Overview: Designing protein-based nanomaterials for medical applications

Proteins are Nature’s building block of choice for the construction of ‘molecular machines’: stable yet dynamic assemblies with unparalleled abilities in molecular recognition and logic. The King group incorporates these features into the design of functional protein-based nanomaterials with the goal of creating new opportunities for the treatment and prevention of disease. We use computational protein design and a variety of biochemical, biophysical, and structural techniques to produce and characterize our novel materials. We are primarily a technology development lab, but our work spans basic science, preclinical evaluation, technology transfer, and commercialization.

Computational design of self-assembling protein nanomaterials

Natural proteins often self-assemble into highly ordered nanoscale objects. The sophisticated functions of these molecular machines suggests that the ability to design novel self-assembling protein nanomaterials with customized structures and functions would have immense practical value. The King Lab develops general computational methods for designing new protein nanomaterials with atomic-level accuracy, with a focus on structures suited for applications in medicine, particularly structure-based vaccine design and targeted delivery of biologics. We characterize the designed materials using a variety of biochemical, biophysical, and structural methods to confirm them as novel starting points for functionalization and to validate and improve our design methods. We are currently working on methods to i) increase the complexity of the architectures accessible to design, ii) genetically encode the ability to sense and respond to environmental changes, and iii) incorporate functional elements into our designed materials.

Representative publications:

• de Haas RJ, et al. (2024) Rapid and automated design of two-component protein nanomaterials using ProteinMPNN. Proc Natl Acad Sci U S A 13(121), e2314646121. doi:10.1073/pnas.2314646121 [PDF]
• Bale JB, et al. (2016) Accurate design of megadalton-scale two-component icosahedral protein complexes. Science 6297(353), 389-94. doi:10.1126/science.aaf8818
• Yang EC, et al. (2024) Computational design of non-porous pH-responsive antibody nanoparticles. Nat Struct Mol Biol 9(31), 1404-1412. doi:10.1038/s41594-024-01288-5 [PDF]

Structure-based design of self-assembling immunogens

Modern vaccine development is largely moving toward subunit vaccines, which comprise antigenic fragments of a pathogen, based on their improved safety profiles and the ineffectiveness or impracticality of vaccines derived from whole pathogens for many diseases. However, subunit vaccines are often inadequately immunogenic to provide durable immunity, and this critical barrier has prevented their more widespread clinical use. We are attacking this problem by developing our designed two-component protein nanomaterials as a next-generation platform for structure-based vaccine design. In collaboration with several world-class vaccinology and immunology groups, we have found that presenting heterologous antigens on our protein nanomaterials in an ordered, repetitive array can induce significantly more potent humoral immune responses than antigen alone. We are currently working on developing new protein nanomaterials that will allow more flexibility and control over antigen presentation as well as the packaging or presentation of other molecules that can be used to tune specific characteristics of the induced immune response.

Representative publications:

• Ellis D, et al. (2023) Antigen spacing on protein nanoparticles influences antibody responses to vaccination. Cell Rep 12(42), 113552. doi:10.1016/j.celrep.2023.113552 [PDF]
• Marcandalli J, et al. (2019) Induction of Potent Neutralizing Antibody Responses by a Designed Protein Nanoparticle Vaccine for Respiratory Syncytial Virus. Cell 6(176), 1420-1431.e17. doi:10.1016/j.cell.2019.01.046
• Miranda MC, et al. (2024) Potent neutralization of SARS-CoV-2 variants by RBD nanoparticle and prefusion-stabilized spike immunogens. NPJ Vaccines 1(9), 184. doi:10.1038/s41541-024-00982-1

Design of protein-based hybrid biomaterials

We have recently begun to extend our efforts to include the design of hybrid biological materials comprising multiple classes of biomolecules. In one example, in collaboration with the Sundquist lab at the University of Utah, we designed self-assembling protein nanocages that direct their own release from cells inside small vesicles in a manner that resembles some viruses. These hybrid biomaterials can fuse their membranes with target cells and deliver their contents, thereby transferring cargoes from one cell to another. This design concept was motivated by the central importance of biological membranes and the opportunity to modulate the activity of membranes through protein design. A key feature of our approach is that it enables control over the biogenesis and contents of the materials through modification of the sequences of our designed proteins. We are currently building additional fundamental capabilities into this platform and developing other classes of protein-based hybrid biomaterials including, for example, co-assemblies of proteins and nucleic acids.

Representative publications:

• Votteler J, et al. (2016) Designed proteins induce the formation of nanocage-containing extracellular vesicles. Nature 7632(540), 292-295. doi:10.1038/nature20607
• Butterfield GL, et al. (2017) Evolution of a designed protein assembly encapsulating its own RNA genome. Nature 7685(552), 415-420. doi:10.1038/nature25157
• Olshefsky A, et al. (2023) In vivo selection of synthetic nucleocapsids for tissue targeting. Proc Natl Acad Sci U S A 46(120), e2306129120. doi:10.1073/pnas.2306129120 [PDF]