1
|
Duan M, Lv C, Zang J, Leng X, Zhao G, Zhang T. Metals at the Helm: Revolutionizing Protein Assembly and Applications. Macromol Biosci 2024:e2400126. [PMID: 39239781 DOI: 10.1002/mabi.202400126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/23/2024] [Indexed: 09/07/2024]
Abstract
Protein assembly is an essential process in biological systems, where proteins self-assemble into complex structures with diverse functions. Inspired by the exquisite control over protein assembly in nature, scientists have been exploring ways to design and assemble protein structures with precise control over their topologies and functions. One promising approach for achieving this goal is through metal coordination, which utilizes metal-binding motifs to mediate protein-protein interactions and assemble protein complexes with controlled stoichiometry and geometry. Metal coordination provides a modular and tunable approach for protein assembly and de novo structure design, where the metal ion acts as a molecular glue that holds the protein subunits together in a specific orientation. Metal-coordinated protein assemblies have shown great potential for developing functional metalloproteinase, novel biomaterials and integrated drug delivery systems. In this review, an overview of the recent advances in protein assemblies benefited from metal coordination is provided, focusing on various protein arrangements in different dimensions including protein oligomers, protein nanocage and higher-order protein architectures. Moreover, the key metal-binding motifs and strategies used to assemble protein structures with precise control over their properties are highlighted. The potential applications of metal-mediated protein assemblies in biotechnology and biomedicine are also discussed.
Collapse
Affiliation(s)
- Maoping Duan
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Chenyan Lv
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Jiachen Zang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Xiaojing Leng
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Guanghua Zhao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Tuo Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
- Center of Food Colloids and Delivery for Functionality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| |
Collapse
|
2
|
Gladkov N, Scott EA, Meador K, Lee EJ, Laganowsky AD, Yeates TO, Castells‐Graells R. Design of a symmetry-broken tetrahedral protein cage by a method of internal steric occlusion. Protein Sci 2024; 33:e4973. [PMID: 38533546 PMCID: PMC10966355 DOI: 10.1002/pro.4973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/05/2024] [Accepted: 03/12/2024] [Indexed: 03/28/2024]
Abstract
Methods in protein design have made it possible to create large and complex, self-assembling protein cages with diverse applications. These have largely been based on highly symmetric forms exemplified by the Platonic solids. Prospective applications of protein cages would be expanded by strategies for breaking the designed symmetry, for example, so that only one or a few (instead of many) copies of an exterior domain or motif might be displayed on their surfaces. Here we demonstrate a straightforward design approach for creating symmetry-broken protein cages able to display singular copies of outward-facing domains. We modify the subunit of an otherwise symmetric protein cage through fusion to a small inward-facing domain, only one copy of which can be accommodated in the cage interior. Using biochemical methods and native mass spectrometry, we show that co-expression of the original subunit and the modified subunit, which is further fused to an outward-facing anti-GFP DARPin domain, leads to self-assembly of a protein cage presenting just one copy of the DARPin protein on its exterior. This strategy of designed occlusion provides a facile route for creating new types of protein cages with unique properties.
Collapse
Affiliation(s)
- Nika Gladkov
- Department of Chemistry and BiochemistryUniversity of CaliforniaLos AngelesCaliforniaUSA
| | - Elena A. Scott
- Department of ChemistryTexas A&M UniversityCollege StationTexasUSA
| | - Kyle Meador
- Department of Chemistry and BiochemistryUniversity of CaliforniaLos AngelesCaliforniaUSA
| | - Eric J. Lee
- Department of Chemistry and BiochemistryUniversity of CaliforniaLos AngelesCaliforniaUSA
| | | | - Todd O. Yeates
- Department of Chemistry and BiochemistryUniversity of CaliforniaLos AngelesCaliforniaUSA
- Molecular Biology InstituteUniversity of CaliforniaLos AngelesCaliforniaUSA
- UCLA‐DOE Institute for Genomics and ProteomicsLos AngelesCaliforniaUSA
| | | |
Collapse
|
3
|
Kavčič L, Kežar A, Koritnik N, Žnidarič MT, Klobučar T, Vičič Ž, Merzel F, Holden E, Benesch JLP, Podobnik M. From structural polymorphism to structural metamorphosis of the coat protein of flexuous filamentous potato virus Y. Commun Chem 2024; 7:14. [PMID: 38233506 PMCID: PMC10794713 DOI: 10.1038/s42004-024-01100-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 01/05/2024] [Indexed: 01/19/2024] Open
Abstract
The structural diversity and tunability of the capsid proteins (CPs) of various icosahedral and rod-shaped viruses have been well studied and exploited in the development of smart hybrid nanoparticles. However, the potential of CPs of the wide-spread flexuous filamentous plant viruses remains to be explored. Here, we show that we can control the shape, size, RNA encapsidation ability, symmetry, stability and surface functionalization of nanoparticles through structure-based design of CP from potato virus Y (PVY). We provide high-resolution insight into CP-based self-assemblies, ranging from large polymorphic or monomorphic filaments to smaller annular, cubic or spherical particles. Furthermore, we show that we can prevent CP self-assembly in bacteria by fusion with a cleavable protein, enabling controlled nanoparticle formation in vitro. Understanding the remarkable structural diversity of PVY CP not only provides possibilities for the production of biodegradable nanoparticles, but may also advance future studies of CP's polymorphism in a biological context.
Collapse
Affiliation(s)
- Luka Kavčič
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
- PhD Program 'Chemical Sciences', Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Andreja Kežar
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Neža Koritnik
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
- PhD Program 'Biomedicine', Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Magda Tušek Žnidarič
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Tajda Klobučar
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
- PhD Program 'Biosciences', Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Žiga Vičič
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Franci Merzel
- Theory Department, National Institute of Chemistry, Ljubljana, Slovenia
| | - Ellie Holden
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Justin L P Benesch
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Marjetka Podobnik
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia.
| |
Collapse
|
4
|
Stupka I, Biela AP, Piette B, Kowalczyk A, Majsterkiewicz K, Borzęcka-Solarz K, Naskalska A, Heddle JG. An artificial protein cage made from a 12-membered ring. J Mater Chem B 2024; 12:436-447. [PMID: 38088805 DOI: 10.1039/d3tb01659e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Artificial protein cages have great potential in diverse fields including as vaccines and drug delivery vehicles. TRAP-cage is an artificial protein cage notable for the way in which the interface between its ring-shaped building blocks can be modified such that the conditions under which cages disassemble can be controlled. To date, TRAP-cages have been constructed from homo-11mer rings, i.e., hendecamers. This is interesting as convex polyhedra with identical regular faces cannot be formed from hendecamers. TRAP-cage overcomes this limitation due to intrinsic flexibility, allowing slight deformation to absorb any error. The resulting TRAP-cage made from 24 TRAP 11mer rings is very close to regular with only very small errors necessary to allow the cage to form. The question arises as to the limits of the error that can be absorbed by a protein structure in this way before the formation of an apparently regular convex polyhedral becomes impossible. Here we use a naturally occurring TRAP variant consisting of twelve identical monomers (i.e., a dodecamer) to probe these limits. We show that it is able to form an apparently regular protein cage consisting of twelve TRAP rings. Comparison of the cryo-EM structure of the new cage with theoretical models and related cages gives insight into the rules of cage formation and allows us to predict other cages that may be formed given TRAP-rings consisting of different numbers of monomers.
Collapse
Affiliation(s)
- Izabela Stupka
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
- Postgraduate School of Molecular Medicine, Warsaw, Poland
| | - Artur P Biela
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
- Institute of Zoology and Biomedical Research, Jagiellonian University, Krakow, Poland
| | - Bernard Piette
- Department of Mathematical Sciences, Durham University, Durham, UK
| | - Agnieszka Kowalczyk
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
- Faculty of Mathematics and Computer Science, Jagiellonian University, Krakow, Poland
| | - Karolina Majsterkiewicz
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
- Postgraduate School of Molecular Medicine, Warsaw, Poland
| | | | - Antonina Naskalska
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
| | - Jonathan G Heddle
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
| |
Collapse
|
5
|
Fatehi F, Twarock R. An interaction network approach predicts protein cage architectures in bionanotechnology. Proc Natl Acad Sci U S A 2023; 120:e2303580120. [PMID: 38060565 PMCID: PMC10723117 DOI: 10.1073/pnas.2303580120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 10/21/2023] [Indexed: 12/17/2023] Open
Abstract
Protein nanoparticles play pivotal roles in many areas of bionanotechnology, including drug delivery, vaccination, and diagnostics. These technologies require control over the distinct particle morphologies that protein nanocontainers can adopt during self-assembly from their constituent protein components. The geometric construction principle of virus-derived protein cages is by now fairly well understood by analogy to viral protein shells in terms of Caspar and Klug's quasi-equivalence principle. However, many artificial, or genetically modified, protein containers exhibit varying degrees of quasi-equivalence in the interactions between identical protein subunits. They can also contain a subset of protein subunits that do not participate in interactions with other assembly units, called capsomers, leading to gaps in the particle surface. We introduce a method that exploits information on the local interactions between the capsomers to infer the geometric construction principle of these nanoparticle architectures. The predictive power of this approach is demonstrated here for a prominent system in nanotechnology, the AaLS pentamer. Our method not only rationalises hitherto discovered cage structures but also predicts geometrically viable options that have not yet been observed. The classification of nanoparticle architecture based on the geometric properties of the interaction network closes a gap in our current understanding of protein container structure and can be widely applied in protein nanotechnology, paving the way to programmable control over particle polymorphism.
Collapse
Affiliation(s)
- Farzad Fatehi
- Departments of Mathematics, University of York, YorkYO10 5DD, United Kingdom
| | - Reidun Twarock
- Departments of Mathematics, University of York, YorkYO10 5DD, United Kingdom
- Department of Biology, University of York, YorkYO10 5DD, United Kingdom
| |
Collapse
|
6
|
Near-Miss Symmetric Polyhedral Cages. Symmetry (Basel) 2023. [DOI: 10.3390/sym15030717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023] Open
Abstract
Following the experimental discovery of several nearly symmetric protein cages, we define the concept of homogeneous symmetric congruent equivalent near-miss polyhedral cages made out of P-gons. We use group theory to parameterize the possible configurations and we minimize the irregularity of the P-gons numerically to construct all such polyhedral cages for P=6 to P=20 with deformation of up to 10%.
Collapse
|