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De novo design of modular and tunable protein biosensors
Open accessAbstract
Naturally occurring protein switches have been repurposed for the development of biosensors and reporters for cellular and clinical applications 1. However, the number of such switches is limited, and reengineering them is challenging. Here we show that a general class of protein-based biosensors can be created by inverting the flow of information through de novo designed protein switches in which the binding of a peptide key triggers biological outputs of interest 2. The designed sensors are modular molecular devices with a closed dark state and an open luminescent state; analyte binding drives the switch from the closed to the open state. Because the sensor is based on the thermodynamic coupling of analyte binding to sensor activation, only one target binding domain is required, which simplifies sensor design and allows direct readout in solution. We create biosensors that can sensitively detect the anti-apoptosis protein BCL-2, the IgG1 Fc domain, the HER2 receptor, and Botulinum neurotoxin B, as well as biosensors for cardiac troponin I and an anti-hepatitis B virus antibody with the high sensitivity required to detect these molecules clinically. Given the need for diagnostic tools to track the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)3, we used the approach to design sensors for the SARS-CoV-2 spike protein and antibodies against the membrane and nucleocapsid proteins. The former, which incorporates a de novo designed spike receptor binding domain (RBD) binder 4, has a limit of detection of 15 pM and a luminescence signal 50-fold higher than the background level. The modularity and sensitivity of the platform should enable the rapid construction of sensors for a wide range of analytes, and highlights the power of de novo protein design to create multi-state protein systems with new and useful functions.
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“The modular nature of the miniprotein binders enables their rapid integration into designed diagnostic biosensors for both influenza and SARS-CoV-2 binders40.”
From Design of protein-binding proteins from the target structure alone (2022) · cites this paper as [40]
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[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
Liebschner, D., Afonine, P. V., Baker, M. L., Bunkóczi, G., Chen, V. B., Croll, T. I., Hintze, B., Hung, L.-W., Jain, S., McCoy, A. J., et al. (2019) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798319011471 · Cited by 7,953
Diagnosing COVID-19: The Disease and Tools for Detection
Udugama, B. N., Kadhiresan, P., Kozlowski, H. N., Malekjahani, A., Osborne, M., Li, V. Y. C., Chen, H., Mubareka, S., Gubbay, J. B., & Chan, W. C. W. (2020) · ACS Nano · doi:10.1021/acsnano.0c02624 · Cited by 1,803
BCL-2 family proteins: changing partners in the dance towards death
Kale, J., Osterlund, E. J., & Andrews, D. W. (2018) · Cell Death & Differentiation · doi:10.1038/cdd.2017.186 · Cited by 1,574
NanoLuc Complementation Reporter Optimized for Accurate Measurement of Protein Interactions in Cells
Dixon, A. S., Schwinn, M. K., Hall, M. P., Zimmerman, K., Otto, P., Lubben, T. H., Butler, B. L., Binkowski, B. F., Machleidt, T., Kirkland, T. A., et al. (2016) · ACS Chemical Biology · doi:10.1021/acschembio.5b00753 · Cited by 1,405
Structure-based design of prefusion-stabilized SARS-CoV-2 spikes
Hsieh, C.-L., Goldsmith, J. A., Schaub, J. M., DiVenere, A. M., Kuo, H.-C., Javanmardi, K., Le, K. C., Wrapp, D., Lee, A. G., Liu, Y., et al. (2020) · Science · doi:10.1126/science.abd0826 · Cited by 1,303
Self-citationDe novo design of picomolar SARS-CoV-2 miniprotein inhibitors
Cao, L., Goreshnik, I., Coventry, B., Case, J. B., Miller, L., Kozodoy, L., Chen, R. E., Carter, L., Walls, A. C., Park, Y.-J., et al. (2020) · Science · doi:10.1126/science.abd9909 · Cited by 742
Self-citationRosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite
Fleishman, S. J., Leaver‐Fay, A., Corn, J. E., Strauch, E., Khare, S. D., Koga, N., Ashworth, J. R., Murphy, P. M., Richter, F. M., Lemmon, G., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0020161 · Cited by 659
Self-citationAlgorithm discovery by protein folding game players
Khatib, F., Cooper, S., Tyka, M. D., Xu, K., Makedon, I., Popović, Z., Baker, D. A., & Players, F. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1115898108 · Cited by 593
Self-citationStructure-based Design of Prefusion-stabilized SARS-CoV-2 SpikesPreprint
Hsieh, C., Goldsmith, J., Schaub, J. M., et al. (2020) · bioRxiv · doi:10.1101/2020.05.30.125484 · Cited by 588
Developments in theCCP4 molecular-graphics project
Potterton, L., McNicholas, S. J., Krissinel, E., Gruber, J., Cowtan, K. D., Emsley, P., Murshudov, G. N., Cohen, S. X., Anastassis Perrakis, A., & Noble, M. E. M. (2004) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444904023716 · Cited by 577
Walls, A. C., Fiala, B., Schäfer, A., Wrenn, S., Pham, M. N., Murphy, M., Tse, L. V., Shehata, L., O’Connor, M. A., Chen, C., et al. (2020) · Cell · doi:10.1016/j.cell.2020.10.043 · Cited by 532
Self-citationGreenwald, E. C., Mehta, S., & Zhang, J. (2018) · Chemical Reviews · doi:10.1021/acs.chemrev.8b00333 · Cited by 502
Massively parallel de novo protein design for targeted therapeutics
Chevalier, A., Silva, D.-A., Rocklin, G. J., Hicks, D. R., Vergara, R., Murapa, P., Bernard, S. M., Zhang, L., Lam, K.-H., Yao, G., et al. (2017) · Nature · doi:10.1038/nature23912 · Cited by 453
Self-citationContext-dependent secondary structure formation of a designed protein sequence
Minor, D. L., & Kim, P. S. (1996) · Nature · doi:10.1038/380730a0 · Cited by 393
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 371
Self-citationTutorial on monoclonal antibody pharmacokinetics and its considerations in early development
Ovacik, M., & Lin, K. (2018) · Clinical and Translational Science · doi:10.1111/cts.12567 · Cited by 299
De novo design of bioactive protein switches
Langan, R. A., Boyken, S. E., Ng, A. H., Samson, J. A., Dods, G., Westbrook, A. M., Nguyen, T. H., Lajoie, M. J., Chen, Z., Berger, S., et al. (2019) · Nature · doi:10.1038/s41586-019-1432-8 · Cited by 268
Self-citationBotulinum neurotoxin B recognizes its protein receptor with high affinity and specificity
Jin, R., Rummel, A., Binz, T., & Brünger, A. T. (2006) · Nature · doi:10.1038/nature05387 · Cited by 235
Structural basis for high-affinity HER2 receptor binding by an engineered protein
Eigenbrot, C. W., Ultsch, M. H., Dubnovitsky, A. P., Abrahmsén, L., & Härd, T. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1005025107 · Cited by 234
Designed protein logic to target cells with precise combinations of surface antigens
Lajoie, M. J., Boyken, S. E., Salter, A. I., Bruffey, J., Rajan, A., Langan, R. A., Olshefsky, A., Muhunthan, V., Bick, M. J., Gewe, M. M., et al. (2020) · Science · doi:10.1126/science.aba6527 · Cited by 223
Self-citationDevelopment and Applications of Bioluminescent and Chemiluminescent Reporters and Biosensors
Yeh, A. H.-W., & Ai, H. (2019) · Annual Review of Analytical Chemistry · doi:10.1146/annurev-anchem-061318-115027 · Cited by 217
Giménez, M. R., Twerenbold, R., Jaeger, C., Schindler, C., Puelacher, C., Wildi, K. S., Reichlin, T., Haaf, P., Merk, S., Honegger, U., et al. (2015) · The American Journal of Medicine · doi:10.1016/j.amjmed.2015.01.046 · Cited by 208
Red-shifted luciferase–luciferin pairs for enhanced bioluminescence imaging
Yeh, A. H.-W., Karmach, O., Ji, A., Carter, D. M., Martins‐Green, M. M., & Ai, H. (2017) · Nature Methods · doi:10.1038/nmeth.4400 · Cited by 194
SARS-CoV-2 Proteome Microarray for Mapping COVID-19 Antibody Interactions at Amino Acid Resolution
Wang, H., Wu, X., Zhang, X., Hou, X., Liang, T., Wang, D., Teng, F., Dai, J., Duan, H., Guo, S., et al. (2020) · ACS Central Science · doi:10.1021/acscentsci.0c00742 · Cited by 188
What has de novo protein design taught us about protein folding and biophysics?
Baker, D. (2019) · Protein Science · doi:10.1002/pro.3588 · Cited by 161
Self-citationSemisynthetic sensor proteins enable metabolic assays at the point of care
Yu, Q., Xue, L., Hiblot, J., Griss, R., Fabritz, S., Roux, C., Binz, P., Haas, D., Okun, J. G., & Johnsson, K. (2018) · Science · doi:10.1126/science.aat7992 · Cited by 159
Synthetic protein switches: design principles and applications
Stein, V., & Alexandrov, K. A. (2014) · Trends in biotechnology · doi:10.1016/j.tibtech.2014.11.010 · Cited by 155
Detection of Antibodies in Blood Plasma Using Bioluminescent Sensor Proteins and a Smartphone
Arts, R., den Hartog, I., Zijlema, S. E., Thijssen, V., van der Beelen, S. H. E., & Merkx, M. (2016) · Analytical Chemistry · doi:10.1021/acs.analchem.6b00534 · Cited by 139
De novo design of picomolar SARS-CoV-2 miniprotein inhibitorsPreprint
Cao, L., Goreshnik, I., Coventry, B., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.08.03.234914 · Cited by 116
Self-citationBerger, S., Procko, E., Margineantu, D. H., Lee, E. F., Shen, B. W., Zelter, A., Silva, D., Chawla, K., Herold, M. J., Garnier, J.-M., et al. (2016) · eLife · doi:10.7554/elife.20352 · Cited by 94
Self-citationThe extracellular domain of Her2 in serum as a biomarker of breast cancer
Perrier, A., Gligorov, J., Lefèvre, G., & Boissan, M. (2018) · Laboratory Investigation · doi:10.1038/s41374-018-0033-8 · Cited by 92
He, Y., Zhou, Y., Siddiqui, P., Niu, J., & Jiang, S. (2005) · Journal of Clinical Microbiology · doi:10.1128/jcm.43.8.3718-3726.2005 · Cited by 84
Bottom-up de novo design of functional proteins with complex structural features
Yang, C., Sesterhenn, F., Bonet, J., van Aalen, E. A., Scheller, L., Abriata, L. A., Cramer, J. T., Wen, X., Rosset, S., Georgeon, S., et al. (2021) · Nature Chemical Biology · doi:10.1038/s41589-020-00699-x · Cited by 84
Mechanistic and structural insights into the proteolytic activation of Vibrio cholerae MARTX toxin
Shen, A., Lupardus, P. J., Albrow, V. E., Guzzetta, A. W., Powers, J. C., García, K. C., & Bogyo, M. S. (2009) · Nature Chemical Biology · doi:10.1038/nchembio.178 · Cited by 78
ATP-Independent Bioluminescent Reporter Variants To Improve in Vivo Imaging
Yeh, A. H.-W., Xiong, Y., Wu, T., Chen, M., Ji, A., Li, X., & Ai, H. (2019) · ACS Chemical Biology · doi:10.1021/acschembio.9b00150 · Cited by 76
Rapid Detection of Botulinum Neurotoxins—A Review
Hobbs, R. J., Thomas, C. A., Halliwell, J., & Gwenin, C. D. (2019) · Toxins · doi:10.3390/toxins11070418 · Cited by 76
Generalizable Protein Biosensors Based on Synthetic Switch Modules
Guo, Z., Johnston, W. A., Whitfield, J. H., Walden, P. M., Cui, Z., Wijker, E., Edwardraja, S., Lantadilla, I. R., Ely, F., Vickers, C. E., et al. (2019) · Journal of the American Chemical Society · doi:10.1021/jacs.8b12298 · Cited by 64
Walls, A. C., Fiala, B., Schäfer, A., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.08.11.247395 · Cited by 60
SARS-CoV-2 proteome microarray for mapping COVID-19 antibody interactions at amino acid resolutionPreprint
Wang, H., Hou, X., Wu, X. W., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.03.26.994756 · Cited by 58
Banala, S., Aper, S. J. A., Schalk, W., & Merkx, M. (2013) · ACS Chemical Biology · doi:10.1021/cb400406x · Cited by 57
A biosensor for measuring NAD+ levels at the point of care
Yu, Q., Pourmandi, N., Xue, L., Gondrand, C., Fabritz, S., Bardy, D., Patiny, L., Katsyuba, E., Auwerx, J. H., & Johnsson, K. (2019) · Nature Metabolism · doi:10.1038/s42255-019-0151-7 · Cited by 55
Dual-Color Bioluminescent Sensor Proteins for Therapeutic Drug Monitoring of Antitumor Antibodies
van Rosmalen, M., Ni, Y., Vervoort, D. F. M., Arts, R., Ludwig, S. K. J., & Merkx, M. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.8b00041 · Cited by 52
Suppression of conformational heterogeneity at a protein–protein interface
Deis, L. N., Wu, Q., Wang, Y., Qi, Y., Daniels, K. G., Zhou, P., & Oas, T. G. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1424724112 · Cited by 48
Panpradist, N., Toley, B. J., Zhang, X., Byrnes, S. A., Buser, J. R., Englund, J. A., & Lutz, B. R. (2014) · PLoS ONE · doi:10.1371/journal.pone.0105786 · Cited by 48
Xue, L., Prifti, E., & Johnsson, K. (2016) · Journal of the American Chemical Society · doi:10.1021/jacs.6b03034 · Cited by 47
Modulating protein activity using tethered ligands with mutually exclusive binding sites
Schena, A., Griss, R., & Johnsson, K. (2015) · Nature Communications · doi:10.1038/ncomms8830 · Cited by 46
Pondé, R. A. D. A. (2019) · Archives of Virology · doi:10.1007/s00705-019-04369-9 · Cited by 43
Arts, R., Ludwig, S. K. J., van Gerven, B., Estirado, E. M., Milroy, L. ‐., & Merkx, M. (2017) · ACS Sensors · doi:10.1021/acssensors.7b00695 · Cited by 40
Chow, S. C. S., Ho, C. Y. S., Tam, T., Wu, C. F., Cheung, T. T., Chan, P. K. S., Ng, M. H. L., Hui, P. K., Ng, H., Au, D. M. Y., et al. (2006) · Journal of Clinical Pathology · doi:10.1136/jcp.2005.029868 · Cited by 36
Chi, S., Maeng, C.-Y., Kim, S. J., Oh, M. S., Ryu, C. J., Kim, S. J., Han, K., Hong, H. J., & Ryu, S. E. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0701279104 · Cited by 33
Self-citationHepatitis B surface antigen quantification: Not what it seems on the surface
Locarnini, S., & Bowden, S. (2012) · Hepatology · doi:10.1002/hep.25732 · Cited by 31
Caged Activators of Artificial Allosteric Protein Biosensors
Edwardraja, S., Guo, Z., Whitfield, J. H., Lantadilla, I. R., Johnston, W. A., Walden, P. M., Vickers, C. E., & Alexandrov, K. A. (2020) · ACS Synthetic Biology · doi:10.1021/acssynbio.9b00500 · Cited by 22
Construction of Protein Switches by Domain Insertion and Directed Evolution
Ribeiro, L. F., Warren, T. D., & Ostermeier, M. (2017) · Methods in molecular biology · doi:10.1007/978-1-4939-6940-1_3 · Cited by 15
Collins, M. H. (2019) · Tropical Medicine and Infectious Disease · doi:10.3390/tropicalmed4020068 · Cited by 14
Kim, J., Gripon, P., Bouezzedine, F., Jeong, M. S., Chi, S., Ryu, S.-E., & Hong, H. J. (2014) · FEBS Letters · doi:10.1016/j.febslet.2014.11.046 · Cited by 10
Self-citationRAPPID: a platform of ratiometric bioluminescent sensors for homogeneous immunoassaysPreprint
Ni, Y., Rosier, B. J. H. M., van Aalen, E. A., Hanckmann, E. T. L., Biewenga, L., Pistikou, A. M., Timmermans, B. J. R., Vu, C., Roos, S., Arts, R., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.10.31.363044 · Cited by 4
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Metadata
- Authors
- Quijano-Rubio, A., Yeh, H.-W., Park, J., Lee, H., Langan, R. A., Boyken, S. E., Lajoie, M. J., Cao, L., Chow, C. M., Miranda, M. C., Wi, J., Hong, H. J., Stewart, L., Oh, B.-H., & Baker, D.
- Affiliations
- University of Washington (US)
- Korea Advanced Institute of Science and Technology (KR)
- Kangwon National University (KR)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Oh, Byung-Ha
- Baker, David
- ORCID
- Venue
- Nature
- Published
- 2021-01-27
- Volume
- 591
- Issue
- 7850
- Pages
- 482-487
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC8074680
- OpenAlex
- W3125484908
- Cited by
- 260
- References
- 57
- Citations by year
- 2026: 34 · 2025: 51 · 2024: 43 · 2023: 42 · 2022: 58 · 2021: 31
- FWCI
- 13.64
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- Washington Research Foundation
- Open Philanthropy Project
- LG Yeonam Cultural Foundation
- National Institute on Aging (U19AG065156)
- National Institute of Allergy and Infectious Diseases (U01AI151698, AI151698)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biochemical and Structural Characterization
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › bioluminescence and chemiluminescence research
- Keywords
- de novo protein design, protein biosensors, protein switches, luminescent biosensors, HER2 receptor, botulinum neurotoxin B, cardiac troponin I, SARS-CoV-2 spike protein, spike protein receptor-binding domain, analyte binding
- MeSH terms
- SARS-CoV-2, Coronavirus Nucleocapsid Proteins, Coronavirus M Proteins, Antibodies, Viral, Botulinum Toxins, Hepatitis B virus, Immunoglobulin G, Phosphoproteins, Sensitivity and Specificity, Viral Matrix Proteins, Biosensing Techniques, Erb-b2 Receptor Tyrosine Kinases, Troponin I, Proto-Oncogene Proteins c-bcl-2, Luminescence, Limit of Detection, Spike Glycoprotein, Coronavirus
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