Hallucinating symmetric protein assemblies.

Journal: Science (New York, N.Y.)
PMID: 36108048

Abstract

Deep learning generative approaches provide an opportunity to broadly explore protein structure space beyond the sequences and structures of natural proteins. Here, we use deep network hallucination to generate a wide range of symmetric protein homo-oligomers given only a specification of the number of protomers and the protomer length. Crystal structures of seven designs are very similar to the computational models (median root mean square deviation: 0.6 angstroms), as are three cryo-electron microscopy structures of giant 10-nanometer rings with up to 1550 residues and symmetry; all differ considerably from previously solved structures. Our results highlight the rich diversity of new protein structures that can be generated using deep learning and pave the way for the design of increasingly complex components for nanomachines and biomaterials.

Authors

  • B I M Wicky
    Department of Biochemistry, University of Washington, Seattle, WA, USA.
  • L F Milles
    Department of Biochemistry, University of Washington, Seattle, WA, USA.
  • A Courbet
    Department of Biochemistry, University of Washington, Seattle, WA, USA.
  • R J Ragotte
    Department of Biochemistry, University of Washington, Seattle, WA, USA.
  • J Dauparas
    Department of Biochemistry, University of Washington, Seattle, WA, USA.
  • E Kinfu
    Department of Biochemistry, University of Washington, Seattle, WA, USA.
  • S Tipps
    Department of Biochemistry, University of Washington, Seattle, WA, USA.
  • R D Kibler
    Department of Biochemistry, University of Washington, Seattle, WA, USA.
  • M Baek
    Department of Biochemistry, University of Washington, Seattle, WA, USA.
  • F DiMaio
    Department of Biochemistry, University of Washington, Seattle, WA, USA.
  • X Li
    1 School of Public Health, Capital Medical University, Beijing, China.
  • L Carter
    Department of Biochemistry, University of Washington, Seattle, WA, USA.
  • A Kang
    Department of Biochemistry, University of Washington, Seattle, WA, USA.
  • H Nguyen
    Department of Biochemistry, University of Washington, Seattle, WA, USA.
  • A K Bera
    Department of Biochemistry, University of Washington, Seattle, WA, USA.
  • D Baker
    Department of Biochemistry, University of Washington, Seattle, WA, USA.

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