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Bhatt S, Dasgupta S, Tupe C, Prashar C, Adhikari U, Pandey KC, Kundu S, Chakraborti S. Antimalarial Delivery with a Ferritin-Based Protein Cage: A Step toward Developing Smart Therapeutics against Malaria. Biochemistry 2024; 63:1738-1751. [PMID: 38975628 DOI: 10.1021/acs.biochem.3c00692] [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: 07/09/2024]
Abstract
Over the past two decades, the utilization of protein cages has witnessed exponential growth driven by their extensive applications in biotechnology and therapeutics. In the context of the recent Covid-19 pandemic, protein-cage-based scaffolds played a pivotal role in vaccine development. Beyond vaccines, these protein cages have proven valuable in diverse drug delivery applications thanks to their distinctive architecture and structural stability. Among the various types of protein cages, ferritin-based cages have taken the lead in drug delivery applications. This is primarily attributed to their ease of production, exceptional thermal stability, and nontoxic nature. While ferritin-based cages are commonly employed in anticancer drug delivery and contrast agent delivery, their efficacy in malarial drug delivery had not been explored until this study. In this investigation, several antimalarial drugs were encapsulated within horse spleen ferritin, and the binding and loading processes were validated through both experimental and computational techniques. The data unequivocally demonstrate the facile incorporation of antimalarial drugs into ferritin without disrupting its three-dimensional structure. Computational docking and molecular dynamics simulations were employed to pinpoint the precise location of the drug binding site within ferritin. Subsequent efficacy testing on Plasmodium revealed that the developed nanoconjugate, comprising the drug-ferritin conjugate, exhibited significant effectiveness in eradicating the parasite. In conclusion, the findings strongly indicate that ferritin-based carrier systems hold tremendous promise for the future of antimalarial drug delivery, offering high selectivity and limited side effects.
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Affiliation(s)
- Shruti Bhatt
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Subrata Dasgupta
- Department of Biosciences & Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Chiging Tupe
- ICMR-National Institute of Malaria Research, Dwarka, New Delhi 110077, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP 201002, India
| | - Cherish Prashar
- ICMR-National Institute of Malaria Research, Dwarka, New Delhi 110077, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP 201002, India
| | - Utpal Adhikari
- National Institute of Technology, Durgapur, West Bengal 713209, India
| | - Kailash C Pandey
- ICMR-National Institute of Malaria Research, Dwarka, New Delhi 110077, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP 201002, India
| | - Suman Kundu
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, K K Birla Goa Campus, Goa 403726, India
| | - Soumyananda Chakraborti
- ICMR-National Institute of Malaria Research, Dwarka, New Delhi 110077, India
- Birla Institute of Technology and Science, Pilani, Hyderabad Campus, Hyderabad 500078, India
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2
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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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3
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Nasu E, Kawakami N, Takamura S, Hotta A, Arai R, Miyamoto K. Thermally Reversible Gel-Sol Transition of Hydrogels via Dissociation and Association of an Artificial Protein Nanocage. Biomacromolecules 2024; 25:2358-2366. [PMID: 38445465 DOI: 10.1021/acs.biomac.3c01285] [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: 03/07/2024]
Abstract
Oligomeric protein nanocages often disassemble into their subunits and reassemble by external stimuli. Thus, using these nanocages as cross-linkers for hydrogel network structures is a promising approach to allow hydrogels to undergo stimuli-responsive gel-sol transitions or self-healing. Here, we report hydrogels that show a reversible gel-sol transition resulting from the heat-induced dissociation and reassociation of protein nanocages. The hydrogel contained the 60-mer artificial protein nanocage, TIP60, as a supramolecular cross-linker for polyethylene glycol network structures. The hydrogel showed a gel-to-sol transition upon heating at a temperature above the melting point of TIP60 and immediately returned to a gel state upon cooling to room temperature. During the heating and cooling treatment of the hydrogel, small-angle X-ray scattering analysis suggested the dissociation and reassociation of TIP60. Furthermore, we demonstrated redox-responsive cargo release from TIP60 in the hydrogel. These results showed the potential of TIP60 as a component of multi-stimuli-responsive hydrogels.
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Affiliation(s)
- Erika Nasu
- Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Norifumi Kawakami
- Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Shuhei Takamura
- Department of Mechanical Engineering, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Atsushi Hotta
- Department of Mechanical Engineering, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Ryoichi Arai
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Ueda, Nagano 386-8567, Japan
- Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Ueda, Nagano 386-8567, Japan
| | - Kenji Miyamoto
- Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan
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Darji S, Aayush A, Estes KM, Strock JD, Thompson DH. Unravelling the Mechanism of Elastin-like Polypeptide-Enzyme Fusion Stabilization in Organic Solvents. Biomacromolecules 2024; 25:272-281. [PMID: 38118170 DOI: 10.1021/acs.biomac.3c00982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Elastin-like polypeptides (ELP) are a class of materials that are widely used as purification tags and in potential therapeutic applications. We have used the hydrophobic nature of ELP to extract them into organic solvents and precipitate them to obtain highly pure materials. Although many different types of ELP have been rapidly purified in this manner, the underlying mechanism for this process and its ability to retain functional proteins within organic phase-rich media has been unclear. A cleavable ELP-Intein construct fused with the enzyme chorismate mutase (ELP-I-Cm2) was used to better understand the organic solvent extraction process for ELP and the factors impacting the retention of enzyme activity. Our extraction studies indicated that a cell lysis step was essential to stabilize the ELP-I-Cm2 in the organic phase, prevent intein cleavage, and extract the fusion protein with high efficiency and retained activity. Circular dichroism and infrared spectroscopic characterization of ELP-I-Cm2 in organic solvents and aqueous solutions of the extracted and precipitated material indicated that the ELP secondary structure was retained in both environments. Atomic force microscopy and negative stain transmission electron microscopy imaging of ELP-I-Cm2 in organic solvents revealed highly regular circular features that were ∼50 nm in diameter, in contrast to larger (>100 nm) irregular features found in aqueous solutions. Since reverse micelles have often been used in catalytic processes, we evaluated the enzymatic activity of the ELP-I-Cm2 reversed micelles in different organic solvent mixtures and found that Cm2-mediated reactions in organic media were of comparable rate and efficiency to those in aqueous media. Based on these findings, we report an exciting new opportunity for ELP-enzyme fusion applications by exploiting their ability to form catalytically active reverse micelles in organic media.
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Affiliation(s)
- Saloni Darji
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Aayush Aayush
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Kiera M Estes
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jocie D Strock
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - David H Thompson
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
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Hu J, Sha X, Li Y, Wu J, Ma J, Zhang Y, Yang R. Multifaceted Applications of Ferritin Nanocages in Delivering Metal Ions, Bioactive Compounds, and Enzymes: A Comprehensive Review. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:19903-19919. [PMID: 37955969 DOI: 10.1021/acs.jafc.3c05510] [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: 11/14/2023]
Abstract
Ferritin, a distinctive iron-storage protein, possesses a unique cage-like nanoscale structure that enables it to encapsulate and deliver a wide range of biomolecules. Recent advances prove that ferritin can serve as an efficient 8 nm diameter carrier for various bioinorganic nutrients, such as minerals, bioactive polyphenols, and enzymes. This review offers a comprehensive summary of ferritin's structural features from different sources and emphasizes its functions in iron supplementation, calcium delivery, single- and coencapsulation of polyphenols, and enzyme package. Additionally, the influence of innovative food processing technologies, including manothermosonication, pulsed electric field, and atmospheric cold plasma, on the structure and function of ferritin are examined. Furthermore, the limitations and prospects of ferritin in food and nutritional applications are discussed. The exploration of ferritin as a multifunctional protein with the capacity to load various biomolecules is crucial to fully harnessing its potential in food applications.
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Affiliation(s)
- Jiangnan Hu
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Xinmei Sha
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Yue Li
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Jincan Wu
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Junrui Ma
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Yuyu Zhang
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing 100048, China
| | - Rui Yang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, China
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Zhang C, Chen X, Liu B, Zang J, Zhang T, Zhao G. Preparation and Unique Three-Dimensional Self-Assembly Property of Starfish Ferritin. Foods 2023; 12:3903. [PMID: 37959022 PMCID: PMC10647799 DOI: 10.3390/foods12213903] [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: 10/09/2023] [Revised: 10/21/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
The structure and assembly properties of ferritin derived from aquatic products remain to be explored. Constructing diverse three-dimensional (3D) protein architectures with the same building blocks has important implications for nutrient delivery, medicine and materials science. Herein, ferritin from Asterias forbesii (AfFer) was prepared, and its crystal structure was resolved at 1.91 Å for the first time. Notably, different from the crystal structure of other reported ferritin, AfFer exhibited a BCT lattice arrangement in its crystals. Bioinspired by the crystal structure of AfFer, we described an effective approach for manufacturing 3D porous, crystalline nanoarchitectures by redesigning the shared protein interface involved in different 3D protein arrays. Based on this strategy, two 3D superlattices of body-centered tetragonal and simple cubicwere constructed with ferritin molecules as the building blocks. This study provided a potentially generalizable strategy for constructing different 3D protein-based crystalline biomaterials with the same building blocks.
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Affiliation(s)
| | | | | | | | | | - Guanghua Zhao
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China; (C.Z.); (X.C.); (B.L.); (J.Z.); (T.Z.)
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7
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Su Y, Liu B, Huang Z, Teng Z, Yang L, Zhu J, Huo S, Liu A. Virus-like particles nanoreactors: from catalysis towards bio-applications. J Mater Chem B 2023; 11:9084-9098. [PMID: 37697810 DOI: 10.1039/d3tb01112g] [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: 09/13/2023]
Abstract
Virus-like particles (VLPs) are self-assembled supramolecular structures found in nature, often used for compartmentalization. Exploiting their inherent properties, including precise nanoscale structures, monodispersity, and high stability, these architectures have been widely used as nanocarriers to protect or enrich catalysts, facilitating catalytic reactions and avoiding interference from the bulk solutions. In this review, we summarize the current progress of virus-like particles (VLPs)-based nanoreactors. First, we briefly introduce the physicochemical properties of the most commonly used virus particles to understand their roles in catalytic reactions beyond the confined space. Next, we summarize the self-assembly of nanoreactors forming higher-order hierarchical structures, highlighting the emerging field of nanoreactors as artificial organelles and their potential biomedical applications. Finally, we discuss the current findings and future perspectives of VLPs-based nanoreactors.
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Affiliation(s)
- Yuqing Su
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
| | - Beibei Liu
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
| | - Zhenkun Huang
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
| | - Zihao Teng
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
| | - Liulin Yang
- State Key Laboratory of Physical Chemistry of Solid Surface, Key Laboratory of Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Jie Zhu
- National-Local Joint Engineering Research and High-Quality Utilization, Changzhou University, Changzhou 213164, China
| | - Shuaidong Huo
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
| | - Aijie Liu
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
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van der Ven AM, Gyamfi H, Suttisansanee U, Ahmad MS, Su Z, Taylor RM, Poole A, Chiorean S, Daub E, Urquhart T, Honek JF. Molecular Engineering of E. coli Bacterioferritin: A Versatile Nanodimensional Protein Cage. Molecules 2023; 28:4663. [PMID: 37375226 DOI: 10.3390/molecules28124663] [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: 04/13/2023] [Revised: 05/23/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Currently, intense interest is focused on the discovery and application of new multisubunit cage proteins and spherical virus capsids to the fields of bionanotechnology, drug delivery, and diagnostic imaging as their internal cavities can serve as hosts for fluorophores or bioactive molecular cargo. Bacterioferritin is unusual in the ferritin protein superfamily of iron-storage cage proteins in that it contains twelve heme cofactors and is homomeric. The goal of the present study is to expand the capabilities of ferritins by developing new approaches to molecular cargo encapsulation employing bacterioferritin. Two strategies were explored to control the encapsulation of a diverse range of molecular guests compared to random entrapment, a predominant strategy employed in this area. The first was the inclusion of histidine-tag peptide fusion sequences within the internal cavity of bacterioferritin. This approach allowed for the successful and controlled encapsulation of a fluorescent dye, a protein (fluorescently labeled streptavidin), or a 5 nm gold nanoparticle. The second strategy, termed the heme-dependent cassette strategy, involved the substitution of the native heme with heme analogs attached to (i) fluorescent dyes or (ii) nickel-nitrilotriacetate (NTA) groups (which allowed for controllable encapsulation of a histidine-tagged green fluorescent protein). An in silico docking approach identified several small molecules able to replace the heme and capable of controlling the quaternary structure of the protein. A transglutaminase-based chemoenzymatic approach to surface modification of this cage protein was also accomplished, allowing for future nanoparticle targeting. This research presents novel strategies to control a diverse set of molecular encapsulations and adds a further level of sophistication to internal protein cavity engineering.
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Affiliation(s)
- Anton M van der Ven
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Hawa Gyamfi
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | | | - Muhammad S Ahmad
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Zhengding Su
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Robert M Taylor
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Amanda Poole
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Sorina Chiorean
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Elisabeth Daub
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Taylor Urquhart
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - John F Honek
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
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Zhu Y, Zhu Y, Cao T, Liu X, Liu X, Yan Y, Shi Y, Wang JC. Ferritin-based nanomedicine for disease treatment. MEDICAL REVIEW (2021) 2023; 3:49-74. [PMID: 37724111 PMCID: PMC10471093 DOI: 10.1515/mr-2023-0001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 02/01/2023] [Indexed: 09/20/2023]
Abstract
Ferritin is an endogenous protein which is self-assembled by 24 subunits into a highly uniform nanocage structure. Due to the drug-encapsulating ability in the hollow inner cavity and abundant modification sites on the outer surface, ferritin nanocage has been demonstrated great potential to become a multi-functional nanomedicine platform. Its good biocompatibility, low toxicity and immunogenicity, intrinsic tumor-targeting ability, high stability, low cost and massive production, together make ferritin nanocage stand out from other nanocarriers. In this review, we summarized ferritin-based nanomedicine in field of disease diagnosis, treatment and prevention. The different types of drugs to be loaded in ferritin, as well as drug-loading methods were classified. The strategies for site-specific and non-specific functional modification of ferritin were investigated, then the application of ferritin for disease imaging, drug delivery and vaccine development were discussed. Finally, the challenges restricting the clinical translation of ferritin-based nanomedicines were analyzed.
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Affiliation(s)
- Yuanjun Zhu
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
- Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Yuefeng Zhu
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Tianmiao Cao
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Xiaoyu Liu
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Xiaoyan Liu
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
- Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Yi Yan
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Yujie Shi
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Jian-Cheng Wang
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
- Laboratory of Innovative Formulations and Pharmaceutical Excipients, Ningbo Institute of Marine Medicine, Peking University, Ningbo, Zhejiang Province, China
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10
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Oh HJ, Jung Y. High order assembly of multiple protein cages with homogeneous sizes and shapes via limited cage surface engineering. Chem Sci 2023; 14:1105-1113. [PMID: 36756339 PMCID: PMC9891371 DOI: 10.1039/d2sc02772k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 12/29/2022] [Indexed: 01/01/2023] Open
Abstract
Protein cages are attractive building blocks to build high order materials such as 3D cage lattices, which offer accurately ordered bio-templates. However, controlling the size or valency of these cage-to-cage assemblies is extremely difficult due to highly multivalent and symmetric cage structures. Here, various high order cage assemblies with homogeneous sizes and geometries are constructed by developing an anisotropic ferritin cage with limitedly exposed binding modules, leucine zipper. The anisotropic ferritin is produced as expressed in cells without the need of complex in vitro cage fabrication by careful subunit manipulation. Ferritin cages with limitedly exposed zippers are assembled around a core ferritin with fully exposed opposing zippers, generating homogeneous high order structures, whereas two fully exposed ferritins are assembled into heterogeneous cage aggregates. Diverse fully exposed core cages are prepared by varying the zipper-ferritin fusion geometries and even by using larger cage structures. With these core cages and the anisotropic ferritin, a range of high order cage assemblies with diverse ferritin valencies (3 to over 12) and sizes (over 40 nm) are created. Cell surface binding and internalization of cage structures are greatly varied by assembly sizes, where high order ferritins are clearly more effective than monomeric ferritin.
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Affiliation(s)
- Hyeok Jin Oh
- Department of Chemistry, KAIST 291 Daehak-ro, Yuseong-gu Daejeon 34141 Republic of Korea +82-42-350-2810 +82-42-350-2817
| | - Yongwon Jung
- Department of Chemistry, KAIST 291 Daehak-ro, Yuseong-gu Daejeon 34141 Republic of Korea +82-42-350-2810 +82-42-350-2817
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11
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Ohara N, Kawakami N, Arai R, Adachi N, Moriya T, Kawasaki M, Miyamoto K. Reversible Assembly of an Artificial Protein Nanocage Using Alkaline Earth Metal Ions. J Am Chem Soc 2023; 145:216-223. [PMID: 36541447 DOI: 10.1021/jacs.2c09537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Protein nanocages are of increasing interest for use as drug capsules, but the encapsulation and release of drug molecules at appropriate times require the reversible association and dissociation of the nanocages. One promising approach to addressing this challenge is the design of metal-dependent associating proteins. Such designed proteins typically have Cys or His residues at the protein surface for connecting the associating proteins through metal-ion coordination. However, Cys and His residues favor interactions with soft and borderline metal ions, such as Au+ and Zn2+, classified by the hard and soft acids and bases concept, restricting the types of metal ions available to drive association. Here, we show the alkaline earth (AE) metal-dependent association of the recently designed artificial protein nanocage TIP60, which is composed of 60-mer fusion proteins. The introduction of a Glu (hard base) mutation to the fusion protein (K67E mutant) prevented the formation of the 60-mer but formed the expected cage structure in the presence of Ca, Sr, or Ba ions (hard acids). Cryogenic electron microscopy (cryo-EM) analysis indicated a Ba ion at the interface of the subunits. Furthermore, we demonstrated the encapsulation and release of single-stranded DNA molecules using this system. Our results provide insights into the design of AE metal-dependent association and dissociation mechanisms for proteins.
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Affiliation(s)
- Naoya Ohara
- Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Norifumi Kawakami
- Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Ryoichi Arai
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Ueda, Nagano 386-8567, Japan.,Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Ueda, Nagano 386-8567, Japan
| | - Naruhiko Adachi
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho, Tsukuba 305-0801, Japan
| | - Toshio Moriya
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho, Tsukuba 305-0801, Japan
| | - Masato Kawasaki
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho, Tsukuba 305-0801, Japan
| | - Kenji Miyamoto
- Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan
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12
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Srivastava AK, Scalcione LJ, Arosio P, Bou‐Abdallah F. Hyperthermostable recombinant human heteropolymer ferritin derived from a novel plasmid design. Protein Sci 2023; 32:e4543. [PMID: 36519270 PMCID: PMC9798250 DOI: 10.1002/pro.4543] [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: 10/05/2022] [Revised: 11/17/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Mammalian ferritins are predominantly heteropolymeric species consisting of 2 structurally similar, but functionally and genetically distinct subunit types, called H (Heavy) and L (Light). The two subunits co-assemble in different H and L ratios to form 24-mer shell-like protein nanocages where thousands of iron atoms can be mineralized inside a hollow cavity. Here, we use differential scanning calorimetry (DSC) to study ferritin stability and understand how various combinations of H and L subunits confer aspects of protein structure-function relationships. Using a recently engineered plasmid design that enables the synthesis of complex ferritin nanostructures with specific H to L subunit ratios, we show that homopolymer L and heteropolymer L-rich ferritins have a remarkable hyperthermostability (Tm = 115 ± 1°C) compared to their H-ferritin homologues (Tm = 93 ± 1°C). Our data reveal a significant linear correlation between protein thermal stability and the number of L subunits present on the ferritin shell. A strong and unexpected iron-induced protein thermal destabilization effect (ΔTm up to 20°C) is observed. To our knowledge, this is the first report of recombinant human homo- and hetero-polymer ferritins that exhibit surprisingly high dissociation temperatures, the highest among all known ferritin species, including many known hyperthermophilic proteins and enzymes. This extreme thermostability of our L and L-rich ferritins may have great potential for biotechnological applications.
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Affiliation(s)
| | | | - Paolo Arosio
- Department of Molecular & Translational MedicineUniversity of BresciaBresciaItaly
| | - Fadi Bou‐Abdallah
- Department of ChemistryState University of New YorkPotsdamNew YorkUSA
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13
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Uchida M, Selivanovitch E, McCoy K, Douglas T. Fabrication of Protein Macromolecular Frameworks (PMFs) and Their Application in Catalytic Materials. Methods Mol Biol 2023; 2671:111-120. [PMID: 37308641 PMCID: PMC11034859 DOI: 10.1007/978-1-0716-3222-2_6] [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] [Indexed: 06/14/2023]
Abstract
The construction of three-dimensional (3D) array materials from nanoscale building blocks has drawn significant interest because of their potential to exhibit collective properties and functions arising from the interactions between individual building blocks. Protein cages such as virus-like particles (VLPs) have distinct advantages as building blocks for higher-order assemblies because they are extremely homogeneous in size and can be engineered with new functionalities by chemical and/or genetic modification. In this chapter, we describe a protocol for constructing a new class of protein-based superlattices, called protein macromolecular frameworks (PMFs). We also describe an exemplary method to evaluate the catalytic activity of enzyme-enclosed PMFs, which exhibit enhanced catalytic activity due to the preferential partitioning of charged substrates into the PMF.
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Affiliation(s)
- Masaki Uchida
- Department of Chemistry and Biochemistry, California State University, Fresno, Fresno, CA, USA.
| | | | - Kimberly McCoy
- Department of Chemistry and Biochemistry, California State University, Fresno, Fresno, CA, USA
| | - Trevor Douglas
- Department of Chemistry, Indiana University, Bloomington, IN, USA
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14
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Zhang X, Zeng R, Zhang T, Lv C, Zang J, Zhao G. Spatiotemporal control over 3D protein nanocage superlattices for the hierarchical encapsulation and release of different cargo molecules. J Mater Chem B 2022; 10:9968-9973. [PMID: 36472186 DOI: 10.1039/d2tb01961b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Taking inspiration from Nature, we have constructed a two-compartment system based on 3D ferritin nanocage superlattices, the self-assembly behavior of which can be spatiotemporally controlled using two designed switches. One pH switch regulates the assembly of the ferritin subunit into its shell-like structure, whereas the other metal switch is responsible for assembly of the 3D superlattices from ferritin nanocages as building blocks. Consequently, this system holds great promise for the hierarchical encapsulation and release of two different cargo molecules.
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Affiliation(s)
- Xiaorong Zhang
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China.
| | - Ruiqi Zeng
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China.
| | - Tuo Zhang
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China.
| | - Chenyan Lv
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China.
| | - Jiachen Zang
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China.
| | - Guanghua Zhao
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China.
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15
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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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16
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Ferritin nanocage based delivery vehicles: From single-, co- to compartmentalized- encapsulation of bioactive or nutraceutical compounds. Biotechnol Adv 2022; 61:108037. [PMID: 36152892 DOI: 10.1016/j.biotechadv.2022.108037] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/15/2022] [Accepted: 09/16/2022] [Indexed: 11/30/2022]
Abstract
Bioactive or nutraceutical ingredients have been widely used in pursuit of health and well-being. However, the environmental instability, poor solubility and bioavailability, and unspecific delivery highly limited their practical values. By virtue of the unique shell-like structure, definite disassembly/reassembly behavior, and excellent safety profile of ferritin protein, it stands out among of various nano-materials and is emerging as one of the most promising vehicles for the encapsulation and delivery of bioactive ingredients or drugs. In this review, we present a systematic overview of recent advances of ferritin-based delivery systems from single-encapsulation, co-encapsulation, to compartmentalized-encapsulation of bioactive ingredients or drugs. Different encapsulation strategies for cargo loading as well as their advantages and drawbacks have been critically reviewed. This study emphasized the importance of the construction of compartmentalized delivery systems through the usage of ferritin nanocages, which exhibit great potential for facilitating the synergistic functionality of different types of cargos. Lastly, the applications of ferritin nanocages for physicochemical improvements and functionality achievements of loaded cargos are summarized. In conclusion, ferritin protein nanocages not only are excellent nanocarriers, but also can act as"multi-seated" vehicles for co-encapsulation and compartmentalized encapsulation of different cargos simultaneously.
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17
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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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18
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Huang J, Jiang Q, Yang M, Dykes GF, Weetman SL, Xin W, He HL, Liu LN. Probing the Internal pH and Permeability of a Carboxysome Shell. Biomacromolecules 2022; 23:4339-4348. [PMID: 36054822 PMCID: PMC9554877 DOI: 10.1021/acs.biomac.2c00781] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The carboxysome is a protein-based nanoscale organelle
in cyanobacteria
and many proteobacteria, which encapsulates the key CO2-fixing enzymes ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco)
and carbonic anhydrase (CA) within a polyhedral protein shell. The
intrinsic self-assembly and architectural features of carboxysomes
and the semipermeability of the protein shell provide the foundation
for the accumulation of CO2 within carboxysomes and enhanced
carboxylation. Here, we develop an approach to determine the interior
pH conditions and inorganic carbon accumulation within an α-carboxysome
shell derived from a chemoautotrophic proteobacterium Halothiobacillus neapolitanus and evaluate the shell
permeability. By incorporating a pH reporter, pHluorin2, within empty
α-carboxysome shells produced in Escherichia
coli, we probe the interior pH of the protein shells
with and without CA. Our in vivo and in vitro results demonstrate a lower interior pH of α-carboxysome shells
than the cytoplasmic pH and buffer pH, as well as the modulation of
the interior pH in response to changes in external environments, indicating
the shell permeability to bicarbonate ions and protons. We further
determine the saturated HCO3– concentration
of 15 mM within α-carboxysome shells and show the CA-mediated
increase in the interior CO2 level. Uncovering the interior
physiochemical microenvironment of carboxysomes is crucial for understanding
the mechanisms underlying carboxysomal shell permeability and enhancement
of Rubisco carboxylation within carboxysomes. Such fundamental knowledge
may inform reprogramming carboxysomes to improve metabolism and recruit
foreign enzymes for enhanced catalytical performance.
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Affiliation(s)
- Jiafeng Huang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom.,School of Life Sciences, Central South University, Changsha 410017, China
| | - Qiuyao Jiang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom.,Department of Central Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, China
| | - Mengru Yang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Gregory F Dykes
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Samantha L Weetman
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Wei Xin
- Department of Central Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, China.,Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 271000, China
| | - Hai-Lun He
- School of Life Sciences, Central South University, Changsha 410017, China
| | - Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom.,College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
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19
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Tsidilkovski L, Mohajerani F, Hagan MF. Microcompartment assembly around multicomponent fluid cargoes. J Chem Phys 2022; 156:245104. [PMID: 35778087 PMCID: PMC9249432 DOI: 10.1063/5.0089556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
This article describes dynamical simulations of the assembly of an icosahedral protein shell around a bicomponent fluid cargo. Our simulations are motivated by bacterial microcompartments, which are protein shells found in bacteria that assemble around a complex of enzymes and other components involved in certain metabolic processes. The simulations demonstrate that the relative interaction strengths among the different cargo species play a key role in determining the amount of each species that is encapsulated, their spatial organization, and the nature of the shell assembly pathways. However, the shell protein–shell protein and shell protein–cargo component interactions that help drive assembly and encapsulation also influence cargo composition within certain parameter regimes. These behaviors are governed by a combination of thermodynamic and kinetic effects. In addition to elucidating how natural microcompartments encapsulate multiple components involved within reaction cascades, these results have implications for efforts in synthetic biology to colocalize alternative sets of molecules within microcompartments to accelerate specific reactions. More broadly, the results suggest that coupling between self-assembly and multicomponent liquid–liquid phase separation may play a role in the organization of the cellular cytoplasm.
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Affiliation(s)
- Lev Tsidilkovski
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Farzaneh Mohajerani
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Michael F Hagan
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
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20
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Linko V, Zhang H, Nonappa, Kostiainen MA, Ikkala O. From Precision Colloidal Hybrid Materials to Advanced Functional Assemblies. Acc Chem Res 2022; 55:1785-1795. [PMID: 35647700 PMCID: PMC9260957 DOI: 10.1021/acs.accounts.2c00093] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
ConspectusThe concept of colloids encompasses a wide range of isotropic and anisotropic particles with diverse sizes, shapes, and functions from synthetic nanoparticles, nanorods, and nanosheets to functional biological units. They are addressed in materials science for various functions, while they are ubiquitous in the biological world for multiple functions. A large variety of synthetic colloids have been researched due to their scientific and technological importance; still they characteristically suffer from finite size distributions, imperfect shapes and interactions, and not fully engineered functions. This contrasts with biological colloids that offer precision in their size, shape, and functionality. Materials science has searched for inspiration from the biological world to allow structural control by self-assembly and hierarchy and to identify novel routes for combinations of functions in bio-inspiration.Herein, we first discuss different approaches for highly defined structural control of technically relevant synthetic colloids based on guided assemblies of biological motifs. First, we describe how polydisperse nanoparticles can be assembled within hollow protein cages to allow well-defined assemblies and hierarchical packings. Another approach relies on DNA nanotechnology-based assemblies, where engineered DNA structures allow programmed assembly. Then we will discuss synthetic colloids that have either particularly narrow size dispersity or even atomically precise structures for new assemblies and potential functions. Such colloids can have well-defined packings for membranes allowing high modulus. They can be switchable using light-responsive moieties, and they can initiate packing of larger assemblies of different geometrical shapes. The emphasis is on atomically defined nanoclusters that allow well-defined assemblies by supramolecular interactions, such as directional hydrogen bonding. Finally, we will discuss stimulus-responsive colloids for new functions, even toward complex responsive functions inspired by life. Therein, stimulus-responsive materials inspired by biological learning could allow the next generation of such materials. Classical conditioning is among the simplest biological learning concepts, requiring two stimuli and triggerable memory. Therein we use thermoresponsive hydrogels with plasmonic gold nanoparticles and a spiropyran photoacid as a model. Heating is the unconditioned stimulus leading to melting of the thermoresponsive gel, whereas light (at a specified wavelength) originally leads to reduced pH without plasmonic or structural changes because of steric gel stabilization. Under heat-induced gel melting, light results in pH-decrease and chain-like aggregation of the gold nanoparticles, allowing a new plasmonic response. Thus, simultaneous heating and light irradiation allow conditioning for a newly derived stimulus, where the logic diagram is analogous to Pavlovian conditioning. The shown assemblies demonstrate the different functionalities achievable using colloids when the sizes and the dispersity are controlled.
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Affiliation(s)
- Veikko Linko
- Department of Bioproducts and Biosystems, Aalto University School of Chemical Engineering, FI-00076 Espoo, Finland
| | - Hang Zhang
- Department of Applied Physics, Aalto University School of Science, FI-00076 Espoo, Finland
| | - Nonappa
- Faculty of Engineering and Natural Sciences, Tampere University, P.O. Box 541, FI-33101 Tampere, Finland
| | - Mauri A. Kostiainen
- Department of Bioproducts and Biosystems, Aalto University School of Chemical Engineering, FI-00076 Espoo, Finland
| | - Olli Ikkala
- Department of Bioproducts and Biosystems, Aalto University School of Chemical Engineering, FI-00076 Espoo, Finland
- Department of Applied Physics, Aalto University School of Science, FI-00076 Espoo, Finland
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21
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Maity B, Taher M, Mazumdar S, Ueno T. Artificial metalloenzymes based on protein assembly. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2022.214593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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22
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Uchida M, Brunk NE, Hewagama ND, Lee B, Prevelige PE, Jadhao V, Douglas T. Multilayered Ordered Protein Arrays Self-Assembled from a Mixed Population of Virus-like Particles. ACS NANO 2022; 16:7662-7673. [PMID: 35549153 DOI: 10.1021/acsnano.1c11272] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Biology shows many examples of spatially controlled assembly of cells and biomacromolecules into hierarchically organized structures, to which many of the complex biological functions are attributed. While such biological structures have inspired the design of synthetic materials, it is still a great challenge to control the spatial arrangement of individual building blocks when assembling multiple types of components into bulk materials. Here, we report self-assembly of multilayered, ordered protein arrays from mixed populations of virus-like particles (VLPs). We systematically tuned the magnitude of the surface charge of the VLPs via mutagenesis to prepare four different types of VLPs for mixing. A mixture of up to four types of VLPs selectively assembled into higher-order structures in the presence of oppositely charged dendrimers during a gradual lowering of the ionic strength of the solution. The assembly resulted in the formation of three-dimensional ordered VLP arrays with up to four distinct layers including a central core, with each layer comprising a single type of VLP. A coarse-grained computational model was developed and simulated using molecular dynamics to probe the formation of the multilayered, core-shell structure. Our findings establish a simple and versatile bottom-up strategy to synthesize multilayered, ordered materials by controlling the spatial arrangement of multiple types of nanoscale building blocks in a one-pot fabrication.
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Affiliation(s)
- Masaki Uchida
- Department of Chemistry and Biochemistry, California State University, Fresno, 2555 E. San Ramon Avenue, Fresno, California 93740, United States
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Nicholas E Brunk
- Intelligent Systems Engineering, Indiana University, 700 N. Woodlawn Avenue, Bloomington, Indiana 47408, United States
- Wolfram Research, 100 Trade Center Drive, Champaign, Illinois 61820, United States
- VeriSIM Life Inc., 1 Sansome Street, Suite 3500, San Francisco, California 94104, United States
| | - Nathasha D Hewagama
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Byeongdu Lee
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - Peter E Prevelige
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Vikram Jadhao
- Intelligent Systems Engineering, Indiana University, 700 N. Woodlawn Avenue, Bloomington, Indiana 47408, United States
| | - Trevor Douglas
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
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23
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Edwardson TGW, Levasseur MD, Tetter S, Steinauer A, Hori M, Hilvert D. Protein Cages: From Fundamentals to Advanced Applications. Chem Rev 2022; 122:9145-9197. [PMID: 35394752 DOI: 10.1021/acs.chemrev.1c00877] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins that self-assemble into polyhedral shell-like structures are useful molecular containers both in nature and in the laboratory. Here we review efforts to repurpose diverse protein cages, including viral capsids, ferritins, bacterial microcompartments, and designed capsules, as vaccines, drug delivery vehicles, targeted imaging agents, nanoreactors, templates for controlled materials synthesis, building blocks for higher-order architectures, and more. A deep understanding of the principles underlying the construction, function, and evolution of natural systems has been key to tailoring selective cargo encapsulation and interactions with both biological systems and synthetic materials through protein engineering and directed evolution. The ability to adapt and design increasingly sophisticated capsid structures and functions stands to benefit the fields of catalysis, materials science, and medicine.
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Affiliation(s)
| | | | - Stephan Tetter
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Angela Steinauer
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Mao Hori
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
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24
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Stupka I, Azuma Y, Biela AP, Imamura M, Scheuring S, Pyza E, Woźnicka O, Maskell DP, Heddle JG. Chemically induced protein cage assembly with programmable opening and cargo release. SCIENCE ADVANCES 2022; 8:eabj9424. [PMID: 34985943 PMCID: PMC8730398 DOI: 10.1126/sciadv.abj9424] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/16/2021] [Indexed: 06/14/2023]
Abstract
Engineered protein cages are promising tools that can be customized for applications in medicine and nanotechnology. A major challenge is developing a straightforward strategy for endowing cages with bespoke, inducible disassembly. Such cages would allow release of encapsulated cargoes at desired timing and location. Here, we achieve such programmable disassembly using protein cages, in which the subunits are held together by different molecular cross-linkers. This modular system enables cage disassembly to be controlled in a condition-dependent manner. Structural details of the resulting cages were determined using cryo–electron microscopy, which allowed observation of bridging cross-linkers at intended positions. Triggered disassembly was demonstrated by high-speed atomic force microscopy and subsequent cargo release using an encapsulated Förster resonance energy transfer pair whose signal depends on the quaternary structure of the cage.
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Affiliation(s)
- Izabela Stupka
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
- Postgraduate School of Molecular Medicine, 02-091 Warsaw, Poland
| | - Yusuke Azuma
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Artur P. Biela
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
- Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
| | - Motonori Imamura
- Department of Anesthesiology, Weill Cornell Medicine, New York City, NY 10065, USA
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York City, NY 10065, USA
| | - Simon Scheuring
- Department of Anesthesiology, Weill Cornell Medicine, New York City, NY 10065, USA
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York City, NY 10065, USA
| | - Elżbieta Pyza
- Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
| | - Olga Woźnicka
- Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
| | - Daniel P. Maskell
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Jonathan G. Heddle
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
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25
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Uchida M, Manzo E, Echeveria D, Jiménez S, Lovell L. Harnessing physicochemical properties of virus capsids for designing enzyme confined nanocompartments. Curr Opin Virol 2021; 52:250-257. [PMID: 34974380 PMCID: PMC8939255 DOI: 10.1016/j.coviro.2021.12.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 12/07/2021] [Accepted: 12/10/2021] [Indexed: 12/13/2022]
Abstract
Viruses have drawn significant scientific interest from a wide variety of disciplines beyond virology because of their elegant architectures and delicately balanced activities. A virus-like particle (VLP), a noninfectious protein cage derived from viruses or other cage-forming proteins, has been exploited as a nano-scale platform for bioinspired engineering and synthetic manipulation with a range of applications. Encapsulation of functional proteins, especially enzymes, is an emerging use of VLPs that is promising not only for developing efficient and robust catalytic materials, but also for providing fundamental insights into the effects of enzyme compartmentalization commonly observed in cells. This review highlights recent advances in employing VLPs as a container for confining enzymes. To accomplish larger and more controlled enzyme loading, various different enzyme encapsulation strategies have been developed; many of these strategies are inspired from assembly and genome loading mechanisms of viral capsids. Characterization of VLPs’ physicochemical properties, such as porosity, could lead to rational manipulation and a better understanding of the catalytic behavior of the materials.
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Affiliation(s)
- Masaki Uchida
- Department of Chemistry and Biochemistry, California State University, Fresno, 2555 E. San Ramon Ave., Fresno, CA 93740, USA.
| | - Elia Manzo
- Department of Chemistry and Biochemistry, California State University, Fresno, 2555 E. San Ramon Ave., Fresno, CA 93740, USA
| | - Dustin Echeveria
- Department of Chemistry and Biochemistry, California State University, Fresno, 2555 E. San Ramon Ave., Fresno, CA 93740, USA
| | - Sophie Jiménez
- Department of Chemistry and Biochemistry, California State University, Fresno, 2555 E. San Ramon Ave., Fresno, CA 93740, USA
| | - Logan Lovell
- Department of Chemistry and Biochemistry, California State University, Fresno, 2555 E. San Ramon Ave., Fresno, CA 93740, USA
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Kojima M, Abe S, Ueno T. Engineering of protein crystals for use as solid biomaterials. Biomater Sci 2021; 10:354-367. [PMID: 34928275 DOI: 10.1039/d1bm01752g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Protein crystals have attracted a great deal of attention as solid biomaterials because they have porous structures created by regular assemblies of proteins. The lattice structures of protein crystals are controlled by designing molecular interfacial interactions via covalent bonds and non-covalent bonds. Protein crystals have been functionalized as templates to immobilize foreign molecules such as metal nanoparticles, metal complexes, and proteins. These hybrid crystals are used as functional materials for catalytic reactions and structural analysis. Furthermore, in-cell protein crystals have been studied extensively, providing progress in rapid protein crystallization and crystallography. This review highlights recent advances in crystal engineering for protein crystallization and generation of solid functional materials both in vitro and within cells.
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Affiliation(s)
- Mariko Kojima
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259-B55, Midori-ku, Yokohama 226-8501, Japan.
| | - Satoshi Abe
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259-B55, Midori-ku, Yokohama 226-8501, Japan.
| | - Takafumi Ueno
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259-B55, Midori-ku, Yokohama 226-8501, Japan.
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Artificial protein assemblies with well-defined supramolecular protein nanostructures. Biochem Soc Trans 2021; 49:2821-2830. [PMID: 34812854 DOI: 10.1042/bst20210808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/28/2021] [Accepted: 11/02/2021] [Indexed: 12/13/2022]
Abstract
Nature uses a wide range of well-defined biomolecular assemblies in diverse cellular processes, where proteins are major building blocks for these supramolecular assemblies. Inspired by their natural counterparts, artificial protein-based assemblies have attracted strong interest as new bio-nanostructures, and strategies to construct ordered protein assemblies have been rapidly expanding. In this review, we provide an overview of very recent studies in the field of artificial protein assemblies, with the particular aim of introducing major assembly methods and unique features of these assemblies. Computational de novo designs were used to build various assemblies with artificial protein building blocks, which are unrelated to natural proteins. Small chemical ligands and metal ions have also been extensively used for strong and bio-orthogonal protein linking. Here, in addition to protein assemblies with well-defined sizes, protein oligomeric and array structures with rather undefined sizes (but with definite repeat protein assembly units) also will be discussed in the context of well-defined protein nanostructures. Lastly, we will introduce multiple examples showing how protein assemblies can be effectively used in various fields such as therapeutics and vaccine development. We believe that structures and functions of artificial protein assemblies will be continuously evolved, particularly according to specific application goals.
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Zhang X, Zhang T, Wang Y, Liu Y, Zang J, Zhao G. Reversible structure transformation between protein nanocages and nanorods controlled by small molecules. Chem Commun (Camb) 2021; 57:12996-12999. [PMID: 34796885 DOI: 10.1039/d1cc04510e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Constructing different protein nanostructures by using identical building blocks, while realizing their structural transformation in response to external stimuli, remains a challenge. Here, we fabricated protein nanocages and nanorods by using dimeric TmFtn as a building block and reacting with Mg2+/(α, L-lysine) with polymerization degrees of 9 (PLL9) and 15 (PLL15), respectively. Notably, the reversible shape transformation of these two supramolecular protein architectures with different dimensions can be achievable in response to external stimuli.
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Affiliation(s)
- Xiaorong Zhang
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China.
| | - Tuo Zhang
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China.
| | - Yingjie Wang
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China.
| | - Yu Liu
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China.
| | - Jiachen Zang
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China.
| | - Guanghua Zhao
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China.
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Bulos JA, Guo R, Wang Z, DeLessio MA, Saven JG, Dmochowski IJ. Design of a Superpositively Charged Enzyme: Human Carbonic Anhydrase II Variant with Ferritin Encapsulation and Immobilization. Biochemistry 2021; 60:3596-3609. [PMID: 34757723 DOI: 10.1021/acs.biochem.1c00515] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Supercharged proteins exhibit high solubility and other desirable properties, but no engineered superpositively charged enzymes have previously been made. Superpositively charged variants of proteins such as green fluorescent protein have been efficiently encapsulated within Archaeoglobus fulgidus thermophilic ferritin (AfFtn). Encapsulation by supramolecular ferritin can yield systems with a variety of sequestered cargo. To advance applications in enzymology and green chemistry, we sought a general method for supercharging an enzyme that retains activity and is compatible with AfFtn encapsulation. The zinc metalloenzyme human carbonic anhydrase II (hCAII) is an attractive encapsulation target based on its hydrolytic activity and physiologic conversion of carbon dioxide to bicarbonate. A computationally designed variant of hCAII contains positively charged residues substituted at 19 sites on the protein's surface, resulting in a shift of the putative net charge from -1 to +21. This designed hCAII(+21) exhibits encapsulation within AfFtn without the need for fusion partners or additional reagents. The hCAII(+21) variant retains esterase activity comparable to the wild type and spontaneously templates the assembly of AfFtn 24mers around itself. The AfFtn-hCAII(+21) host-guest complex exhibits both greater activity and thermal stability when compared to hCAII(+21). Upon immobilization on a solid support, AfFtn-hCAII(+21) retains enzymatic activity and exhibits an enhancement of activity at elevated temperatures.
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Affiliation(s)
- Joshua A Bulos
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Rui Guo
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Zhiheng Wang
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Maegan A DeLessio
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Jeffery G Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Ivan J Dmochowski
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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Zhu J, Avakyan N, Kakkis AA, Hoffnagle AM, Han K, Li Y, Zhang Z, Choi TS, Na Y, Yu CJ, Tezcan FA. Protein Assembly by Design. Chem Rev 2021; 121:13701-13796. [PMID: 34405992 PMCID: PMC9148388 DOI: 10.1021/acs.chemrev.1c00308] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins are nature's primary building blocks for the construction of sophisticated molecular machines and dynamic materials, ranging from protein complexes such as photosystem II and nitrogenase that drive biogeochemical cycles to cytoskeletal assemblies and muscle fibers for motion. Such natural systems have inspired extensive efforts in the rational design of artificial protein assemblies in the last two decades. As molecular building blocks, proteins are highly complex, in terms of both their three-dimensional structures and chemical compositions. To enable control over the self-assembly of such complex molecules, scientists have devised many creative strategies by combining tools and principles of experimental and computational biophysics, supramolecular chemistry, inorganic chemistry, materials science, and polymer chemistry, among others. Owing to these innovative strategies, what started as a purely structure-building exercise two decades ago has, in short order, led to artificial protein assemblies with unprecedented structures and functions and protein-based materials with unusual properties. Our goal in this review is to give an overview of this exciting and highly interdisciplinary area of research, first outlining the design strategies and tools that have been devised for controlling protein self-assembly, then describing the diverse structures of artificial protein assemblies, and finally highlighting the emergent properties and functions of these assemblies.
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Affiliation(s)
| | | | - Albert A. Kakkis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Alexander M. Hoffnagle
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Kenneth Han
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Yiying Li
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Zhiyin Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Tae Su Choi
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Youjeong Na
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Chung-Jui Yu
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
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Zeng R, Lv C, Wang C, Zhao G. Bionanomaterials based on protein self-assembly: Design and applications in biotechnology. Biotechnol Adv 2021; 52:107835. [PMID: 34520791 DOI: 10.1016/j.biotechadv.2021.107835] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/06/2021] [Accepted: 09/08/2021] [Indexed: 01/13/2023]
Abstract
Elegant protein assembly to generate new biomaterials undergoes extremely rapid development for wide extension of biotechnology applications, which can be a powerful tool not only for creating nanomaterials but also for advancing understanding of the structure of life. Unique biological properties of proteins bestow these artificial biomaterials diverse functions that can permit them to be applied in encapsulation, bioimaging, biocatalysis, biosensors, photosynthetic apparatus, electron transport, magnetogenetic applications, vaccine development and antibodies design. This review gives a perspective view of the latest advances in the construction of protein-based nanomaterials. We initially start with distinguishable, specific interactions to construct sundry nanomaterials through protein self-assembly and concisely expound the assembly mechanism from the design strategy. And then, the design and construction of 0D, 1D, 2D, 3D protein assembled nanomaterials are especially highlighted. Furthermore, the potential applications have been discussed in detail. Overall, this review will illustrate how to fabricate highly sophisticated nanomaterials oriented toward applications in biotechnology based on the rules of supramolecular chemistry.
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Affiliation(s)
- Ruiqi Zeng
- College of Food Science & Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education, Beijing 100083, China
| | - Chenyan Lv
- College of Food Science & Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education, Beijing 100083, China
| | - Chengtao Wang
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University, No. 11 Fucheng Road, Haidian District, Beijing 100048, China
| | - Guanghua Zhao
- College of Food Science & Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education, Beijing 100083, China.
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Vallerinteavide Mavelli G, Sadeghi S, Vaidya SS, Kong SN, Drum CL. Nanoencapsulation as a General Solution for Lyophilization of Labile Substrates. Pharmaceutics 2021; 13:1790. [PMID: 34834205 PMCID: PMC8622885 DOI: 10.3390/pharmaceutics13111790] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/15/2021] [Accepted: 10/15/2021] [Indexed: 11/17/2022] Open
Abstract
Protein macromolecules occur naturally at the nanoscale. The use of a dedicated nanoparticle as a lyophilization excipient, however, has not been reported. Because biopolymeric and lipid nanoparticles often denature protein macromolecules and commonly lack the structural rigidity to survive the freeze-drying process, we hypothesized that surrounding an individual protein substrate with a nanoscale, thermostable exoshell (tES) would prevent aggregation and protect the substrate from denaturation during freezing, sublimation, and storage. We systematically investigated the properties of tES, including secondary structure and its homogeneity, throughout the process of lyophilization and found that tES have a near 100% recovery following aqueous reconstitution. We then tested the hypothesis that tES could encapsulate a model substrate, horseradish peroxidase (HRP), using charge complementation and pH-mediated controlled assembly. HRP were encapsulated within the 8 nm internal tES aqueous cavity using a simplified loading procedure. Time-course experiments demonstrated that unprotected HRP loses 95% of activity after 1 month of lyophilized storage. After encapsulation within tES nanoparticles, 70% of HRP activity was recovered, representing a 14-fold improvement and this effect was reproducible across a range of storage temperatures. To our knowledge, these results represent the first reported use of nanoparticle encapsulation to stabilize a functional macromolecule during lyophilization. Thermostable nanoencapsulation may be a useful method for the long-term storage of labile proteins.
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Affiliation(s)
- Girish Vallerinteavide Mavelli
- Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore; (G.V.M.); (S.S.); (S.S.V.); (S.N.K.)
| | - Samira Sadeghi
- Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore; (G.V.M.); (S.S.); (S.S.V.); (S.N.K.)
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*Star), Singapore 138672, Singapore
| | - Siddhesh Sujit Vaidya
- Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore; (G.V.M.); (S.S.); (S.S.V.); (S.N.K.)
| | - Shik Nie Kong
- Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore; (G.V.M.); (S.S.); (S.S.V.); (S.N.K.)
| | - Chester Lee Drum
- Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore; (G.V.M.); (S.S.); (S.S.V.); (S.N.K.)
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33
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Song N, Zhang J, Zhai J, Hong J, Yuan C, Liang M. Ferritin: A Multifunctional Nanoplatform for Biological Detection, Imaging Diagnosis, and Drug Delivery. Acc Chem Res 2021; 54:3313-3325. [PMID: 34415728 DOI: 10.1021/acs.accounts.1c00267] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Ferritins are spherical iron storage proteins within cells that are composed of a combination of 24 subunits of two types, heavy-chain ferritin (HFn) and light-chain ferritin (LFn). They autoassemble naturally into a spherical hollow nanocage with an outer diameter of 12 nm and an interior cavity that is 8 nm in diameter. In recent years, with the constantly emerging safety issues and the concerns about unfavorable uniformity and indefinite in vivo behavior of traditional nanomedicines, the characteristics of native ferritin nanocages, such as the unique nanocage structure, excellent safety profile, and definite in vivo behavior, make ferritin-based formulations uniquely attractive for nanomedicine development. To date, a variety of cargo molecules, including therapeutic drugs (e.g., cisplatin, carboplatin, paclitaxel, curcumin, atropine, quercetin, gefitinib, daunomycin, epirubicin, doxorubicin, etc.), imaging agents (e.g., fluorescence dyes, radioisotopes, and MRI contrast agents), nucleic acids (e.g., siRNA and miRNA), and metal nanoparticles (e.g., Fe3O4, CeO2, AuPd, CuS, CoPt, FeCo, Ag, etc.) have been loaded into the interior cavity of ferritin nanocages for a broad range of biomedical applications from in vitro biosensing to targeted delivery of cargo molecules in living systems with the aid of modified targeting ligands either genetically or chemically. We reported that human HFn could selectively deliver a large amount of cargo into tumors in vivo via transferrin receptor 1 (TfR1)-mediated tumor-cell-specific targeting followed by rapid internalization. By the use of the intrinsic tumor-targeting property and unique nanocage structure of human HFn, a broad variety of cargo-loaded HFn formulations have been developed for biological analysis, imaging diagnosis, and medicine development. In view of the intrinsic tumor-targeting property, unique nanocage structure, lack of immunogenicity, and definite in vivo behavior, human HFn holds promise to promote therapeutic drugs, diagnostic imaging agents, and targeting moieties into multifunctional nanomedicines.Since the report of the intrinsic tumor-targeting property of human HFn, we have extensively explored human HFn as an ideal nanocarrier for tumor-targeted delivery of anticancer drugs, MRI contrast agents, inorganic nanoparticles, and radioisotopes. In particular, by the use of genetic tools, we also have genetically engineered human HFn nanocages to recognize a broader range of disease biomarkers. In this Account, we systematically review human ferritins from characterizing their tumor-binding property and understanding their mechanism and kinetics for cargo loading to exploring their biomedical applications. We finally discuss the prospect of ferritin-based formulations to become next-generation nanomedicines. We expect that ferritin formulations with unique physicochemical characteristics and intrinsic tumor-targeting property will attract broad interest in fundamental drug research and offer new opportunities for nanomedicine development.
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Affiliation(s)
- Ningning Song
- Experimental Center of Advanced Materials, School of Materials Science & Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Jianlin Zhang
- Experimental Center of Advanced Materials, School of Materials Science & Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Jiao Zhai
- Tung Foundation Biomedical Sciences Centre/Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Juanji Hong
- Experimental Center of Advanced Materials, School of Materials Science & Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Chang Yuan
- Experimental Center of Advanced Materials, School of Materials Science & Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Minmin Liang
- Experimental Center of Advanced Materials, School of Materials Science & Engineering, Beijing Institute of Technology, Beijing 100081, China
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Zhang X, Liu Y, Zheng B, Zang J, Lv C, Zhang T, Wang H, Zhao G. Protein interface redesign facilitates the transformation of nanocage building blocks to 1D and 2D nanomaterials. Nat Commun 2021; 12:4849. [PMID: 34381032 PMCID: PMC8357837 DOI: 10.1038/s41467-021-25199-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 07/28/2021] [Indexed: 01/09/2023] Open
Abstract
Although various artificial protein nanoarchitectures have been constructed, controlling the transformation between different protein assemblies has largely been unexplored. Here, we describe an approach to realize the self-assembly transformation of dimeric building blocks by adjusting their geometric arrangement. Thermotoga maritima ferritin (TmFtn) naturally occurs as a dimer; twelve of these dimers interact with each other in a head-to-side manner to generate 24-meric hollow protein nanocage in the presence of Ca2+ or PEG. By tuning two contiguous dimeric proteins to interact in a fully or partially side-by-side fashion through protein interface redesign, we can render the self-assembly transformation of such dimeric building blocks from the protein nanocage to filament, nanorod and nanoribbon in response to multiple external stimuli. We show similar dimeric protein building blocks can generate three kinds of protein materials in a manner that highly resembles natural pentamer building blocks from viral capsids that form different protein assemblies.
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Affiliation(s)
- Xiaorong Zhang
- grid.22935.3f0000 0004 0530 8290College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing, 100083 China
| | - Yu Liu
- grid.22935.3f0000 0004 0530 8290College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing, 100083 China
| | - Bowen Zheng
- grid.22935.3f0000 0004 0530 8290College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing, 100083 China
| | - Jiachen Zang
- grid.22935.3f0000 0004 0530 8290College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing, 100083 China
| | - Chenyan Lv
- grid.22935.3f0000 0004 0530 8290College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing, 100083 China
| | - Tuo Zhang
- grid.22935.3f0000 0004 0530 8290College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing, 100083 China
| | - Hongfei Wang
- grid.163032.50000 0004 1760 2008Key Laboratory of Chemical Biology and Molecular Engineering of Education Ministry, Key Laboratory of Energy Conversion and Storage Materials of Shanxi Province, Institute of Molecular Science, Shanxi University, Taiyuan, China
| | - Guanghua Zhao
- grid.22935.3f0000 0004 0530 8290College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing, 100083 China
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Kumar M, Markiewicz-Mizera J, Janna Olmos JD, Wilk P, Grudnik P, Biela AP, Jemioła-Rzemińska M, Górecki A, Chakraborti S, Heddle JG. A single residue can modulate nanocage assembly in salt dependent ferritin. NANOSCALE 2021; 13:11932-11942. [PMID: 34195748 DOI: 10.1039/d1nr01632f] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Cage forming proteins have numerous potential applications in biomedicine and biotechnology, where the iron storage ferritin is a widely used example. However, controlling ferritin cage assembly/disassembly remains challenging, typically requiring extreme conditions incompatible with many desirable cargoes, particularly for more fragile biopharmaceuticals. Recently, a ferritin from the hyperthermophile bacterium Thermotoga maritima (TmFtn) has been shown to have reversible assembly under mild conditions, offering greater potential biocompatibility in terms of cargo access and encapsulation. Like Archeoglobus fulgidus ferritin (AfFtn), TmFtn forms 24mer cages mediated by metal ions (Mg2+). We have solved the crystal structure of the wild type TmFtn and several mutants displaying different assembly/disassembly properties. These data combined with other biophysical studies allow us to suggest candidate interfacial amino acids crucial in controlling assembly. This work deepens our understanding of how these ferritin complexes assemble and is a useful step towards production of triggerable ferritins in which these properties can be finely designed and controlled.
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Affiliation(s)
- Mantu Kumar
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-392 Krakow, Poland.
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36
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Sun R, Lim S. Protein cages as building blocks for superstructures. ENGINEERING BIOLOGY 2021; 5:35-42. [PMID: 36969478 PMCID: PMC9996708 DOI: 10.1049/enb2.12010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 11/20/2022] Open
Abstract
Proteins naturally self-assemble to function. Protein cages result from the self-assembly of multiple protein subunits that interact to form hollow symmetrical structures with functions that range from cargo storage to catalysis. Driven by self-assembly, building elegant higher-order superstructures with protein cages as building blocks has been an increasingly attractive field in recent years. It presents an engineering challenge not only at the molecular level but also at the supramolecular level. The higher-order constructs are proposed to provide access to diverse functional materials. Focussing on design strategy as a perspective, current work on protein cage supramolecular self-assembly are reviewed from three principles that are electrostatic, metal-ligand coordination and inherent symmetry. The review also summarises possible applications of the superstructure architecture built using modified protein cages.
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Affiliation(s)
- Ruoxuan Sun
- School of Chemical and Biomedical Engineering Nanyang Technological University Singapore
| | - Sierin Lim
- School of Chemical and Biomedical Engineering Nanyang Technological University Singapore
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37
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Oerlemans RAJF, Timmermans SBPE, van Hest JCM. Artificial Organelles: Towards Adding or Restoring Intracellular Activity. Chembiochem 2021; 22:2051-2078. [PMID: 33450141 PMCID: PMC8252369 DOI: 10.1002/cbic.202000850] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/15/2021] [Indexed: 12/15/2022]
Abstract
Compartmentalization is one of the main characteristics that define living systems. Creating a physically separated microenvironment allows nature a better control over biological processes, as is clearly specified by the role of organelles in living cells. Inspired by this phenomenon, researchers have developed a range of different approaches to create artificial organelles: compartments with catalytic activity that add new function to living cells. In this review we will discuss three complementary lines of investigation. First, orthogonal chemistry approaches are discussed, which are based on the incorporation of catalytically active transition metal-containing nanoparticles in living cells. The second approach involves the use of premade hybrid nanoreactors, which show transient function when taken up by living cells. The third approach utilizes mostly genetic engineering methods to create bio-based structures that can be ultimately integrated with the cell's genome to make them constitutively active. The current state of the art and the scope and limitations of the field will be highlighted with selected examples from the three approaches.
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Affiliation(s)
- Roy A. J. F. Oerlemans
- Bio-Organic Chemistry Research GroupInstitute for Complex Molecular SystemsEindhoven University of TechnologyP.O. Box 513 (STO3.41)5600 MBEindhovenThe Netherlands
| | - Suzanne B. P. E. Timmermans
- Bio-Organic Chemistry Research GroupInstitute for Complex Molecular SystemsEindhoven University of TechnologyP.O. Box 513 (STO3.41)5600 MBEindhovenThe Netherlands
| | - Jan C. M. van Hest
- Bio-Organic Chemistry Research GroupInstitute for Complex Molecular SystemsEindhoven University of TechnologyP.O. Box 513 (STO3.41)5600 MBEindhovenThe Netherlands
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38
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Zhang JT, Ma J, Kankala RK, Yu Q, Wang SB, Chen AZ. Recent Advances in Fabrication of Well-Organized Protein-Based Nanostructures. ACS APPLIED BIO MATERIALS 2021; 4:4039-4048. [DOI: 10.1021/acsabm.1c00156] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jian-Ting Zhang
- Institute of Biomaterials and Tissue Engineering, Huaqiao University, Xiamen 361021, People’s Republic of China
- Fujian Provincial Key Laboratory of Biochemical Technology, Huaqiao University, Xiamen 361021, People’s Republic of China
| | - Jingyao Ma
- Institute of Biomaterials and Tissue Engineering, Huaqiao University, Xiamen 361021, People’s Republic of China
- Fujian Provincial Key Laboratory of Biochemical Technology, Huaqiao University, Xiamen 361021, People’s Republic of China
| | - Ranjith Kumar Kankala
- Institute of Biomaterials and Tissue Engineering, Huaqiao University, Xiamen 361021, People’s Republic of China
- Fujian Provincial Key Laboratory of Biochemical Technology, Huaqiao University, Xiamen 361021, People’s Republic of China
| | - Qianqian Yu
- Institute of Biomaterials and Tissue Engineering, Huaqiao University, Xiamen 361021, People’s Republic of China
- Fujian Provincial Key Laboratory of Biochemical Technology, Huaqiao University, Xiamen 361021, People’s Republic of China
| | - Shi-Bin Wang
- Institute of Biomaterials and Tissue Engineering, Huaqiao University, Xiamen 361021, People’s Republic of China
- Fujian Provincial Key Laboratory of Biochemical Technology, Huaqiao University, Xiamen 361021, People’s Republic of China
| | - Ai-Zheng Chen
- Institute of Biomaterials and Tissue Engineering, Huaqiao University, Xiamen 361021, People’s Republic of China
- Fujian Provincial Key Laboratory of Biochemical Technology, Huaqiao University, Xiamen 361021, People’s Republic of China
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Sprenger J, Carey J, Schulz A, Drouard F, Lawson CL, von Wachenfeldt C, Linse S, Lo Leggio L. Guest-protein incorporation into solvent channels of a protein host crystal (hostal). Acta Crystallogr D Struct Biol 2021; 77:471-485. [PMID: 33825708 PMCID: PMC8025882 DOI: 10.1107/s2059798321001078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 01/29/2021] [Indexed: 11/10/2022] Open
Abstract
Soaking small molecules into the solvent channels of protein crystals is the most common method of obtaining crystalline complexes with ligands such as substrates or inhibitors. The solvent channels of some protein crystals are large enough to allow the incorporation of macromolecules, but soaking of protein guests into protein crystals has not been reported. Such protein host crystals (here given the name hostals) incorporating guest proteins may be useful for a wide range of applications in biotechnology, for example as cargo systems or for diffraction studies analogous to the crystal sponge method. The present study takes advantage of crystals of the Escherichia coli tryptophan repressor protein (ds-TrpR) that are extensively domain-swapped and suitable for incorporating guest proteins by diffusion, as they are robust and have large solvent channels. Confocal fluorescence microscopy is used to follow the migration of cytochrome c and fluorophore-labeled calmodulin into the solvent channels of ds-TrpR crystals. The guest proteins become uniformly distributed in the crystal within weeks and enriched within the solvent channels. X-ray diffraction studies on host crystals with high concentrations of incorporated guests demonstrate that diffraction limits of ∼2.5 Å can still be achieved. Weak electron density is observed in the solvent channels, but the guest-protein structures could not be determined by conventional crystallographic methods. Additional approaches that increase the ordering of guests in the host crystal are discussed that may support protein structure determination using the hostal system in the future. This host system may also be useful for biotechnological applications where crystallographic order of the guest is not required.
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Affiliation(s)
- Janina Sprenger
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
- Center for Molecular Protein Science, Lund University, SE-221 00 Lund, Sweden
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Jannette Carey
- Chemistry Department, Princeton University, Princeton, NJ 08544, USA
| | - Alexander Schulz
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg, Denmark
| | - Fleur Drouard
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Catherine L. Lawson
- Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ 08854, USA
| | | | - Sara Linse
- Center for Molecular Protein Science, Lund University, SE-221 00 Lund, Sweden
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
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40
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Electrostatic Self-Assembly of Protein Cage Arrays. Methods Mol Biol 2021. [PMID: 32856259 DOI: 10.1007/978-1-0716-0928-6_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Protein and peptide cages are nanoscale containers, which are of particular interest in nanoscience due to their well-defined dimensions and enclosed central cavities that can be filled with material that is protected from the outside environment. Ferritin is a typical example of protein cage, formed by 24 polypeptide chains that self-assemble into a hollow, roughly spherical protein cage with external and internal diameters of approximately 12 nm and 8 nm, respectively. The interior cavity of ferritin provides a unique reaction vessel to carry out reactions separated from the exterior environment. In nature, the cavity is utilized for sequestration and biomineralization to render iron inert and safe by shielding from the external environment. Materials scientists have been inspired by this system and exploited a range of ferritin superfamily proteins as supramolecular templates to encapsulate cargoes ranging from cancer drugs to therapeutic proteins. Interesting possibilities arise if such containers can themselves be arranged into even higher-order structures such as crystalline arrays. Here, we describe how crystalline arrays of negatively charged ferritin protein cages can be built by taking advantage of electrostatic interactions with cationic gold nanoparticles.
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41
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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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42
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Tan YQ, Xue B, Yew WS. Genetically Encodable Scaffolds for Optimizing Enzyme Function. Molecules 2021; 26:molecules26051389. [PMID: 33806660 PMCID: PMC7961827 DOI: 10.3390/molecules26051389] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 02/27/2021] [Accepted: 03/01/2021] [Indexed: 12/13/2022] Open
Abstract
Enzyme engineering is an indispensable tool in the field of synthetic biology, where enzymes are challenged to carry out novel or improved functions. Achieving these goals sometimes goes beyond modifying the primary sequence of the enzyme itself. The use of protein or nucleic acid scaffolds to enhance enzyme properties has been reported for applications such as microbial production of chemicals, biosensor development and bioremediation. Key advantages of using these assemblies include optimizing reaction conditions, improving metabolic flux and increasing enzyme stability. This review summarizes recent trends in utilizing genetically encodable scaffolds, developed in line with synthetic biology methodologies, to complement the purposeful deployment of enzymes. Current molecular tools for constructing these synthetic enzyme-scaffold systems are also highlighted.
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Affiliation(s)
- Yong Quan Tan
- Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore; (Y.Q.T.); (B.X.)
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore
| | - Bo Xue
- Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore; (Y.Q.T.); (B.X.)
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | - Wen Shan Yew
- Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore; (Y.Q.T.); (B.X.)
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
- Correspondence: ; Tel.: +65-6516-8624
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Fernández-Penas R, Verdugo-Escamilla C, Martínez-Rodríguez S, Gavira JA. Production of Cross-Linked Lipase Crystals at a Preparative Scale. CRYSTAL GROWTH & DESIGN 2021; 21:1698-1707. [PMID: 34602865 PMCID: PMC8479976 DOI: 10.1021/acs.cgd.0c01608] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 02/10/2021] [Indexed: 05/14/2023]
Abstract
The autoimmobilization of enzymes via cross-linked enzyme crystals (CLECs) has regained interest in recent years, boosted by the extensive knowledge gained in protein crystallization, the decrease of cost and laboriousness of the process, and the development of potential applications. In this work, we present the crystallization and preparative-scale production of reinforced cross-linked lipase crystals (RCLLCs) using a commercial detergent additive as a raw material. Bulk crystallization was carried out in 500 mL of agarose media using the batch technique. Agarose facilitates the homogeneous production of crystals, their cross-linking treatment, and their extraction. RCLLCs were active in an aqueous solution and in hexane, as shown by the hydrolysis of p-nitrophenol butyrate and α-methylbenzyl acetate, respectively. RCLLCs presented both high thermal and robust operational stability, allowing the preparation of a packed-bed chromatographic column to work in a continuous flow. Finally, we determined the three-dimensional (3D) models of this commercial lipase crystallized with and without phosphate at 2.0 and 1.7 Å resolutions, respectively.
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Affiliation(s)
- Raquel Fernández-Penas
- Laboratorio
de Estudios Cristalográficos, Instituto Andaluz de Ciencias
de la Tierra, Consejo Superior de Investigaciones
Científicas-Universidad de Granada, Avenida de las Palmeras 4, Armilla, 18100 Granada, Spain
| | - Cristóbal Verdugo-Escamilla
- Laboratorio
de Estudios Cristalográficos, Instituto Andaluz de Ciencias
de la Tierra, Consejo Superior de Investigaciones
Científicas-Universidad de Granada, Avenida de las Palmeras 4, Armilla, 18100 Granada, Spain
| | - Sergio Martínez-Rodríguez
- Laboratorio
de Estudios Cristalográficos, Instituto Andaluz de Ciencias
de la Tierra, Consejo Superior de Investigaciones
Científicas-Universidad de Granada, Avenida de las Palmeras 4, Armilla, 18100 Granada, Spain
- Departamento
de Bioquímica y Biología Molecular III e Inmunología, Universidad de Granada, Avenida de la Investigación 11, 18071 Granada, Spain
| | - José A. Gavira
- Laboratorio
de Estudios Cristalográficos, Instituto Andaluz de Ciencias
de la Tierra, Consejo Superior de Investigaciones
Científicas-Universidad de Granada, Avenida de las Palmeras 4, Armilla, 18100 Granada, Spain
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44
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Du M, Zhou K, Yu R, Zhai Y, Chen G, Wang Q. Noncovalent Self-Assembly of Protein Crystals with Tunable Structures. NANO LETTERS 2021; 21:1749-1757. [PMID: 33556245 DOI: 10.1021/acs.nanolett.0c04587] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Engineering noncovalent interactions for assembling nonspherical proteins into supramolecular architectures with tunable morphologies and dynamics is challenging due to the structural heterogeneity and complexity of protein surfaces. Herein, we employed an anisotropic building block l-rhamnulose-1-phosphate aldolase (RhuA) to control supramolecular polymorphism in highly ordered protein assemblies by introducing histidine residues. Histidine-based π-π stacking interactions enabled thermodynamically controlled self-organization of RhuA to form three-dimensional (3D) nanoribbons and crystals. Self-assembly of different 3D crystal phases was kinetically modulated by the strong metal ion-histidine chelation, and double-helical protein superstructures were formed by engineering increased histidine interactions at the RhuA binding surface. Their structural properties and dynamics were determined via fluorescence microscopy, transmission electron microscopy, atomic force microscopy, and small-angle X-ray scattering. This work is aimed at expanding the toolbox for the programming of tunable, highly ordered, protein superstructures and increasing the understanding of the mechanisms of protein interfacial interactions.
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Affiliation(s)
- Mingming Du
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Kun Zhou
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Runze Yu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yufeng Zhai
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Gang Chen
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Qiangbin Wang
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
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Kalathiya U, Padariya M, Fahraeus R, Chakraborti S, Hupp TR. Multivalent Display of SARS-CoV-2 Spike (RBD Domain) of COVID-19 to Nanomaterial, Protein Ferritin Nanocages. Biomolecules 2021; 11:297. [PMID: 33671255 PMCID: PMC7923090 DOI: 10.3390/biom11020297] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 02/12/2021] [Accepted: 02/13/2021] [Indexed: 11/17/2022] Open
Abstract
SARS-CoV-2, or COVID-19, has a devastating effect on our society, both in terms of quality of life and death rates; hence, there is an urgent need for developing safe and effective therapeutics against SARS-CoV-2. The most promising strategy to fight against this deadly virus is to develop an effective vaccine. Internalization of SARS-CoV-2 into the human host cell mainly occurs through the binding of the coronavirus spike protein (a trimeric surface glycoprotein) to the human angiotensin-converting enzyme 2 (ACE2) receptor. The spike-ACE2 protein-protein interaction is mediated through the receptor-binding domain (RBD) of the spike protein. Mutations in the spike RBD can significantly alter interactions with the ACE2 host receptor. Due to its important role in virus transmission, the spike RBD is considered to be one of the key molecular targets for vaccine development. In this study, a spike RBD-based subunit vaccine was designed by utilizing a ferritin protein nanocage as a scaffold. Several fusion protein constructs were designed in silico by connecting the spike RBD via a synthetic linker (different sizes) to different ferritin subunits (H-ferritin and L-ferritin). The stability and the dynamics of the engineered nanocage constructs were tested by extensive molecular dynamics simulation (MDS). Based on our MDS analysis, a five amino acid-based short linker (S-Linker) was the most effective for displaying the spike RBD over the surface of ferritin. The behavior of the spike RBD binding regions from the designed chimeric nanocages with the ACE2 receptor was highlighted. These data propose an effective multivalent synthetic nanocage, which might form the basis for new vaccine therapeutics designed against viruses such as SARS-CoV-2.
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Affiliation(s)
- Umesh Kalathiya
- University of Gdansk, International Centre for Cancer Vaccine Science, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (R.F.)
| | - Monikaben Padariya
- University of Gdansk, International Centre for Cancer Vaccine Science, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (R.F.)
| | - Robin Fahraeus
- University of Gdansk, International Centre for Cancer Vaccine Science, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (R.F.)
| | | | - Ted R. Hupp
- University of Gdansk, International Centre for Cancer Vaccine Science, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (R.F.)
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH4 2XR, UK
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46
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Wang Y, Uchida M, Waghwani HK, Douglas T. Synthetic Virus-like Particles for Glutathione Biosynthesis. ACS Synth Biol 2020; 9:3298-3310. [PMID: 33232156 DOI: 10.1021/acssynbio.0c00368] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein-based nanocompartments found in nature have inspired the development of functional nanomaterials for a range of applications including delivery of catalytic activities with therapeutic effects. As glutathione (GSH) plays a vital role in metabolic adaptation and many diseases are associated with its deficiency, supplementation of GSH biosynthetic activity might be a potential therapeutic when delivered directly to the disease site. Here, we report the successful design and production of active nanoreactors capable of catalyzing the partial or complete pathway for GSH biosynthesis, which was realized by encapsulating essential enzymes of the pathway inside the virus-like particle (VLP) derived from the bacteriophage P22. These nanoreactors are the first examples of nanocages specifically designed for the biosynthesis of oligomeric biomolecules. A dense packing of enzymes is achieved within the cavities of the nanoreactors, which allows us to study enzyme behavior, in a crowded and confined environment, including enzymatic kinetics and protein stability. In addition, the biomedical utility of the nanoreactors in protection against oxidative stress was confirmed using an in vitro cell culture model. Given that P22 VLP capsid was suggested as a potential liver-tropic nanocarrier in vivo, it will be promising to test the efficacy of these GSH nanoreactors as a novel treatment for GSH-deficient hepatic diseases.
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Affiliation(s)
- Yang Wang
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Masaki Uchida
- Department of Chemistry and Biochemistry, California State University Fresno, Fresno, California 93740, United States
| | - Hitesh Kumar Waghwani
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Trevor Douglas
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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47
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Stupka I, Heddle JG. Artificial protein cages – inspiration, construction, and observation. Curr Opin Struct Biol 2020; 64:66-73. [DOI: 10.1016/j.sbi.2020.05.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 05/05/2020] [Accepted: 05/19/2020] [Indexed: 12/29/2022]
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48
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Zhang C, Zhang X, Zhao G. Ferritin Nanocage: A Versatile Nanocarrier Utilized in the Field of Food, Nutrition, and Medicine. NANOMATERIALS 2020; 10:nano10091894. [PMID: 32971961 PMCID: PMC7557750 DOI: 10.3390/nano10091894] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 12/21/2022]
Abstract
Compared with other nanocarriers such as liposomes, mesoporous silica, and cyclodextrin, ferritin as a typical protein nanocage has received considerable attention in the field of food, nutrition, and medicine owing to its inherent cavity size, excellent water solubility, and biocompatibility. Additionally, ferritin nanocage also serves as a versatile bio-template for the synthesis of a variety of nanoparticles. Recently, scientists have explored the ferritin nanocage structure for encapsulation and delivery of guest molecules such as nutrients, bioactive molecules, anticancer drugs, and mineral metal ions by taking advantage of its unique reversible disassembly and reassembly property and biomineralization. In this review, we mainly focus on the preparation and structure of ferritin-based nanocarriers, and regulation of their self-assembly. Moreover, the recent advances of their applications in food nutrient delivery and medical diagnostics are highlighted. Finally, the main challenges and future development in ferritin-directed nanoparticles’ synthesis and multifunctional applications are discussed.
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49
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Chen H, Liu Y, Zhang T, Zhao G. Construction of three-dimensional interleaved protein hetero-superlattices in solution by cooperative electrostatic and aromatic stacking interactions. J Colloid Interface Sci 2020; 582:1-11. [PMID: 32814217 DOI: 10.1016/j.jcis.2020.08.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 07/26/2020] [Accepted: 08/04/2020] [Indexed: 12/14/2022]
Abstract
HYPOTHESIS Hierarchical assembly of naturally occurring assemblies is accurate and responsible for performing various cellular functions. However, Nature's wisdom in navigating the assembly process to desired protein assemblies by the cooperation of multiple noncovalent interactions has been underexploited for protein superstructures constructions. Owing to the chemical diversity of noncovalent interactions, it should be possible to fabricate protein assemblies with novel properties in high efficiency through the cooperation of different noncovalent interaction. EXPERIMENTS Both charged residues and aromatic residues are introduced on the exterior surface of ferritin centered at their symmetry axes, mixing of complementary variants forms ordered assemblies through the cooperation of two kinds of chemical-diverse noncovalent interactions. The assemblies were further characterized in terms of their assembly behavior, structure, size, assembly kinetics, properties and stabilities. FINDINGS We utilized both electrostatic and π-π stacking interactions between complementary nanocages to cooperatively trigger the self-assembly into predesigned interleaved hetero-superlattices which exhibit high electrolyte stability and thermal stability. The size of the hetero-superlattices can be well controlled with ranges from nanometers to micrometers in solution in response to external stimuli such as pH and salt concentration. The hetero-superlattice may have the potential applications in hybrid bio-templating, light-harvesting and compartmentalized encapsulation.
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Affiliation(s)
- Hai Chen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China
| | - Yu Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China
| | - Tuo Zhang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China
| | - Guanghua Zhao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China.
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50
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Majsterkiewicz K, Azuma Y, Heddle JG. Connectability of protein cages. NANOSCALE ADVANCES 2020; 2:2255-2264. [PMID: 36133365 PMCID: PMC9416917 DOI: 10.1039/d0na00227e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 04/27/2020] [Indexed: 06/14/2023]
Abstract
Regular, hollow proteinaceous nanoparticles are widespread in nature. The well-defined structures as well as diverse functions of naturally existing protein cages have inspired the development of new nanoarchitectures with desired capabilities. In such approaches, a key functionality is "connectability". Engineering of interfaces between cage building blocks to modulate intra-cage connectability leads to protein cages with new morphologies and assembly-disassembly properties. Modification of protein cage surfaces to control inter-cage connectability enables their arrangement into lattice-like nanomaterials. Here, we review the current progress in control of intra- and inter-cage connectability for protein cage-based nanotechnology development.
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Affiliation(s)
- Karolina Majsterkiewicz
- Małopolska Centre of Biotechnology, Jagiellonian University Gronostajowa 7A 30-387 Krakow Poland
- Postgraduate School of Molecular Medicine Trojdena 2a 02-091 Warsaw Poland
| | - Yusuke Azuma
- Małopolska Centre of Biotechnology, Jagiellonian University Gronostajowa 7A 30-387 Krakow Poland
| | - Jonathan G Heddle
- Małopolska Centre of Biotechnology, Jagiellonian University Gronostajowa 7A 30-387 Krakow Poland
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