1
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Jones AA, Snow CD. Porous protein crystals: synthesis and applications. Chem Commun (Camb) 2024; 60:5790-5803. [PMID: 38756076 DOI: 10.1039/d4cc00183d] [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: 05/18/2024]
Abstract
Large-pore protein crystals (LPCs) are an emerging class of biomaterials. The inherent diversity of proteins translates to a diversity of crystal lattice structures, many of which display large pores and solvent channels. These pores can, in turn, be functionalized via directed evolution and rational redesign based on the known crystal structures. LPCs possess extremely high solvent content, as well as extremely high surface area to volume ratios. Because of these characteristics, LPCs continue to be explored in diverse applications including catalysis, targeted therapeutic delivery, templating of nanostructures, structural biology. This Feature review article will describe several of the existing platforms in detail, with particular focus on LPC synthesis approaches and reported applications.
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Affiliation(s)
- Alec Arthur Jones
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523-1301, USA.
| | - Christopher D Snow
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523-1301, USA.
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523-1301, USA
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2
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Liu B, Li X, Zhang JP, Li X, Yuan Y, Hou GH, Zhang HJ, Zhang H, Li Y, Mezzenga R. Protein Nanotubes as Advanced Material Platforms and Delivery Systems. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2307627. [PMID: 37921269 DOI: 10.1002/adma.202307627] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 10/22/2023] [Indexed: 11/04/2023]
Abstract
Protein nanotubes (PNTs) as state-of-the-art nanocarriers are promising for various potential applications both in the food and pharmaceutical industries. Derived from edible starting sources like α-lactalbumin, lysozyme, and ovalbumin, PNTs bear properties of biocompatibility and biodegradability. Their large specific surface area and hydrophobic core facilitate chemical modification and loading of bioactive substances, respectively. Moreover, their enhanced permeability and penetration ability across biological barriers such as intestinal mucus, extracellular matrix, and thrombus clot, make it promising platforms for health-related applications. Most importantly, their simple preparation processes enable large-scale production, supporting applications in the biomedical and nanotechnological fields. Understanding the self-assembly principles is crucial for controlling their morphology, size, and shape, and thus provides the ground to a multitude of applications. Here, the current state-of-the-art of PNTs including their building materials, physicochemical properties, and self-assembly mechanisms are comprehensively reviewed. The advantages and limitations, as well as challenges and prospects for their successful applications in biomaterial and pharmaceutical sectors are then discussed and highlighted. Potential cytotoxicity of PNTs and the need of regulations as critical factors for enabling in vivo applications are also highlighted. In the end, a brief summary and future prospects for PNTs as advanced platforms and delivery systems are included.
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Affiliation(s)
- Bin Liu
- Key Laboratory of Precision Nutrition and Food Quality, Research Center of Food Colloids and Delivery of Functionality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
- Department of Nutrition and Health, China Agricultural University, Beijing, 100091, P. R. China
| | - Xing Li
- Key Laboratory of Precision Nutrition and Food Quality, Research Center of Food Colloids and Delivery of Functionality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Ji Peng Zhang
- Key Laboratory of Precision Nutrition and Food Quality, Research Center of Food Colloids and Delivery of Functionality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Xin Li
- Key Laboratory of Precision Nutrition and Food Quality, Research Center of Food Colloids and Delivery of Functionality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Yu Yuan
- Key Laboratory of Precision Nutrition and Food Quality, Research Center of Food Colloids and Delivery of Functionality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Guo Hua Hou
- Key Laboratory of Precision Nutrition and Food Quality, Research Center of Food Colloids and Delivery of Functionality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Hui Juan Zhang
- Key Laboratory of Precision Nutrition and Food Quality, Research Center of Food Colloids and Delivery of Functionality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Hui Zhang
- Key Laboratory of Precision Nutrition and Food Quality, Research Center of Food Colloids and Delivery of Functionality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Yuan Li
- Key Laboratory of Precision Nutrition and Food Quality, Research Center of Food Colloids and Delivery of Functionality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Raffaele Mezzenga
- Department of Health Sciences and Technology, ETH Zurich, Zürich, 8092, Switzerland
- Department of Materials, ETH Zurich, Zürich, 8092, Switzerland
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3
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Oohora K, Hayashi T. Preparation of Cage-Like Micellar Assemblies of Engineered Hemoproteins. Methods Mol Biol 2023; 2671:95-108. [PMID: 37308640 DOI: 10.1007/978-1-0716-3222-2_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Natural protein assemblies have encouraged scientists to create large supramolecular systems consisting of various protein motifs. In the case of hemoproteins containing heme as a cofactor, several approaches have been reported to form artificial assemblies with various structures such as fibers, sheets, networks, and cages. This chapter describes the design, preparation, and characterization of cage-like micellar assemblies for chemically modified hemoproteins including hydrophilic protein units attached to hydrophobic molecules. Detailed procedures are described for constructing specific systems using cytochrome b562 and hexameric tyrosine-coordinated heme protein as hemoprotein units with heme-azobenzene conjugate and poly-N-isopropylacrylamide as attached molecules.
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Affiliation(s)
- Koji Oohora
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Yamadaoka, Suita, Japan.
| | - Takashi Hayashi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Yamadaoka, Suita, Japan.
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4
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Hiromoto T, Ikura T, Honjo E, Blaber M, Kuroki R, Tamada T. Creation of Cross-Linked Crystals With Intermolecular Disulfide Bonds Connecting Symmetry-Related Molecules Allows Retention of Tertiary Structure in Different Solvent Conditions. Front Mol Biosci 2022; 9:908394. [PMID: 35755825 PMCID: PMC9213883 DOI: 10.3389/fmolb.2022.908394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/05/2022] [Indexed: 11/13/2022] Open
Abstract
Protein crystals are generally fragile and sensitive to subtle changes such as pH, ionic strength, and/or temperature in their crystallization mother liquor. Here, using T4 phage lysozyme as a model protein, the three-dimensional rigidification of protein crystals was conducted by introducing disulfide cross-links between neighboring molecules in the crystal. The effect of cross-linking on the stability of the crystals was evaluated by microscopic observation and X-ray diffraction. When soaking the obtained cross-linked crystals into a precipitant-free solution, the crystals held their shape without dissolution and diffracted to approximately 1.1 Å resolution, comparable to that of the non-cross-linked crystals. Such cross-linked crystals maintained their diffraction even when immersed in other solutions with pH values from 4 to 10, indicating that the disulfide cross-linking made the packing contacts enforced and resulted in some mechanical strength in response to changes in the preservation conditions. Furthermore, the cross-linked crystals gained stability to permit soaking into solutions containing high concentrations of organic solvents. The results suggest the possibility of obtaining protein crystals for effective drug screening by introducing appropriate cross-linked disulfide bonds.
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Affiliation(s)
- Takeshi Hiromoto
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Ibaraki, Japan
| | - Teikichi Ikura
- Institute for Human Life Science, Ochanomizu University, Tokyo, Japan
| | - Eijiro Honjo
- Research and Development Division, ADTEC Co., Ltd., Oita, Japan
| | - Michael Blaber
- College of Medicine, Florida State University, Tallahassee, FL, United states
| | - Ryota Kuroki
- Quantum Beam Science Center, Japan Atomic Energy Agency, Ibaraki, Japan
| | - Taro Tamada
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Ibaraki, Japan
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5
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Zeng R, Lv C, Zang J, Zhang T, Zhao G. Designing Stacked Assembly of Type III Rubisco for CO 2 Fixation with Higher Efficiency. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:7049-7057. [PMID: 35670363 DOI: 10.1021/acs.jafc.2c02521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The slow catalytic rate of the carboxylation enzyme d-ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is a major barrier to increasing the rate of carbon assimilation from the atmosphere into the biosphere. It is of great importance to establish a method to improve the carboxylation efficiency of Rubisco. Inspired by the assembly of Rubisco in carboxysomes, herein, we presented a rational protein engineering approach for the construction of one-dimensional (1D) protein arrays of type III Rubisco through designed π-π stacking interactions by using crystal structural information as a guide. In aqueous solutions, the dimensions of these 1D protein arrays collectively span nearly the entire nano- and micrometer scale (200 nm to 5.0 μm) by adjusting protein and NaCl concentrations. As a result, the stacked Rubisco assemblies increase by 40% in the carboxylase activity, while their turnover number (kcat) is around twofold larger than that of wild-type III Rubisco. Notably, upon heat treatment at temperature up to 75 °C for 30 min, most of the assembled nanostructures and the enzyme activity are retained. More importantly, the initial relative activity of stacked assemblies retained 91% after 10 cycles of reuse. This work provides a simple, effective solution for the improvement of the CO2 carboxylation efficiency of Rubisco.
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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
| | - Jiachen Zang
- College of Food Science & Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education, Beijing 100083, China
| | - Tuo Zhang
- College of Food Science & Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education, Beijing 100083, 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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6
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Han K, Na Y, Zhang L, Tezcan FA. Dynamic, Polymer-Integrated Crystals for Efficient, Reversible Protein Encapsulation. J Am Chem Soc 2022; 144:10139-10144. [PMID: 35666988 DOI: 10.1021/jacs.2c02584] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Crystalline materials are increasingly being used as platforms for encapsulating proteins to create stable, functional materials. However, the uptake efficiencies and stimuli-responsiveness of crystalline frameworks are limited by their rigidities. We have recently reported a new form of materials, polymer-integrated crystals (PIX), which combine the structural order of protein crystals with the dynamic, stimuli-responsive properties of synthetic polymers. Here we show that the crystallinity, flexibility, and chemical tunability of PIX can be exploited to encapsulate guest proteins with high loading efficiencies (up to 46% w/w). The electrostatic host-guest interactions enable reversible, pH-controlled uptake/release of guest proteins as well as the mutual stabilization of the host and the guest, thus creating a uniquely synergistic platform toward the development of functional biomaterials and the controlled delivery of biological macromolecules.
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Affiliation(s)
- Kenneth Han
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Youjeong Na
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Ling Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - F Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States.,Materials Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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7
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Mouli MSSV, Agrawal HG, Kumar M, Mishra AK. Luminescent and morphological behavior of the aromatic dipeptide pair having singular structural variability. LUMINESCENCE 2022. [PMID: 35560861 DOI: 10.1002/bio.4275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/15/2022] [Accepted: 05/07/2022] [Indexed: 11/07/2022]
Abstract
In the present manuscript, the luminescence and the self-assembly behavior of the two aromatic dipeptides having singular structure variable are investigated. The terminally protected dipeptides tryptophan-tyrosine (WYp ) and tryptophan-phenylalanine (WFp ) were synthesized using standard solution phase procedure. Significant solvatochromic effect was observed for both the dipeptidyl entities; while the influence was more pronounced in case of the WYp entity when compared to WFp . Interesting morphological variation was observed for WFp and WYp , wherein discrete and interconnected nanospheres were observed for the respective dipeptides. The results obtained signifies the influence of the singular structural variation on modulating the overall functional behavior of the short peptides motifs.
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Affiliation(s)
- M S S Vinod Mouli
- Department of chemistry, Indian Institute of Technology Hyderabad, Sangareddy, Telangana, India
| | - Harsha Gopal Agrawal
- Department of chemistry, Indian Institute of Technology Hyderabad, Sangareddy, Telangana, India
| | - Mohit Kumar
- Department of chemistry, Indian Institute of Technology Hyderabad, Sangareddy, Telangana, India
| | - Ashutosh Kumar Mishra
- Department of chemistry, Indian Institute of Technology Hyderabad, Sangareddy, Telangana, India
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8
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Soon JW, Oohora K, Hayashi T. A disulphide bond-mediated hetero-dimer of a hemoprotein and a fluorescent protein exhibiting efficient energy transfer †. RSC Adv 2022; 12:28519-28524. [PMID: 36320522 PMCID: PMC9535469 DOI: 10.1039/d2ra05249k] [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: 08/21/2022] [Accepted: 09/22/2022] [Indexed: 11/07/2022] Open
Abstract
Artificial protein hetero-dimerization is one of the promising strategies to construct protein-based chemical tools. In this work, cytochrome b562, an electron transfer hemoprotein, and green fluorescent protein (GFP) mutants with cysteine residues added to their surfaces were conjugated via a pyridyl disulphide-based thiol–disulfide exchange reaction. The eight hetero-dimers, which have cysteine residues at different positions to form the disulphide bonds, were obtained and characterized by gel-electrophoresis, mass spectrometry and size exclusion chromatography. The fluorescence properties of the hetero-dimers were evaluated by fluorescence spectroscopy and fluorescence lifetime measurements. Efficient photoinduced energy transfer from the GFP chromophore to the heme cofactor was observed in each of the hetero-dimers. The energy transfer efficiency is strongly dependent on the cross-linking residues, reaching 96%. Furthermore, the estimated Förster distance and the structure-based maximum possible distances of the donor and acceptor suggest that one of the hetero-dimers has a rigid protein–protein structure with favourable properties for energy transfer. The disulphide bond-mediated protein hetero-dimerization is useful for screening functional protein systems towards further developments. Hetero-dimerization of a hemoprotein and green fluorescent protein via a thiol–disulphide exchange reaction is achieved. The heterodimer has suitable cross-linking points and displays efficient energy transfer.![]()
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Affiliation(s)
- Julian Wong Soon
- Department of Applied Chemistry, Graduate School of Engineering, Osaka UniversitySuita565-0871Japan
| | - Koji Oohora
- Department of Applied Chemistry, Graduate School of Engineering, Osaka UniversitySuita565-0871Japan
| | - Takashi Hayashi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka UniversitySuita565-0871Japan
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9
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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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10
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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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11
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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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12
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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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13
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Abe S, Pham TT, Negishi H, Yamashita K, Hirata K, Ueno T. Design of an In‐Cell Protein Crystal for the Environmentally Responsive Construction of a Supramolecular Filament. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Satoshi Abe
- School of Life Science and Technology Tokyo Institute of Technology Nagatsuta 4259-B-55, Midori-ku Yokohama 226-8501 Japan
| | - Thuc Toan Pham
- School of Life Science and Technology Tokyo Institute of Technology Nagatsuta 4259-B-55, Midori-ku Yokohama 226-8501 Japan
| | - Hashiru Negishi
- School of Life Science and Technology Tokyo Institute of Technology Nagatsuta 4259-B-55, Midori-ku Yokohama 226-8501 Japan
| | - Keitaro Yamashita
- SR Life Science Instrumentation Unit RIKEN/SPring-8 RIKEN/SPring-8 Center 1-1-1, Kouto, Sayo-cho Sayo-gun Hyogo 679-5148 Japan
| | - Kunio Hirata
- SR Life Science Instrumentation Unit RIKEN/SPring-8 RIKEN/SPring-8 Center 1-1-1, Kouto, Sayo-cho Sayo-gun Hyogo 679-5148 Japan
| | - Takafumi Ueno
- School of Life Science and Technology Tokyo Institute of Technology Nagatsuta 4259-B-55, Midori-ku Yokohama 226-8501 Japan
- Tokyo Tech World Research Hub Initiative (WRHI) Tokyo Institute of Technology Japan
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14
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Abe S, Pham TT, Negishi H, Yamashita K, Hirata K, Ueno T. Design of an In‐Cell Protein Crystal for the Environmentally Responsive Construction of a Supramolecular Filament. Angew Chem Int Ed Engl 2021; 60:12341-12345. [DOI: 10.1002/anie.202102039] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/17/2021] [Indexed: 12/20/2022]
Affiliation(s)
- Satoshi Abe
- School of Life Science and Technology Tokyo Institute of Technology Nagatsuta 4259-B-55, Midori-ku Yokohama 226-8501 Japan
| | - Thuc Toan Pham
- School of Life Science and Technology Tokyo Institute of Technology Nagatsuta 4259-B-55, Midori-ku Yokohama 226-8501 Japan
| | - Hashiru Negishi
- School of Life Science and Technology Tokyo Institute of Technology Nagatsuta 4259-B-55, Midori-ku Yokohama 226-8501 Japan
| | - Keitaro Yamashita
- SR Life Science Instrumentation Unit RIKEN/SPring-8 RIKEN/SPring-8 Center 1-1-1, Kouto, Sayo-cho Sayo-gun Hyogo 679-5148 Japan
| | - Kunio Hirata
- SR Life Science Instrumentation Unit RIKEN/SPring-8 RIKEN/SPring-8 Center 1-1-1, Kouto, Sayo-cho Sayo-gun Hyogo 679-5148 Japan
| | - Takafumi Ueno
- School of Life Science and Technology Tokyo Institute of Technology Nagatsuta 4259-B-55, Midori-ku Yokohama 226-8501 Japan
- Tokyo Tech World Research Hub Initiative (WRHI) Tokyo Institute of Technology Japan
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15
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A Supramolecular Assembly of Hemoproteins Formed in a Star-Shaped Structure via Heme-Heme Pocket Interactions. Int J Mol Sci 2021; 22:ijms22031012. [PMID: 33498330 PMCID: PMC7864044 DOI: 10.3390/ijms22031012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/16/2021] [Accepted: 01/17/2021] [Indexed: 11/17/2022] Open
Abstract
Proteins have been used as building blocks to provide various supramolecular structures in efforts to develop nano-biomaterials possessing broad biological functionalities. A series of unique structures have been obtained from the engineering of hemoproteins which contain the iron porphyrin known as heme, as a prosthetic group. This work in developing assembling systems is extended using cytochrome b562, a small electron transfer hemoprotein engineered to include an externally-attached heme moiety. The engineered units, which form a one-dimensional assembly via interprotein heme–heme pocket interactions, are conjugated to an apo-form of hexameric tyrosine-coordinated hemoprotein (apoHTHP) to provide a branching unit promoting the assembly of a star-shaped structure. The incorporation of the heme moiety attached to the protein surface of cytochrome b562 into apoHTHP can be accelerated by elevating the reaction temperature to generate a new assembly. The formation of a new larger assembly structure was confirmed by size exclusion chromatography. The ratio of the heme-containing units in the assemblies was analyzed by UV-Vis spectroscopy and the population of protein units estimated from SDS PAGE suggests the presence of plausible star-shaped structures, which are supported by hydrodynamic diameter data obtained by dynamic light scattering.
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16
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Groeer S, Walther A. Switchable supracolloidal 3D DNA origami nanotubes mediated through fuel/antifuel reactions. NANOSCALE 2020; 12:16995-17004. [PMID: 32780076 PMCID: PMC7612458 DOI: 10.1039/d0nr04209a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
3D DNA origami provide access to the de novo design of monodisperse and functional bio(organic) nanoparticles, and complement structural protein engineering and inorganic and organic nanoparticle synthesis approaches for the design of self-assembling colloidal systems. We show small 3D DNA origami nanoparticles, which polymerize and depolymerize reversibly to nanotubes of micrometer lengths by applying fuel/antifuel switches. 3D DNA nanocylinders are engineered as a basic building block with different numbers of overhang strands at the open sides to allow for their assembly via fuel strands that bridge both overhangs, resulting in the supracolloidal polymerization. The influence of the multivalent interaction patterns and the length of the bridging fuel strand on efficient polymerization and nanotube length distribution is investigated. The polymerized multivalent nanotubes disassemble through toehold-mediated rehybridization by adding equimolar amounts of antifuel strands. Finally, Förster resonance energy transfer yields in situ insights into the kinetics and reversibility of the nanotube polymerization and depolymerization.
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Affiliation(s)
- Saskia Groeer
- A3BMS Lab - Active, Adaptive and Autonomous Bioinspired Material Systems, Institute for Macromolecular Chemistry, University of Freiburg, Stefan-Meier-Straße 31, 79104 Freiburg, Germany. and Freiburg Materials Research Center (FMF), University of Freiburg, Stefan-Meier-Str. 21, 79104 Freiburg, Germany and Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Andreas Walther
- A3BMS Lab - Active, Adaptive and Autonomous Bioinspired Material Systems, Institute for Macromolecular Chemistry, University of Freiburg, Stefan-Meier-Straße 31, 79104 Freiburg, Germany. and Freiburg Materials Research Center (FMF), University of Freiburg, Stefan-Meier-Str. 21, 79104 Freiburg, Germany and Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany and Cluster of Excellence livMatS @ FIT, 79110 Freiburg, Germany
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17
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Sun H, Li Y, Yu S, Liu J. Hierarchical Self-Assembly of Proteins Through Rationally Designed Supramolecular Interfaces. Front Bioeng Biotechnol 2020; 8:295. [PMID: 32426335 PMCID: PMC7212437 DOI: 10.3389/fbioe.2020.00295] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Accepted: 03/19/2020] [Indexed: 12/11/2022] Open
Abstract
With the increasing advances in the basic understanding of pathogenesis mechanism and fabrication of advanced biological materials, protein nanomaterials are being developed for their potential bioengineering research and biomedical applications. Among different fabrication strategies, supramolecular self-assembly provides a versatile approach to construct hierarchical nanostructures from polyhedral cages, filaments, tubules, monolayer sheets to even cubic crystals through rationally designed supramolecular interfaces. In this mini review, we will briefly recall recent progress in reconstituting protein interfaces for hierarchical self-assembly and classify by the types of designed protein-protein interactions into receptor-ligand recognition, electrostatic interaction, metal coordination, and non-specific interaction networks. Moreover, some attempts on functionalization of protein superstructures for bioengineering and/or biomedical applications are also shortly discussed. We believe this mini review will outline the stream of hierarchical self-assembly of proteins through rationally designed supramolecular interfaces, which would open minds in visualizing protein-protein recognition and assembly in living cells and organisms, and even constructing multifarious functional bionanomaterials.
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Affiliation(s)
- Hongcheng Sun
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou, China
| | - Yan Li
- Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Hangzhou Normal University, Hangzhou, China
| | - Shuangjiang Yu
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou, China
| | - Junqiu Liu
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou, China
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18
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Oohora K, Hirayama S, Uchihashi T, Hayashi T. Construction of a Hexameric Hemoprotein Sheet and Direct Observation of Dynamic Processes of Its Formation. CHEM LETT 2020. [DOI: 10.1246/cl.190855] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Koji Oohora
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
- Frontier Research Base for Global Young Researchers, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Shota Hirayama
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Takayuki Uchihashi
- Department of Physics, Nagoya University, Nagoya, Aichi 464-8602, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | - Takashi Hayashi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
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19
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Alex JM, Brancatelli G, Volpi S, Bonaccorso C, Casnati A, Geremia S, Crowley PB. Probing the determinants of porosity in protein frameworks: co-crystals of cytochrome c and an octa-anionic calix[4]arene. Org Biomol Chem 2020; 18:211-214. [DOI: 10.1039/c9ob02275a] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In contrast to sulfonato-calix[4]arene (sclx4), which mediates close-packed assemblies, the higher charge carboxylate-containing sclx4mc induced a crystalline framework of cytochrome c.
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Affiliation(s)
- Jimi M. Alex
- School of Chemistry
- National University of Ireland Galway
- University Road
- Galway
- Ireland
| | - Giovanna Brancatelli
- Centre of Excellence in Biocrystallography
- Department of Chemical and Pharmaceutical Sciences
- University of Trieste
- 34127 Trieste
- Italy
| | - Stefano Volpi
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale
- Università degli Studi di Parma
- 43124 Parma
- Italy
| | - Carmela Bonaccorso
- Dipartimento di Scienze Chimiche
- Università degli Studi di Catania
- Catania
- Italy
| | - Alessandro Casnati
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale
- Università degli Studi di Parma
- 43124 Parma
- Italy
| | - Silvano Geremia
- Centre of Excellence in Biocrystallography
- Department of Chemical and Pharmaceutical Sciences
- University of Trieste
- 34127 Trieste
- Italy
| | - Peter B. Crowley
- School of Chemistry
- National University of Ireland Galway
- University Road
- Galway
- Ireland
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20
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Affiliation(s)
- Aleksei Solomonov
- Department of Materials and Interfaces Weizmann Institute of Science 7610001 Rehovot Israel
| | - Ulyana Shimanovich
- Department of Materials and Interfaces Weizmann Institute of Science 7610001 Rehovot Israel
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21
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Engilberge S, Rennie ML, Dumont E, Crowley PB. Tuning Protein Frameworks via Auxiliary Supramolecular Interactions. ACS NANO 2019; 13:10343-10350. [PMID: 31490058 DOI: 10.1021/acsnano.9b04115] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Protein crystals with their precise, periodic array of functional building blocks have potential applications in biomaterials, sensing, and catalysis. This paper describes how a highly porous crystalline framework of a cationic redox protein and an anionic macrocycle can be modulated by a small cationic effector. Ternary composites of protein (∼13 kDa), calix[8]arene (∼1.5 kDa), and effector (∼0.2 kDa) formed distinct crystalline architectures, dependent on the effector concentration and the crystallization technique. A combination of X-ray crystallography and density functional theory (DFT) calculations was used to decipher the framework variations, which appear to be dependent on a calixarene conformation change mediated by the effector. This "switch" calixarene was observed in three states, each of which is associated with a different interaction network. Two structures obtained by co-crystallization with the effector contained an additional protein "pillar", resulting in framework duplication and decreased porosity. These results suggest how protein assembly can be engineered by supramolecular host-guest interactions.
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Affiliation(s)
- Sylvain Engilberge
- School of Chemistry , National University of Ireland Galway , University Road , Galway H91 TK33 , Ireland
| | - Martin L Rennie
- School of Chemistry , National University of Ireland Galway , University Road , Galway H91 TK33 , Ireland
| | - Elise Dumont
- Université de Lyon, ENS de Lyon, CNRS UMR 5182 , Université Claude Bernard Lyon 1, Laboratoire de Chimie , 69342 Lyon , France
| | - Peter B Crowley
- School of Chemistry , National University of Ireland Galway , University Road , Galway H91 TK33 , Ireland
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22
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Katouzian I, Jafari SM. Protein nanotubes as state-of-the-art nanocarriers: Synthesis methods, simulation and applications. J Control Release 2019; 303:302-318. [PMID: 31009647 DOI: 10.1016/j.jconrel.2019.04.026] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 04/16/2019] [Accepted: 04/17/2019] [Indexed: 12/16/2022]
Abstract
Application of food proteins as a tool to form nanostructures (especially nanotubular shapes) has been an interesting topic for both the food and pharmaceutical sectors. Organic and protein nanostructures have better biocompatibility and biodegradability compared to inorganic counterparts like carbon nanotubes; in addition, they can undergo surface modifications. Several organic nanotubes have been developed, meanwhile, the engineered protein nanotubes in the food science have been prepared from α-lactalbumin, ovalbumin, cyclic peptide nanotubes, collagen, bovine serum albumin, lysozyme and hydrophobins which are of great interest to be applied in the food industry considering their outstanding properties. This revision underlines the production of protein nanotubular structures and their applications as well as introducing the in silico studies which is a novel field in predicting the interactions of proteins with different molecules before running experimental tests and finally exploring the safety of protein nanotubes. Protein nanotubes have several advantages over other morphologies, such as the functionalizing ability of both the outer and inner layers, enabling an efficient delivery and controlled release and their ability as gelling agents. Also, regarding their natural source in foods, they are promising alternatives to carbon nanotubes.
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Affiliation(s)
- Iman Katouzian
- Department of Food Materials and Process Design Engineering, Gorgan University of Agricultural Science and Natural Resources, Gorgan, Iran; Nano-encapsulation in the Food, Nutraceutical, and Pharmaceutical Industries Group (NFNPIG), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Seid Mahdi Jafari
- Department of Food Materials and Process Design Engineering, Gorgan University of Agricultural Science and Natural Resources, Gorgan, Iran.
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23
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Ross JF, Wildsmith GC, Johnson M, Hurdiss DL, Hollingsworth K, Thompson RF, Mosayebi M, Trinh CH, Paci E, Pearson AR, Webb ME, Turnbull WB. Directed Assembly of Homopentameric Cholera Toxin B-Subunit Proteins into Higher-Order Structures Using Coiled-Coil Appendages. J Am Chem Soc 2019; 141:5211-5219. [PMID: 30856321 PMCID: PMC6449800 DOI: 10.1021/jacs.8b11480] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
![]()
The self-assembly
of proteins into higher order structures is ubiquitous
in living systems. It is also an essential process for the bottom-up
creation of novel molecular architectures and devices for synthetic
biology. However, the complexity of protein–protein interaction
surfaces makes it challenging to mimic natural assembly processes
in artificial systems. Indeed, many successful computationally designed
protein assemblies are prescreened for “designability”,
limiting the choice of components. Here, we report a simple and pragmatic
strategy to assemble chosen multisubunit proteins into more complex
structures. A coiled-coil domain appended to one face of the pentameric
cholera toxin B-subunit (CTB) enabled the ordered assembly of tubular
supra-molecular complexes. Analysis of a tubular structure determined
by X-ray crystallography has revealed a hierarchical assembly process
that displays features reminiscent of the polymorphic assembly of
polyomavirus proteins. The approach provides a simple and straightforward
method to direct the assembly of protein building blocks which present
either termini on a single face of an oligomer. This scaffolding approach
can be used to generate bespoke supramolecular assemblies of functional
proteins. Additionally, structural resolution of the scaffolded assemblies
highlight “native-state” forced protein–protein
interfaces, which may prove useful as starting conformations for future
computational design.
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Affiliation(s)
- James F Ross
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Chemistry , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Molecular and Cellular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Gemma C Wildsmith
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Chemistry , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Michael Johnson
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Chemistry , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Daniel L Hurdiss
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Molecular and Cellular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Kristian Hollingsworth
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Chemistry , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Rebecca F Thompson
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Molecular and Cellular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Majid Mosayebi
- School of Mathematics , University of Bristol , Bristol BS8 1TW , United Kingdom.,BrisSynBio, Life Sciences Building , University of Bristol , Bristol BS8 1TQ , United Kingdom
| | - Chi H Trinh
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Molecular and Cellular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Emanuele Paci
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Molecular and Cellular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Arwen R Pearson
- Institute for Nanostructure and Solid State Physics , Universität Hamburg , Hamburg D-22761 , Germany
| | - Michael E Webb
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Chemistry , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - W Bruce Turnbull
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Chemistry , University of Leeds , Leeds LS2 9JT , United Kingdom
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