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Buchanan CJ, Gaunt B, Harrison PJ, Yang Y, Liu J, Khan A, Giltrap AM, Le Bas A, Ward PN, Gupta K, Dumoux M, Tan TK, Schimaski L, Daga S, Picchiotti N, Baldassarri M, Benetti E, Fallerini C, Fava F, Giliberti A, Koukos PI, Davy MJ, Lakshminarayanan A, Xue X, Papadakis G, Deimel LP, Casablancas-Antràs V, Claridge TDW, Bonvin AMJJ, Sattentau QJ, Furini S, Gori M, Huo J, Owens RJ, Schaffitzel C, Berger I, Renieri A, Naismith JH, Baldwin AJ, Davis BG. Pathogen-sugar interactions revealed by universal saturation transfer analysis. Science 2022; 377:eabm3125. [PMID: 35737812 DOI: 10.1126/science.abm3125] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Many pathogens exploit host cell-surface glycans. However, precise analyses of glycan ligands binding with heavily modified pathogen proteins can be confounded by overlapping sugar signals and/or compounded with known experimental constraints. Universal saturation transfer analysis (uSTA) builds on existing nuclear magnetic resonance spectroscopy to provide an automated workflow for quantitating protein-ligand interactions. uSTA reveals that early-pandemic, B-origin-lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike trimer binds sialoside sugars in an "end-on" manner. uSTA-guided modeling and a high-resolution cryo-electron microscopy structure implicate the spike N-terminal domain (NTD) and confirm end-on binding. This finding rationalizes the effect of NTD mutations that abolish sugar binding in SARS-CoV-2 variants of concern. Together with genetic variance analyses in early pandemic patient cohorts, this binding implicates a sialylated polylactosamine motif found on tetraantennary N-linked glycoproteins deep in the human lung as potentially relevant to virulence and/or zoonosis.
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Affiliation(s)
- Charles J Buchanan
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK.,Kavli Institute of Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | - Ben Gaunt
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK
| | - Peter J Harrison
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK.,Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire, UK
| | - Yun Yang
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK
| | - Jiwei Liu
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK
| | - Aziz Khan
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Andrew M Giltrap
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Audrey Le Bas
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK
| | - Philip N Ward
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK
| | - Kapil Gupta
- Max Planck Bristol Centre for Minimal Biology, University of Bristol, Bristol, UK
| | - Maud Dumoux
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK
| | - Tiong Kit Tan
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Lisa Schimaski
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Sergio Daga
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Nicola Picchiotti
- Department of Information Engineering and Mathematics, University of Siena, Siena, Italy.,Department of Mathematics, University of Pavia, Pavia, Italy
| | - Margherita Baldassarri
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Elisa Benetti
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Chiara Fallerini
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Francesca Fava
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Annarita Giliberti
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Panagiotis I Koukos
- Bijvoet Centre for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Matthew J Davy
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK
| | - Abirami Lakshminarayanan
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Xiaochao Xue
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK.,Sir William Dunn School of Pathology, Oxford, UK
| | | | | | - Virgínia Casablancas-Antràs
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK.,Kavli Institute of Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | | | - Alexandre M J J Bonvin
- Bijvoet Centre for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | | | - Simone Furini
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Marco Gori
- Department of Information Engineering and Mathematics, University of Siena, Siena, Italy.,Maasai, I3S CNRS, Université Côte d'Azur, Nice, France
| | - Jiandong Huo
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK
| | - Raymond J Owens
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK
| | - Christiane Schaffitzel
- Bijvoet Centre for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Imre Berger
- Bijvoet Centre for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | | | - James H Naismith
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK
| | - Andrew J Baldwin
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK.,Kavli Institute of Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | - Benjamin G Davis
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK.,Department of Pharmacology, University of Oxford, Oxford OX1 3QT, UK
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