Local structural flexibility drives oligomorphism in computationally designed protein assemblies
Open accessPublished version of a preprint
Abstract
Many naturally occurring protein assemblies have dynamic structures that allow them to perform specialized functions. For example, clathrin coats adopt a wide variety of architectures to adapt to vesicular cargos of various sizes. Although computational methods for designing novel self-assembling proteins have advanced substantially over the past decade, most existing methods focus on designing static structures with high accuracy. Here we characterize the structures of three distinct computationally designed protein assemblies that each form multiple unanticipated architectures, and identify flexibility in specific regions of the subunits of each assembly as the source of structural diversity. Cryo-EM single-particle reconstructions and native mass spectrometry showed that only two distinct architectures were observed in two of the three cases, while we obtained six cryo-EM reconstructions that likely represent a subset of the architectures present in solution in the third case. Structural modeling and molecular dynamics simulations indicated that the surprising observation of a defined range of architectures, instead of non-specific aggregation, can be explained by constrained flexibility within the building blocks. Our results suggest that deliberate use of structural flexibility as a design principle will allow exploration of previously inaccessible structural and functional space in designed protein assemblies.
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- Authors
- Khmelinskaia, A., Bethel, N. P., Fatehi, F., Mallik, B. B., Antanasijevic, A., Borst, A. J., Lai, S.-H., Chim, H. Y., Wang, J. Y. ‘., Miranda, M. C., Watkins, A. M., Ogohara, C., Caldwell, S., Wu, M., Heck, A. J. R., Veesler, D., Ward, A. B., Baker, D., Twarock, R., & King, N. P.
- Affiliations
- University of Bonn (DE)
- University of Washington (US)
- University of York (GB)
- Scripps Research Institute (US)
- Utrecht University (NL)
- Ludwig-Maximilians-Universität München (DE)
- Genentech (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Khmelinskaia, Alena
- King, Neil P.
- ORCID
- Khmelinskaia, Alena
- Bethel, Neville P.
- Fatehi, Farzad
- Mallik, Bhoomika Basu
- Antanasijevic, Aleksandar
- Borst, Andrew J.
- Lai, Szu-Hsueh
- Chim, Ho Yeung
- Wang, Jing Yang ‘John’
- Miranda, Marcos C.
- Watkins, Andrew M.
- Caldwell, Shane
- Wu, Mengyu
- Heck, Albert J. R.
- Veesler, David
- Ward, Andrew B.
- Baker, David
- Twarock, Reidun
- King, Neil P.
- Venue
- Nature Structural & Molecular Biology
- Published
- 2025-02-26
- Volume
- 32
- Issue
- 6
- Pages
- 1050-1060
- ISSN
- 1545-9985 (ISSN-L)
- 1545-9993
- PMC
- PMC12170342
- OpenAlex
- W4407988683
- Cited by
- 18
- References
- 13
- Citations by year
- 2026: 9 · 2025: 8 · 2024: 1
- FWCI
- 5.11
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Nature Structural & Molecular Biology (publishedVersion, cc-by-nc-nd)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- White Rose Research Online (University of Leeds, The University of Sheffield, University of York) (acceptedVersion)
- PubMed Central (submittedVersion)
- Utrecht University Repository (Utrecht University) (submittedVersion)
- Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
- Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion)
- Funders
- National Science Foundation (1629214, P30 GM124169)
- Howard Hughes Medical Institute (GT11817)
- U.S. Department of Energy (180009, P30 GM124169, GM124169)
- Bill and Melinda Gates Foundation (INV-002916, INV-010680)
- amfAR, The Foundation for AIDS Research (110182-69-RKVA)
- University of Washington
- Wellcome Trust (110145, 110146, DP1AI158186)
- Open Philanthropy Project
- Australian Government
- Deutsche Forschungsgemeinschaft (SFB1032,)
- École Polytechnique Fédérale de Lausanne
- Bundesministerium für Bildung und Forschung
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek (SPI.2017.028, ENPPS.LIFT.019.001)
- Engineering and Physical Sciences Research Council (EP/R023204/1)
- Leibniz-Gemeinschaft
- National Institute of General Medical Sciences (P30GM124169)
- National Institute of Allergy and Infectious Diseases (DP1AI158186, P01AI167966, 75N93022C00036, U54AI170856)
- Basic Energy Sciences
- Biological and Environmental Research (P30 GM124169)
- Lawrence Berkeley National Laboratory
- 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
- Physical Sciences › Materials Science › Biomaterials › Supramolecular Self-Assembly in Materials
- Keywords
- protein self-assembly, structural flexibility, structural diversity, protein architecture, native mass spectrometry, molecular dynamics simulation, protein design
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