IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v12y2021i1d10.1038_s41467-021-27325-1.html
   My bibliography  Save this article

Molecular insights into receptor binding energetics and neutralization of SARS-CoV-2 variants

Author

Listed:
  • Melanie Koehler

    (Université catholique de Louvain)

  • Ankita Ray

    (Université catholique de Louvain)

  • Rodrigo A. Moreira

    (Polish Academy of Sciences)

  • Blinera Juniku

    (Université catholique de Louvain)

  • Adolfo B. Poma

    (Lodz University of Technology)

  • David Alsteens

    (Université catholique de Louvain
    Walloon Excellence in Life sciences and Biotechnology (WELBIO))

Abstract

Despite an unprecedented global gain in knowledge since the emergence of SARS-CoV-2, almost all mechanistic knowledge related to the molecular and cellular details of viral replication, pathology and virulence has been generated using early prototypic isolates of SARS-CoV-2. Here, using atomic force microscopy and molecular dynamics, we investigated how these mutations quantitatively affected the kinetic, thermodynamic and structural properties of RBD—ACE2 complex formation. We observed for several variants of concern a significant increase in the RBD—ACE2 complex stability. While the N501Y and E484Q mutations are particularly important for the greater stability, the N501Y mutation is unlikely to significantly affect antibody neutralization. This work provides unprecedented atomistic detail on the binding of SARS-CoV-2 variants and provides insight into the impact of viral mutations on infection-induced immunity.

Suggested Citation

  • Melanie Koehler & Ankita Ray & Rodrigo A. Moreira & Blinera Juniku & Adolfo B. Poma & David Alsteens, 2021. "Molecular insights into receptor binding energetics and neutralization of SARS-CoV-2 variants," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
  • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-27325-1
    DOI: 10.1038/s41467-021-27325-1
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-021-27325-1
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-021-27325-1?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. Jun Lan & Jiwan Ge & Jinfang Yu & Sisi Shan & Huan Zhou & Shilong Fan & Qi Zhang & Xuanling Shi & Qisheng Wang & Linqi Zhang & Xinquan Wang, 2020. "Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor," Nature, Nature, vol. 581(7807), pages 215-220, May.
    2. Jinsung Yang & Simon J. L. Petitjean & Melanie Koehler & Qingrong Zhang & Andra C. Dumitru & Wenzhang Chen & Sylvie Derclaye & Stéphane P. Vincent & Patrice Soumillion & David Alsteens, 2020. "Molecular interaction and inhibition of SARS-CoV-2 binding to the ACE2 receptor," Nature Communications, Nature, vol. 11(1), pages 1-10, December.
    3. Melanie Koehler & Pavithra Aravamudhan & Camila Guzman-Cardozo & Andra C. Dumitru & Jinsung Yang & Serena Gargiulo & Patrice Soumillion & Terence S. Dermody & David Alsteens, 2019. "Glycan-mediated enhancement of reovirus receptor binding," Nature Communications, Nature, vol. 10(1), pages 1-14, December.
    4. Wenhui Li & Michael J. Moore & Natalya Vasilieva & Jianhua Sui & Swee Kee Wong & Michael A. Berne & Mohan Somasundaran & John L. Sullivan & Katherine Luzuriaga & Thomas C. Greenough & Hyeryun Choe & M, 2003. "Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus," Nature, Nature, vol. 426(6965), pages 450-454, November.
    5. Bryan A. Johnson & Xuping Xie & Adam L. Bailey & Birte Kalveram & Kumari G. Lokugamage & Antonio Muruato & Jing Zou & Xianwen Zhang & Terry Juelich & Jennifer K. Smith & Lihong Zhang & Nathen Bopp & C, 2021. "Loss of furin cleavage site attenuates SARS-CoV-2 pathogenesis," Nature, Nature, vol. 591(7849), pages 293-299, March.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Rong Zhu & Daniel Canena & Mateusz Sikora & Miriam Klausberger & Hannah Seferovic & Ahmad Reza Mehdipour & Lisa Hain & Elisabeth Laurent & Vanessa Monteil & Gerald Wirnsberger & Ralph Wieneke & Robert, 2022. "Force-tuned avidity of spike variant-ACE2 interactions viewed on the single-molecule level," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    2. Amanda R. Goldberg & Kate E. Langwig & Katherine L. Brown & Jeffrey M. Marano & Pallavi Rai & Kelsie M. King & Amanda K. Sharp & Alessandro Ceci & Christopher D. Kailing & Macy J. Kailing & Russell Br, 2024. "Widespread exposure to SARS-CoV-2 in wildlife communities," Nature Communications, Nature, vol. 15(1), pages 1-13, December.

    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. Alexander J. Pak & Alvin Yu & Zunlong Ke & John A. G. Briggs & Gregory A. Voth, 2022. "Cooperative multivalent receptor binding promotes exposure of the SARS-CoV-2 fusion machinery core," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    2. David Chmielewski & Eric A. Wilson & Grigore Pintilie & Peng Zhao & Muyuan Chen & Michael F. Schmid & Graham Simmons & Lance Wells & Jing Jin & Abhishek Singharoy & Wah Chiu, 2023. "Structural insights into the modulation of coronavirus spike tilting and infectivity by hinge glycans," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    3. Chunyan Wang & Emma L. Hesketh & Tatiana M. Shamorkina & Wentao Li & Peter J. Franken & Dubravka Drabek & Rien Haperen & Sarah Townend & Frank J. M. Kuppeveld & Frank Grosveld & Neil A. Ranson & Joost, 2022. "Antigenic structure of the human coronavirus OC43 spike reveals exposed and occluded neutralizing epitopes," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    4. Weiwei Ji & Qi Peng & Xueqiong Fang & Zehou Li & Yaxin Li & Cunfa Xu & Shuqing Zhao & Jizong Li & Rong Chen & Guoxiang Mo & Zhanyong Wei & Ying Xu & Bin Li & Shuijun Zhang, 2022. "Structures of a deltacoronavirus spike protein bound to porcine and human receptors," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    5. Zhenzhen Wang & Shiqi Hu & Kristen D. Popowski & Shuo Liu & Dashuai Zhu & Xuan Mei & Junlang Li & Yilan Hu & Phuong-Uyen C. Dinh & Xiaojie Wang & Ke Cheng, 2024. "Inhalation of ACE2-expressing lung exosomes provides prophylactic protection against SARS-CoV-2," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    6. Behrooz Darbani, 2020. "The Expression and Polymorphism of Entry Machinery for COVID-19 in Human: Juxtaposing Population Groups, Gender, and Different Tissues," IJERPH, MDPI, vol. 17(10), pages 1-8, May.
    7. Hannah McClymont & Wenbiao Hu, 2021. "Weather Variability and COVID-19 Transmission: A Review of Recent Research," IJERPH, MDPI, vol. 18(2), pages 1-19, January.
    8. Indrikis A. Krams & Priit Jõers & Severi Luoto & Giedrius Trakimas & Vilnis Lietuvietis & Ronalds Krams & Irena Kaminska & Markus J. Rantala & Tatjana Krama, 2021. "The Obesity Paradox Predicts the Second Wave of COVID-19 to Be Severe in Western Countries," IJERPH, MDPI, vol. 18(3), pages 1-10, January.
    9. Nikhil Kumar Tulsian & Raghuvamsi Venkata Palur & Xinlei Qian & Yue Gu & Bhuvaneshwari D/O Shunmuganathan & Firdaus Samsudin & Yee Hwa Wong & Jianqing Lin & Kiren Purushotorman & Mary McQueen Kozma & , 2023. "Defining neutralization and allostery by antibodies against COVID-19 variants," Nature Communications, Nature, vol. 14(1), pages 1-23, December.
    10. Shelly J. Robertson & Olivia Bedard & Kristin L. McNally & Carl Shaia & Chad S. Clancy & Matthew Lewis & Rebecca M. Broeckel & Abhilash I. Chiramel & Jeffrey G. Shannon & Gail L. Sturdevant & Rebecca , 2023. "Genetically diverse mouse models of SARS-CoV-2 infection reproduce clinical variation in type I interferon and cytokine responses in COVID-19," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    11. Joseph Dodd-o & Abhishek Roy & Zain Siddiqui & Roya Jafari & Francesco Coppola & Santhamani Ramasamy & Afsal Kolloli & Dilip Kumar & Soni Kaundal & Boyang Zhao & Ranjeet Kumar & Alicia S. Robang & Jef, 2024. "Antiviral fibrils of self-assembled peptides with tunable compositions," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    12. Jian Rong & Ahmed Haider & Troels E. Jeppesen & Lee Josephson & Steven H. Liang, 2023. "Radiochemistry for positron emission tomography," Nature Communications, Nature, vol. 14(1), pages 1-23, December.
    13. Ravindra B. Malabadi & Neelambika T. Meti & Raju K. Chalannavar, 2021. "Role of herbal medicine for controlling coronavirus (SARS-CoV-2) disease (COVID-19)," International Journal of Research and Scientific Innovation, International Journal of Research and Scientific Innovation (IJRSI), vol. 8(2), pages 135-165, February.
    14. Oskar Staufer & Kapil Gupta & Jochen Estebano Hernandez Bücher & Fabian Kohler & Christian Sigl & Gunjita Singh & Kate Vasileiou & Ana Yagüe Relimpio & Meline Macher & Sebastian Fabritz & Hendrik Diet, 2022. "Synthetic virions reveal fatty acid-coupled adaptive immunogenicity of SARS-CoV-2 spike glycoprotein," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    15. Tomokazu Tamura & Jumpei Ito & Keiya Uriu & Jiri Zahradnik & Izumi Kida & Yuki Anraku & Hesham Nasser & Maya Shofa & Yoshitaka Oda & Spyros Lytras & Naganori Nao & Yukari Itakura & Sayaka Deguchi & Ri, 2023. "Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
    16. Diego Fernández-Lázaro & Jerónimo J. González-Bernal & Nerea Sánchez-Serrano & Lourdes Jiménez Navascués & Ana Ascaso-del-Río & Juan Mielgo-Ayuso, 2020. "Physical Exercise as a Multimodal Tool for COVID-19: Could It Be Used as a Preventive Strategy?," IJERPH, MDPI, vol. 17(22), pages 1-13, November.
    17. James Brett Case & Samantha Mackin & John M. Errico & Zhenlu Chong & Emily A. Madden & Bradley Whitener & Barbara Guarino & Michael A. Schmid & Kim Rosenthal & Kuishu Ren & Ha V. Dang & Gyorgy Snell &, 2022. "Resilience of S309 and AZD7442 monoclonal antibody treatments against infection by SARS-CoV-2 Omicron lineage strains," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    18. Simon J. L. Petitjean & Wenzhang Chen & Melanie Koehler & Ravikumar Jimmidi & Jinsung Yang & Danahe Mohammed & Blinera Juniku & Megan L. Stanifer & Steeve Boulant & Stéphane P. Vincent & David Alsteen, 2022. "Multivalent 9-O-Acetylated-sialic acid glycoclusters as potent inhibitors for SARS-CoV-2 infection," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    19. Marysia Wrona & Damian Skrypnik, 2022. "New-Onset Diabetes Mellitus, Hypertension, Dyslipidaemia as Sequelae of COVID-19 Infection—Systematic Review," IJERPH, MDPI, vol. 19(20), pages 1-10, October.
    20. Peter Radvak & Hyung-Joon Kwon & Martina Kosikova & Uriel Ortega-Rodriguez & Ruoxuan Xiang & Je-Nie Phue & Rong-Fong Shen & James Rozzelle & Neeraj Kapoor & Taylor Rabara & Jeff Fairman & Hang Xie, 2021. "SARS-CoV-2 B.1.1.7 (alpha) and B.1.351 (beta) variants induce pathogenic patterns in K18-hACE2 transgenic mice distinct from early strains," Nature Communications, Nature, vol. 12(1), pages 1-15, 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:12:y:2021:i:1:d:10.1038_s41467-021-27325-1. 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.