Generation, Functionalization and Distribution of de novo Designed Protein Nanomaterials
Proteins are large molecules that have complex three-dimensional (3D) structures that give them sophisticated cellular functions. To provide access to complex protein structures not found in nature, Professors Baker and King of the University of Washington and Professor Yeates of University of California Los Angeles collaborate to compute and precisely control the assembly of proteins into 3D architectures. The research team shares these capabilities with the engineering and scientific communities and constructs a Designed Protein Nanomaterial (DPN) database to enable others to rapidly build on these advances. The long-term goal is to allow predictable design of protein-based materials for use in a wide range of applications such as targeted drug delivery, functional materials for energy conversion, and other chemical technologies. The interdisciplinary project provides excellent research training opportunities to postdoctoral researchers and students.
Publications
Computational design of non-porous pH-responsive antibody nanoparticles
E. C. Yang, R. Divine, M. C. Miranda, A. J. Borst, W. Sheffler, J. Z. Zhang, J. Decarreau, A. Saragovi, M. Abedi, N. Goldbach, M. Ahlrichs, C. Dobbins, A. Hand, S. Cheng, M. Lamb, P. M. Levine, S. Chan, R. Skotheim, J. Fallas, G. Ueda, J. Lubner, M. Somiya, A. Khmelinskaia, N. P. King, and D. Baker
5/9/2024
Blueprinting extendable nanomaterials with standardized protein blocks
T. F. Huddy, Y. Hsia, R. D. Kibler, J. Xu, N. Bethel, D. Nagarajan, R. Redler, P. J. Y. Leung, C. Weidle, A. Courbet, E. C. Yang, A. K. Bera, N. Coudray, S. J. Calise, F. A. Davila-Hernandez, H. L. Han, K. D. Carr, Z. Li, R. McHugh, G. Reggiano, A. Kang, B. Sankaran, M. S. Dickinson, B. Coventry, T. J. Brunette, Y. Liu, J. Dauparas, A. J. Borst, D. Ekiert, J. M. Kollman, G. Bhabha, and D. Baker
3/13/2024
Macromolecular Cargo Encapsulation via In Vitro Assembly of Two‐Component Protein Nanoparticles
K. Herpoldt, C. L. López, I. Sappington, M. N. Pham, S. Srinivasan, J. Netland, K. S. Montgomery, D. Roy, A. N. Prossnitz, D. Ellis, A. J. Wargacki, M. Pepper, A. J. Convertine, P. S. Stayton, and N. P. King
2/11/2024
Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock
W. Sheffler, E. C. Yang, Q. Dowling, Y. Hsia, C. N. Fries, J. Stanislaw, M. D. Langowski, M. Brandys, Z. Li, R. Skotheim, A. J. Borst, A. Khmelinskaia, N. P. King, and D. Baker
5/22/2023
De novo design of obligate ABC-type heterotrimeric proteins
S. Bermeo, A. Favor, Y. Chang, A. Norris, S. E. Boyken, Y. Hsia, H. K. Haddox, C. Xu, T. J. Brunette, V. H. Wysocki, G. Bhabha, D. C. Ekiert, and D. Baker
12/1/2022
Increasing Computational Protein Design Literacy through Cohort-Based Learning for Undergraduate Students
E. C. Yang, R. Divine, C. S. Kang, S. Chan, E. Arenas, Z. Subol, P. Tinker, H. Manninen, A. Feichtenbiner, T. Mustafa, J. Hallowell, I. Orr, H. Haddox, B. Koepnick, J. O’Connor, I. C. Haydon, K. Herpoldt, K. V. Wormer, C. Abell, D. Baker, A. Khmelinskaia, and N. P. King
8/5/2022
De novo design of protein homodimers containing tunable symmetric protein pockets
D. R. Hicks, M. A. Kennedy, K. A. Thompson, M. DeWitt, B. Coventry, A. Kang, A. K. Bera, T. J. Brunette, B. Sankaran, B. Stoddard, and D. Baker
7/21/2022
Designing Protease-Triggered Protein Cages
J. E. Miller, Y. Srinivasan, N. P. Dharmaraj, A. Liu, P. L. Nguyen, S. D. Taylor, and T. O. Yeates
7/8/2022
Engineering Self-Assembling Protein Nanoparticles for Therapeutic Delivery
A. Olshefsky, C. Richardson, S. H. Pun, and N. P. King
4/29/2022
Computational design of mechanically coupled axle-rotor protein assemblies
A. Courbet, J. Hansen, Y. Hsia, N. Bethel, Y. -. Park, C. Xu, A. Moyer, S. E. Boyken, G. Ueda, U. Nattermann, D. Nagarajan, D. -. Silva, W. Sheffler, J. Quispe, A. Nord, N. King, P. Bradley, D. Veesler, J. Kollman, and D. Baker
4/22/2022
Hallmarks of icosahedral virus capsids emerged during laboratory evolution of a bacterial enzyme
A. Olshefsky, and N. P. King
11/1/2021
Polyclonal antibody responses to HIV Env immunogens resolved using cryoEM
A. Antanasijevic, L. M. Sewall, C. A. Cottrell, D. G. Carnathan, L. E. Jimenez, J. T. Ngo, J. B. Silverman, B. Groschel, E. Georgeson, J. Bhiman, R. Bastidas, C. LaBranche, J. D. Allen, J. Copps, H. R. Perrett, K. Rantalainen, F. Cannac, Y. R. Yang, A. T. de la Peña, R. F. Rocha, Z. T. Berndsen, D. Baker, N. P. King, R. W. Sanders, J. P. Moore, S. Crotty, M. Crispin, D. C. Montefiori, D. R. Burton, W. R. Schief, G. Silvestri, and A. B. Ward
8/10/2021
Structure-based design of novel polyhedral protein nanomaterials
A. Khmelinskaia, A. Wargacki, and N. P. King
6/1/2021
Generation of ordered protein assemblies using rigid three-body fusion
I. Vulovic, Q. Yao, Y. Park, A. Courbet, A. Norris, F. Busch, A. Sahasrabuddhe, H. Merten, D. D. Sahtoe, G. Ueda, J. A. Fallas, S. J. Weaver, Y. Hsia, R. A. Langan, A. Plückthun, V. H. Wysocki, D. Veesler, G. J. Jensen, and D. Baker
5/31/2021
Design of multi-scale protein complexes by hierarchical building block fusion
Y. Hsia, R. Mout, W. Sheffler, N. I. Edman, I. Vulovic, Y. Park, R. L. Redler, M. J. Bick, A. K. Bera, A. Courbet, A. Kang, T. J. Brunette, U. Nattermann, E. Tsai, A. Saleem, C. M. Chow, D. Ekiert, G. Bhabha, D. Veesler, and D. Baker
4/16/2021
Designed proteins assemble antibodies into modular nanocages
R. Divine, H. V. Dang, G. Ueda, J. A. Fallas, I. Vulovic, W. Sheffler, S. Saini, Y. T. Zhao, I. X. Raj, P. A. Morawski, M. F. Jennewein, L. J. Homad, Y. Wan, M. R. Tooley, F. Seeger, A. Etemadi, M. L. Fahning, J. Lazarovits, A. Roederer, A. C. Walls, L. Stewart, M. Mazloomi, N. P. King, D. J. Campbell, A. T. McGuire, L. Stamatatos, H. Ruohola-Baker, J. Mathieu, D. Veesler, and D. Baker
4/2/2021
Geometric Lessons and Design Strategies for Nanoscale Protein Cages
J. Laniado, K. A. Cannon, J. E. Miller, M. R. Sawaya, D. E. McNamara, and T. O. Yeates
3/8/2021
Complete and cooperative in vitro assembly of computationally designed self-assembling protein nanomaterials
A. J. Wargacki, T. P. Wörner, M. van de Waterbeemd, D. Ellis, A. J. R. Heck, and N. P. King
2/9/2021
A fragment-based protein interface design algorithm for symmetric assemblies
J. Laniado, K. Meador, and T. O. Yeates
1/1/2021
A complete rule set for designing symmetry combination materials from protein molecules
J. Laniado, and T. O. Yeates
11/25/2020
Designed protein logic to target cells with precise combinations of surface antigens
M. J. Lajoie, S. E. Boyken, A. I. Salter, J. Bruffey, A. Rajan, R. A. Langan, A. Olshefsky, V. Muhunthan, M. J. Bick, M. Gewe, A. Quijano-Rubio, J. Johnson, G. Lenz, A. Nguyen, S. Pun, C. E. Correnti, S. R. Riddell, and D. Baker
9/25/2020
Computational design of transmembrane pores
C. Xu, P. Lu, T. M. Gamal El-Din, X. Y. Pei, M. C. Johnson, A. Uyeda, M. J. Bick, Q. Xu, D. Jiang, H. Bai, G. Reggiano, Y. Hsia, T. J. Brunette, J. Dou, D. Ma, E. M. Lynch, S. E. Boyken, P. Huang, L. Stewart, F. DiMaio, J. M. Kollman, B. F. Luisi, T. Matsuura, W. A. Catterall, and D. Baker
8/26/2020
Structural and functional evaluation of de novo-designed, two-component nanoparticle carriers for HIV Env trimer immunogens
A. Antanasijevic, G. Ueda, P. J. M. Brouwer, J. Copps, D. Huang, J. D. Allen, C. A. Cottrell, A. Yasmeen, L. M. Sewall, I. Bontjer, T. J. Ketas, H. L. Turner, Z. T. Berndsen, D. C. Montefiori, P. J. Klasse, M. Crispin, D. Nemazee, J. P. Moore, R. W. Sanders, N. P. King, D. Baker, and A. B. Ward
8/11/2020
Tailored design of protein nanoparticle scaffolds for multivalent presentation of viral glycoprotein antigens
G. Ueda, A. Antanasijevic, J. A. Fallas, W. Sheffler, J. Copps, D. Ellis, G. B. Hutchinson, A. Moyer, A. Yasmeen, Y. Tsybovsky, Y. Park, M. J. Bick, B. Sankaran, R. A. Gillespie, P. J. Brouwer, P. H. Zwart, D. Veesler, M. Kanekiyo, B. S. Graham, R. W. Sanders, J. P. Moore, P. J. Klasse, A. B. Ward, N. P. King, and D. Baker
8/4/2020
Design and Characterization of an Icosahedral Protein Cage Formed by a Double-Fusion Protein Containing Three Distinct Symmetry Elements
K. A. Cannon, V. N. Nguyen, C. Morgan, and T. O. Yeates
2/12/2020
Design and structure of two new protein cages illustrate successes and ongoing challenges in protein engineering
K. A. Cannon, R. U. Park, S. E. Boyken, U. Nattermann, S. Yi, D. Baker, N. P. King, and T. O. Yeates
12/26/2019
De novo design of tunable, pH-driven conformational changes
S. E. Boyken, M. A. Benhaim, F. Busch, M. Jia, M. J. Bick, H. Choi, J. C. Klima, Z. Chen, C. Walkey, A. Mileant, A. Sahasrabuddhe, K. Y. Wei, E. A. Hodge, S. Byron, A. Quijano-Rubio, B. Sankaran, N. P. King, J. Lippincott-Schwartz, V. H. Wysocki, K. K. Lee, and D. Baker
5/17/2019
High-symmetry protein assemblies: patterns and emerging applications
K. A. Cannon, J. M. Ochoa, and T. O. Yeates
4/1/2019
View All Publications
Research Highlights
Blueprinting Extendable Nanomaterials with Standardized Protein Blocks
David Baker (U. Washington)
10/25/2024
Increasing Computational Protein Design Literacy through Cohort-based Learning for Undergraduate Students
David Baker and Neil King (U. Washington)
10/25/2024
Computational Design of Mechanically Coupled Axle-rotor Protein Assemblies
Neil King and David Baker (U. Washington)
10/25/2024