De novo design of a fluorescence-activating β-barrel
Open accessAbstract
The regular arrangements of β-strands around a central axis in β-barrels and of α-helices in coiled coils contrast with the irregular tertiary structures of most globular proteins, and have fascinated structural biologists since they were first discovered. Simple parametric models have been used to design a wide range of α-helical coiled-coil structures, but to date there has been no success with β-barrels. Here we show that accurate de novo design of β-barrels requires considerable symmetry-breaking to achieve continuous hydrogen-bond connectivity and eliminate backbone strain. We then build ensembles of β-barrel backbone models with cavity shapes that match the fluorogenic compound DFHBI, and use a hierarchical grid-based search method to simultaneously optimize the rigid-body placement of DFHBI in these cavities and the identities of the surrounding amino acids to achieve high shape and chemical complementarity. The designs have high structural accuracy and bind and fluorescently activate DFHBI in vitro and in Escherichia coli, yeast and mammalian cells. This de novo design of small-molecule binding activity, using backbones custom-built to bind the ligand, should enable the design of increasingly sophisticated ligand-binding proteins, sensors and catalysts that are not limited by the backbone geometries available in known protein structures.
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RIFDock resulted in better Rosetta binding energy (ddG) values and packing (contact molecular surface) after sequence design than shape matching alone with PatchDock, and more extensive nonpolar interactions with the target than hierarchical search without PatchDock shape matching.
“This approach resulted in better Rosetta binding energy (ddG) values and packing (contact molecular surface, see below) after sequence design than shape matching alone with PatchDock (Fig. 1b, red and green), and more extensive nonpolar interactions with the target than hierarchical search without PatchDock shape matching (Extended Data Fig. 2a) 6.”
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- Authors
- Dou, J., Vorobieva, A. A., Sheffler, W., Doyle, L. A., Park, H., Bick, M. J., Mao, B., Foight, G. W., Lee, M. Y., Gagnon, L. A., Carter, L., Sankaran, B., Ovchinnikov, S., Marcos, E., Huang, P.-S., Vaughan, J. C., Stoddard, B. L., & Baker, D.
- Affiliations
- University of Washington (US)
- Fred Hutch Cancer Center (US)
- Lawrence Berkeley National Laboratory (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Baker, David
- ORCID
- Venue
- Nature
- Published
- 2018-09-12
- Volume
- 561
- Issue
- 7724
- Pages
- 485-491
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC6275156
- OpenAlex
- W2891841439
- Cited by
- 351
- References
- 58
- Citations by year
- 2026: 35 · 2025: 42 · 2024: 45 · 2023: 44 · 2022: 48 · 2021: 56 · 2020: 42 · 2019: 30 · 2018: 8
- FWCI
- 12.09
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Licence
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (acceptedVersion, other-oa)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- VUBIR (Vrije Universiteit Brussel) (submittedVersion)
- Funders
- Howard Hughes Medical Institute (DE-AC02-05CH11231)
- U.S. Department of Energy (-AC02-05CH11231, 05CH11231, DE AC02 05CH11231, DE-AC02-)
- Open Philanthropy Project
- US-UK Fulbright Commission
- European Commission (298976)
- National Institutes of Health (DE-AC02–05CH11231)
- National Institute of General Medical Sciences (R01GM115545, DE-AC02-05CH11231, T32GM007270)
- FP7 People: Marie-Curie Actions (FP7-PEOPLE-2011-IOF)
- 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 › Chemical Synthesis and Analysis
- Keywords
- de novo protein design, beta-barrel proteins, fluorescence activation, ligand binding, symmetry breaking, protein-ligand binding
- MeSH terms
- Protein Domains, Animals, Benzyl Compounds, Chlorocebus aethiops, Escherichia coli, Fluorescence, Hydrogen Bonding, Ligands, Protein Binding, Proteins, Yeasts, Reproducibility of Results, Protein Structure, Secondary, Protein Folding, COS Cells, Imidazolines, Green Fluorescent Proteins, Protein Stability
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