Local structural flexibility drives oligomorphism in computationally designed protein assemblies
Many naturally occurring protein assemblies have dynamic structures that allow them to perform specialized functions. Although computational methods for designing novel self-assembling proteins have advanced substantially over the past decade, they primarily focus on designing static structures. Here we characterize three distinct computationally designed protein assemblies that exhibit unanticipated structural diversity arising from flexibility in their subunits. Cryo-EM single-particle reconstructions and native mass spectrometry reveal two distinct architectures for two assemblies, while six cryo-EM reconstructions for the third likely represent a subset of its solution-phase structures. Structural modeling and molecular dynamics simulations indicate that constrained flexibility within the subunits of each assembly promotes a defined range of architectures rather than nonspecific aggregation. Redesigning the flexible region in one building block rescues the intended monomorphic assembly. These findings highlight structural flexibility as a powerful design principle, enabling exploration of new structural and functional spaces in protein assembly design.
Authors
- Andrew M. Watkins (ORCID: https://orcid.org/0000-0003-1617-1720)
- Marcos C. Miranda (ORCID: https://orcid.org/0000-0002-2839-6997)
- S.J. Caldwell (ORCID: https://orcid.org/0000-0002-9518-0168)
- Neil P. King (ORCID: https://orcid.org/0000-0002-2978-4692)
- Bhoomika Basu Mallik (ORCID: https://orcid.org/0000-0002-0592-4267)
- Alena Khmelinskaia (ORCID: https://orcid.org/0000-0003-1584-9800)
- Andrew J. Borst (ORCID: https://orcid.org/0000-0003-4297-7824)
- Szu‐Hsueh Lai (ORCID: https://orcid.org/0000-0001-9698-1496)
- David A. Baker (ORCID: https://orcid.org/0000-0001-7896-6217)
- Albert J. R. Heck (ORCID: https://orcid.org/0000-0002-2405-4404)
- Jing Yang Wang (ORCID: https://orcid.org/0000-0002-1511-6976)
- Aleksandar Antanasijevic (ORCID: https://orcid.org/0000-0001-9452-8954)
- Neville P. Bethel (ORCID: https://orcid.org/0000-0001-7576-9613)
- Cassandra Ogohara
- Andrew B. Ward (ORCID: https://orcid.org/0000-0001-7153-3769)
- Mengyu Wu (ORCID: https://orcid.org/0000-0002-2248-9383)
- David Veesler (ORCID: https://orcid.org/0000-0002-6019-8675)
- Reidun Twarock
- Farzad Fatehi (ORCID: https://orcid.org/0000-0003-3743-5772)
- Ho Yeung Chim
Institutions
- Scripps Research Institute (US)
- Howard Hughes Medical Institute (US)
- University of Bonn (DE)
- Utrecht University (NL)
- University of Washington (US)
- University Hospital Bonn (DE)
- École Polytechnique Fédérale de Lausanne (CH)
- University of York (GB)
- Ludwig-Maximilians-Universität München (DE)
- National Cheng Kung University (TW)
Publication Details
- Journal
- Nature Structural & Molecular Biology
- Published
- 2025-02-26
- DOI
- https://doi.org/10.1038/s41594-025-01490-z
- Citations
- 8
- Primary Topic
- Protein Structure and Dynamics
- Type
- article
- Field-Weighted Citation Impact
- 6.45
Funders
- National Science Foundation
- Howard Hughes Medical Institute
- U.S. Department of Energy
- Bill and Melinda Gates Foundation
- amfAR, The Foundation for AIDS Research
- University of Washington
- Wellcome Trust
- Open Philanthropy Project
- Australian Government
- Deutsche Forschungsgemeinschaft
- École Polytechnique Fédérale de Lausanne
- Bundesministerium für Bildung und Forschung
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek
- Engineering and Physical Sciences Research Council
- Leibniz-Gemeinschaft
- Basic Energy Sciences
- Biological and Environmental Research
- Lawrence Berkeley National Laboratory