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  • Perspective
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Engineering complexity into protein-based biomaterials for biomedical applications

Abstract

Protein-based biomaterials are growing in popularity for biomedical applications, in part owing to their innate ability to interface with biological systems. These materials, in the form of fibres, nanoparticles and hydrogels, have shown promise as drug delivery vehicles, tissue scaffolds and vaccines. Moreover, the explosion of protein engineering tools and the inception of de novo protein design have transformed our ability to explore new protein structures, enabling the creation of novel materials with diverse properties and furthering their customization for various applications. In this Perspective, we explore the coming of age of protein engineering technologies and their impact on biomaterials. Starting with naturally sourced materials, we highlight common protein building blocks and fabrication methods, as well as recent applications of each. We subsequently explore rationally designed materials and conclude by discussing the potential impacts that de novo design will have on the biomaterials field.

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Fig. 1: Overview of the three approaches to designing protein-based materials.
Fig. 2: Examples of methods used to fabricate and design protein-based biomaterials.
Fig. 3: Functionalizing protein-based biomaterials for therapeutic effects.

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References

  1. Marin, E., Boschetto, F. & Pezzotti, G. Biomaterials and biocompatibility: an historical overview. J. Biomed. Mater. Res. Part A 108, 1617–1633 (2020).

    Article  CAS  Google Scholar 

  2. Bookstaver, M. L., Tsai, S. J., Bromberg, J. S. & Jewell, C. M. Improving vaccine and immunotherapy design using biomaterials. Trends Immunol. 39, 135–150 (2018).

    Article  CAS  PubMed  Google Scholar 

  3. Ratner, B. D. & Bryant, S. J. Biomaterials: where we have been and where we are going. Annu. Rev. Biomed. Eng. 6, 41–75 (2004).

    Article  CAS  PubMed  Google Scholar 

  4. Gomes, S., Leonor, I. B., Mano, J. F., Reis, R. L. & Kaplan, D. L. Natural and genetically engineered proteins for tissue engineering. Prog. Polym. Sci. 37, 1–17 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Chu, S., Wang, A. L., Bhattacharya, A. & Montclare, J. K. Protein based biomaterials for therapeutic and diagnostic applications. Prog. Biomed. Eng. 4, 012003 (2022).

    Article  CAS  Google Scholar 

  6. Catoira, M. C., Fusaro, L., Di Francesco, D., Ramella, M. & Boccafoschi, F. Overview of natural hydrogels for regenerative medicine applications. J. Mater. Sci: Mater. Med. 30, 115 (2019).

    PubMed  Google Scholar 

  7. Kianfar, E. Protein nanoparticles in drug delivery: animal protein, plant proteins and protein cages, albumin nanoparticles. J. Nanobiotechnol. 19, 159 (2021).

    Article  CAS  Google Scholar 

  8. Duan, T., Bian, Q. & Li, H. Light-responsive dynamic protein hydrogels based on LOVTRAP. Langmuir 37, 10214–10222 (2021).

    Article  CAS  PubMed  Google Scholar 

  9. Gregorio, N. E. et al. PhoCoil: a photodegradable and injectable single-component recombinant protein hydrogel for minimally invasive delivery and degradation. Sci. Adv. 11, eadx3472 (2025).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Wang, R., Yang, Z., Luo, J., Hsing, I.-M. & Sun, F. B12-dependent photoresponsive protein hydrogels for controlled stem cell/protein release. Proc. Natl Acad. Sci. USA 114, 5912–5917 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Jensen, M. M. et al. Temperature-responsive silk-elastin-like protein polymer enhancement of intravesical drug delivery of a therapeutic glycosaminoglycan for treatment of interstitial cystitis/painful bladder syndrome. Biomaterials 217, 119293 (2019). This work demonstrates the utility of silk–elastin-like polypeptide hydrogels as an extended-release delivery vehicle for glycosaminoglycans to the bladder for the treatment of interstitial cystitis, which currently has minimal treatment options that do not provide relief for most patients.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Yang, E. C. et al. Computational design of non-porous pH-responsive antibody nanoparticles. Nat. Struct. Mol. Biol. https://doi.org/10.1038/s41594-024-01288-5 (2024).

    Article  PubMed  PubMed Central  Google Scholar 

  13. Ballister, E. R., Lai, A. H., Zuckermann, R. N., Cheng, Y. & Mougous, J. D. In vitro self-assembly of tailorable nanotubes from a simple protein building block. Proc. Natl Acad. Sci. USA 105, 3733–3738 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Bian, Q., Kong, N., Arslan, S. & Li, H. Calmodulin-based dynamic protein hydrogels with three distinct mechanical stiffness. Adv. Funct. Mater. 34, 2404934 (2024).

    Article  CAS  Google Scholar 

  15. Cao, Y., Wei, X., Lin, Y. & Sun, F. Synthesis of bio-inspired viscoelastic molecular networks by metal-induced protein assembly. Mol. Syst. Des. Eng. 5, 117–124 (2020).

    Article  CAS  Google Scholar 

  16. Brodin, J. D., Smith, S. J., Carr, J. R. & Tezcan, F. A. Designed, helical protein nanotubes with variable diameters from a single building block. J. Am. Chem. Soc. 137, 10468–10471 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Suzuki, Y. et al. Self-assembly of coherently dynamic, auxetic, two-dimensional protein crystals. Nature 533, 369–373 (2016). This study creates 2D self-assembling protein layers by designing specific intermolecular interactions involving metal coordination or disulfide bonds.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Arunachalam, P. S. et al. Durable protection against the SARS-CoV-2 Omicron variant is induced by an adjuvanted subunit vaccine. Sci. Transl. Med. 14, eabq4130 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Ou, B. S. et al. Broad and durable humoral responses following single hydrogel immunization of SARS-CoV-2 subunit vaccine. Adv. Healthc. Mater. 12, 2301495 (2023).

    Article  CAS  Google Scholar 

  20. Ols, S. et al. Multivalent antigen display on nanoparticle immunogens increases B cell clonotype diversity and neutralization breadth to pneumoviruses. Immunity 56, 2425–2441.e14 (2023).

    Article  CAS  PubMed  Google Scholar 

  21. Yuan, Y. et al. Intestinal-targeted nanotubes-in-microgels composite carriers for capsaicin delivery and their effect for alleviation of Salmonella induced enteritis. Biomaterials 287, 121613 (2022). This paper is one of the only published applications of nanotubes to meet a biomedical need, in this case as a delivery system for insoluble drugs such as capsaicin that enable their transport through the mucosal layer for the treatment of enteritis.

    Article  CAS  PubMed  Google Scholar 

  22. Yang, Y. et al. Small molecules combined with collagen hydrogel direct neurogenesis and migration of neural stem cells after spinal cord injury. Biomaterials 269, 120479 (2021). This study demonstrated the efficacy of a collagen hydrogel as a small-molecule delivery vehicle for inducing neurogenesis after spinal cord injury by modulating cell fate at the injury site.

    Article  CAS  PubMed  Google Scholar 

  23. Liu, C., Jiang, T., Yuan, Z. & Lu, Y. Self-assembled casein nanoparticles loading triptolide for the enhancement of oral bioavailability. Nat. Product Commun. https://doi.org/10.1177/1934578X20948352 (2020).

    Article  Google Scholar 

  24. Jiang, B. et al. Injectable, photoresponsive hydrogels for delivering neuroprotective proteins enabled by metal-directed protein assembly. Sci. Adv. 6, eabc4824 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Maity, B., Samanta, S., Sarkar, S., Alam, S. & Govindaraju, T. Injectable silk fibroin-based hydrogel for sustained insulin delivery in diabetic rats. ACS Appl. Bio Mater. 3, 3544–3552 (2020).

    Article  CAS  PubMed  Google Scholar 

  26. Bennett, J. I. et al. Genetically encoded XTEN-based hydrogels with tunable viscoelasticity and biodegradability for injectable cell therapies. Adv. Sci. https://doi.org/10.1002/advs.202301708 (2024).

  27. Sudhadevi, T., Vijayakumar, H. S., Hariharan, E. V., Sandhyamani, S. & Krishnan, L. K. Optimizing fibrin hydrogel toward effective neural progenitor cell delivery in spinal cord injury. Biomed. Mater. 17, 014102 (2021).

    Article  Google Scholar 

  28. Kortemme, T. De novo protein design — from new structures to programmable functions. Cell 187, 526–544 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Abramson, J. et al. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature 630, 493–500 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Dauparas, J. et al. Robust deep learning-based protein sequence design using ProteinMPNN. Science 378, 49–56 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Watson, J. L. et al. De novo design of protein structure and function with RFdiffusion. Nature 620, 1089–1100 (2023). This article demonstrates one of the first examples of use of diffusion-based machine-learning models to generate various protein backbones for many use-cases.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Panahi, R. & Baghban-Salehi, M. in Cellulose-Based Superabsorbent Hydrogels (ed. Mondal, Md. I. H.) 1561–1600 (Springer, 2019).

  34. Liu, B. et al. Protein nanotubes as advanced material platforms and delivery systems. Adv. Mater. 36, 2307627 (2024).

    Article  CAS  Google Scholar 

  35. Petrov, A. & Audette, G. F. Peptide and protein-based nanotubes for nanobiotechnology. WIREs Nanomed. Nanobiotechnol. 4, 575–585 (2012).

    Article  CAS  Google Scholar 

  36. Audette, G. F., Yaseen, A., Bragagnolo, N. & Bawa, R. Protein nanotubes: from bionanotech towards medical applications. Biomedicines 7, 46 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Medalsy, I. et al. SP1 protein-based nanostructures and arrays. Nano Lett. 8, 473–477 (2008).

    Article  CAS  PubMed  Google Scholar 

  38. Uddin, I., Frank, S., Warren, M. J. & Pickersgill, R. W. A generic self-assembly process in microcompartments and synthetic protein nanotubes. Small 14, 1704020 (2018).

    Article  Google Scholar 

  39. Shapiro, D. M. et al. Protein nanowires with tunable functionality and programmable self-assembly using sequence-controlled synthesis. Nat. Commun. 13, 829 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Kumara, M. T., Srividya, N., Muralidharan, S. & Tripp, B. C. Bioengineered flagella protein nanotubes with cysteine loops:  self-assembly and manipulation in an optical trap. Nano Lett. 6, 2121–2129 (2006).

    Article  CAS  PubMed  Google Scholar 

  41. Yin, L. et al. Engineered coiled-coil protein for delivery of inverse agonist for osteoarthritis. Biomacromolecules 19, 1614–1624 (2018).

    Article  CAS  PubMed  Google Scholar 

  42. Akhmetova, A. & Heinz, A. Electrospinning proteins for wound healing purposes: opportunities and challenges. Pharmaceutics 13, 4 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  43. Zhang, C., Zhang, Y., Shao, H. & Hu, X. Hybrid silk fibers dry-spun from regenerated silk fibroin/graphene oxide aqueous solutions. ACS Appl. Mater. Interfaces 8, 3349–3358 (2016).

    Article  CAS  PubMed  Google Scholar 

  44. Rohani Shirvan, A., Nouri, A. & Sutti, A. A perspective on the wet spinning process and its advancements in biomedical sciences. Eur. Polym. J. 181, 111681 (2022).

    Article  CAS  Google Scholar 

  45. Kong, B. et al. Tailoring micro/nano-fibers for biomedical applications. Bioact. Mater. 19, 328–347 (2023).

    CAS  PubMed  Google Scholar 

  46. Miranda, C. S. et al. Tunable spun fiber constructs in biomedicine: influence of processing parameters in the fibers’ architecture. Pharmaceutics 14, 164 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Blackstone, B. N., Gallentine, S. C. & Powell, H. M. Collagen-based electrospun materials for tissue engineering: a systematic review. Bioengineering 8, 39 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Abrishamkar, A., Nilghaz, A., Saadatmand, M., Naeimirad, M. & deMello, A. J. Microfluidic-assisted fiber production: potentials, limitations, and prospects. Biomicrofluidics 16, 061504 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Komatsu, T. Protein-based nanotubes for biomedical applications. Nanoscale 4, 1910–1918 (2012).

    Article  CAS  PubMed  Google Scholar 

  50. Landoulsi, J., Roy, C. J., Dupont-Gillain, C. & Demoustier-Champagne, S. Synthesis of collagen nanotubes with highly regular dimensions through membrane-templated layer-by-layer assembly. Biomacromolecules 10, 1021–1024 (2009).

    Article  CAS  PubMed  Google Scholar 

  51. Hou, S., Wang, J. & Martin, C. R. Template-synthesized protein nanotubes. Nano Lett. 5, 231–234 (2005).

    Article  CAS  PubMed  Google Scholar 

  52. Pum, D., Toca-Herrera, J. & Sleytr, U. S-layer protein self-assembly. Int. J. Mol. Sci. 14, 2484–2501 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Ilk, N., Egelseer, E. M. & Sleytr, U. B. S-layer fusion proteins — construction principles and applications. Curr. Opin. Biotechnol. 22, 824–831 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Padilla, J. E., Colovos, C. & Yeates, T. O. Nanohedra: using symmetry to design self assembling protein cages, layers, crystals, and filaments. Proc. Natl Acad. Sci. USA 98, 2217–2221 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Karuppannan, C. et al. Fabrication of progesterone-loaded nanofibers for the drug delivery applications in bovine. Nanoscale Res. Lett. 12, 116 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  56. Brahatheeswaran, D. et al. Hybrid fluorescent curcumin loaded zein electrospun nanofibrous scaffold for biomedical applications. Biomed. Mater. 7, 045001 (2012).

    Article  PubMed  Google Scholar 

  57. Nangare, S., Dugam, S., Patil, P., Tade, R. & Jadhav, N. Silk industry waste protein: isolation, purification and fabrication of electrospun silk protein nanofibers as a possible nanocarrier for floating drug delivery. Nanotechnology 32, 035101 (2020).

    Article  Google Scholar 

  58. Xu, L. et al. Mesenchymal stem cell-seeded regenerated silk fibroin complex matrices for liver regeneration in an animal model of acute liver failure. ACS Appl. Mater. Interfaces 9, 14716–14723 (2017).

    Article  CAS  PubMed  Google Scholar 

  59. Xu, H., Cai, S., Sellers, A. & Yang, Y. Intrinsically water-stable electrospun three-dimensional ultrafine fibrous soy protein scaffolds for soft tissue engineering using adipose derived mesenchymal stem cells. RSC Adv. 4, 15451–15457 (2014).

    Article  CAS  Google Scholar 

  60. Varshney, N., Sahi, A. K., Poddar, S. & Mahto, S. K. Soy protein isolate supplemented silk fibroin nanofibers for skin tissue regeneration: fabrication and characterization. Int. J. Biol. Macromol. 160, 112–127 (2020).

    Article  CAS  PubMed  Google Scholar 

  61. Zhou, T. et al. Electrospun tilapia collagen nanofibers accelerating wound healing via inducing keratinocytes proliferation and differentiation. Colloids Surf. B Biointerfaces 143, 415–422 (2016).

    Article  CAS  PubMed  Google Scholar 

  62. Bao, C. et al. Enhanced transport of shape and rigidity-tuned α-lactalbumin nanotubes across intestinal mucus and cellular barriers. Nano Lett. 20, 1352–1361 (2020).

    Article  CAS  PubMed  Google Scholar 

  63. Azzaroni, O. & Lau, K. H. A. Layer-by-layer assemblies in nanoporous templates: nano-organized design and applications of soft nanotechnology. Soft Matter 7, 8709–8724 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Komatsu, T. et al. Virus trap in human serum albumin nanotube. J. Am. Chem. Soc. 133, 3246–3248 (2011).

    Article  CAS  PubMed  Google Scholar 

  65. Yuge, S. et al. Glycoprotein nanotube traps influenza virus. Chem. Lett. 46, 95–97 (2017).

    Article  CAS  Google Scholar 

  66. Komatsu, T., Terada, H. & Kobayashi, N. Protein nanotubes with an enzyme interior surface. Chem. Eur. J. 17, 1849–1854 (2011).

    Article  CAS  PubMed  Google Scholar 

  67. Qu, X. & Komatsu, T. Molecular capture in protein nanotubes. ACS Nano 4, 563–573 (2010).

    Article  CAS  PubMed  Google Scholar 

  68. Moll, D. et al. S-layer–streptavidin fusion proteins as template for nanopatterned molecular arrays. Proc. Natl Acad. Sci. USA 99, 14646–14651 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Riedmann, E. M. et al. Construction of recombinant S-layer proteins (rSbsA) and their expression in bacterial ghosts — a delivery system for the nontypeable Haemophilus influenzae antigen Omp26. FEMS Immunol. Med. Microbiol. 37, 185–192 (2003).

    Article  CAS  PubMed  Google Scholar 

  70. Pleschberger, M. et al. An S-layer heavy chain camel antibody fusion protein for generation of a nanopatterned sensing layer to detect the prostate-specific antigen by surface plasmon resonance technology. Bioconjug. Chem. 15, 664–671 (2004).

    Article  CAS  PubMed  Google Scholar 

  71. Tariq, H., Batool, S., Asif, S., Ali, M. & Abbasi, B. H. Virus-like particles: revolutionary platforms for developing vaccines against emerging infectious diseases. Front. Microbiol. 12, 790121 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  72. Pretto, C. et al. Cowpea chlorotic mottle virus-like particles as potential platform for antisense oligonucleotide delivery in posterior segment ocular diseases. Macromol. Biosci. 21, 2100095 (2021).

    Article  CAS  Google Scholar 

  73. Zhang, J. et al. Advances of structural design and biomedical applications of tobacco mosaic virus coat protein. Adv. NanoBiomed Res. 4, 2300135 (2024).

    Article  Google Scholar 

  74. Hartzell, E. J., Lieser, R. M., Sullivan, M. O. & Chen, W. Modular hepatitis B virus-like particle platform for biosensing and drug delivery. ACS Nano 14, 12642–12651 (2020).

    Article  CAS  PubMed  Google Scholar 

  75. Hashemi, K. et al. Optimizing the synthesis and purification of MS2 virus like particles. Sci. Rep. 11, 19851 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Chang, J.-Y., Gorzelnik, K. V., Thongchol, J. & Zhang, J. Structural assembly of Qβ virion and its diverse forms of virus-like particles. Viruses 14, 225 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Cho, K. J. et al. The crystal structure of ferritin from Helicobacter pylori reveals unusual conformational changes for iron uptake. J. Mol. Biol. 390, 83–98 (2009).

    Article  CAS  PubMed  Google Scholar 

  78. Zhang, X., Meining, W., Fischer, M., Bacher, A. & Ladenstein, R. X-ray structure analysis and crystallographic refinement of lumazine synthase from the hyperthermophile Aquifex aeolicus at 1.6 Å resolution: determinants of thermostability revealed from structural comparisons. J. Mol. Biol. 306, 1099–1114 (2001).

    Article  CAS  PubMed  Google Scholar 

  79. Van Zon, A., Mossink, M. H., Scheper, R. J., Sonneveld, P. & Wiemer, E. A. C. The vault complex. Cell. Mol. Life Sci. 60, 1828–1837 (2003).

    Article  PubMed  PubMed Central  Google Scholar 

  80. Chmelyuk, N. S., Oda, V. V., Gabashvili, A. N. & Abakumov, M. A. Encapsulins: structure, properties, and biotechnological applications. Biochemistry 88, 35–49 (2023).

    CAS  PubMed  Google Scholar 

  81. Feng, R., Lan, J., Goh, M. C., Du, M. & Chen, Z. Advances in the application of gas vesicles in medical imaging and disease treatment. J. Biol. Eng. 18, 41 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Yasmin, R., Shah, M., Khan, S. A. & Ali, R. Gelatin nanoparticles: a potential candidate for medical applications. Nanotechnol. Rev. 6, 191–207 (2017).

    Article  CAS  Google Scholar 

  83. Pham, D. T. & Tiyaboonchai, W. Fibroin nanoparticles: a promising drug delivery system. Drug Deliv. 27, 431–448 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Hornok, V. Serum albumin nanoparticles: problems and prospects. Polymers 13, 3759 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Gandhi, S. & Roy, I. Drug delivery applications of casein nanostructures: a minireview. J. Drug Deliv. Sci. Technol. 66, 102843 (2021).

    Article  CAS  Google Scholar 

  86. Lu, L., Duong, V. T., Shalash, A. O., Skwarczynski, M. & Toth, I. Chemical conjugation strategies for the development of protein-based subunit nanovaccines. Vaccines 9, 563 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Royal, J. M. et al. Development of a SARS-CoV-2 vaccine candidate using plant-based manufacturing and a tobacco mosaic virus-like nano-particle. Vaccines 9, 1347 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Pomwised, R., Intamaso, U., Teintze, M., Young, M. & Pincus, S. Coupling peptide antigens to virus-like particles or to protein carriers influences the Th1/Th2 polarity of the resulting immune response. Vaccines 4, 15 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  89. Kanekiyo, M. et al. Self-assembling influenza nanoparticle vaccines elicit broadly neutralizing H1N1 antibodies. Nature 499, 102–106 (2013). This paper demonstrates an early example of fusing an antigen to the self-assembling protein nanoparticle ferritin to develop a potential vaccine.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Jardine, J. et al. Rational HIV immunogen design to target specific germline B cell receptors. Science 340, 711–716 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Collins, L. T. et al. Encapsulation of AAVs into protein vault nanoparticles as a novel solution to gene therapy’s neutralizing antibody problem. Preprint at bioRxiv https://doi.org/10.1101/2023.11.29.569229 (2024).

  92. Gause, K. T. et al. Immunological principles guiding the rational design of particles for vaccine delivery. ACS Nano 11, 54–68 (2017).

    Article  CAS  PubMed  Google Scholar 

  93. Zhai, L. & Tumban, E. Gardasil-9: a global survey of projected efficacy. Antivir. Res. 130, 101–109 (2016).

    Article  CAS  PubMed  Google Scholar 

  94. Laurens, M. B. RTS,S/AS01 vaccine (MosquirixTM): an overview. Hum. Vaccin. Immunother. 16, 480–489 (2020).

    Article  CAS  PubMed  Google Scholar 

  95. Jardine, J. G. et al. Priming a broadly neutralizing antibody response to HIV-1 using a germline-targeting immunogen. Science 349, 156–161 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Willis, J. R. et al. Vaccination with mRNA-encoded nanoparticles drives early maturation of HIV bnAb precursors in humans. Science 389, eadr8382 (2025).

    Article  CAS  PubMed  Google Scholar 

  97. Roier, S. et al. mRNA-based VP8* nanoparticle vaccines against rotavirus are highly immunogenic in rodents. npj Vaccines 8, 190 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Khaleeq, S. et al. Neutralizing efficacy of encapsulin nanoparticles against SARS-CoV2 variants of concern. Viruses 15, 346 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Hu, X., Cebe, P., Weiss, A. S., Omenetto, F. & Kaplan, D. L. Protein-based composite materials. Mater. Today 15, 208–215 (2012).

    Article  CAS  Google Scholar 

  100. Jonker, A. M., Löwik, D. W. P. M. & van Hest, J. C. M. Peptide- and protein-based hydrogels. Chem. Mater. 24, 759–773 (2012).

    Article  CAS  Google Scholar 

  101. Silva, N. H. C. S. et al. Protein-based materials: from sources to innovative sustainable materials for biomedical applications. J. Mater. Chem. B 2, 3715–3740 (2014).

    Article  CAS  PubMed  Google Scholar 

  102. Antoine, E. E., Vlachos, P. P. & Rylander, M. N. Review of collagen I hydrogels for bioengineered tissue microenvironments: characterization of mechanics, structure, and transport. Tissue Eng. Part B Rev. 20, 683–696 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Zhang, H., Xu, D., Zhang, Y., Li, M. & Chai, R. Silk fibroin hydrogels for biomedical applications. Smart Med. 1, e20220011 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  104. Kong, B. et al. Recombinant human collagen hydrogels with hierarchically ordered microstructures for corneal stroma regeneration. Chem. Eng. J. 428, 131012 (2022).

    Article  CAS  Google Scholar 

  105. Arndt, T. et al. Tuneable recombinant spider silk protein hydrogels for drug release and 3D cell culture. Adv. Funct. Mater. 34, 2303622 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  106. Sindhi, K. et al. The role of biomaterials-based scaffolds in advancing skin tissue construct. J. Tissue Viability 34, 100858 (2025).

    Article  PubMed  Google Scholar 

  107. Nikolova, M. P. & Chavali, M. S. Recent advances in biomaterials for 3D scaffolds: a review. Bioact. Mater. 4, 271–292 (2019).

    PubMed  PubMed Central  Google Scholar 

  108. Veiga, A., Silva, I. V., Duarte, M. M. & Oliveira, A. L. Current trends on protein driven bioinks for 3D printing. Pharmaceutics 13, 1444 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Huerta-López, C. & Alegre-Cebollada, J. Protein hydrogels: the Swiss Army Knife for enhanced mechanical and bioactive properties of biomaterials. Nanomaterials 11, 1656 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  110. He, J., Zhang, N., Zhu, Y., Jin, R. & Wu, F. MSC spheroids-loaded collagen hydrogels simultaneously promote neuronal differentiation and suppress inflammatory reaction through PI3K-Akt signaling pathway. Biomaterials 265, 120448 (2021).

    Article  CAS  PubMed  Google Scholar 

  111. Liu, Y. et al. Construction of adhesive and bioactive silk fibroin hydrogel for treatment of spinal cord injury. Acta Biomater. 158, 178–189 (2023).

    Article  CAS  PubMed  Google Scholar 

  112. Muangsanit, P., Roberton, V., Costa, E. & Phillips, J. B. Engineered aligned endothelial cell structures in tethered collagen hydrogels promote peripheral nerve regeneration. Acta Biomater. 126, 224–237 (2021).

    Article  CAS  PubMed  Google Scholar 

  113. Wei, S.-Y. et al. Engineering large and geometrically controlled vascularized nerve tissue in collagen hydrogels to restore large-sized volumetric muscle loss. Biomaterials 303, 122402 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  114. Zhang, W. et al. Hydrogel-based dressings designed to facilitate wound healing. Mater. Adv. 5, 1364–1394 (2024).

    Article  CAS  Google Scholar 

  115. Li, J., Li, Y., Guo, C. & Wu, X. Development of quercetin loaded silk fibroin/soybean protein isolate hydrogels for burn wound healing. Chem. Eng. J. 481, 148458 (2024).

    Article  CAS  Google Scholar 

  116. Jelodari, S. et al. Assessment of the efficacy of an LL-37-encapsulated keratin hydrogel for the treatment of full-thickness wounds. ACS Appl. Bio Mater. 6, 2122–2136 (2023).

    Article  CAS  PubMed  Google Scholar 

  117. Bakadia, B. M. et al. Teicoplanin-decorated reduced graphene oxide incorporated silk protein hybrid hydrogel for accelerating infectious diabetic wound healing and preventing diabetic foot osteomyelitis. Adv. Healthc. Mater. 13, 2304572 (2024).

    Article  CAS  Google Scholar 

  118. Gong, W. et al. Construction of a sustained-release hydrogel using gallic acid and lysozyme with antimicrobial properties for wound treatment. Biomater. Sci. 10, 6836–6849 (2022).

    Article  CAS  PubMed  Google Scholar 

  119. Chen, J. et al. Converting lysozyme to hydrogel: a multifunctional wound dressing that is more than antibacterial. Colloids Surf. B Biointerfaces 219, 112854 (2022).

    Article  CAS  PubMed  Google Scholar 

  120. Tian, D.-M. et al. In-situ formed elastin-based hydrogels enhance wound healing via promoting innate immune cells recruitment and angiogenesis. Mater. Today Bio 15, 100300 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  121. Gagliardi, A. et al. Rutin-loaded zein gel as a green biocompatible formulation for wound healing application. Int. J. Biol. Macromol. 269, 132071 (2024).

    Article  CAS  PubMed  Google Scholar 

  122. Baptista-Silva, S. et al. In situ forming silk sericin-based hydrogel: a novel wound healing biomaterial. ACS Biomater. Sci. Eng. 7, 1573–1586 (2021).

    Article  CAS  PubMed  Google Scholar 

  123. Raza, A. et al. Injectable zein gel with in situ self-assembly as hemostatic material. Biomater. Adv. 145, 213225 (2023).

    Article  CAS  PubMed  Google Scholar 

  124. Tan, J. et al. Biofunctionalized fibrin gel co-embedded with BMSCs and VEGF for accelerating skin injury repair. Mater. Sci. Eng. C 121, 111749 (2021).

    Article  CAS  Google Scholar 

  125. Tang, A. et al. Injectable keratin hydrogels as hemostatic and wound dressing materials. Biomater. Sci. 9, 4169–4177 (2021).

    Article  CAS  PubMed  Google Scholar 

  126. Xeroudaki, M. et al. A porous collagen-based hydrogel and implantation method for corneal stromal regeneration and sustained local drug delivery. Sci. Rep. 10, 16936 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  127. Wang, Y. et al. A microengineered collagen scaffold for generating a polarized crypt-villus architecture of human small intestinal epithelium. Biomaterials 128, 44–55 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  128. McLaughlin, S. et al. Recombinant human collagen hydrogel rapidly reduces methylglyoxal adducts within cardiomyocytes and improves borderzone contractility after myocardial infarction in mice. Adv. Funct. Mater. 32, 2204076 (2022).

    Article  CAS  Google Scholar 

  129. Kim, W., Jang, C. H. & Kim, G. H. A myoblast-laden collagen bioink with fully aligned Au nanowires for muscle-tissue regeneration. Nano Lett. 19, 8612–8620 (2019).

    Article  CAS  PubMed  Google Scholar 

  130. Briquez, P. S., Tsai, H.-M., Watkins, E. A. & Hubbell, J. A. Engineered bridge protein with dual affinity for bone morphogenetic protein-2 and collagen enhances bone regeneration for spinal fusion. Sci. Adv. 7, eabh4302 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  131. Bellas, E. et al. Injectable silk foams for soft tissue regeneration. Adv. Healthc. Mater. 4, 452–459 (2015).

    Article  CAS  PubMed  Google Scholar 

  132. Wang, T. et al. Intraarticularly injectable silk hydrogel microspheres with enhanced mechanical and structural stability to attenuate osteoarthritis. Biomaterials 286, 121611 (2022).

    Article  CAS  PubMed  Google Scholar 

  133. Lee, K. Z. et al. Protein-based hydrogels and their biomedical applications. Molecules 28, 4988 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  134. Miranda, F. F. et al. A self-assembled protein nanotube with high aspect ratio. Small 5, 2077–2084 (2009).

    Article  CAS  PubMed  Google Scholar 

  135. Hou, C. et al. Construction of protein nanowires through cucurbit[8]uril-based highly specific host–guest interactions: an approach to the assembly of functional proteins. Angew. Chem. Int. Ed. 52, 5590–5593 (2013).

    Article  CAS  Google Scholar 

  136. Zhang, X. et al. Protein interface redesign facilitates the transformation of nanocage building blocks to 1D and 2D nanomaterials. Nat. Commun. 12, 4849 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  137. Brodin, J. D. et al. Metal-directed, chemically tunable assembly of one-, two- and three-dimensional crystalline protein arrays. Nat. Chem. 4, 375–382 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  138. Sinclair, J. C., Davies, K. M., Vénien-Bryan, C. & Noble, M. E. M. Generation of protein lattices by fusing proteins with matching rotational symmetry. Nat. Nanotechnol. 6, 558–562 (2011).

    Article  CAS  PubMed  Google Scholar 

  139. Gonen, S., DiMaio, F., Gonen, T. & Baker, D. Design of ordered two-dimensional arrays mediated by noncovalent protein–protein interfaces. Science 348, 1365–1368 (2015).

    Article  CAS  PubMed  Google Scholar 

  140. Ben-Sasson, A. J. et al. Design of biologically active binary protein 2D materials. Nature 589, 468–473 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  141. Tetter, S. et al. Evolution of a virus-like architecture and packaging mechanism in a repurposed bacterial protein. Science 372, 1220–1224 (2021). This work uses principles of directed evolution to create a much larger version of lumazine synthase that can package RNA.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  142. Lai, Y.-T. et al. Structure of a designed protein cage that self-assembles into a highly porous cube. Nat. Chem. 6, 1065–1071 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  143. Cannon, K. A., Nguyen, V. N., Morgan, C. & Yeates, T. O. Design and characterization of an icosahedral protein cage formed by a double-fusion protein containing three distinct symmetry elements. ACS Synth. Biol. 9, 517–524 (2020).

    Article  CAS  PubMed  Google Scholar 

  144. Lai, Y.-T., Cascio, D. & Yeates, T. O. Structure of a 16-nm cage designed by using protein oligomers. Science 336, 1129 (2012).

    Article  CAS  PubMed  Google Scholar 

  145. Patterson, D. P. et al. Characterization of a highly flexible self-assembling protein system designed to form nanocages. Protein Sci. 23, 190–199 (2014).

    Article  CAS  PubMed  Google Scholar 

  146. Sciore, A. et al. Flexible, symmetry-directed approach to assembling protein cages. Proc. Natl Acad. Sci. USA 113, 8681–8686 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  147. Badieyan, S. et al. Symmetry-directed self-assembly of a tetrahedral protein cage mediated by de novo-designed coiled coils. ChemBiochem 18, 1888–1892 (2017).

    Article  CAS  PubMed  Google Scholar 

  148. Indelicato, G. et al. Principles governing the self-assembly of coiled-coil protein nanoparticles. Biophys. J. 110, 646–660 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  149. Fletcher, J. M. et al. Self-assembling cages from coiled-coil peptide modules. Science 340, 595–599 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  150. Lai, Y.-T., Jiang, L., Chen, W. & Yeates, T. O. On the predictability of the orientation of protein domains joined by a spanning alpha-helical linker. Protein Eng. Des. Sel. 28, 491–499 (2015).

    Article  CAS  PubMed  Google Scholar 

  151. Milligan, J. J., Saha, S., Jenkins, I. C. & Chilkoti, A. Genetically encoded elastin-like polypeptide nanoparticles for drug delivery. Curr. Opin. Biotechnol. 74, 146–153 (2022).

    Article  CAS  PubMed  Google Scholar 

  152. King, N. P. et al. Computational design of self-assembling protein nanomaterials with atomic level accuracy. Science 336, 1171–1174 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  153. Hsia, Y. et al. Design of a hyperstable 60-subunit protein icosahedron. Nature 535, 136–139 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  154. Bale, J. B. et al. Accurate design of megadalton-scale two-component icosahedral protein complexes. Science 353, 389–394 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  155. Wang, J. Y.(J.) et al. Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains. Proc. Natl Acad. Sci. USA 120, e2214556120 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  156. Dowling, Q. M. et al. Hierarchical design of pseudosymmetric protein nanocages. Nature 638, 553–561 (2025).

    Article  CAS  PubMed  Google Scholar 

  157. Lee, S. et al. Four-component protein nanocages designed by programmed symmetry breaking. Nature 638, 546–552 (2025).

    Article  CAS  PubMed  Google Scholar 

  158. Huard, D. J. E., Kane, K. M. & Tezcan, F. A. Re-engineering protein interfaces yields copper-inducible ferritin cage assembly. Nat. Chem. Biol. 9, 169–176 (2013).

    Article  CAS  PubMed  Google Scholar 

  159. Cristie-David, A. S. & Marsh, E. N. G. Metal-dependent assembly of a protein nano-cage. Protein Sci. 28, 1620–1629 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  160. Golub, E. et al. Constructing protein polyhedra via orthogonal chemical interactions. Nature 578, 172–176 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  161. Aupič, J. et al. Metal ion-regulated assembly of designed modular protein cages. Sci. Adv. 8, eabm8243 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  162. Subramanian, R. H. et al. Design of metal-mediated protein assemblies via hydroxamic acid functionalities. Nat. Protoc. 16, 3264–3297 (2021).

    Article  CAS  PubMed  Google Scholar 

  163. Marcandalli, J. et al. Induction of potent neutralizing antibody responses by a designed protein nanoparticle vaccine for respiratory syncytial virus. Cell 176, 1420–1431.e17 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  164. Brouwer, P. J. M. et al. Enhancing and shaping the immunogenicity of native-like HIV-1 envelope trimers with a two-component protein nanoparticle. Nat. Commun. 10, 4272 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  165. Ueda, G. et al. Tailored design of protein nanoparticle scaffolds for multivalent presentation of viral glycoprotein antigens. eLife 9, e57659 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  166. Song, J. Y. et al. Immunogenicity and safety of SARS-CoV-2 recombinant protein nanoparticle vaccine GBP510 adjuvanted with AS03: interim results of a randomised, active-controlled, observer-blinded, phase 3 trial. eClinicalMedicine 64, 102140 (2023). These results demonstrate the successful use of a computationally designed protein nanoparticle as a viable clinical vaccine candidate in humans.

    Article  PubMed  PubMed Central  Google Scholar 

  167. Hendricks, G. G. et al. Computationally designed mRNA-launched protein nanoparticle immunogens elicit protective antibody and T cell responses in mice. Sci. Transl. Med. 17, eadu2085 (2025).

    Article  CAS  PubMed  Google Scholar 

  168. Walls, A. C. et al. Distinct sensitivities to SARS-CoV-2 variants in vaccinated humans and mice. Cell Rep. 40, 111299 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  169. Divine, R. et al. Designed proteins assemble antibodies into modular nanocages. Science 372, eabd9994 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  170. Olshefsky, A. et al. In vivo selection of synthetic nucleocapsids for tissue targeting. Proc. Natl Acad. Sci. USA 120, e2306129120 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  171. Herpoldt, K. et al. Macromolecular cargo encapsulation via in vitro assembly of two-component protein nanoparticles. Adv. Healthc. Mater. 13, 2303910 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  172. Edwardson, T. G. W., Mori, T. & Hilvert, D. Rational engineering of a designed protein cage for siRNA delivery. J. Am. Chem. Soc. 140, 10439–10442 (2018).

    Article  CAS  PubMed  Google Scholar 

  173. Garcia Garcia, C., Patkar, S. S., Wang, B., Abouomar, R. & Kiick, K. L. Recombinant protein-based injectable materials for biomedical applications. Adv. Drug Deliv. Rev. 193, 114673 (2023).

    Article  CAS  PubMed  Google Scholar 

  174. Petka, W. A., Harden, J. L., McGrath, K. P., Wirtz, D. & Tirrell, D. A. Reversible hydrogels from self-assembling artificial proteins. Science 281, 389–392 (1998).

    Article  CAS  PubMed  Google Scholar 

  175. Shen, W., Zhang, K., Kornfield, J. A. & Tirrell, D. A. Tuning the erosion rate of artificial protein hydrogels through control of network topology. Nat. Mater. 5, 153–158 (2006).

    Article  CAS  PubMed  Google Scholar 

  176. Olsen, B. D., Kornfield, J. A. & Tirrell, D. A. Yielding behavior in injectable hydrogels from telechelic proteins. Macromolecules 43, 9094–9099 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  177. Sun, W., Duan, T., Cao, Y. & Li, H. An injectable self-healing protein hydrogel with multiple dissipation modes and tunable dynamic response. Biomacromolecules 20, 4199–4207 (2019).

    Article  CAS  PubMed  Google Scholar 

  178. Meleties, M., Katyal, P., Lin, B., Britton, D. & Montclare, J. K. Self-assembly of stimuli-responsive coiled-coil fibrous hydrogels. Soft Matter 17, 6470–6476 (2021).

    Article  CAS  PubMed  Google Scholar 

  179. Wong Po Foo, C. T. S., Lee, J. S., Mulyasasmita, W., Parisi-Amon, A. & Heilshorn, S. C. Two-component protein-engineered physical hydrogels for cell encapsulation. Proc. Natl Acad. Sci. USA 106, 22067–22072 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  180. Gao, X., Fang, J., Xue, B., Fu, L. & Li, H. Engineering protein hydrogels using SpyCatcher–SpyTag chemistry. Biomacromolecules 17, 2812–2819 (2016).

    Article  CAS  PubMed  Google Scholar 

  181. Sun, F., Zhang, W.-B., Mahdavi, A., Arnold, F. H. & Tirrell, D. A. Synthesis of bioactive protein hydrogels by genetically encoded SpyTag–SpyCatcher chemistry. Proc. Natl Acad. Sci. USA 111, 11269–11274 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  182. Lu, Y. et al. Stimuli-responsive protein hydrogels: their design, properties, and biomedical applications. Polymers 2023 15, 4652 (2023).

    CAS  Google Scholar 

  183. Lyu, S. et al. Optically controlled reversible protein hydrogels based on photoswitchable fluorescent protein Dronpa. Chem. Commun. 53, 13375–13378 (2017).

    Article  CAS  Google Scholar 

  184. Yang, Z. et al. B12-induced reassembly of split photoreceptor protein enables photoresponsive hydrogels with tunable mechanics. Sci. Adv. 8, eabm5482 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  185. Lao, U. L., Sun, M., Matsumoto, M., Mulchandani, A. & Chen, W. Genetic engineering of self-assembled protein hydrogel based on elastin-like sequences with metal binding functionality. Biomacromolecules 8, 3736–3739 (2007).

    Article  CAS  PubMed  Google Scholar 

  186. Luo, J. & Sun, F. Calcium-responsive hydrogels enabled by inducible protein–protein interactions. Polym. Chem. 11, 4973–4977 (2020).

    Article  CAS  Google Scholar 

  187. Lee, J. S., Kang, M. J., Lee, J. H. & Lim, D. W. Injectable hydrogels of stimuli-responsive elastin and calmodulin-based triblock copolypeptides for controlled drug release. Biomacromolecules 23, 2051–2063 (2022).

    Article  CAS  PubMed  Google Scholar 

  188. Wang, Y., Katyal, P. & Montclare, J. K. Protein-engineered functional materials. Adv. Healthc. Mater. 8, 1801374 (2019).

    Article  Google Scholar 

  189. Mout, R. et al. De novo design of modular protein hydrogels with programmable intra- and extracellular viscoelasticity. Proc. Natl Acad. Sci. USA 121, e2309457121 (2024). This paper demonstrates the application of de novo design towards the development of hydrogel materials with variable mechanical properties.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  190. Kong, N., Peng, Q. & Li, H. Rationally designed dynamic protein hydrogels with reversibly tunable mechanical properties. Adv. Funct. Mater. 24, 7310–7317 (2014).

    Article  CAS  Google Scholar 

  191. Zhang, Y.-N. et al. A highly elastic and rapidly crosslinkable elastin-like polypeptide-based hydrogel for biomedical applications. Adv. Funct. Mater. 25, 4814–4826 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  192. Pescador, D. et al. Regeneration of hyaline cartilage promoted by xenogeneic mesenchymal stromal cells embedded within elastin-like recombinamer-based bioactive hydrogels. J. Mater. Sci. Mater. Med. 28, 115 (2017).

    Article  PubMed  Google Scholar 

  193. Cipriani, F. et al. Cartilage regeneration in preannealed silk elastin-like co-recombinamers injectable hydrogel embedded with mature chondrocytes in an ex vivo culture platform. Biomacromolecules 19, 4333–4347 (2018).

    Article  CAS  PubMed  Google Scholar 

  194. Hatlevik, Ø et al. Translational development of a silk-elastinlike protein polymer embolic for transcatheter arterial embolization. Macromol. Biosci. 22, 2100401 (2022).

    Article  CAS  Google Scholar 

  195. Jiang, X. et al. A bi-layer hydrogel cardiac patch made of recombinant functional proteins. Adv. Mater. 34, 2201411 (2022). This paper showcases the power of fusing proteins to design hydrogels with varied properties, in this case to enable the creation of a bilayer material in which the layers have unique functions contributing to their overall utility as a cardiac patch.

    Article  CAS  Google Scholar 

  196. Britton, D. et al. Exosome loaded protein hydrogel for enhanced gelation kinetics and wound healing. ACS Appl. Bio Mater. https://doi.org/10.1021/acsabm.4c00569 (2024).

    Article  PubMed  PubMed Central  Google Scholar 

  197. Crick, F. H. C. The Fourier transform of a coiled-coil. Acta Cryst. 6, 685–689 (1953).

    Article  CAS  Google Scholar 

  198. Harbury, P. B., Plecs, J. J., Tidor, B., Alber, T. & Kim, P. S. High-resolution protein design with backbone freedom. Science 282, 1462–1467 (1998).

    Article  CAS  PubMed  Google Scholar 

  199. Hill, R. B., Raleigh, D. P., Lombardi, A. & DeGrado, W. F. De novo design of helical bundles as models for understanding protein folding and function. Acc. Chem. Res. 33, 745–754 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  200. Vázquez Torres, S. et al. De novo designed proteins neutralize lethal snake venom toxins. Nature https://doi.org/10.1038/s41586-024-08393-x (2025).

    Article  PubMed  PubMed Central  Google Scholar 

  201. Huang, B. et al. De novo design of miniprotein antagonists of cytokine storm inducers. Nat. Commun. 15, 7064 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  202. Shen, H. et al. De novo design of self-assembling helical protein filaments. Science 362, 705–709 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  203. Shen, H. et al. De novo design of pH-responsive self-assembling helical protein filaments. Nat. Nanotechnol. 19, 1016–1021 (2024). This work exhibits the utility of de novo design to mimic naturally occurring responsive material behaviours that are otherwise difficult to design.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  204. Pyles, H., Zhang, S., De Yoreo, J. J. & Baker, D. Controlling protein assembly on inorganic crystals through designed protein interfaces. Nature 571, 251–256 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  205. Hsia, Y. et al. Design of multi-scale protein complexes by hierarchical building block fusion. Nat. Commun. 12, 2294 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  206. Pillai, A. et al. De novo design of allosterically switchable protein assemblies. Nature 632, 911–920 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  207. Wang, S. et al. Bond-centric modular design of protein assemblies. Nat. Mater. https://doi.org/10.1038/s41563-025-02297-5 (2025).

    Article  PubMed  PubMed Central  Google Scholar 

  208. Rankovic, S. et al. Computational design of bifaceted protein nanomaterials. Nat. Mater. 24, 1635–1643 (2025).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  209. Haas, C. M. et al. From sequence to scaffold: computational design of protein nanoparticle vaccines from AlphaFold2-predicted building blocks. Proc. Natl Acad. Sci. USA 122, e2409566122 (2025).

    Article  PubMed  PubMed Central  Google Scholar 

  210. Gregorio, N. E., Li, Z., Baker, D. & DeForest, C. A. Stimuli-triggered formation of de novo-designed protein biomaterials. Cell Biomater. https://doi.org/10.1016/j.celbio.2025.100239 (2025).

    Article  Google Scholar 

  211. Wicky, B. I. M. et al. Hallucinating symmetric protein assemblies. Science 378, 56–61 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  212. Chen, Z. et al. Programmable design of orthogonal protein heterodimers. Nature 565, 106–111 (2019).

    Article  CAS  PubMed  Google Scholar 

  213. Cao, L., Zhang, Z., Yuan, D., Yu, M. & Min, J. Tissue engineering applications of recombinant human collagen: a review of recent progress. Front. Bioeng. Biotechnol. 12, 1358246 (2024).

    Article  PubMed  PubMed Central  Google Scholar 

  214. Heinrich, M. A., Mangia, M. & Prakash, J. Impact of endotoxins on bioengineered tissues and models. Trends Biotechnol. 40, 532–534 (2022).

    Article  CAS  PubMed  Google Scholar 

  215. Varadi, M. et al. AlphaFold protein structure database in 2024: providing structure coverage for over 214 million protein sequences. Nucleic Acids Res. 52, D368–D375 (2024).

    Article  CAS  PubMed  Google Scholar 

  216. Lin, Z. et al. Evolutionary-scale prediction of atomic-level protein structure with a language model. Science 379, 1123–1130 (2023).

    Article  CAS  PubMed  Google Scholar 

  217. Barroca, M. et al. Antibiotic free selection for the high level biosynthesis of a silk-elastin-like protein. Sci. Rep. 6, 39329 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  218. de Haas, R. J. et al. Rapid and automated design of two-component protein nanomaterials using ProteinMPNN. Proc. Natl Acad. Sci. USA 121, e2314646121 (2024).

    Article  PubMed  PubMed Central  Google Scholar 

  219. Kellmann, S. J. et al. SpyDisplay: a versatile phage display selection system using SpyTag/SpyCatcher technology. mAbs 15, 2177978 (2003).

    Article  Google Scholar 

  220. Baek, M. et al. Accurate prediction of protein structures and interactions using a three-track neural network. Science 373, 871–876 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  221. Dieckhaus, H., Brocidiacono, M., Randolph, N. Z. & Kuhlman, B. Transfer learning to leverage larger datasets for improved prediction of protein stability changes. Proc. Natl Acad. Sci. USA 121, e2314853121 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  222. Hsu, C. et al. Learning inverse folding from millions of predicted structures. Preprint at bioRxiv https://doi.org/10.1101/2022.04.10.487779 (2022).

  223. Nijkamp, E., Ruffolo, J. A., Weinstein, E. N., Naik, N. & Madani, A. ProGen2: exploring the boundaries of protein language models. Cell Syst. 14, 968–978.e3 (2023).

    Article  CAS  PubMed  Google Scholar 

  224. Ingraham, J. B. et al. Illuminating protein space with a programmable generative model. Nature 623, 1070–1078 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

The authors acknowledge support for this work in the form of two Graduate Research Fellowships Program Awards (DGE-2140004 to N.E.G. and C.M.H.) from the National Science Foundation, a Maximizing Investigators’ Research Award (R35GM138036 to C.A.D.) and Other Awards (P01AI167966 and 1U19AI181881 to N.P.K.) from the NIH, and an Award (HR00112420369 to C.A.D.) from the Defense Advanced Research Projects Agency.

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Gregorio, N.E., Haas, C.M., King, N.P. et al. Engineering complexity into protein-based biomaterials for biomedical applications. Nat Rev Mater (2025). https://doi.org/10.1038/s41578-025-00861-8

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