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Xia X, Li H, Zang J, Cheng S, Du M. Advancements of the Molecular Directed Design and Structure-Activity Relationship of Ferritin Nanocage. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:7629-7654. [PMID: 38518374 DOI: 10.1021/acs.jafc.3c09903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/24/2024]
Abstract
Ferritin nanocages possess remarkable structural properties and biological functions, making them highly attractive for applications in functional materials and biomedicine. This comprehensive review presents an overview of the molecular characteristics, extraction and identification of ferritin, ferritin receptors, as well as the advancements in the directional design of high-order assemblies of ferritin and the applications based on its unique structural properties. Specifically, this Review focuses on the regulation of ferritin assembly from one to three dimensions, leveraging the symmetry of ferritin and modifications on key interfaces. Furthermore, it discusses targeted delivery of nutrition and drugs through facile loading and functional modification of ferritin. The aim of this Review is to inspire the design of micro/nano functional materials using ferritin and the development of nanodelivery vehicles for nutritional fortification and disease treatment.
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Affiliation(s)
- Xiaoyu Xia
- SKL of Marine Food Processing & Safety Control, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China
- National Engineering Research Center of Seafood, Collaborative Innovation Centre of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Han Li
- SKL of Marine Food Processing & Safety Control, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China
- National Engineering Research Center of Seafood, Collaborative Innovation Centre of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Jiachen Zang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Shuzhen Cheng
- SKL of Marine Food Processing & Safety Control, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China
- National Engineering Research Center of Seafood, Collaborative Innovation Centre of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Ming Du
- SKL of Marine Food Processing & Safety Control, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China
- National Engineering Research Center of Seafood, Collaborative Innovation Centre of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
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2
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Bacterioferritin nanocage: Structure, biological function, catalytic mechanism, self-assembly and potential applications. Biotechnol Adv 2022; 61:108057. [DOI: 10.1016/j.biotechadv.2022.108057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/24/2022] [Accepted: 10/26/2022] [Indexed: 11/22/2022]
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3
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Bradley JM, Gray E, Richardson J, Moore GR, Le Brun NE. Protein encapsulation within the internal cavity of a bacterioferritin. NANOSCALE 2022; 14:12322-12331. [PMID: 35969005 PMCID: PMC9439638 DOI: 10.1039/d2nr01780f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The thermal and chemical stability of 24mer ferritins has led to attempts to exploit their naturally occurring nanoscale (8 nm) internal cavities for biotechnological applications. An area of increasing interest is the encapsulation of molecules either for medical or biocatalysis applications. Encapsulation requires ferritin dissociation, typically induced using high temperature or acidic conditions (pH ≥ 2), which generally precludes the inclusion of fragile cargo such as proteins or peptide fragments. Here we demonstrate that minimizing salt concentration combined with adjusting the pH to ≤8.5 (i.e. low proton/metal ion concentration) reversibly shifts the naturally occurring equilibrium between dimeric and 24meric assemblies of Escherichia coli bacterioferritin (Bfr) in favour of the disassembled form. Interconversion between the different oligomeric forms of Bfr is sufficiently slow under these conditions to allow the use of size exclusion chromatography to obtain wild type protein in the purely dimeric and 24meric forms. This control over association state was exploited to bind heme at natural sites that are not accessible in the assembled protein. The potential for biotechnological applications was demonstrated by the encapsulation of a small, acidic [3Fe-4S] cluster-containing ferredoxin within the Bfr internal cavity. The capture of ∼4-6 negatively charged ferredoxin molecules per cage indicates that charge complementarity with the inner protein surface is not an essential determinant of successful encapsulation.
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Affiliation(s)
- Justin M Bradley
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Elizabeth Gray
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Jake Richardson
- Bioimaging Facility, John Innes Centre, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Geoffrey R Moore
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Nick E Le Brun
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
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4
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Dang DT. Molecular Approaches to Protein Dimerization: Opportunities for Supramolecular Chemistry. Front Chem 2022; 10:829312. [PMID: 35211456 PMCID: PMC8861298 DOI: 10.3389/fchem.2022.829312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 01/14/2022] [Indexed: 11/17/2022] Open
Abstract
Protein dimerization plays a key role in many biological processes. Most cellular events such as enzyme activation, transcriptional cofactor recruitment, signal transduction, and even pathogenic pathways are significantly regulated via protein-protein interactions. Understanding and controlling the molecular mechanisms that regulate protein dimerization is crucial for biomedical applications. The limitations of engineered protein dimerization provide an opportunity for molecular chemistry to induce dimerization of protein in biological events. In this review, molecular control over dimerization of protein and activation in this respect are discussed. The well known molecule glue-based approaches to induced protein dimerization provide powerful tools to modulate the functionality of dimerized proteins and are shortly highlighted. Subsequently metal ion, nucleic acid and host-guest chemistry are brought forward as novel approaches for orthogonal control over dimerization of protein. The specific focus of the review will be on host-guest systems as novel, robust and versatile supramolecular approaches to modulate the dimerization of proteins, using functional proteins as model systems.
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5
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Lv C, Zhang X, Liu Y, Zhang T, Chen H, Zang J, Zheng B, Zhao G. Redesign of protein nanocages: the way from 0D, 1D, 2D to 3D assembly. Chem Soc Rev 2021; 50:3957-3989. [PMID: 33587075 DOI: 10.1039/d0cs01349h] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Compartmentalization is a hallmark of living systems. Through compartmentalization, ubiquitous protein nanocages such as viral capsids, ferritin, small heat shock proteins, and DNA-binding proteins from starved cells fulfill a variety of functions, while their shell-like structures hold great promise for various applications in the field of nanomedicine and nanotechnology. However, the number and structure of natural protein nanocages are limited, and these natural protein nanocages may not be suited for a given application, which might impede their further application as nanovehicles, biotemplates or building blocks. To overcome these shortcomings, different strategies have been developed by scientists to construct artificial protein nanocages, and 1D, 2D and 3D protein arrays with protein nanocages as building blocks through genetic and chemical modification to rival the size and functionality of natural protein nanocages. This review outlines the recent advances in the field of the design and construction of artificial protein nanocages and their assemblies with higher order, summarizes the strategies for creating the assembly of protein nanocages from zero-dimension to three dimensions, and introduces their corresponding applications in the preparation of nanomaterials, electrochemistry, and drug delivery. The review will highlight the roles of both the inter-subunit/intermolecular interactions at the key interface and the protein symmetry in constructing and controlling protein nanocage assemblies with different dimensions.
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Affiliation(s)
- Chenyan Lv
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China.
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Le Vay K, Carter BM, Watkins DW, Dora Tang TY, Ting VP, Cölfen H, Rambo RP, Smith AJ, Ross Anderson JL, Perriman AW. Controlling Protein Nanocage Assembly with Hydrostatic Pressure. J Am Chem Soc 2020; 142:20640-20650. [PMID: 33252237 DOI: 10.1021/jacs.0c07285] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Controlling the assembly and disassembly of nanoscale protein cages for the capture and internalization of protein or non-proteinaceous components is fundamentally important to a diverse range of bionanotechnological applications. Here, we study the reversible, pressure-induced dissociation of a natural protein nanocage, E. coli bacterioferritin (Bfr), using synchrotron radiation small-angle X-ray scattering (SAXS) and circular dichroism (CD). We demonstrate that hydrostatic pressures of 450 MPa are sufficient to completely dissociate the Bfr 24-mer into protein dimers, and the reversibility and kinetics of the reassembly process can be controlled by selecting appropriate buffer conditions. We also demonstrate that the heme B prosthetic group present at the subunit dimer interface influences the stability and pressure lability of the cage, despite its location being discrete from the interdimer interface that is key to cage assembly. This indicates a major cage-stabilizing role for heme within this family of ferritins.
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Affiliation(s)
- Kristian Le Vay
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K
- Bristol Centre for Functional Nanomaterials, HH Wills Physics Laboratory, University of Bristol, Tyndall Avenue, Bristol BS8 1TL, U.K
| | - Ben M Carter
- School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD, U.K
| | - Daniel W Watkins
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K
| | - T-Y Dora Tang
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K
| | - Valeska P Ting
- Bristol Composites Institute (ACCIS), Department of Mechanical Engineering, University of Bristol, Queen's Building, Bristol BS8 1TR, U.K
| | - Helmut Cölfen
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Robert P Rambo
- Diamond House, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Fermi Ave., Didcot OX11 0DE, U.K
| | - Andrew J Smith
- Diamond House, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Fermi Ave., Didcot OX11 0DE, U.K
| | - J L Ross Anderson
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K
- BrisSynBio Synthetic Biology Research Centre, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K
| | - Adam W Perriman
- School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD, U.K
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7
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Zhao Y, Choi S, Yu J. In Situ Generated Silver Nanodot Förster Resonance Energy Transfer Pair Reveals Nanocage Sizes. J Phys Chem Lett 2020; 11:6867-6872. [PMID: 32787207 DOI: 10.1021/acs.jpclett.0c01950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Characterizing nanocages in macromolecules is one of the keys to understanding various biological activities and further utilizing nanocages for novel materials synthesis. However, fast and straightforward detection of the nanocage size remains challenging. Here, we present a new approach to detect the diameter of a nanocage by Förster resonance energy transfer (FRET) of luminescent silver nanodot pairs with reverse micelles as a model. Silver nanodot FRET pairs can be generated in situ from a single silver nanodot species with critical energy transfer distances, R0, of 4.8-6.5 nm. We have applied this approach to clarify the size variation of the water nanocage in nonionic surfactant Triton X-100-based reverse micelles. FRET efficiency decreases as more water is added, indicating that the size of the reverse micelles continuously expands with water content. The silver element in the nanocage also enhances the visualization of the nanocage under cryo-TEM imaging. The diameter of the water nanocage measured with the above approach is consistent with that obtained by cryo-TEM, demonstrating that the FRET measurement of silver nanodots can be a fast and accurate tool to detect nanocage dimensions. The above demonstration allows us to apply our strategy to other protein-based nanocages.
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Affiliation(s)
- Yanlu Zhao
- Department of Chemistry Education, Seoul National University, Seoul 08826, Republic of Korea
| | - Sungmoon Choi
- Department of Chemistry Education, Seoul National University, Seoul 08826, Republic of Korea
| | - Junhua Yu
- Department of Chemistry Education, Seoul National University, Seoul 08826, Republic of Korea
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8
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Li R, Ma Y, Dong Y, Zhao Z, You C, Huang S, Li X, Wang F, Zhang Y. Novel Paclitaxel-Loaded Nanoparticles Based on Human H Chain Ferritin for Tumor-Targeted Delivery. ACS Biomater Sci Eng 2019; 5:6645-6654. [PMID: 33423483 DOI: 10.1021/acsbiomaterials.9b01533] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Paclitaxel (PTX), an excellent chemotherapeutic antitumor drug, is widely used to treat patients with various cancers. However, its clinical applications are greatly restricted by poor solubility and lack of targeting. Herein, we applied natural human H chain ferritin (HFtn) nanocages that can bind to tumor cells via interacting with the human transferritin receptor 1 (TfR1) leading to its endocytosis as the PTX carrier for the targeted delivery. PTX molecules were encapsulated into HFtn cavity using disassembly/reassembly method through adjusting pH. According to the requirements of drugs suitable for clinical trials, HFtn can be easily purified in high yields with no ligand modification or property modulation. We demonstrated that PTX molecules were successfully encapsulated in the protein nanocages. The HFtn-PTX nanoparticles exhibited similar morphology and structural characteristics to the hollow cage and showed significant cytotoxicity in vitro than the naked PTX. Flow cytometry, confocal laser scanning microscopy, and in vivo imaging of MDA-MB-231 tumor demonstrated the HFtn-PTX nanoparticles targeting ability to tumor cells. Cell apoptosis assay showed that HFtn-PTX had similar apoptotic characteristics on MDA-MB-231 cells as that of the free PTX. HFtn-PTX nanoparticles have higher in vivo therapeutic efficacy and lower systemic toxicity. The BALB/c mice model also confirmed the effectiveness of the nanoparticles. Specifically targeting to tumors and solving the solubility issue of water-insoluble drugs thus alleviating the side effects, HFtn can be an efficient hydrophobic drug delivery nanocarrier for further applications in cancer therapy.
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Affiliation(s)
- Ruike Li
- College of Chemical Engineering, Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Products, Nanjing Forestry University, Nanjing 210037, P. R. China
| | - Yuanmeng Ma
- College of Chemical Engineering, Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Products, Nanjing Forestry University, Nanjing 210037, P. R. China
| | - Yixin Dong
- College of Chemical Engineering, Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Products, Nanjing Forestry University, Nanjing 210037, P. R. China
| | - Zhujun Zhao
- College of Chemical Engineering, Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Products, Nanjing Forestry University, Nanjing 210037, P. R. China
| | - Chaoqun You
- College of Chemical Engineering, Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Products, Nanjing Forestry University, Nanjing 210037, P. R. China.,School of Chemistry and Chemical Engineering, Southeast University, Nanjing 210089, P. R. China
| | - Shenlin Huang
- College of Chemical Engineering, Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Products, Nanjing Forestry University, Nanjing 210037, P. R. China
| | - Xun Li
- College of Chemical Engineering, Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Products, Nanjing Forestry University, Nanjing 210037, P. R. China
| | - Fei Wang
- College of Chemical Engineering, Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Products, Nanjing Forestry University, Nanjing 210037, P. R. China
| | - Yu Zhang
- College of Chemical Engineering, Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Products, Nanjing Forestry University, Nanjing 210037, P. R. China
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9
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Wang Z, Xu L, Yu H, Lv P, Lei Z, Zeng Y, Liu G, Cheng T. Ferritin nanocage-based antigen delivery nanoplatforms: epitope engineering for peptide vaccine design. Biomater Sci 2019; 7:1794-1800. [PMID: 30888360 DOI: 10.1039/c9bm00098d] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Biomedical applications and nanotechnological advances, including constrained synthesis, multimodal imaging, drug delivery, and bioassay, have strongly benefited from employing ferritin nanocages due to their remarkable properties of easy engineering, great biocompatible features, large capacity and so on. In this study, ferritin nanocages were used to display epitopes (model antigens derived from Enterovirus 71 (EV71) with different length) on C- and N-terminals and the loop zone to search for the optimal position for the fusion of the epitopes to the vaccine platform. The longest epitope displayed on the N-terminal and loop zone as well as the second longest peptide displayed on the loop zone of ferritin resulted in 100% passive protection of newborn BALB/c mice from the lethal EV71. This suggests that peptides fused onto the loop zone of ferritin could induce strong immune response. Our results increase the versatility of the vaccine platform and provide more options for the production of stable constructs, suggesting the potential future clinical applicability of ferritin-based antigen delivery nanoplatforms.
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Affiliation(s)
- Zhantong Wang
- Department of pharmacology, Xiamen Medical College, Xiamen, 361008, China.
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10
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Medium throughput cage state stability screen of conditions for the generation of gold nanoparticles encapsulated within a mini-ferritin. Bioorg Med Chem 2018; 26:5253-5258. [DOI: 10.1016/j.bmc.2018.03.036] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 03/15/2018] [Accepted: 03/23/2018] [Indexed: 12/26/2022]
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11
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Diaz D, Care A, Sunna A. Bioengineering Strategies for Protein-Based Nanoparticles. Genes (Basel) 2018; 9:E370. [PMID: 30041491 PMCID: PMC6071185 DOI: 10.3390/genes9070370] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 07/16/2018] [Accepted: 07/17/2018] [Indexed: 12/16/2022] Open
Abstract
In recent years, the practical application of protein-based nanoparticles (PNPs) has expanded rapidly into areas like drug delivery, vaccine development, and biocatalysis. PNPs possess unique features that make them attractive as potential platforms for a variety of nanobiotechnological applications. They self-assemble from multiple protein subunits into hollow monodisperse structures; they are highly stable, biocompatible, and biodegradable; and their external components and encapsulation properties can be readily manipulated by chemical or genetic strategies. Moreover, their complex and perfect symmetry have motivated researchers to mimic their properties in order to create de novo protein assemblies. This review focuses on recent advances in the bioengineering and bioconjugation of PNPs and the implementation of synthetic biology concepts to exploit and enhance PNP's intrinsic properties and to impart them with novel functionalities.
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Affiliation(s)
- Dennis Diaz
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Andrew Care
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics, Macquarie University, Sydney, NSW 2109, Australia.
| | - Anwar Sunna
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics, Macquarie University, Sydney, NSW 2109, Australia.
- Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, NSW 2109, Australia.
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12
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Cornell TA, Ardejani MS, Fu J, Newland SH, Zhang Y, Orner BP. A Structure-Based Assembly Screen of Protein Cage Libraries in Living Cells: Experimentally Repacking a Protein–Protein Interface To Recover Cage Formation in an Assembly-Frustrated Mutant. Biochemistry 2018; 57:604-613. [DOI: 10.1021/acs.biochem.7b01000] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Thomas A. Cornell
- Department
of Chemistry, King’s College London, London, U.K
- Division
of Chemistry and Biological Chemistry, Nanyang Technological University, Singapore
| | - Maziar S. Ardejani
- Department
of Chemistry, King’s College London, London, U.K
- Division
of Chemistry and Biological Chemistry, Nanyang Technological University, Singapore
| | - Jing Fu
- Division
of Chemistry and Biological Chemistry, Nanyang Technological University, Singapore
| | | | - Yu Zhang
- Division
of Chemistry and Biological Chemistry, Nanyang Technological University, Singapore
| | - Brendan P. Orner
- Department
of Chemistry, King’s College London, London, U.K
- Division
of Chemistry and Biological Chemistry, Nanyang Technological University, Singapore
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13
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Zhang Y, Zhou J, Ardejani MS, Li X, Wang F, Orner BP. Designability of Aromatic Interaction Networks at E. coli Bacterioferritin B-Type Channels. Molecules 2017; 22:E2184. [PMID: 29292762 PMCID: PMC6149950 DOI: 10.3390/molecules22122184] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/01/2017] [Accepted: 12/06/2017] [Indexed: 02/02/2023] Open
Abstract
The bacterioferritin from E. coli (BFR), a maxi-ferritin made of 24 subunits, has been utilized as a model to study the fundamentals of protein folding and self-assembly. Through structural and computational analyses, two amino acid residues at the B-site interface of BFR were chosen to investigate the role they play in the self-assembly of nano-cage formation, and the possibility of building aromatic interaction networks at B-type protein-protein interfaces. Three mutants were designed, expressed, purified, and characterized using transmission electron microscopy, size exclusion chromatography, native gel electrophoresis, and temperature-dependent circular dichroism spectroscopy. All of the mutants fold into α-helical structures and possess lowered thermostability. The double mutant D132W/N34W was 12 °C less stable than the wild type, and was also the only mutant for which cage-like nanostructures could not be detected in the dried, surface-immobilized conditions of transmission electron microscopy. Two mutants-N34W and D132W/N34W-only formed dimers in solution, while mutant D132W favored the 24-mer even more robustly than the wild type, suggesting that we were successful in designing proteins with enhanced assembly properties. This investigation into the structure of this important class of proteins could help to understand the self-assembly of proteins in general.
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Affiliation(s)
- Yu Zhang
- College of Chemical Engineering, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Ago-Forest Biomass, Jiangsu Key Lab of Biomass-Based Green Fuels and Chemicals, Nanjing Forestry University, Nanjing 210037, China.
| | - Jinhua Zhou
- College of Chemical Engineering, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Ago-Forest Biomass, Jiangsu Key Lab of Biomass-Based Green Fuels and Chemicals, Nanjing Forestry University, Nanjing 210037, China.
| | - Maziar S Ardejani
- Division of Chemistry and Biological Chemistry, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore.
- Department of Chemistry, King's College London, London SE1 1DB, UK.
| | - Xun Li
- College of Chemical Engineering, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Ago-Forest Biomass, Jiangsu Key Lab of Biomass-Based Green Fuels and Chemicals, Nanjing Forestry University, Nanjing 210037, China.
| | - Fei Wang
- College of Chemical Engineering, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Ago-Forest Biomass, Jiangsu Key Lab of Biomass-Based Green Fuels and Chemicals, Nanjing Forestry University, Nanjing 210037, China.
| | - Brendan P Orner
- Department of Chemistry, King's College London, London SE1 1DB, UK.
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14
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Cornell TA, Srivastava Y, Jauch R, Fan R, Orner BP. The Crystal Structure of a Maxi/Mini-Ferritin Chimera Reveals Guiding Principles for the Assembly of Protein Cages. Biochemistry 2017; 56:3894-3899. [PMID: 28682051 DOI: 10.1021/acs.biochem.7b00312] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Cage proteins assemble into nanoscale structures with large central cavities. They play roles, including those as virus capsids and chaperones, and have been applied to drug delivery and nanomaterials. Furthermore, protein cages have been used as model systems to understand and design protein quaternary structure. Ferritins are ubiquitous protein cages that manage iron homeostasis and oxidative damage. Two ferritin subfamilies have strongly similar tertiary structure yet distinct quaternary structure: maxi-ferritins normally assemble into 24-meric, octahedral cages with C-terminal E-helices centered around 4-fold symmetry axes, and mini-ferritins are 12-meric, tetrahedral cages with 3-fold axes defined by C-termini lacking E-domains. To understand the role E-domains play in ferritin quaternary structure, we previously designed a chimera of a maxi-ferritin E-domain fused to the C-terminus of a mini-ferritin. The chimera is a 12-mer cage midway in size between those of the maxi- and mini-ferritin. The research described herein sets out to understand (a) whether the increase in size over a typical mini-ferritin is due to a frozen state where the E-domain is flipped out of the cage and (b) whether the symmetrical preference of the E-domain in the maxi-ferritin (4-fold axis) overrules the C-terminal preference in the mini-ferritin (3-fold axis). With a 1.99 Å resolution crystal structure, we determined that the chimera assembles into a tetrahedral cage that can be nearly superimposed with the parent mini-ferritin, and that the E-domains are flipped external to the cage at the 3-fold symmetry axes.
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Affiliation(s)
- Thomas A Cornell
- Department of Chemistry, King's College London , London, U.K.,Division of Chemistry and Biological Chemistry, Nanyang Technological University , Singapore
| | - Yogesh Srivastava
- Genome Regulation Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , Guangzhou, China
| | - Ralf Jauch
- Genome Institute of Singapore , Singapore.,Genome Regulation Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , Guangzhou, China
| | - Rongli Fan
- Division of Chemistry and Biological Chemistry, Nanyang Technological University , Singapore
| | - Brendan P Orner
- Department of Chemistry, King's College London , London, U.K.,Division of Chemistry and Biological Chemistry, Nanyang Technological University , Singapore
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15
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Pulsipher KW, Villegas JA, Roose BW, Hicks TL, Yoon J, Saven JG, Dmochowski IJ. Thermophilic Ferritin 24mer Assembly and Nanoparticle Encapsulation Modulated by Interdimer Electrostatic Repulsion. Biochemistry 2017; 56:3596-3606. [PMID: 28682599 DOI: 10.1021/acs.biochem.7b00296] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Protein cage self-assembly enables encapsulation and sequestration of small molecules, macromolecules, and nanomaterials for many applications in bionanotechnology. Notably, wild-type thermophilic ferritin from Archaeoglobus fulgidus (AfFtn) exists as a stable dimer of four-helix bundle proteins at a low ionic strength, and the protein forms a hollow assembly of 24 protomers at a high ionic strength (∼800 mM NaCl). This assembly process can also be initiated by highly charged gold nanoparticles (AuNPs) in solution, leading to encapsulation. These data suggest that salt solutions or charged AuNPs can shield unfavorable electrostatic interactions at AfFtn dimer-dimer interfaces, but specific "hot-spot" residues controlling assembly have not been identified. To investigate this further, we computationally designed three AfFtn mutants (E65R, D138K, and A127R) that introduce a single positive charge at sites along the dimer-dimer interface. These proteins exhibited different assembly kinetics and thermodynamics, which were ranked in order of increasing 24mer propensity: A127R < wild type < D138K ≪ E65R. E65R assembled into the 24mer across a wide range of ionic strengths (0-800 mM NaCl), and the dissociation temperature for the 24mer was 98 °C. X-ray crystal structure analysis of the E65R mutant identified a more compact, closed-pore cage geometry. A127R and D138K mutants exhibited wild-type ability to encapsulate and stabilize 5 nm AuNPs, whereas E65R did not encapsulate AuNPs at the same high yields. This work illustrates designed protein cages with distinct assembly and encapsulation properties.
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Affiliation(s)
- Katherine W Pulsipher
- Department of Chemistry, University of Pennsylvania , 231 South 34th Street, Philadelphia, Pennsylvania 19104, United States
| | - Jose A Villegas
- Department of Chemistry, University of Pennsylvania , 231 South 34th Street, Philadelphia, Pennsylvania 19104, United States
| | - Benjamin W Roose
- Department of Chemistry, University of Pennsylvania , 231 South 34th Street, Philadelphia, Pennsylvania 19104, United States
| | - Tacey L Hicks
- Department of Chemistry, University of Pennsylvania , 231 South 34th Street, Philadelphia, Pennsylvania 19104, United States
| | - Jennifer Yoon
- Department of Chemistry, University of Pennsylvania , 231 South 34th Street, Philadelphia, Pennsylvania 19104, United States
| | - Jeffery G Saven
- Department of Chemistry, University of Pennsylvania , 231 South 34th Street, Philadelphia, Pennsylvania 19104, United States
| | - Ivan J Dmochowski
- Department of Chemistry, University of Pennsylvania , 231 South 34th Street, Philadelphia, Pennsylvania 19104, United States
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Zhang Y, Wang L, Ardejani MS, Aris NF, Li X, Orner BP, Wang F. Mutagenesis study to disrupt electrostatic interactions on the twofold symmetry interface of Escherichia coli bacterioferritin. J Biochem 2015; 158:505-12. [PMID: 26115686 DOI: 10.1093/jb/mvv065] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 05/26/2015] [Indexed: 12/23/2022] Open
Abstract
Ferritins and other cage proteins have been utilized as models to understand the fundamentals of protein folding and self-assembly. The bacterioferritin (BFR) from Escherichia coli, a maxi-ferritin made up of 24 subunits, was chosen as the basis for a mutagenesis study to investigate the role of electrostatic intermolecular interactions mediated through charged amino acids. Through structural and computational analyses, three charged amino acids R30, D56 and E60 which involved in an electrostatic interaction network were mutated to the opposite charge. Four mutants, R30D, D56R, E60H and D56R-E60H, were expressed, purified and characterized. All of the mutants fold into α-helical structures. Consistent with the computational prediction, they all show a lowered thermostability; double mutant D56R-E60H was found to be 16°C less stable than the wild type. Except for the mutant E60H, all the other mutations completely shut down the formation of protein cages to favour the dimer state in solution. The mutants, however, retain their ability to form cage-like nanostructures in the dried, surface immobilized conditions of transmission electron microscopy. Our findings confirm that even a single charge-inversion mutation at the 2-fold interface of BFR can affect the quaternary structure of its dimers and their ability to self-assemble into cage structures.
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Affiliation(s)
- Yu Zhang
- College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China; Jiangsu Key Lab of Biomass-Based Green Fuels and Chemicals, Nanjing 210037, China
| | - Lijun Wang
- College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Maziar S Ardejani
- Department of Chemistry, King's College London, London, SE1 1DB, UK; and
| | - Nur Fazlina Aris
- School of Life Sciences and Chemical Technology, Ngee Ann Polytechnic 599489, Singapore
| | - Xun Li
- College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China; Jiangsu Key Lab of Biomass-Based Green Fuels and Chemicals, Nanjing 210037, China
| | - Brendan P Orner
- Department of Chemistry, King's College London, London, SE1 1DB, UK; and
| | - Fei Wang
- College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China; Jiangsu Key Lab of Biomass-Based Green Fuels and Chemicals, Nanjing 210037, China;
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17
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Yao H, Rui H, Kumar R, Eshelman K, Lovell S, Battaile KP, Im W, Rivera M. Concerted motions networking pores and distant ferroxidase centers enable bacterioferritin function and iron traffic. Biochemistry 2015; 54:1611-27. [PMID: 25640193 DOI: 10.1021/bi501255r] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
X-ray crystallography, molecular dynamics (MD) simulations, and biochemistry were utilized to investigate the effect of introducing hydrophobic interactions in the 4-fold (N148L and Q151L) and B-pores (D34F) of Pseudomonas aeruginosa bacterioferritin B (BfrB) on BfrB function. The structures show only local structural perturbations and confirm the anticipated hydrophobic interactions. Surprisingly, structures obtained after soaking crystals in Fe2+-containing crystallization solution revealed that although iron loads into the ferroxidase centers of the mutants, the side chains of ferroxidase ligands E51 and H130 do not reorganize to bind the iron ions, as is seen in the wt BfrB structures. Similar experiments with a double mutant (C89S/K96C) prepared to introduce changes outside the pores show competent ferroxidase centers that function akin to those in wt BfrB. MD simulations comparing wt BfrB with the D34F and N148L mutants show that the mutants exhibit significantly reduced flexibility and reveal a network of concerted motions linking ferroxidase centers and 4-fold and B-pores, which are important for imparting ferroxidase centers in BfrB with the required flexibility to function efficiently. In agreement, the efficiency of Fe2+ oxidation and uptake of the 4-fold and B-pore mutants in solution is significantly compromised relative to wt or C89S/K96C BfrB. Finally, our structures show a large number of previously unknown iron binding sites in the interior cavity and B-pores of BfrB, which reveal in unprecedented detail conduits followed by iron and phosphate ions across the BfrB shell, as well as paths in the interior cavity that may facilitate nucleation of the iron phosphate mineral.
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Affiliation(s)
- Huili Yao
- Department of Chemistry, ‡Del Shankel Structural Biology Center, and §Department of Molecular Biosciences and Center for Bioinformatics, University of Kansas , Multidisciplinary Research Building, 2030 Becker Drive, Lawrence, Kansas 66047, United States
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18
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Zhang Y, Ardejani MS. Differential scanning calorimetry to quantify the stability of protein cages. Methods Mol Biol 2015; 1252:101-113. [PMID: 25358777 DOI: 10.1007/978-1-4939-2131-7_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Differential scanning calorimetry (DSC) is an experimental technique through which the differences in amount of heat required to maintain equal temperature between a sample and a reference cell are measured at various temperatures. The quantified heat relates to the differences in apparent heat capacity of the analytes. The data from DSC studies will thereby provide direct information about the energetics of thermally induced processes in the sample. Here we present a detailed protocol to quantify the thermostability of protein cage, bacterioferritin (BFR), using differential scanning calorimetry.
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Affiliation(s)
- Yu Zhang
- College of Chemical Engineering, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu, 210037, China,
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19
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Abstract
We describe a method for the detection of specific protein-protein interactions in protein cages through the exploitation of designed binding sites for bisarsenic fluorescent probes. These sites are engineered to be protein-protein interface specific. We have adapted this method to ferritins; however, it could conceivably be applied to other protein cages. It is thought that this technique could be utilized in the thermodynamic and kinetic characterization of cage assembly mechanisms and in the high-throughput screening of protein cage libraries for the discovery of proteins with new assembly properties or of optimized conditions for assembly.
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Affiliation(s)
- Thomas A Cornell
- Department of Chemistry, King's College London, Guys Campus, London, SE1 1DB, UK,
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20
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Ardejani MS, Orner BP. Computationally assisted engineering of protein cages. Methods Mol Biol 2015; 1252:51-59. [PMID: 25358772 DOI: 10.1007/978-1-4939-2131-7_5] [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: 06/04/2023]
Abstract
A hybrid computational method incorporating topographic analysis of protein surfaces and free-energy calculations of protein-protein interactions in protein nanocages is described. This design strategy can be used to engineer protein cages for enhanced structural stability and assembly.
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Affiliation(s)
- Maziar S Ardejani
- Department of Chemistry, School of Natural and Mathematical Sciences, King's College London, London, UK
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21
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Cornell TA, Fu J, Newland SH, Orner BP. Detection of Specific Protein–Protein Interactions in Nanocages by Engineering Bipartite FlAsH Binding Sites. J Am Chem Soc 2013; 135:16618-24. [DOI: 10.1021/ja4085034] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Thomas A. Cornell
- Department
of Chemistry, King’s College London, London, SE1 1DB, United Kingdom
- Division
of Chemistry and Biological Chemistry, Nanyang Technological University, Singapore, 637371
| | - Jing Fu
- Division
of Chemistry and Biological Chemistry, Nanyang Technological University, Singapore, 637371
| | - Stephanie H. Newland
- School
of Chemistry, University of Southampton, Southampton, SO17 1BJ, United Kingdom
| | - Brendan P. Orner
- Department
of Chemistry, King’s College London, London, SE1 1DB, United Kingdom
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22
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Ardejani MS, Chok XL, Foo CJ, Orner BP. Complete shift of ferritin oligomerization toward nanocage assembly via engineered protein–protein interactions. Chem Commun (Camb) 2013; 49:3528-30. [DOI: 10.1039/c3cc40886h] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Zhang Y, Fu J, Chee SY, Ang EXW, Orner BP. Rational disruption of the oligomerization of the mini-ferritin E. coli DPS through protein-protein interface mutation. Protein Sci 2011; 20:1907-17. [PMID: 21898653 DOI: 10.1002/pro.731] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Revised: 08/24/2011] [Accepted: 08/26/2011] [Indexed: 11/06/2022]
Abstract
DNA-binding protein from starved cells (DPS), a mini-ferritin capable of self-assembling into a 12-meric nano-cage, was chosen as the basis for an alanine-shaving mutagenesis study to investigate the importance of key amino acid residues, located at symmetry-related protein-protein interfaces, in controlling protein stability and self-assembly. Nine mutants were designed through simple inspection, synthesized, and subjected to transmission electron microscopy, circular dichroism, size exclusion chromatography, and "virtual alanine scanning" computational analysis. The data indicate that many of these residues may be hot spot residues. Most remarkably, two residues, R83 and R133, were observed to shift the oligomerization state to ~50% dimer. Based on the hypothesis that these two residues constitute a "hot strip," located at the ferritin-like threefold axis, the double mutant was generated which completely shuts down detectable formation of 12-mer in solution, favoring a cooperatively folded dimer. The fact that this effect logically builds upon the single mutants emphasizes that complex self-assembly has the potential to be manipulated rationally. This study should have an impact on the fundamental understanding of the assembly of DPS protein cages specifically and protein quaternary structure in general. In addition, as there is much interest in applying these and similar systems to the templation of nano-materials and drug delivery, the ability to control this ferritin's oligomerization state and stability could prove especially valuable.
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Affiliation(s)
- Yu Zhang
- Division of Chemistry and Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University, Singapore 637371
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