of Washington)

  • Maggie Ahlrichs

    (University of Washington
    University of Washington)

  • Sidney Chan

    (University of Washington
    University of Washington)

  • Andrew J. Borst

    (University of Washington
    University of Washington)

  • Young-Jun Park

    (University of Washington
    University of Washington)

  • Kelly K. Lee

    (University of Washington)

  • Barney S. Graham

    (National Institutes of Health)

  • David Veesler

    (University of Washington
    University of Washington)

  • Neil P. King

    (University of Washington
    University of Washington)

  • Masaru Kanekiyo

    (National Institutes of Health)

Abstract

Influenza virus neuraminidase (NA) is a major antiviral drug target and has recently reemerged as a key target of antibody-mediated protective immunity. Here we show that recombinant NAs across non-bat subtypes adopt various tetrameric conformations, including an “open” state that may help explain poorly understood variations in NA stability across viral strains and subtypes. We use homology-directed protein design to uncover the structural principles underlying these distinct tetrameric conformations and stabilize multiple recombinant NAs in the “closed” state, yielding two near-atomic resolution structures of NA by cryo-EM. In addition to enhancing thermal stability, conformational stabilization improves affinity to protective antibodies elicited by viral infection, including antibodies targeting a quaternary epitope and the broadly conserved catalytic site. Stabilized NAs can also be integrated into viruses without affecting fitness. Our findings provide a deeper understanding of NA structure, stability, and antigenicity, and establish design strategies for reinforcing the conformational integrity of recombinant NA proteins.

Suggested Citation

  • Daniel Ellis & Julia Lederhofer & Oliver J. Acton & Yaroslav Tsybovsky & Sally Kephart & Christina Yap & Rebecca A. Gillespie & Adrian Creanga & Audrey Olshefsky & Tyler Stephens & Deleah Pettie & Mic, 2022. "Structure-based design of stabilized recombinant influenza neuraminidase tetramers," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-29416-z
    DOI: 10.1038/s41467-022-29416-z
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-022-29416-z
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-022-29416-z?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. Susu Duan & Elena A. Govorkova & Justin Bahl & Hassan Zaraket & Tatiana Baranovich & Patrick Seiler & Kristi Prevost & Robert G. Webster & Richard J. Webby, 2014. "Epistatic interactions between neuraminidase mutations facilitated the emergence of the oseltamivir-resistant H1N1 influenza viruses," Nature Communications, Nature, vol. 5(1), pages 1-12, December.
    2. Sarel J Fleishman & Andrew Leaver-Fay & Jacob E Corn & Eva-Maria Strauch & Sagar D Khare & Nobuyasu Koga & Justin Ashworth & Paul Murphy & Florian Richter & Gordon Lemmon & Jens Meiler & David Baker, 2011. "RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite," PLOS ONE, Public Library of Science, vol. 6(6), pages 1-10, June.
    3. Kwinten Sliepen & Byung Woo Han & Ilja Bontjer & Petra Mooij & Fernando Garces & Anna-Janina Behrens & Kimmo Rantalainen & Sonu Kumar & Anita Sarkar & Philip J. M. Brouwer & Yuanzi Hua & Monica Tolazz, 2019. "Structure and immunogenicity of a stabilized HIV-1 envelope trimer based on a group-M consensus sequence," Nature Communications, Nature, vol. 10(1), pages 1-16, December.
    4. Gabriel Ozorowski & Jesper Pallesen & Natalia de Val & Dmitry Lyumkis & Christopher A. Cottrell & Jonathan L. Torres & Jeffrey Copps & Robyn L. Stanfield & Albert Cupo & Pavel Pugach & John P. Moore &, 2017. "Open and closed structures reveal allostery and pliability in the HIV-1 envelope spike," Nature, Nature, vol. 547(7663), pages 360-363, July.
    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. Thomas W. Linsky & Kyle Noble & Autumn R. Tobin & Rachel Crow & Lauren Carter & Jeffrey L. Urbauer & David Baker & Eva-Maria Strauch, 2022. "Sampling of structure and sequence space of small protein folds," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    2. Durgadevi Parthasarathy & Karunakar Reddy Pothula & Sneha Ratnapriya & Héctor Cervera Benet & Ruth Parsons & Xiao Huang & Salam Sammour & Katarzyna Janowska & Miranda Harris & Joseph Sodroski & Priyam, 2024. "Conformational flexibility of HIV-1 envelope glycoproteins modulates transmitted/founder sensitivity to broadly neutralizing antibodies," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    3. Alexander M Sevy & Tim M Jacobs & James E Crowe Jr. & Jens Meiler, 2015. "Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences," PLOS Computational Biology, Public Library of Science, vol. 11(7), pages 1-23, July.
    4. Jinliang Guo & Shangrong Li & Lisha Bai & Huimin Zhao & Wenyu Shang & Zhaojun Zhong & Tuerxunjiang Maimaiti & Xueyan Gao & Ning Ji & Yanjie Chao & Zhaofei Li & Dijun Du, 2024. "Structural transition of GP64 triggered by a pH-sensitive multi-histidine switch," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    5. Jonathan Yaacov Weinstein & Carlos Martí-Gómez & Rosalie Lipsh-Sokolik & Shlomo Yakir Hoch & Demian Liebermann & Reinat Nevo & Haim Weissman & Ekaterina Petrovich-Kopitman & David Margulies & Dmitry I, 2023. "Designed active-site library reveals thousands of functional GFP variants," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    6. Zhi Yang & Kim-Marie A. Dam & Michael D. Bridges & Magnus A. G. Hoffmann & Andrew T. DeLaitsch & Harry B. Gristick & Amelia Escolano & Rajeev Gautam & Malcolm A. Martin & Michel C. Nussenzweig & Wayne, 2022. "Neutralizing antibodies induced in immunized macaques recognize the CD4-binding site on an occluded-open HIV-1 envelope trimer," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    7. Jared Adolf-Bryfogle & Oleks Kalyuzhniy & Michael Kubitz & Brian D Weitzner & Xiaozhen Hu & Yumiko Adachi & William R Schief & Roland L Dunbrack Jr., 2018. "RosettaAntibodyDesign (RAbD): A general framework for computational antibody design," PLOS Computational Biology, Public Library of Science, vol. 14(4), pages 1-38, April.
    8. Vishruth Mullapudi & Jaime Vaquer-Alicea & Vaibhav Bommareddy & Anthony R. Vega & Bryan D. Ryder & Charles L. White & Marc. I. Diamond & Lukasz A. Joachimiak, 2023. "Network of hotspot interactions cluster tau amyloid folds," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    9. Jun Niu & Qi Wang & Wenwen Zhao & Bing Meng & Youwei Xu & Xianfang Zhang & Yi Feng & Qilian Qi & Yanling Hao & Xuan Zhang & Ying Liu & Jiangchao Xiang & Yiming Shao & Bei Yang, 2023. "Structures and immune recognition of Env trimers from two Asia prevalent HIV-1 CRFs," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    10. P. Konstantin Richter & Paula Blázquez-Sánchez & Ziyue Zhao & Felipe Engelberger & Christian Wiebeler & Georg Künze & Ronny Frank & Dana Krinke & Emanuele Frezzotti & Yuliia Lihanova & Patricia Falken, 2023. "Structure and function of the metagenomic plastic-degrading polyester hydrolase PHL7 bound to its product," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    11. Jorge Roel-Touris & Marta Nadal & Enrique Marcos, 2023. "Single-chain dimers from de novo immunoglobulins as robust scaffolds for multiple binding loops," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    12. Yi-Nan Zhang & Jennifer Paynter & Aleksandar Antanasijevic & Joel D. Allen & Mor Eldad & Yi-Zong Lee & Jeffrey Copps & Maddy L. Newby & Linling He & Deborah Chavez & Pat Frost & Anna Goodroe & John Du, 2023. "Single-component multilayered self-assembling protein nanoparticles presenting glycan-trimmed uncleaved prefusion optimized envelope trimers as HIV-1 vaccine candidates," Nature Communications, Nature, vol. 14(1), pages 1-29, December.
    13. Ruipeng Lei & Timothy J. C. Tan & Andrea Hernandez Garcia & Yiquan Wang & Meghan Diefenbacher & Chuyun Teo & Gopika Gopan & Zahra Tavakoli Dargani & Qi Wen Teo & Claire S. Graham & Christopher B. Broo, 2022. "Prevalence and mechanisms of evolutionary contingency in human influenza H3N2 neuraminidase," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    14. Diego del Alamo & Kevin L Jagessar & Jens Meiler & Hassane S Mchaourab, 2021. "Methodology for rigorous modeling of protein conformational changes by Rosetta using DEER Distance Restraints," PLOS Computational Biology, Public Library of Science, vol. 17(6), pages 1-18, June.
    15. Julia Skokowa & Birte Hernandez Alvarez & Murray Coles & Malte Ritter & Masoud Nasri & Jérémy Haaf & Narges Aghaallaei & Yun Xu & Perihan Mir & Ann-Christin Krahl & Katherine W. Rogers & Kateryna Maks, 2022. "A topological refactoring design strategy yields highly stable granulopoietic proteins," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    16. Tamuka M. Chidyausiku & Soraia R. Mendes & Jason C. Klima & Marta Nadal & Ulrich Eckhard & Jorge Roel-Touris & Scott Houliston & Tibisay Guevara & Hugh K. Haddox & Adam Moyer & Cheryl H. Arrowsmith & , 2022. "De novo design of immunoglobulin-like domains," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    17. Jaume Bonet & Sarah Wehrle & Karen Schriever & Che Yang & Anne Billet & Fabian Sesterhenn & Andreas Scheck & Freyr Sverrisson & Barbora Veselkova & Sabrina Vollers & Roxanne Lourman & Mélanie Villard , 2018. "Rosetta FunFolDes – A general framework for the computational design of functional proteins," PLOS Computational Biology, Public Library of Science, vol. 14(11), pages 1-30, November.
    18. Sowmiya Palani & Yuka Machida & Julia R. Alvey & Vandana Mishra & Allison L. Welter & Gaofeng Cui & Benoît Bragantini & Maria Victoria Botuyan & Anh T. Q. Cong & Georges Mer & Matthew J. Schellenberg , 2024. "Dimerization-dependent serine protease activity of FAM111A prevents replication fork stalling at topoisomerase 1 cleavage complexes," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    19. Mathieu Claireaux & Tom G. Caniels & Marlon Gast & Julianna Han & Denise Guerra & Gius Kerster & Barbera D. C. Schaik & Aldo Jongejan & Angela I. Schriek & Marloes Grobben & Philip J. M. Brouwer & Kar, 2022. "A public antibody class recognizes an S2 epitope exposed on open conformations of SARS-CoV-2 spike," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    20. Kristin J. Adolfsen & Isolde Callihan & Catherine E. Monahan & Per Jr. Greisen & James Spoonamore & Munira Momin & Lauren E. Fitch & Mary Joan Castillo & Lindong Weng & Lauren Renaud & Carl J. Weile &, 2021. "Improvement of a synthetic live bacterial therapeutic for phenylketonuria with biosensor-enabled enzyme engineering," Nature Communications, Nature, vol. 12(1), pages 1-13, December.

    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:13:y:2022:i:1:d:10.1038_s41467-022-29416-z. 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.