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De novo designed ice-binding proteins from twist-constrained helices
Open accessPublished version of a preprint
Abstract
Attaining molecular-level control over solidification processes is a crucial aspect of materials science. To control ice formation, organisms have evolved bewildering arrays of ice-binding proteins (IBPs), but these have poorly understood structure–activity relationships. We propose that reverse engineering using de novo computational protein design can shed light on structure–activity relationships of IBPs. We hypothesized that the model alpha-helical winter flounder antifreeze protein uses an unusual undertwisting of its alpha-helix to align its putative ice-binding threonine residues in exactly the same direction. We test this hypothesis by designing a series of straight three-helix bundles with an ice-binding helix projecting threonines and two supporting helices constraining the twist of the ice-binding helix. Our findings show that ice-recrystallization inhibition by the designed proteins increases with the degree of designed undertwisting, thus validating our hypothesis, and opening up avenues for the computational design of IBPs.
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Cites
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Robust deep learning–based protein sequence design using ProteinMPNN
Dauparas, J., Anishchenko, I., Bennett, N., Bai, H., Ragotte, R. J., Milles, L. F., Wicky, B. I. M., Courbet, A., de Haas, R. J., Bethel, N., et al. (2022) · Science · doi:10.1126/science.add2187 · Cited by 2,210
Self-citationRobust deep learning based protein sequence design using ProteinMPNN
Dauparas, J., Anishchenko, I., Bennett, N., Bai, H., Ragotte, R. J., Milles, L. F., Wicky, B. I. M., Courbet, A., de Haas, R. J., Bethel, N., et al. (2022) · doi:10.1101/2022.06.03.494563 · Cited by 2,107
Self-citationThe Rosetta All-Atom Energy Function for Macromolecular Modeling and Design
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Metadata
- Authors
- de Haas, R. J., Tas, R. P., van den Broek, D., Zheng, C., Nguyen, H., Kang, A., Bera, A. K., King, N. P., Voets, I. K., & de Vries, R.
- Affiliations
- Wageningen University & Research (NL)
- Eindhoven University of Technology (NL)
- University of Washington (US)
- Corresponding author
- Voets, Ilja K.
- de Vries, Renko
- ORCID
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2023-06-26
- Volume
- 120
- Issue
- 27
- Pages
- e2220380120-e2220380120
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC10319034
- OpenAlex
- W4382047596
- Cited by
- 12
- References
- 7
- Citations by year
- 2026: 6 · 2025: 5 · 2024: 1
- FWCI
- 1.07
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion, cc-by-nc-nd)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- TU/e Research Portal (publishedVersion, cc-by-nc-nd)
- Socio-Environmental Systems Modeling (submittedVersion, cc-by-nc-nd)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- TU/e Research Portal (submittedVersion)
- Funders
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek (202.220)
- EC | European Research Council (ERC-2020-CoG 101001965)
- HHS | NIH | National Institute of General Medical Sciences (P30 GM124165)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Chemistry › Physical and Theoretical Chemistry › nanoparticles nucleation surface interactions
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- antifreeze proteins, de novo protein design, ice recrystallization inhibition, structure-activity relationship, three-helix bundle
- MeSH terms
- Animals, Flounder, Ice, Caspase 1, Antifreeze Proteins
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