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Duan M, Lv C, Zang J, Leng X, Zhao G, Zhang T. Metals at the Helm: Revolutionizing Protein Assembly and Applications. Macromol Biosci 2024:e2400126. [PMID: 39239781 DOI: 10.1002/mabi.202400126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/23/2024] [Indexed: 09/07/2024]
Abstract
Protein assembly is an essential process in biological systems, where proteins self-assemble into complex structures with diverse functions. Inspired by the exquisite control over protein assembly in nature, scientists have been exploring ways to design and assemble protein structures with precise control over their topologies and functions. One promising approach for achieving this goal is through metal coordination, which utilizes metal-binding motifs to mediate protein-protein interactions and assemble protein complexes with controlled stoichiometry and geometry. Metal coordination provides a modular and tunable approach for protein assembly and de novo structure design, where the metal ion acts as a molecular glue that holds the protein subunits together in a specific orientation. Metal-coordinated protein assemblies have shown great potential for developing functional metalloproteinase, novel biomaterials and integrated drug delivery systems. In this review, an overview of the recent advances in protein assemblies benefited from metal coordination is provided, focusing on various protein arrangements in different dimensions including protein oligomers, protein nanocage and higher-order protein architectures. Moreover, the key metal-binding motifs and strategies used to assemble protein structures with precise control over their properties are highlighted. The potential applications of metal-mediated protein assemblies in biotechnology and biomedicine are also discussed.
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Affiliation(s)
- Maoping Duan
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Chenyan Lv
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Jiachen Zang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Xiaojing Leng
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Guanghua Zhao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Tuo Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
- Center of Food Colloids and Delivery for Functionality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
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2
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Han K, Zhang Z, Tezcan FA. Spatially Patterned, Porous Protein Crystals as Multifunctional Materials. J Am Chem Soc 2023; 145:19932-19944. [PMID: 37642457 DOI: 10.1021/jacs.3c06348] [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: 08/31/2023]
Abstract
While the primary use of protein crystals has historically been in crystallographic structure determination, they have recently emerged as promising materials with many advantageous properties such as high porosity, biocompatibility, stability, structural and functional versatility, and genetic/chemical tailorability. Here, we report that the utility of protein crystals as functional materials can be further augmented through their spatial patterning and control of their morphologies. To this end, we took advantage of the chemically and kinetically controllable nature of ferritin self-assembly and constructed core-shell crystals with chemically distinct domains, tunable structural patterns, and morphologies. The spatial organization within ferritin crystals enabled the generation of patterned, multi-enzyme frameworks with cooperative catalytic behavior. We further exploited the differential growth kinetics of ferritin crystal facets to assemble Janus-type architectures with an anisotropic arrangement of chemically distinct domains. These examples represent a step toward using protein crystals as reaction vessels for complex multi-step reactions and broadening their utility as functional, solid-state materials. Our results demonstrate that morphology control and spatial patterning, which are key concepts in materials science and nanotechnology, can also be applied for engineering protein crystals.
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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
| | - Zhiyin 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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3
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Oohora K. Supramolecular assembling systems of hemoproteins using chemical modifications. J INCL PHENOM MACRO 2023. [DOI: 10.1007/s10847-023-01181-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2023]
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4
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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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5
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Lee J, Yang M, Song WJ. The expanded landscape of metalloproteins by genetic incorporation of noncanonical amino acids. B KOREAN CHEM SOC 2022. [DOI: 10.1002/bkcs.12635] [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)
- Jaehee Lee
- Department of Chemistry Seoul National University Seoul South Korea
| | - Minwoo Yang
- Department of Chemistry Seoul National University Seoul South Korea
| | - Woon Ju Song
- Department of Chemistry Seoul National University Seoul South Korea
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6
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Oranges M, Wort JL, Fukushima M, Fusco E, Ackermann K, Bode BE. Pulse Dipolar Electron Paramagnetic Resonance Spectroscopy Reveals Buffer-Modulated Cooperativity of Metal-Templated Protein Dimerization. J Phys Chem Lett 2022; 13:7847-7852. [PMID: 35976741 PMCID: PMC9421889 DOI: 10.1021/acs.jpclett.2c01719] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/10/2022] [Indexed: 05/26/2023]
Abstract
Self-assembly of protein monomers directed by metal ion coordination constitutes a promising strategy for designing supramolecular architectures complicated by the noncovalent interaction between monomers. Herein, two pulse dipolar electron paramagnetic resonance spectroscopy (PDS) techniques, pulse electron-electron double resonance and relaxation-induced dipolar modulation enhancement, were simultaneously employed to study the CuII-templated dimerization behavior of a model protein (Streptococcus sp. group G, protein G B1 domain) in both phosphate and Tris-HCl buffers. A cooperative binding model could simultaneously fit all data and demonstrate that the cooperativity of protein dimerization across α-helical double-histidine motifs in the presence of CuII is strongly modulated by the buffer, representing a platform for highly tunable buffer-switchable templated dimerization. Hence, PDS enriches the family of techniques for monitoring binding processes, supporting the development of novel strategies for bioengineering structures and stable architectures assembled by an initial metal-templated dimerization.
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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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8
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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: 100] [Impact Index Per Article: 33.3] [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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Zou Z, He L, Deng X, Wang H, Huang Z, Xue Q, Qing Z, Lei Y, Yang R, Liu J. Zn
2+
‐Coordination‐Driven RNA Assembly with Retained Integrity and Biological Functions. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202110404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Zhen Zou
- School of Chemistry and Food Engineering Hunan Provincial Key Laboratory of Cytochemistry Changsha University of Science and Technology Changsha 410114 China
| | - Libei He
- School of Chemistry and Food Engineering Hunan Provincial Key Laboratory of Cytochemistry Changsha University of Science and Technology Changsha 410114 China
| | - Xiangxi Deng
- School of Chemistry and Food Engineering Hunan Provincial Key Laboratory of Cytochemistry Changsha University of Science and Technology Changsha 410114 China
| | - Huangxiang Wang
- School of Chemistry and Food Engineering Hunan Provincial Key Laboratory of Cytochemistry Changsha University of Science and Technology Changsha 410114 China
| | - Ziyun Huang
- School of Chemistry and Food Engineering Hunan Provincial Key Laboratory of Cytochemistry Changsha University of Science and Technology Changsha 410114 China
| | - Qian Xue
- School of Chemistry and Food Engineering Hunan Provincial Key Laboratory of Cytochemistry Changsha University of Science and Technology Changsha 410114 China
| | - Zhihe Qing
- School of Chemistry and Food Engineering Hunan Provincial Key Laboratory of Cytochemistry Changsha University of Science and Technology Changsha 410114 China
| | - Yanli Lei
- School of Chemistry and Food Engineering Hunan Provincial Key Laboratory of Cytochemistry Changsha University of Science and Technology Changsha 410114 China
| | - Ronghua Yang
- School of Chemistry and Food Engineering Hunan Provincial Key Laboratory of Cytochemistry Changsha University of Science and Technology Changsha 410114 China
- Laboratory of Chemical Biology & Traditional Chinese Medicine Research Ministry of Education College of Chemistry and Chemical Engineering Hunan Normal University Changsha 410081 China
| | - Juewen Liu
- Department of Chemistry Waterloo Institute for Nanotechnology University of Waterloo Waterloo Ontario N2L 3G1 Canada
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10
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Zou Z, He L, Deng X, Wang H, Huang Z, Xue Q, Qing Z, Lei Y, Yang R, Liu J. Zn 2+ -Coordination-Driven RNA Assembly with Retained Integrity and Biological Functions. Angew Chem Int Ed Engl 2021; 60:22970-22976. [PMID: 34405498 DOI: 10.1002/anie.202110404] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Indexed: 12/29/2022]
Abstract
Metal-coordination-directed biomolecule crosslinking in nature has been used for synthesizing various biopolymers, including DNA, peptides, proteins, and polysaccharides. However, the RNA biopolymer has been avoided so far, as due to the poor stability of the RNA molecules, the formation of a biopolymer may alter the biological function of the molecules. Herein, for the first time, we report Zn2+ -driven RNA self-assembly forming spherical nanoparticles while retaining the integrity and biological function of RNA. Various functional RNAs of different compositions, shapes, and lengths from 20 to nearly 1000 nucleotides were used, highlighting the versatility of this approach. The assembled nanospheres possess a superior RNA-loading efficiency, pharmacokinetics, and bioavailability. In-vitro and in-vivo evaluation demonstrated mRNA delivery for expressing GFP proteins, and microRNA delivery to triple-negative breast cancer. This coordination-directed self-assembly behavior amplifies the horizons of RNA coordination chemistry and the application scope of RNA-based therapeutics.
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Affiliation(s)
- Zhen Zou
- School of Chemistry and Food Engineering, Hunan Provincial Key Laboratory of Cytochemistry, Changsha University of Science and Technology, Changsha, 410114, China
| | - Libei He
- School of Chemistry and Food Engineering, Hunan Provincial Key Laboratory of Cytochemistry, Changsha University of Science and Technology, Changsha, 410114, China
| | - Xiangxi Deng
- School of Chemistry and Food Engineering, Hunan Provincial Key Laboratory of Cytochemistry, Changsha University of Science and Technology, Changsha, 410114, China
| | - Huangxiang Wang
- School of Chemistry and Food Engineering, Hunan Provincial Key Laboratory of Cytochemistry, Changsha University of Science and Technology, Changsha, 410114, China
| | - Ziyun Huang
- School of Chemistry and Food Engineering, Hunan Provincial Key Laboratory of Cytochemistry, Changsha University of Science and Technology, Changsha, 410114, China
| | - Qian Xue
- School of Chemistry and Food Engineering, Hunan Provincial Key Laboratory of Cytochemistry, Changsha University of Science and Technology, Changsha, 410114, China
| | - Zhihe Qing
- School of Chemistry and Food Engineering, Hunan Provincial Key Laboratory of Cytochemistry, Changsha University of Science and Technology, Changsha, 410114, China
| | - Yanli Lei
- School of Chemistry and Food Engineering, Hunan Provincial Key Laboratory of Cytochemistry, Changsha University of Science and Technology, Changsha, 410114, China
| | - Ronghua Yang
- School of Chemistry and Food Engineering, Hunan Provincial Key Laboratory of Cytochemistry, Changsha University of Science and Technology, Changsha, 410114, China.,Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
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11
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Kim S, Yun J, Yoo H, Kim S, Kim HM, Lee HS. Metal-Mediated Protein Assembly Using a Genetically Incorporated Metal-Chelating Amino Acid. Biomacromolecules 2020; 21:5021-5028. [PMID: 33253537 DOI: 10.1021/acs.biomac.0c01194] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many natural proteins function in oligomeric forms, which are critical for their sophisticated functions. The construction of protein assemblies has great potential for biosensors, enzyme catalysis, and biomedical applications. In designing protein assemblies, a critical process is to create protein-protein interaction (PPI) networks at defined sites of a target protein. Although a few methods are available for this purpose, most of them are dependent on existing PPIs of natural proteins to some extent. In this report, a metal-chelating amino acid, 2,2'-bipyridylalanine (BPA), was genetically introduced into defined sites of a monomeric protein and used to form protein oligomers. Depending on the number of BPAs introduced into the protein and the species of metal ions (Ni2+ and Cu2+), dimers or oligomers with different oligomerization patterns were formed by complexation with a metal ion. Oligomer sizes could also be controlled by incorporating two BPAs at different locations with varied angles to the center of the protein. When three BPAs were introduced, the monomeric protein formed a large complex with Ni2+. In addition, when Cu2+ was used for complex formation with the protein containing two BPAs, a linear complex was formed. The method proposed in this report is technically simple and generally applicable to various proteins with interesting functions. Therefore, this method would be useful for the design and construction of functional protein assemblies.
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Affiliation(s)
- Sanggil Kim
- Department of Chemistry, Sogang University, 35 Baekbeomro Mapogu, Seoul 121-742, Republic of Korea
| | - Jeongwon Yun
- Graduate School of Medical Science & Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Hyunjung Yoo
- Department of Chemistry, Sogang University, 35 Baekbeomro Mapogu, Seoul 121-742, Republic of Korea
| | - Sooin Kim
- Department of Chemistry, Sogang University, 35 Baekbeomro Mapogu, Seoul 121-742, Republic of Korea
| | - Ho Min Kim
- Graduate School of Medical Science & Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.,Center for Biomolecular & Cellular Structure, Institution for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - Hyun Soo Lee
- Department of Chemistry, Sogang University, 35 Baekbeomro Mapogu, Seoul 121-742, Republic of Korea
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Abstract
As the hardest tissue formed by vertebrates, enamel represents nature's engineering masterpiece with complex organizations of fibrous apatite crystals at the nanometer scale. Supramolecular assemblies of enamel matrix proteins (EMPs) play a key role as the structural scaffolds for regulating mineral morphology during enamel development. However, to achieve maximum tissue hardness, most organic content in enamel is digested and removed at the maturation stage, and thus knowledge of a structural protein template that could guide enamel mineralization is limited at this date. Herein, by examining a gene-modified mouse that lacked enzymatic degradation of EMPs, we demonstrate the presence of protein nanoribbons as the structural scaffolds in developing enamel matrix. Using in vitro mineralization assays we showed that both recombinant and enamel-tissue-based amelogenin nanoribbons are capable of guiding fibrous apatite nanocrystal formation. In accordance with our understanding of the natural process of enamel formation, templated crystal growth was achieved by interaction of amelogenin scaffolds with acidic macromolecules that facilitate the formation of an amorphous calcium phosphate precursor which gradually transforms into oriented apatite fibers along the protein nanoribbons. Furthermore, this study elucidated that matrix metalloproteinase-20 is a critical regulator of the enamel mineralization as only a recombinant analog of a MMP20-cleavage product of amelogenin was capable of guiding apatite mineralization. This study highlights that supramolecular assembly of the scaffold protein, its enzymatic processing, and its ability to interact with acidic carrier proteins are critical steps for proper enamel development.
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13
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Learte‐Aymamí S, Rodríguez J, Vázquez ME, Mascareñas JL. Assembly of a Ternary Metallopeptide Complex at Specific DNA Sites Mediated by an AT‐Hook Adaptor. Chemistry 2020; 26:8875-8878. [DOI: 10.1002/chem.202001277] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Indexed: 12/25/2022]
Affiliation(s)
- Soraya Learte‐Aymamí
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) andDepartamento de Química OrgánicaUniversidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - Jéssica Rodríguez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) andDepartamento de Química OrgánicaUniversidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - M. Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) andDepartamento de Química OrgánicaUniversidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - José L. Mascareñas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) andDepartamento de Química OrgánicaUniversidade de Santiago de Compostela 15782 Santiago de Compostela Spain
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14
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Bowen BJ, McGarrity AR, Szeto JYA, Pudney CR, Jones DD. Switching protein metalloporphyrin binding specificity by design from iron to fluorogenic zinc. Chem Commun (Camb) 2020; 56:4308-4311. [PMID: 32186552 DOI: 10.1039/d0cc00596g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Metalloporphyrins play important roles in areas ranging from biology to nanoscience. Using computational design, we converted metalloporphyrin specificity of cytochrome b562 from iron to fluorogenic zinc. The new variant had a near total preference for zinc representing a switch in specificity, which greatly enhanced the negligible aqueous fluorescence of free ZnPP in vitro and in vivo.
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15
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Oohora K, Hirayama S, Mashima T, Hayashi T. Supramolecular dimerization of a hexameric hemoprotein via multiple pyrene-pyrene interactions. J PORPHYR PHTHALOCYA 2020. [DOI: 10.1142/s1088424619500949] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Protein assemblies are being investigated as a new-class of biomaterials. A supramolecular assembly of a mutant hexameric tyrosine coordinated hemoprotein (HTHP) modified with a pyrene derivative is described. Cysteine was first introduced as a site-specific reaction point at position V44 which is located at the bottom surface of the cylindrical structure of HTHP. [Formula: see text]-(1-pyrenyl)maleimide was then reacted with the mutant. The modification was confirmed by MALDI-TOF mass spectrometry and UV-vis absorption spectroscopy, indicating that approximately 90% cysteine residues are attached via the pyrene derivative. Size exclusion chromatography (SEC) measurements for pyrene-attached HTHP include a single peak which elutes earlier than the unmodified HTHP. Further investigation by SEC and dynamic light scattering (DLS) measurements indicate the desired size corresponding to the dimer of the hemoprotein hexamers. The multivalent effect of pyrene–pyrene interactions including hydrophobic and [Formula: see text]–[Formula: see text] stacking interactions appears to be responsible for including formation of the stable dimer of the hexamers. Interestingly, the assembly dissociates to the hexamer by removal of heme. In the case of the apo-form of pyrene-attached HTHP, the pyrene moiety appears to be incorporated into the heme pocket because the modification point is located at the adjacent residue of the Tyr45 coordinating to heme in the holo-form of HTHP. Subsequent addition of heme into the apo-form of pyrene-attached HTHP regenerates the dimer of the hexamers. The present study demonstrates a unique heme-dependent system in which HTHP is assembled to form a dimer of hexamers in the presence of heme and disassembled by removal of heme.
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Affiliation(s)
- Koji Oohora
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, 565-0871, Japan
- Frontier Research Base for Global Young Researchers, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan
| | - Shota Hirayama
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, 565-0871, Japan
| | - Tsuyoshi Mashima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, 565-0871, Japan
| | - Takashi Hayashi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, 565-0871, Japan
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16
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Diverse protein assembly driven by metal and chelating amino acids with selectivity and tunability. Nat Commun 2019; 10:5545. [PMID: 31804480 PMCID: PMC6895169 DOI: 10.1038/s41467-019-13491-w] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 11/08/2019] [Indexed: 01/01/2023] Open
Abstract
Proteins are versatile natural building blocks with highly complex and multifunctional architectures, and self-assembled protein structures have been created by the introduction of covalent, noncovalent, or metal-coordination bonding. Here, we report the robust, selective, and reversible metal coordination properties of unnatural chelating amino acids as the sufficient and dominant driving force for diverse protein self-assembly. Bipyridine-alanine is genetically incorporated into a D3 homohexamer. Depending on the position of the unnatural amino acid, 1-directional, crystalline and noncrystalline 2-directional, combinatory, and hierarchical architectures are effectively created upon the addition of metal ions. The length and shape of the structures is tunable by altering conditions related to thermodynamics and kinetics of metal-coordination and subsequent reactions. The crystalline 1-directional and 2-directional biomaterials retain their native enzymatic activities with increased thermal stability, suggesting that introducing chelating ligands provides a specific chemical basis to synthesize diverse protein-based functional materials while retaining their native structures and functions. Precise manipulation of protein self-assembly in vitro is challenging. Here, the authors developed an approach for driving metal-mediated reversible protein assembly by genetically installing a bipyridine residue into an oligomeric (D3) protein.
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17
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Covalently-assembled single-chain protein nanostructures with ultra-high stability. Nat Commun 2019; 10:3317. [PMID: 31346167 PMCID: PMC6658521 DOI: 10.1038/s41467-019-11285-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 07/02/2019] [Indexed: 12/20/2022] Open
Abstract
Protein nanostructures with precisely defined geometries have many potential applications in catalysis, sensing, signal processing, and drug delivery. While many de novo protein nanostructures have been assembled via non-covalent intramolecular and intermolecular interactions, a largely unexplored strategy is to construct nanostructures by covalently linking multiple individually folded proteins through site-specific ligations. Here, we report the synthesis of single-chain protein nanostructures with triangular and square shapes made using multiple copies of a three-helix bundle protein and split intein chemistry. Coarse-grained simulations confirm the experimentally observed flexibility of these nanostructures, which is optimized to produce triangular structures with high regularity. These single-chain nanostructures also display ultra-high thermostability, resist denaturation by chaotropes and organic solvents, and have applicability as scaffolds for assembling materials with nanometer resolution. Our results show that site-specific covalent ligation can be used to assemble individually folded proteins into single-chain nanostructures with bespoke architectures and high stabilities. De novo protein nanostructures are typically assembled via top-down approaches. Here, the authors developed a bottom-up approach, using split inteins to ligate multiple copies of a three-helix bundle to create 2D triangular and square-shaped structures with high stability.
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18
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Maniaci B, Lipper CH, Anipindi DL, Erlandsen H, Cole JL, Stec B, Huxford T, Love JJ. Design of High-Affinity Metal-Controlled Protein Dimers. Biochemistry 2019; 58:2199-2207. [DOI: 10.1021/acs.biochem.9b00055] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Brian Maniaci
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, California 92182, United States
| | - Colin H. Lipper
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, California 92182, United States
| | - Deepthi L. Anipindi
- Structural Biochemistry Laboratory, Department of Chemistry and Biochemistry, San Diego State University, San Diego, California 92182, United States
| | - Heidi Erlandsen
- Center for Open Research Resources and Equipment, University of Connecticut, Storrs, Connecticut 06269, United States
| | - James L. Cole
- Department of Molecular and Cell Biology and Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Boguslaw Stec
- Structural Biochemistry Laboratory, Department of Chemistry and Biochemistry, San Diego State University, San Diego, California 92182, United States
| | - Tom Huxford
- Structural Biochemistry Laboratory, Department of Chemistry and Biochemistry, San Diego State University, San Diego, California 92182, United States
| | - John J. Love
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, California 92182, United States
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19
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Combes S, Tran KT, Ayhan MM, Karoui H, Rockenbauer A, Tonetto A, Monnier V, Charles L, Rosas R, Viel S, Siri D, Tordo P, Clair S, Wang R, Bardelang D, Ouari O. Triangular Regulation of Cucurbit[8]uril 1:1 Complexes. J Am Chem Soc 2019; 141:5897-5907. [PMID: 30808163 DOI: 10.1021/jacs.9b00150] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Triangular shapes have inspired scientists over time and are common in nature, such as the flower petals of oxalis triangularis, the triangular faces of tetrahedrite crystals, and the icosahedron faces of virus capsids. Supramolecular chemistry has enabled the construction of triangular assemblies, many of which possess functional features. Among these structures, cucurbiturils have been used to build supramolecular triangles, and we recently reported paramagnetic cucurbit[8]uril (CB[8]) triangles, but the reasons for their formation remain unclear. Several parameters have now been identified to explain their formation. At first sight, the radical nature of the guest was of prime importance in obtaining the triangles, and we focused on extending this concept to biradicals to get supramolecular hexaradicals. Two sodium ions were systematically observed by ESI-MS in trimer structures, and the presence of Na+ triggered or strengthened the triangulation of CB[8]/guest 1:1 complexes in solution. X-ray crystallography and molecular modeling have allowed the proposal of two plausible sites of residence for the two sodium cations. We then found that a diamagnetic guest with an H-bond acceptor function is equally good at forming CB[8] triangles. Hence, a guest molecule containing a ketone function has been precisely triangulated thanks to CB[8] and sodium cations as determined by DOSY-NMR and DLS. A binding constant for the triangulation of 1:1 to 3:3 complexes is proposed. This concept has finally been extended to the triangulation of ditopic guests toward network formation by the reticulation of CB[8] triangles using dinitroxide biradicals.
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Affiliation(s)
- Sébastien Combes
- Aix Marseille Univ , CNRS, ICR , Marseille , France.,Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes , Aix Marseille Univ, UM105 , 13009 Marseille , France
| | | | - Mehmet Menaf Ayhan
- Aix Marseille Univ , CNRS, ICR , Marseille , France.,Department of Chemistry , Gebze Technical University , P.K.141 , 41400 Gebze , Kocaeli , Turkey
| | - Hakim Karoui
- Aix Marseille Univ , CNRS, ICR , Marseille , France
| | - Antal Rockenbauer
- Institute of Materials and Environmental Chemistry , Hungarian Academy of Sciences , P.O. Box. 286, 1519 Budapest , Hungary.,Department of Physics , Budapest University of Technology and Economics , 1111 Budapest , Hungary
| | - Alain Tonetto
- Aix Marseille Univ , CNRS, Centrale Marseille, FSCM (FR1739), PRATIM , F-13397 Marseille , France
| | - Valérie Monnier
- Aix Marseille Univ , CNRS, Centrale Marseille, FSCM, Spectropole , Marseille , France
| | | | - Roselyne Rosas
- Aix Marseille Univ , CNRS, Centrale Marseille, FSCM, Spectropole , Marseille , France
| | - Stéphane Viel
- Aix Marseille Univ , CNRS, ICR , Marseille , France.,Institut Universitaire de France , F-75005 Paris , France
| | - Didier Siri
- Aix Marseille Univ , CNRS, ICR , Marseille , France
| | - Paul Tordo
- Aix Marseille Univ , CNRS, ICR , Marseille , France
| | - Sylvain Clair
- Aix Marseille Univ, University of Toulon , CNRS, IM2NP, Marseille , France
| | - Ruibing Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences , University of Macau , Taipa , Macau , China
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20
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Oohora K, Kajihara R, Fujimaki N, Uchihashi T, Hayashi T. A ring-shaped hemoprotein trimer thermodynamically controlled by the supramolecular heme-heme pocket interaction. Chem Commun (Camb) 2019; 55:1544-1547. [PMID: 30565588 DOI: 10.1039/c8cc09314h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Engineered cytochrome b562, a small hemoprotein, with an externally-attached heme moiety via a moderately long linker at a suitable position predominantly forms a thermodynamically stable ring-shaped trimer in dilute solution. In an equilibrium between supramolecular polymerization and depolymerization, the ring-shaped trimer is kinetically trapped even in a concentrated solution.
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Affiliation(s)
- Koji Oohora
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, 565-0871, Japan.
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21
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Kuan SL, Bergamini FRG, Weil T. Functional protein nanostructures: a chemical toolbox. Chem Soc Rev 2018; 47:9069-9105. [PMID: 30452046 PMCID: PMC6289173 DOI: 10.1039/c8cs00590g] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Indexed: 01/08/2023]
Abstract
Nature has evolved an optimal synthetic factory in the form of translational and posttranslational processes by which millions of proteins with defined primary sequences and 3D structures can be built. Nature's toolkit gives rise to protein building blocks, which dictates their spatial arrangement to form functional protein nanostructures that serve a myriad of functions in cells, ranging from biocatalysis, formation of structural networks, and regulation of biochemical processes, to sensing. With the advent of chemical tools for site-selective protein modifications and recombinant engineering, there is a rapid development to develop and apply synthetic methods for creating structurally defined, functional protein nanostructures for a broad range of applications in the fields of catalysis, materials and biomedical sciences. In this review, design principles and structural features for achieving and characterizing functional protein nanostructures by synthetic approaches are summarized. The synthetic customization of protein building blocks, the design and introduction of recognition units and linkers and subsequent assembly into structurally defined protein architectures are discussed herein. Key examples of these supramolecular protein nanostructures, their unique functions and resultant impact for biomedical applications are highlighted.
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Affiliation(s)
- Seah Ling Kuan
- Max-Planck Institute for Polymer Research
,
Ackermannweg 10
, 55128 Mainz
, Germany
.
;
- Institute of Inorganic Chemistry I – Ulm University
,
Albert-Einstein-Allee 11
, 89081 Ulm
, Germany
| | - Fernando R. G. Bergamini
- Institute of Chemistry
, Federal University of Uberlândia – UFU
,
38400-902 Uberlândia
, MG
, Brazil
| | - Tanja Weil
- Max-Planck Institute for Polymer Research
,
Ackermannweg 10
, 55128 Mainz
, Germany
.
;
- Institute of Inorganic Chemistry I – Ulm University
,
Albert-Einstein-Allee 11
, 89081 Ulm
, Germany
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22
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Taylor LLK, Riddell IA, Smulders MMJ. Selbstorganisation von funktionellen diskreten dreidimensionalen Architekturen in Wasser. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806297] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Lauren L. K. Taylor
- School of Chemistry; University of Manchester; Oxford Road M13 9PL Großbritannien
| | - Imogen A. Riddell
- School of Chemistry; University of Manchester; Oxford Road M13 9PL Großbritannien
| | - Maarten M. J. Smulders
- Laboratory of Organic Chemistry; Wageningen University, P.O. Box 8026; 6700EG Wageningen Niederlande
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23
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Taylor LLK, Riddell IA, Smulders MMJ. Self-Assembly of Functional Discrete Three-Dimensional Architectures in Water. Angew Chem Int Ed Engl 2018; 58:1280-1307. [DOI: 10.1002/anie.201806297] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Indexed: 01/01/2023]
Affiliation(s)
| | - Imogen A. Riddell
- School of Chemistry; University of Manchester; Oxford Road M13 9PL UK
| | - Maarten M. J. Smulders
- Laboratory of Organic Chemistry; Wageningen University, P.O. Box 8026; 6700EG Wageningen The Netherlands
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24
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Hecht MH, Zarzhitsky S, Karas C, Chari S. Are natural proteins special? Can we do that? Curr Opin Struct Biol 2018; 48:124-132. [DOI: 10.1016/j.sbi.2017.11.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 11/29/2017] [Indexed: 12/23/2022]
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25
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Yang G, Wu L, Chen G, Jiang M. Precise protein assembly of array structures. Chem Commun (Camb) 2018; 52:10595-605. [PMID: 27384233 DOI: 10.1039/c6cc04190f] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The assembly of proteins into various nano-objects with regular and periodic microstructures, i.e. protein arrays, is a fast-growing field in materials science. Due to the structural complexity of proteins, reports in this field are still quite limited. In this review, we summarize the recent developments in protein array construction by different driving forces, including electrostatic interactions, metal-ligand interactions, molecular recognition and protein-protein interactions. In line with our particular interest, assemblies driven by molecular recognition are particularly explored. Finally, functionalities of the obtained protein arrays are briefly discussed.
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Affiliation(s)
- Guang Yang
- State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, China.
| | - Libin Wu
- State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, China.
| | - Guosong Chen
- State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, China.
| | - Ming Jiang
- State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, China.
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26
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Learte-Aymamí S, Curado N, Rodríguez J, Vázquez ME, Mascareñas JL. Metal-Dependent DNA Recognition and Cell Internalization of Designed, Basic Peptides. J Am Chem Soc 2017; 139:16188-16193. [PMID: 29056048 PMCID: PMC5741177 DOI: 10.1021/jacs.7b07422] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Indexed: 12/18/2022]
Abstract
A fragment of the DNA basic region (br) of the GCN4 bZIP transcription factor has been modified to include two His residues at designed i and i+4 positions of its N-terminus. The resulting monomeric peptide (brHis2) does not bind to its consensus target DNA site (5'-GTCAT-3'). However, addition of Pd(en)Cl2 (en, ethylenediamine) promotes a high-affinity interaction with exquisite selectivity for this sequence. The peptide-DNA complex is disassembled by addition of a slight excess of a palladium chelator, and the interaction can be reversibly switched multiple times by playing with controlled amounts of either the metal complex or the chelator. Importantly, while the peptide brHis2 fails to translocate across cell membranes on its own, addition of the palladium reagent induces an efficient cell internalization of this peptide. In short, we report (1) a designed, short peptide that displays highly selective, major groove DNA binding, (2) a reversible, metal-dependent DNA interaction, and (3) a metal-promoted cell internalization of this basic peptide.
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Affiliation(s)
- Soraya Learte-Aymamí
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS)
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Natalia Curado
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS)
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Jéssica Rodríguez
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS)
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - M. Eugenio Vázquez
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS)
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - José L. Mascareñas
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS)
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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27
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Tian Y, Zhang HV, Kiick KL, Saven JG, Pochan DJ. Transition from disordered aggregates to ordered lattices: kinetic control of the assembly of a computationally designed peptide. Org Biomol Chem 2017; 15:6109-6118. [PMID: 28639674 PMCID: PMC8783983 DOI: 10.1039/c7ob01197k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2023]
Abstract
Natural biomolecular self-assembly typically occurs under a narrow range of solution conditions, and the design of sequences that can form prescribed structures under a range of such conditions would be valuable in the bottom-up assembly of predetermined nanostructures. We present a computationally designed peptide that robustly self-assembles into regular arrays under a wide range of solution pH and temperature conditions. Controling the solution conditions provides the opportunity to exploit a simple and reproducible approach for altering the pathway of peptide solution self-assembly. The computationally designed peptide forms a homotetrameric coiled-coil bundle that further self-assembles into 2-D plate structures with well-defined inter-bundle symmetry. Herein, we present how modulation of solution conditions, such as pH and temperature, can be used to control the kinetics of the inter-bundle assembly and manipulate the final morphology. Changes in solution pH primarily influence the inter-bundle assembly by affecting the charged state of ionizable residues on the bundle exterior while leaving the homotetrameric coiled-coil structure intact. At low pH, repulsive interactions prevent 2-D lattice nanostructure formation. Near the estimated isoelectric point of the peptide, bundle aggregation is rapid and yields disordered products, which subsequently transform into ordered nanostructures over days to weeks. At elevated temperatures (T = 40 °C or 50 °C), the formation of disordered, kinetically-trapped products largely can be eliminated, allowing the system to quickly assemble into plate-like nanostructured lattices. Moreover, subtle changes in pH and in the peptide charge state have a significant influence on the thickness of formed plates and on the hierarchical manner in which plates fuse into larger material structures with observable grain boundaries. These findings confirm the ability to finely tune the peptide assembly process to achieve a range of engineered structures with one simple 29-residue peptide building block.
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Affiliation(s)
- Yu Tian
- Materials Science and Engineering Department, University of Delaware, Newark, Delaware 19716, USA.
| | - Huixi Violet Zhang
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | - Kristi L Kiick
- Materials Science and Engineering Department, University of Delaware, Newark, Delaware 19716, USA.
| | - Jeffery G Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | - Darrin J Pochan
- Materials Science and Engineering Department, University of Delaware, Newark, Delaware 19716, USA.
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28
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Repurposing proteins for new bioinorganic functions. Essays Biochem 2017; 61:245-258. [DOI: 10.1042/ebc20160068] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/17/2017] [Accepted: 01/23/2017] [Indexed: 02/06/2023]
Abstract
Inspired by the remarkable sophistication and complexity of natural metalloproteins, the field of protein design and engineering has traditionally sought to understand and recapitulate the design principles that underlie the interplay between metals and protein scaffolds. Yet, some recent efforts in the field demonstrate that it is possible to create new metalloproteins with structural, functional and physico-chemical properties that transcend evolutionary boundaries. This essay aims to highlight some of these efforts and draw attention to the ever-expanding scope of bioinorganic chemistry and its new connections to synthetic biology, biotechnology, supramolecular chemistry and materials engineering.
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29
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30
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Jeong WH, Lee H, Song DH, Eom JH, Kim SC, Lee HS, Lee H, Lee JO. Connecting two proteins using a fusion alpha helix stabilized by a chemical cross linker. Nat Commun 2016; 7:11031. [PMID: 26980593 PMCID: PMC4799363 DOI: 10.1038/ncomms11031] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 02/15/2016] [Indexed: 11/23/2022] Open
Abstract
Building a sophisticated protein nano-assembly requires a method for linking protein components in a predictable and stable structure. Most of the cross linkers available have flexible spacers. Because of this, the linked hybrids have significant structural flexibility and the relative structure between their two components is largely unpredictable. Here we describe a method of connecting two proteins via a ‘fusion α helix' formed by joining two pre-existing helices into a single extended helix. Because simple ligation of two helices does not guarantee the formation of a continuous helix, we used EY-CBS, a synthetic cross linker that has been shown to react selectively with cysteines in α-helices, to stabilize the connecting helix. Formation and stabilization of the fusion helix was confirmed by determining the crystal structures of the fusion proteins with and without bound EY-CBS. Our method should be widely applicable for linking protein building blocks to generate predictable structures. Linking protein components in a controlled manner is crucial for assembling protein nanostructures with pre-determined architecture. Here, the authors use a chemical cross-linker to fuse the terminal helices of two proteins into a single one, forcing the protein domains in a specific orientation.
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Affiliation(s)
| | - Haerim Lee
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | | | - Jae-Hoon Eom
- Department of Chemistry, KAIST, Daejeon 34141, Korea
| | - Sun Chang Kim
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Hee-Seung Lee
- Department of Chemistry, KAIST, Daejeon 34141, Korea
| | - Hayyoung Lee
- Institute of Biotechnology, Chungnam National University, Daejeon 34134, Korea
| | - Jie-Oh Lee
- Department of Chemistry, KAIST, Daejeon 34141, Korea
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31
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Qiao SP, Lang C, Wang RD, Li XM, Yan TF, Pan TZ, Zhao LL, Fan XT, Zhang X, Hou CX, Luo Q, Xu JY, Liu JQ. Metal induced self-assembly of designed V-shape protein into 2D wavy supramolecular nanostructure. NANOSCALE 2016; 8:333-341. [PMID: 26612683 DOI: 10.1039/c5nr06378g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
In order to understand and imitate the more complex bio-processes and fascinating functions in nature, protein self-assembly has been studied and has attracted more and more interest in recent years. Artificial self-assemblies of proteins have been constructed through many strategies. However, the design of complicated protein self-assemblies utilizing the special profile of building blocks remains a challenge. We herein report linear and 2D nanostructures constructed from a V shape SMAC protein and induced by metal coordination. Zigzag nanowires and wavy 2D nanostructures have been demonstrated by AFM and TEM. The zigzag nanowires can translate to a 2D nanostructure with an excess of metal ions, which reveals the step by step assembly process. Fluorescence and UV/Vis spectra have also been obtained to further study the mechanism and process of self-assembly. Upon the protein nanostructure, fluorescence resonance energy transfer (FRET) could also be detected using fluorescein modified proteins as building blocks. This article provides an approach for designing and controlling self-assembled protein nanostructures with a distinctive topological morphology.
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Affiliation(s)
- S P Qiao
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China.
| | - C Lang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China.
| | - R D Wang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China.
| | - X M Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China.
| | - T F Yan
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China.
| | - T Z Pan
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China.
| | - L L Zhao
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China.
| | - X T Fan
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China.
| | - X Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China.
| | - C X Hou
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China.
| | - Q Luo
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China.
| | - J Y Xu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China.
| | - J Q Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China.
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32
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Miyamoto T, Kuribayashi M, Nagao S, Shomura Y, Higuchi Y, Hirota S. Domain-swapped cytochrome cb562 dimer and its nanocage encapsulating a Zn-SO 4 cluster in the internal cavity. Chem Sci 2015; 6:7336-7342. [PMID: 28791095 PMCID: PMC5519777 DOI: 10.1039/c5sc02428e] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 09/22/2015] [Indexed: 01/01/2023] Open
Abstract
Three domain-swapped cytochrome cb562 dimers formed a unique cage structure with a Zn–SO4 cluster inside the cavity.
Protein nanostructures have been gaining in interest, along with developments in new methods for construction of novel nanostructures. We have previously shown that c-type cytochromes and myoglobin form oligomers by domain swapping. Herein, we show that a four-helix bundle protein cyt cb562, with the cyt b562 heme attached to the protein moiety by two Cys residues insertion, forms a domain-swapped dimer. Dimeric cyt cb562 did not dissociate to monomers at 4 °C, whereas dimeric cyt b562 dissociated under the same conditions, showing that heme attachment to the protein moiety stabilizes the domain-swapped structure. According to X-ray crystallographic analysis of dimeric cyt cb562, the two helices in the N-terminal region of one protomer interacted with the other two helices in the C-terminal region of the other protomer, where Lys51–Asp54 served as a hinge loop. The heme coordination structure of the dimer was similar to that of the monomer. In the crystal, three domain-swapped cyt cb562 dimers formed a unique cage structure with a Zn–SO4 cluster inside the cavity. The Zn–SO4 cluster consisted of fifteen Zn2+ and seven SO42– ions, whereas six additional Zn2+ ions were detected inside the cavity. The cage structure was stabilized by coordination of the amino acid side chains of the dimers to the Zn2+ ions and connection of two four-helix bundle units through the conformation-adjustable hinge loop. These results show that domain swapping can be applied in the construction of unique protein nanostructures.
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Affiliation(s)
- Takaaki Miyamoto
- Graduate School of Materials Science , Nara Institute of Science and Technology , 8916-5 Takayama, Ikoma , Nara 630-0192 , Japan .
| | - Mai Kuribayashi
- Graduate School of Materials Science , Nara Institute of Science and Technology , 8916-5 Takayama, Ikoma , Nara 630-0192 , Japan .
| | - Satoshi Nagao
- Graduate School of Materials Science , Nara Institute of Science and Technology , 8916-5 Takayama, Ikoma , Nara 630-0192 , Japan .
| | - Yasuhito Shomura
- Graduate School of Science and Engineering , Ibaraki University , 4-12-1, Nakanarusawa , Hitachi , Ibaraki 316-8511 , Japan
| | - Yoshiki Higuchi
- Department of Life Science , Graduate School of Life Science , University of Hyogo , 3-2-1 Koto, Kamigori-cho, Ako-gun , Hyogo 678-1297 , Japan.,RIKEN SPring-8 Center , 1-1-1 Koto, Sayo-cho, Sayo-gun , Hyogo 679-5148 , Japan
| | - Shun Hirota
- Graduate School of Materials Science , Nara Institute of Science and Technology , 8916-5 Takayama, Ikoma , Nara 630-0192 , Japan .
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33
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Sontz PA, Bailey JB, Ahn S, Tezcan FA. A Metal Organic Framework with Spherical Protein Nodes: Rational Chemical Design of 3D Protein Crystals. J Am Chem Soc 2015; 137:11598-601. [PMID: 26305584 DOI: 10.1021/jacs.5b07463] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We describe here the construction of a three-dimensional, porous, crystalline framework formed by spherical protein nodes that assemble into a prescribed lattice arrangement through metal-organic linker-directed interactions. The octahedral iron storage enzyme, ferritin, was engineered in its C3 symmetric pores with tripodal Zn coordination sites. Dynamic light scattering and crystallographic studies established that this Zn-ferritin construct could robustly self-assemble into the desired bcc-type crystals upon coordination of a ditopic linker bearing hydroxamic acid functional groups. This system represents the first example of a ternary protein-metal-organic crystalline framework whose formation is fully dependent on each of its three components.
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Affiliation(s)
- Pamela A Sontz
- Department of Chemistry and Biochemistry, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Jake B Bailey
- Department of Chemistry and Biochemistry, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Sunhyung Ahn
- 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
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34
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Brodin JD, Smith SJ, Carr JR, Tezcan FA. Designed, Helical Protein Nanotubes with Variable Diameters from a Single Building Block. J Am Chem Soc 2015; 137:10468-71. [PMID: 26256820 PMCID: PMC6855837 DOI: 10.1021/jacs.5b05755] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Due to their structural and mechanical properties, 1D helical protein assemblies represent highly attractive design targets for biomolecular engineering and protein design. Here we present a designed, tetrameric protein building block, Zn8R4, which assembles via Zn coordination interactions into a series of crystalline, helical nanotubes whose widths can be controlled by solution conditions. X-ray crystallography and transmission electron microscopy (TEM) measurements indicate that all classes of protein nanotubes are constructed through the same 2D arrangement of Zn8R4 tetramers held together by Zn coordination. The mechanical properties of these nanotubes are correlated with their widths. All Zn8R4 nanotubes are found to be highly flexible despite possessing crystalline order, owing to their minimal interbuilding-block interactions mediated solely by metal coordination.
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Affiliation(s)
| | | | - Jessica R. Carr
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0356
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0356
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35
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Tabbasum K, Rao CP. Zn2+ and Cu2+ induced nanosheets and nanotubes in six different lectins by TEM. RSC Adv 2015. [DOI: 10.1039/c5ra00481k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Zn2+ and Cu2+ induced supramolecular assemblies of lectins resulted in the formation of nanosheets in case of Zn2+ and both nanosheets and nanotubes in case of Cu2+ having different features characteristic of the lectin and the metal ion present. These nanostructures are unprecedented and would lead to major advances in nanobiomaterial science.
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Affiliation(s)
- Khatija Tabbasum
- Bioinorganic Laboratory
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai 400 076
- India
| | - Chebrolu Pulla Rao
- Bioinorganic Laboratory
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai 400 076
- India
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36
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Sánchez MI, Mosquera J, Vázquez ME, Mascareñas JL. Reversible Supramolecular Assembly at Specific DNA Sites: Nickel-Promoted Bivalent DNA Binding with Designed Peptide and Bipyridyl-Bis(benzamidine) Components. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405726] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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37
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Sánchez MI, Mosquera J, Vázquez ME, Mascareñas JL. Reversible Supramolecular Assembly at Specific DNA Sites: Nickel-Promoted Bivalent DNA Binding with Designed Peptide and Bipyridyl-Bis(benzamidine) Components. Angew Chem Int Ed Engl 2014; 53:9917-21. [DOI: 10.1002/anie.201405726] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Indexed: 01/20/2023]
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38
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Luo Q, Dong Z, Hou C, Liu J. Protein-based supramolecular polymers: progress and prospect. Chem Commun (Camb) 2014; 50:9997-10007. [DOI: 10.1039/c4cc03143a] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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39
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Oohora K, Hayashi T. Hemoprotein-based supramolecular assembling systems. Curr Opin Chem Biol 2014; 19:154-61. [PMID: 24658057 DOI: 10.1016/j.cbpa.2014.02.014] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 02/11/2014] [Accepted: 02/13/2014] [Indexed: 12/11/2022]
Abstract
Hemoproteins are metalloproteins which include iron porphyrin as a cofactor. These proteins have received much attention as promising building blocks for development of new types of biomaterials. This review summarizes recent efforts in the rational design of supramolecular hemoprotein assemblies using myoglobin, horseradish peroxidase, cytochrome b562 and cytochrome c as a monomer unit. The processes of coordination bond-mediated assembly or domain swapping-mediated assembly provide defined oligomers, while hemoprotein reconstitution with synthetic heme derivatives provides submicrometer-sized structures such as fibrils, vesicles/micelles, or networks. Interestingly, several of these assembled structures maintain the intrinsic functions of monomer units. The chemical and/or biological strategies described in this review will lead to the creation of unique hemoprotein-based functional biomaterials.
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Affiliation(s)
- Koji Oohora
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University Suita, 565-0871, Japan
| | - Takashi Hayashi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University Suita, 565-0871, Japan.
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40
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Jensen KJ. Leonidas Zervas award lecture:
Abiotic ligands for new quaternary architectures of peptides and proteins. J Pept Sci 2013; 19:537-44. [DOI: 10.1002/psc.2545] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 07/12/2013] [Accepted: 07/11/2013] [Indexed: 02/06/2023]
Affiliation(s)
- Knud J. Jensen
- Department of Chemistry; University of Copenhagen; Thorvaldsensvej 40 DK-1871 Frederiksberg Denmark
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41
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Bai Y, Luo Q, Zhang W, Miao L, Xu J, Li H, Liu J. Highly Ordered Protein Nanorings Designed by Accurate Control of Glutathione S-Transferase Self-Assembly. J Am Chem Soc 2013; 135:10966-9. [DOI: 10.1021/ja405519s] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yushi Bai
- State Key Laboratory of Supramolecular
Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Quan Luo
- State Key Laboratory of Supramolecular
Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Wei Zhang
- State Key Laboratory of Supramolecular
Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Lu Miao
- State Key Laboratory of Supramolecular
Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Jiayun Xu
- State Key Laboratory of Supramolecular
Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Hongbin Li
- Department of Chemistry, University of British Columbia, Vancouver, British
Columbia, Canada V6T 1Z1
| | - Junqiu Liu
- State Key Laboratory of Supramolecular
Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
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42
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Pattammattel A, Deshapriya IK, Chowdhury R, Kumar CV. Metal-enzyme frameworks: role of metal ions in promoting enzyme self-assembly on α-zirconium(IV) phosphate nanoplates. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:2971-2981. [PMID: 23373444 DOI: 10.1021/la304979s] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Previously, an ion-coupled protein binding (ICPB) model was proposed to explain the thermodynamics of protein binding to negatively charged α-Zr(IV) phosphate (α-ZrP). This model is tested here using glucose oxidase (GO) and met-hemoglobin (Hb) and several cations (Zr(IV), Cr(III), Au(III), Al(III), Ca(II), Mg(II), Zn(II), Ni(II), Na(I), and H(I)). The binding constant of GO with α-ZrP was increased ∼380-fold by the addition of either 1 mM Zr(IV) or 1 mM Ca(II), and affinities followed the trend Zr(IV) ≃ Ca(II) > Cr(III) > Mg(II) ≫ H(I) > Na(I). Binding studies could not be conducted with Au(III), Al(III), Zn(II), Cu(II), and Ni(II), as these precipitated both proteins. Zr(IV) increased Hb binding constant to α-ZrP by 43-fold, and affinity enhancements followed the trend Zr(IV) > H(I) > Mg(II) > Na(I) > Ca(II) > Cr(III). Zeta potential studies clearly showed metal ion binding to α-ZrP and affinities followed the trend, Zr(IV) ≫ Cr(III) > Zn(II) > Ni(II) > Mg(II) > Ca(II) > Au(III) > Na(I) > H(I). Electron microscopy showed highly ordered structures of protein/metal/α-ZrP intercalates on micrometer length scales, and protein intercalation was also confirmed by powder X-ray diffraction. Specific activities of GO/Zr(IV)/α-ZrP and Hb/Zr(IV)/α-ZrP ternary complexes were 2.0 × 10(-3) and 6.5 × 10(-4) M(-1) s(-1), respectively. While activities of all GO/cation/α-ZrP samples were comparable, those of Hb/cation/α-ZrP followed the trend Mg(II) > Na(I) > H(I) > Cr(III) > Ca(II) ≃ Zr(IV). Metal ions enhanced protein binding by orders of magnitude, as predicted by the ICPB model, and binding enhancements depended on charge as well as the phosphophilicity/oxophilicity of the cation.
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Affiliation(s)
- Ajith Pattammattel
- Department of Chemistry, University of Connecticut, U-3060, Storrs, Connecticut 06269, USA
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43
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Geotti-Bianchini P, Darbre T, Reymond JL. pH-tuned metal coordination and peroxidase activity of a peptide dendrimer enzyme model with a Fe(II)bipyridine at its core. Org Biomol Chem 2012; 11:344-52. [PMID: 23172354 DOI: 10.1039/c2ob26551f] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peptide dendrimer BP1 was obtained by double thioether bond formation between 5,5'-bis(bromomethyl)-2,2'-bipyridine and two equivalents of peptide dendrimer N1 (Ac-Glu-Ser)(8)(Dap-Glu-Ala)(4)(Dap-Amb-Tyr)(2)Dap-Cys-Asp-NH(2) (Dap = branching 2,3-diaminopropanoic acid, Amb = 4-aminomethyl-benzoic acid). At pH 4.0 BP1 bound Fe(ii) to form the expected tris-coordinated complex [Fe(II)(BP1)(3)] (K(f) = 2.1 × 10(15) M(-3)). At pH 6.5 a monocoordinated complex [Fe(II)(BP1)] was formed instead (K(f) = 2.1 × 10(5) M(-1)) due to electrostatic repulsion between the polyanionic dendrimer branches, as confirmed by the behavior of three analogues where glutamates were partially or completely replaced by neutral glutamines or positive lysines. [Fe(II)(BP1)] catalyzed the oxidation of o-phenylenediamine with H(2)O(2) with enzyme-like kinetics (k(cat) = 1.0 min(-1), K(M) = 1.5 mM, k(cat)/k(uncat) = 90 000) and multiple turnover, while Fe(2+) or [Fe(bipy)(3)](2+) were inactive. The labile coordination positions allowing coordination to H(2)O(2) and to the substrate are likely responsible for the enhanced peroxidase activity of the metallopeptide dendrimer.
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Affiliation(s)
- Piero Geotti-Bianchini
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, CH-3012 Berne, Switzerland
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44
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Shaw WJ. The Outer-Coordination Sphere: Incorporating Amino Acids and Peptides as Ligands for Homogeneous Catalysts to Mimic Enzyme Function. CATALYSIS REVIEWS-SCIENCE AND ENGINEERING 2012. [DOI: 10.1080/01614940.2012.679453] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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45
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Zhang W, Luo Q, Miao L, Hou C, Bai Y, Dong Z, Xu J, Liu J. Self-assembly of glutathione S-transferase into nanowires. NANOSCALE 2012; 4:5847-5851. [PMID: 22907071 DOI: 10.1039/c2nr31244a] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
This study presents the Ni-ion-directed self-assembly of a C(2)-symmetric homodimeric enzyme into nanowires. A genetically introduced His-tag arm stretches out of the central structure of a C(2)-symmetric homodimer of glutathione S-transferase, which is used as a linker to recruit a second building block through interprotein metal coordination, forming self-assembled one-dimensional nanostructures with excellent enzymatic activity.
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Affiliation(s)
- Wei Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Road, Changchun 130012, China
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46
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Lai YT, King NP, Yeates TO. Principles for designing ordered protein assemblies. Trends Cell Biol 2012; 22:653-61. [PMID: 22975357 DOI: 10.1016/j.tcb.2012.08.004] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 08/10/2012] [Accepted: 08/12/2012] [Indexed: 11/18/2022]
Abstract
In nature, many proteins have evolved to have self-complementary shapes. This drives them to assemble into supramolecular structures, sometimes of great complexity, and often carrying out sophisticated cellular functions. Designing novel proteins that can self-assemble into similarly complex structures is a longstanding goal in bioengineering. New ideas, combined with continually improving computer algorithms, are making it possible to advance on that goal, bringing wide-ranging applications in synthetic biology within reach. Prospective applications range from vaccine design to molecular delivery to bioactive materials. Recent strategies and examples of successfully designed protein cages, layers, and crystals are reviewed.
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Affiliation(s)
- Yen-Ting Lai
- Biomedical Engineering Interdepartmental Degree Program, University of California, Los Angeles, CA, USA
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47
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48
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Uchida M, Morris DS, Kang S, Jolley CC, Lucon J, Liepold LO, LaFrance B, Prevelige PE, Douglas T. Site-directed coordination chemistry with P22 virus-like particles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:1998-2006. [PMID: 22166052 DOI: 10.1021/la203866c] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Protein cage nanoparticles (PCNs) are attractive platforms for developing functional nanomaterials using biomimetic approaches for functionalization and cargo encapsulation. Many strategies have been employed to direct the loading of molecular cargos inside a wide range of PCN architectures. Here we demonstrate the exploitation of a metal-ligand coordination bond with respect to the direct packing of guest molecules on the interior interface of a virus-like PCN derived from Salmonella typhimurium bacteriophage P22. The incorporation of these guest species was assessed using mass spectrometry, multiangle laser light scattering, and analytical ultracentrifugation. In addition to small-molecule encapsulation, this approach was also effective for the directed synthesis of a large macromolecular coordination polymer packed inside of the P22 capsid and initiated on the interior surface. A wide range of metals and ligands with different thermodynamic affinities and kinetic stabilities are potentially available for this approach, highlighting the potential for metal-ligand coordination chemistry to direct the site-specific incorporation of cargo molecules for a variety of applications.
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Affiliation(s)
- Masaki Uchida
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
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49
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Garner DK, Liang L, Barrios DA, Zhang JL, Lu Y. Covalent Anchor Positions Play an Important Role in Tuning Catalytic Properties of a Rationally Designed MnSalen-containing Metalloenzyme. ACS Catal 2011; 1:1083-1089. [PMID: 22013554 PMCID: PMC3194002 DOI: 10.1021/cs200258e] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Two questions important to the success in metalloenzyme design are how to attach or anchor metal cofactors inside protein scaffolds, and in what way such positioning affects enzymatic properties. We have previously reported a dual anchoring method to position a nonnative cofactor, MnSalen (1), inside the heme cavity of apo sperm whale myoglobin (Mb) and showed that the dual anchoring can increase both the activity and enantioselectivity over the single anchoring methods, making this artificial enzyme an ideal system to address the above questions. Here we report systematic investigations of the effect of different covalent attachment or anchoring positions on reactivity and selectivity of sulfoxidation by the MnSalen-containing Mb enzymes. We have found that changing the left anchor from Y103C to T39C has an almost identical effect of increasing rate by 1.8-fold and increasing selectivity by +14% for S, whether the right anchor is L72C or S108C. At the same time, regardless of the identity of the left anchor, changing the right anchor from S108C to L72C increases rate by 4-fold and selectivity by +66%. The right anchor site was observed to have a greater influence than the left anchor site on the reactivity and selectivity in sulfoxidation of a wide scope of other ortho-, meta- and para- substituted substrates. The 1•Mb(T39C/L72C) showed the highest reactivity (TON up to 2.31 min(-1)) and selectivity (ee% up to 83%) among the different anchoring positions examined. Molecular dynamic simulations indicate that these changes in reactivity and selectivity may be due to the steric effects of the linker arms inside the protein cavity. These results indicate that small differences in the anchor positions can result in significant changes in reactivity and enantioselectivity, probably through steric interactions with substrates when they enter the substrate-binding pocket, and that the effects of right and left anchor positions are independent and additive in nature. The finding that the anchoring arms can influence both the positioning of the cofactor and steric control of substrate entrance will help design better functional metalloenzymes with predicted catalytic activity and selectivity.
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Affiliation(s)
- Dewain K. Garner
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Lei Liang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - David A. Barrios
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jun-Long Zhang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Yi Lu
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
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50
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Bogdan ND, Matache M, Roiban GD, Dobrotă C, Meier VM, Funeriu DP. Metal Ion Mediated Self-Assembly Directed Formation of Protein Arrays. Biomacromolecules 2011; 12:3400-5. [DOI: 10.1021/bm200833k] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Niculina D. Bogdan
- Department of Chemistry, Marie
Curie Excellence Team, Technical University München, 4 Lichtenberg str., 85748 Garching, Germany
| | - Mihaela Matache
- Department of Chemistry, University of Bucharest, 90-92 Panduri str., 050663
Bucharest, Romania
| | - Gheorghe-Doru Roiban
- Department of Chemistry, Marie
Curie Excellence Team, Technical University München, 4 Lichtenberg str., 85748 Garching, Germany
| | - Cristian Dobrotă
- Department of Chemistry, Marie
Curie Excellence Team, Technical University München, 4 Lichtenberg str., 85748 Garching, Germany
| | - Veronika M. Meier
- Department of Chemistry, Marie
Curie Excellence Team, Technical University München, 4 Lichtenberg str., 85748 Garching, Germany
| | - Daniel P. Funeriu
- Department of Chemistry, Marie
Curie Excellence Team, Technical University München, 4 Lichtenberg str., 85748 Garching, Germany
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