Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site
Open accessAbstract
Many viral surface glycoproteins and cell surface receptors are homo-oligomers, and thus can potentially be targeted by geometrically matched homo-oligomers that engage all subunits simultaneously to attain high avidity and/or lock subunits together. The adaptive immune system cannot generally employ this strategy since the individual antibody binding sites are not arranged with appropriate geometry to simultaneously engage multiple sites in a single target homo-oligomer. We describe a general strategy for the computational design of homo-oligomeric protein assemblies with binding functionality precisely matched to homo-oligomeric target sites. In the first step, a small protein is designed that binds a single site on the target. In the second step, the designed protein is assembled into a homo-oligomer such that the designed binding sites are aligned with the target sites. We use this approach to design high-avidity trimeric proteins that bind influenza A hemagglutinin (HA) at its conserved receptor binding site. The designed trimers can both capture and detect HA in a paper-based diagnostic format, neutralizes influenza in cell culture, and completely protects mice when given as a single dose 24 h before or after challenge with influenza.
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Most current computational methods used to design proteins that bind to a target surface utilize information derived from structures of the native complex on specific side-chain interactions or protein backbone placements optimal for binding.
“Most current computational methods used to design proteins that bind to a target surface utilize information derived from structures of the native complex on specific side-chain interactions or protein backbone placements optimal for binding1–3.”
From Design of protein-binding proteins from the target structure alone (2022) · cites this paper as [2]
Designing proteins that bind to a specific site on the surface of a target protein using no information other than the three-dimensional structure of the target remains a challenge.
“The design of proteins that bind to a specific site on the surface of a target protein using no information other than the three-dimensional structure of the target remains a challenge1–5.”
From Design of protein-binding proteins from the target structure alone (2022) · cites this paper as [2]
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Cites
[20] Processing of X-ray diffraction data collected in oscillation mode
Otwinowski, Z., & Minor, W. (1997) · Methods in Enzymology · doi:10.1016/s0076-6879(97)76066-x · Cited by 33,475 · see citing works
<i>Coot</i> : model-building tools for molecular graphics
Emsley, P., & Cowtan, K. (2004) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444904019158 · Cited by 30,571 · see citing works
<i>PHENIX</i> : a comprehensive Python-based system for macromolecular structure solution
Adams, P. D., Afonine, P. V., Bunkóczi, G., Chen, V. B., Davis, I. W., Echols, N., Headd, J. J., Hung, L.-W., Kapral, G. J., Grosse-Kunstleve, R. W., et al. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444909052925 · Cited by 23,716 · see citing works
<i>Phaser</i> crystallographic software
McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C., & Read, R. J. (2007) · Journal of Applied Crystallography · doi:10.1107/s0021889807021206 · Cited by 20,612 · see citing works
<i>MolProbity</i> : all-atom structure validation for macromolecular crystallography
Chen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S., & Richardson, D. C. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444909042073 · Cited by 14,115 · see citing works
MUSCLE: a multiple sequence alignment method with reduced time and space complexity
Edgar, R. C. (2004) · BMC Bioinformatics · doi:10.1186/1471-2105-5-113 · Cited by 8,879 · see citing works
PHENIX: a comprehensive Python-based system for macromolecular structure solution
Adams, P. D., Afonine, P. V., Bunkòczi, G., Chen, V. B., Davis, I., Echols, N., Headd, J. J., Hung, L., Kapral, G. J., Grosse‐Kunstleve, R. W., et al. (2012) · International Tables for Crystallography · doi:10.1107/97809553602060000865 · Cited by 7,334 · see citing works
Svergun, D. I. (1992) · Journal of Applied Crystallography · doi:10.1107/s0021889892001663 · Cited by 3,709 · see citing works
TGF-β signalling from cell membrane to nucleus through SMAD proteins
Heldin, C., Miyazono, K., & ten Dijke, P. (1997) · Nature · doi:10.1038/37284 · Cited by 3,697 · see citing works
EMAN2: An extensible image processing suite for electron microscopy
Tang, G., Peng, L., Baldwin, P. R., Mann, D. S., Jiang, W., Rees, I., & Ludtke, S. J. (2006) · Journal of Structural Biology · doi:10.1016/j.jsb.2006.05.009 · Cited by 2,914 · see citing works
PRIMUS: a Windows PC-based system for small-angle scattering data analysis
Konarev, P. V., Волков, В. В., Sokolova, A. V., Koch, M. H. J., & Svergun, D. I. (2003) · Journal of Applied Crystallography · doi:10.1107/s0021889803012779 · Cited by 2,850 · see citing works
Structure of the haemagglutinin membrane glycoprotein of influenza virus at 3 Å resolution
Wilson, I. A., Skehel, J. J., & Wiley, D. C. (1981) · Nature · doi:10.1038/289366a0 · Cited by 2,535 · see citing works
Self-citationLeaver-Fay (2011) · doi:10.1016/b978-0-12-381270-4.00019-6 · Cited by 1,904 · see citing works
Automated molecular microscopy: The new Leginon system
Suloway, C. J. M., Pulokas, J., Fellmann, D., Cheng, A., Guerra, F., Quispe, J. D., Stagg, S. M., Potter, C. S., & Carragher, B. O. (2005) · Journal of Structural Biology · doi:10.1016/j.jsb.2005.03.010 · Cited by 1,681 · see citing works
Dimerization of cell surface receptors in signal transduction
Heldin, C.-H. (1995) · Cell · doi:10.1016/0092-8674(95)90404-2 · Cited by 1,634 · see citing works
Predicting protein structures with a multiplayer online game
Cooper, S., Khatib, F., Treuille, A., Barbero, J., Lee, J., Beenen, M., Leaver-Fay, A., Baker, D., Popović, Z., & players, F. (2010) · Nature · doi:10.1038/nature09304 · Cited by 1,368 · see citing works
Self-citationA New Generation of the IMAGIC Image Processing System
van Heel, M., Harauz, G., Orlova, E. V., Schmidt, R., & Schatz, M. X. (1996) · Journal of Structural Biology · doi:10.1006/jsbi.1996.0004 · Cited by 1,229 · see citing works
Corti, D., Voss, J., Gamblin, S. J., Codoni, G., Macagno, A., Jarrossay, D., Vachieri, S. G., Pinna, D., Minola, A., Vanzetta, F., et al. (2011) · Science · doi:10.1126/science.1205669 · Cited by 1,203 · see citing works
ProDy : Protein Dynamics Inferred from Theory and Experiments
Bakan, A., Meireles, L., & Bahar, İ. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr168 · Cited by 1,113 · see citing works
Isolating and engineering human antibodies using yeast surface display
Chao, G., Lau, W. L., Hackel, B. J., Sazinsky, S. L., Lippow, S. M., & Wittrup, K. D. (2006) · Nature Protocols · doi:10.1038/nprot.2006.94 · Cited by 913 · see citing works
A Highly Conserved Neutralizing Epitope on Group 2 Influenza A Viruses
Ekiert, D. C., Friesen, R. H. E., Bhabha, G., Kwaks, T., Jongeneelen, M. A. C., Yu, W., Ophorst, C., Cox, F., Korse, H. J. W. M., Brandenburg, B., et al. (2011) · Science · doi:10.1126/science.1204839 · Cited by 823 · see citing works
Self-citationDiLillo, D. J., Tan, G. S., Palese, P., & Ravetch, J. V. (2014) · Nature Medicine · doi:10.1038/nm.3443 · Cited by 749 · see citing works
Influenza vaccine: The challenge of antigenic drift
Carrat, F., & Flahault, A. (2007) · Vaccine · doi:10.1016/j.vaccine.2007.07.027 · Cited by 711 · see citing works
Cryo-EM Structure of a Fully Glycosylated Soluble Cleaved HIV-1 Envelope Trimer
Lyumkis, D., Julien, J., de Val, N., Cupo, A., Potter, C. S., Klasse, P.-J., Burton, D. R., Sanders, R. W., Moore, J. P., Carragher, B. O., et al. (2013) · Science · doi:10.1126/science.1245627 · Cited by 669 · see citing works
Self-citationPermissive Secondary Mutations Enable the Evolution of Influenza Oseltamivir Resistance
Bloom, J. D., Gong, L. I., & Baltimore, D. (2010) · Science · doi:10.1126/science.1187816 · Cited by 659 · see citing works
Self-citationComputational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin
Fleishman, S. J., Whitehead, T. A., Ekiert, D. C., Dreyfus, C., Corn, J. E., Strauch, E.-M., Wilson, I. A., & Baker, D. (2011) · Science · doi:10.1126/science.1202617 · Cited by 585 · see citing works
Self-citationAccurate SAXS Profile Computation and its Assessment by Contrast Variation Experiments
Schneidman‐Duhovny, D., Hammel, M., Tainer, J. A., & Šali, A. (2013) · Biophysical Journal · doi:10.1016/j.bpj.2013.07.020 · Cited by 555 · see citing works
FoXS: a web server for rapid computation and fitting of SAXS profiles
Schneidman‐Duhovny, D., Hammel, M., & Šali, A. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq461 · Cited by 524 · see citing works
Cross-neutralization of influenza A viruses mediated by a single antibody loop
Ekiert, D. C., Kashyap, A. K., Steel, J., Rubrum, A. M., Bhabha, G., Khayat, R., Lee, J. H., Dillon, M. A., O’Neil, R. E., Faynboym, A. M., et al. (2012) · Nature · doi:10.1038/nature11414 · Cited by 483 · see citing works
Self-citationAn improved yeast transformation method for the generation of very large human antibody libraries
Benatuil, L., Perez, J. M., Belk, J., & Hsieh, C.-M. (2010) · Protein Engineering Design and Selection · doi:10.1093/protein/gzq002 · Cited by 435 · see citing works
Structure and flexibility within proteins as identified through small angle X-ray scattering
Pelikán, M., Hura, G. L., & Hammel, M. (2009) · General Physiology and Biophysics · doi:10.4149/gpb_2009_02_174 · Cited by 434 · see citing works
RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design
Huang, P., Ban, Y. A., Richter, F. M., André, I., Vernon, R. M., Schief, W. R., & Baker, D. A. (2011) · PLoS ONE · doi:10.1371/journal.pone.0024109 · Cited by 373 · see citing works
Self-citationSPARX, a new environment for Cryo-EM image processing
Hohn, M. H., Tang, G., Goodyear, G., Baldwin, P. R., Huang, Z. X., Penczek, P. A., Yang, C., Glaeser, R. M., Adams, P. D., & Ludtke, S. J. (2006) · Journal of Structural Biology · doi:10.1016/j.jsb.2006.07.003 · Cited by 364 · see citing works
Sauter, N. K., Bednarski, M. D., Wurzburg, B. A., Hanson, J. E., Whitesides, G. M., Skehel, J. J., & Wiley, D. C. (1989) · Biochemistry · doi:10.1021/bi00447a018 · Cited by 354 · see citing works
Both, G. W., Sleigh, M. J., Cox, N. J., & Kendal, A. P. (1983) · Journal of Virology · doi:10.1128/jvi.48.1.52-60.1983 · Cited by 327 · see citing works
Schäffr, J. R., Kawaoka, Y., Bean, W. J., Süß, J., Senne, D. A., & Webster, R. G. (1993) · Virology · doi:10.1006/viro.1993.1319 · Cited by 245 · see citing works
Schmidt, A. G., Xu, H., Khan, A. R., O’Donnell, T. J., Khurana, S., King, L. R., Manischewitz, J. F., Golding, H., Suphaphiphat, P., Carfı́, A., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1218256109 · Cited by 243 · see citing works
Computation-Guided Backbone Grafting of a Discontinuous Motif onto a Protein Scaffold
Azoitei, M. L., Correia, B. E., Ban, Y.-E. A., Carrico, C., Kalyuzhniy, O., Chen, L., Schroeter, A., Huang, P.-S., McLellan, J. S., Kwong, P. D., et al. (2011) · Science · doi:10.1126/science.1209368 · Cited by 224 · see citing works
Self-citationAnalysis of X-ray and neutron scattering from biomacromolecular solutions
Petoukhov, M. V., & Svergun, D. I. (2007) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2007.06.009 · Cited by 215 · see citing works
Sorzano, C. Ó. S., Bilbao-Castro, J. R., Shkolnisky, Y., Alcorlo, M., Melero, R., Caffarena, G., Li, M., Xu, G., Marabini, R., & Carazo, J. M. (2010) · Journal of Structural Biology · doi:10.1016/j.jsb.2010.03.011 · Cited by 206 · see citing works
Simonsen, L., Viboud, C. G., Grenfell, B. T., et al. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm103 · Cited by 185 · see citing works
Lee, P. S., Yoshida, R., Ekiert, D. C., Sakai, N., Suzuki, Y., Takada, A., & Wilson, I. A. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1212371109 · Cited by 179 · see citing works
Self-citationViral Receptor-Binding Site Antibodies with Diverse Germline Origins
Schmidt, A. G., Therkelsen, M. D., Stewart, S. M., Kepler, T. B., Liao, H., Moody, M. A., Haynes, B. F., & Harrison, S. C. (2015) · Cell · doi:10.1016/j.cell.2015.04.028 · Cited by 172 · see citing works
Influenza: historical aspects of epidemics and pandemics
Cunha, B. A. (2004) · Infectious Disease Clinics of North America · doi:10.1016/s0891-5520(03)00095-3 · Cited by 142 · see citing works
Control over overall shape and size in de novo designed proteins
Lin, Y., Koga, N., Koga, R., Liu, G., Clouser, A. F., Montelione, G. T., & Baker, D. A. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1509508112 · Cited by 134 · see citing works
Self-citationA recurring motif for antibody recognition of the receptor-binding site of influenza hemagglutinin
Xu, R., Krause, J. C., McBride, R., Paulson, J. C., Crowe, J. E., & Wilson, I. A. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2500 · Cited by 133 · see citing works
Self-citationIntra-Spike Crosslinking Overcomes Antibody Evasion by HIV-1
Galimidi, R. P., Klein, J. S., Politzer, M. S., Bai, S., Seaman, M. S., Nussenzweig, M. C., West, A. P., & Björkman, P. J. (2015) · Cell · doi:10.1016/j.cell.2015.01.016 · Cited by 121 · see citing works
Computational Design of High-Affinity Epitope Scaffolds by Backbone Grafting of a Linear Epitope
Azoitei, M. L., Ban, Y. A., Julien, J., Bryson, S., Schroeter, A., Kalyuzhniy, O., Porter, J. R., Adachi, Y., Baker, D. A., PAI, E. F., et al. (2011) · Journal of Molecular Biology · doi:10.1016/j.jmb.2011.10.003 · Cited by 101 · see citing works
Self-citationA Nanomolar Multivalent Ligand as Entry Inhibitor of the Hemagglutinin of Avian Influenza
Waldmann, M., Jirmann, R., Hoelscher, K., Wienke, M., Niemeyer, F. C., Rehders, D., & Meyer, B. (2013) · Journal of the American Chemical Society · doi:10.1021/ja410918a · Cited by 92 · see citing works
Immobilizing affinity proteins to nitrocellulose: a toolbox for paper-based assay developers
Holstein, C. A., Chevalier, A. A., Bennett, S. P., Anderson, C. E., Keniston, K., Olsen, C., Li, B., Bales, B., Moore, D. R., Fu, E. S., et al. (2015) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-015-9052-0 · Cited by 92 · see citing works
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Strauch, E., Fleishman, S. J., & Baker, D. A. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1313605111 · Cited by 91 · see citing works
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Hooper, K. A., & Bloom, J. D. (2013) · Journal of Virology · doi:10.1128/jvi.01889-13 · Cited by 82 · see citing works
Self-citationAll-Atom Ensemble Modeling to Analyze Small-Angle X-Ray Scattering of Glycosylated Proteins
Guttman, M., Weinkam, P., Šali, A., et al. (2013) · Structure · doi:10.1016/j.str.2013.02.004 · Cited by 81 · see citing works
Dynamic Changes during Acid-Induced Activation of Influenza Hemagglutinin
Garcia, N. K., Guttman, M., Ebner, J. L., & Lee, K. K. (2015) · Structure · doi:10.1016/j.str.2015.02.006 · Cited by 72 · see citing works
Self-citationRecent Anti-Influenza Strategies in Multivalent Sialyloligosaccharides and Sialylmimetics Approaches
Sun, X. (2007) · Current Medicinal Chemistry · doi:10.2174/092986707781696582 · Cited by 45 · see citing works
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- Authors
- Strauch, E.-M., Bernard, S. M., La, D., Bohn, A. J., Lee, P. S., Anderson, C. E., Nieusma, T., Holstein, C. A., Garcia, N. K., Hooper, K. A., Ravichandran, R., Nelson, J. W., Sheffler, W., Bloom, J. D., Lee, K. K., Ward, A. B., Yager, P., Fuller, D. H., Wilson, I. A., & Baker, D.
- Affiliations
- University of Washington (US)
- Scripps Research Institute (US)
- Fred Hutch Cancer Center (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Baker, David
- ORCID
- Venue
- Nature Biotechnology
- Published
- 2017-06-12
- Volume
- 35
- Issue
- 7
- Pages
- 667-671
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- PMC
- PMC5512607
- OpenAlex
- W2624703541
- Cited by
- 119
- References
- 55
- Citations by year
- 2026: 4 · 2025: 6 · 2024: 10 · 2023: 11 · 2022: 12 · 2021: 12 · 2020: 17 · 2019: 22 · 2018: 15 · 2017: 9
- FWCI
- 13.71
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Howard Hughes Medical Institute
- National Institutes of Health (5t32ai007354-30, P51OD010425)
- National Institute of General Medical Sciences (R01GM099989, T32GM007270, P41GM103393, R01GM102198)
- National Institute of Allergy and Infectious Diseases (R56AI117675, R21AI119258, R33AI119258, T32-AI007354., R01AI096184)
- Topics
- Health Sciences › Medicine › Epidemiology › Influenza Virus Research Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
- Keywords
- computational protein design, trimeric protein, homo-oligomerization, influenza A hemagglutinin, receptor binding sites, neutralizing antibodies, protein assembly, paper-based diagnostics, influenza vaccination
- MeSH terms
- Binding Sites, Models, Chemical, Protein Binding, Protein Engineering, Hemagglutinin Glycoproteins, Influenza Virus, Protein Multimerization, Molecular Docking Simulation
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