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De novo design of self-assembling helical protein filaments.

Shen H, Fallas JA, Lynch E, Sheffler W, Parry B, Jannetty N, Decarreau J, Wagenbach M, Vicente JJ, Chen J, Wang L, Dowling Q, Oberdorfer G, Stewart L, Wordeman L, De Yoreo J, Jacobs-Wagner C, Kollman J, Baker D
Science 362 705-709 (2018)
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Cited: 46 times
EuropePMC logo PMID: 30409885

Abstract

We describe a general computational approach to designing self-assembling helical filaments from monomeric proteins and use this approach to design proteins that assemble into micrometer-scale filaments with a wide range of geometries in vivo and in vitro. Cryo-electron microscopy structures of six designs are close to the computational design models. The filament building blocks are idealized repeat proteins, and thus the diameter of the filaments can be systematically tuned by varying the number of repeat units. The assembly and disassembly of the filaments can be controlled by engineered anchor and capping units built from monomers lacking one of the interaction surfaces. The ability to generate dynamic, highly ordered structures that span micrometers from protein monomers opens up possibilities for the fabrication of new multiscale metamaterials.

Articles - 6e9z mentioned but not cited (1)

  1. De novo design of self-assembling helical protein filaments. Shen H, Fallas JA, Lynch E, Sheffler W, Parry B, Jannetty N, Decarreau J, Wagenbach M, Vicente JJ, Chen J, Wang L, Dowling Q, Oberdorfer G, Stewart L, Wordeman L, De Yoreo J, Jacobs-Wagner C, Kollman J, Baker D. Science 362 705-709 (2018)


Reviews citing this publication (18)

  1. Advances in protein structure prediction and design. Kuhlman B, Bradley P. Nat Rev Mol Cell Biol 20 681-697 (2019)
  2. De novo protein design, a retrospective. Korendovych IV, DeGrado WF. Q Rev Biophys 53 e3 (2020)
  3. Recent advances in de novo protein design: Principles, methods, and applications. Pan X, Kortemme T. J Biol Chem 296 100558 (2021)
  4. Protein Engineering for Improving and Diversifying Natural Product Biosynthesis. Li C, Zhang R, Wang J, Wilson LM, Yan Y. Trends Biotechnol 38 729-744 (2020)
  5. Protein Assembly by Design. Zhu J, Avakyan N, Kakkis A, Hoffnagle AM, Han K, Li Y, Zhang Z, Choi TS, Na Y, Yu CJ, Tezcan FA. Chem Rev 121 13701-13796 (2021)
  6. Advances in intracellular delivery through supramolecular self-assembly of oligonucleotides and peptides. Kim J, Narayana A, Patel S, Sahay G. Theranostics 9 3191-3212 (2019)
  7. Protein design via deep learning. Ding W, Nakai K, Gong H. Brief Bioinform 23 bbac102 (2022)
  8. Protein Design: From the Aspect of Water Solubility and Stability. Qing R, Hao S, Smorodina E, Jin D, Zalevsky A, Zhang S. Chem Rev 122 14085-14179 (2022)
  9. Cryo-EM of Helical Polymers. Wang F, Gnewou O, Solemanifar A, Conticello VP, Egelman EH. Chem Rev 122 14055-14065 (2022)
  10. Infinite Assembly of Folded Proteins in Evolution, Disease, and Engineering. Garcia-Seisdedos H, Villegas JA, Levy ED. Angew Chem Int Ed Engl 58 5514-5531 (2019)
  11. Nanoreactor Design Based on Self-Assembling Protein Nanocages. Ren H, Zhu S, Zheng G. Int J Mol Sci 20 E592 (2019)
  12. Electrical energy storage with engineered biological systems. Salimijazi F, Parra E, Barstow B. J Biol Eng 13 38 (2019)
  13. Supramolecular assembly of protein building blocks: from folding to function. Kim NH, Choi H, Shahzad ZM, Ki H, Lee J, Chae H, Kim YH. Nano Converg 9 4 (2022)
  14. From structure to application: Progress and opportunities in peptide materials development. Lopez-Silva TL, Schneider JP. Curr Opin Chem Biol 64 131-144 (2021)
  15. Greater than the sum of parts: Mechanisms of metabolic regulation by enzyme filaments. Hvorecny KL, Kollman JM. Curr Opin Struct Biol 79 102530 (2023)
  16. Rationally Designed Protein Building Blocks for Programmable Hierarchical Architectures. Zhang W, Mo S, Liu M, Liu L, Yu L, Wang C. Front Chem 8 587975 (2020)
  17. Natural Voltage-Gated Sodium Channel Ligands: Biosynthesis and Biology. Lukowski AL, Narayan ARH. Chembiochem 20 1231-1241 (2019)
  18. Intelligent Protein Design and Molecular Characterization Techniques: A Comprehensive Review. Wang J, Chen C, Yao G, Ding J, Wang L, Jiang H. Molecules 28 7865 (2023)

Articles citing this publication (27)



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