1
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Maity B, Shoji M, Luo F, Nakane T, Abe S, Owada S, Kang J, Tono K, Tanaka R, Pham TT, Kojima M, Hishikawa Y, Tanaka J, Tian J, Nagama M, Suzuki T, Noya H, Nakasuji Y, Asanuma A, Yao X, Iwata S, Shigeta Y, Nango E, Ueno T. Real-time observation of a metal complex-driven reaction intermediate using a porous protein crystal and serial femtosecond crystallography. Nat Commun 2024; 15:5518. [PMID: 38951539 PMCID: PMC11217357 DOI: 10.1038/s41467-024-49814-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 06/14/2024] [Indexed: 07/03/2024] Open
Abstract
Determining short-lived intermediate structures in chemical reactions is challenging. Although ultrafast spectroscopic methods can detect the formation of transient intermediates, real-space structures cannot be determined directly from such studies. Time-resolved serial femtosecond crystallography (TR-SFX) has recently proven to be a powerful method for capturing molecular changes in proteins on femtosecond timescales. However, the methodology has been mostly applied to natural proteins/enzymes and limited to reactions promoted by synthetic molecules due to structure determination challenges. This work demonstrates the applicability of TR-SFX for investigations of chemical reaction mechanisms of synthetic metal complexes. We fix a light-induced CO-releasing Mn(CO)3 reaction center in porous hen egg white lysozyme (HEWL) microcrystals. By controlling light exposure and time, we capture the real-time formation of Mn-carbonyl intermediates during the CO release reaction. The asymmetric protein environment is found to influence the order of CO release. The experimentally-observed reaction path agrees with quantum mechanical calculations. Therefore, our demonstration offers a new approach to visualize atomic-level reactions of small molecules using TR-SFX with real-space structure determination. This advance holds the potential to facilitate design of artificial metalloenzymes with precise mechanisms, empowering design, control and development of innovative reactions.
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Affiliation(s)
- Basudev Maity
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, Japan.
| | - Mitsuo Shoji
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan.
| | - Fangjia Luo
- JASRI, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
| | - Takanori Nakane
- Institute of Protein Research, Osaka University, Osaka, Japan
| | - Satoshi Abe
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, Japan
| | - Shigeki Owada
- JASRI, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
- RIKEN SPring-8 Center, Hyogo, 679-5148, Japan
| | | | - Kensuke Tono
- JASRI, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
- RIKEN SPring-8 Center, Hyogo, 679-5148, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, Hyogo, 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Thuc Toan Pham
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, Japan
| | - Mariko Kojima
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, Japan
| | - Yuki Hishikawa
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, Japan
| | - Junko Tanaka
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, Japan
| | - Jiaxin Tian
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, Japan
| | - Misaki Nagama
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, Japan
| | - Taiga Suzuki
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, Japan
| | - Hiroki Noya
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, Japan
| | - Yuto Nakasuji
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, Japan
| | - Asuka Asanuma
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, Japan
| | - Xinchen Yao
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, Japan
| | - So Iwata
- RIKEN SPring-8 Center, Hyogo, 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Eriko Nango
- RIKEN SPring-8 Center, Hyogo, 679-5148, Japan.
- Tohoku University. Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Japan.
| | - Takafumi Ueno
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, Japan.
- Research Center for Autonomous Systems Materialogy (ASMat), Institute of Innovative Research, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, Japan.
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2
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Savchenko M, Sebastian V, Lopez-Lopez MT, Rodriguez-Navarro A, Alvarez De Cienfuegos L, Jimenez-Lopez C, Gavira JA. Magnetite Mineralization inside Cross-Linked Protein Crystals. CRYSTAL GROWTH & DESIGN 2023; 23:4032-4040. [PMID: 37304398 PMCID: PMC10251750 DOI: 10.1021/acs.cgd.2c01436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 04/19/2023] [Indexed: 06/13/2023]
Abstract
Crystallization in confined spaces is a widespread process in nature that also has important implications for the stability and durability of many man-made materials. It has been reported that confinement can alter essential crystallization events, such as nucleation and growth and, thus, have an impact on crystal size, polymorphism, morphology, and stability. Therefore, the study of nucleation in confined spaces can help us understand similar events that occur in nature, such as biomineralization, design new methods to control crystallization, and expand our knowledge in the field of crystallography. Although the fundamental interest is clear, basic models at the laboratory scale are scarce mainly due to the difficulty in obtaining well-defined confined spaces allowing a simultaneous study of the mineralization process outside and inside the cavities. Herein, we have studied magnetite precipitation in the channels of cross-linked protein crystals (CLPCs) with different channel pore sizes, as a model of crystallization in confined spaces. Our results show that nucleation of an Fe-rich phase occurs inside the protein channels in all cases, but, by a combination of chemical and physical effects, the channel diameter of CLPCs exerted a precise control on the size and stability of those Fe-rich nanoparticles. The small diameters of protein channels restrain the growth of metastable intermediates to around 2 nm and stabilize them over time. At larger pore diameters, recrystallization of the Fe-rich precursors into more stable phases was observed. This study highlights the impact that crystallization in confined spaces can have on the physicochemical properties of the resulting crystals and shows that CLPCs can be interesting substrates to study this process.
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Affiliation(s)
- Mariia Savchenko
- Departamento
de Química Orgánica, Facultad de Ciencias, Unidad de
Excelencia de Química Aplicada a Biomedicina y Medioambiente
(UEQ), Universidad de Granada, 18002 Granada, Spain
- Laboratorio
de Estudios Cristalográficos, Instituto
Andaluz de Ciencias de la Tierra (Consejo Superior de Investigaciones
Científicas-Universidad de Granada), Avenida de las Palmeras 4, 18100 Armilla, Granada, Spain
- Departamento
de Física Aplicada, Facultad de Ciencias, Universidad de Granada, 18002 Granada, Spain
| | - Victor Sebastian
- Department
of Chemical Engineering and Environmental Technology, Instituto de
Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain
- Networking
Research Center on Bioengineering Biomaterials and Nanomedicine (CIBER-
BBN), Madrid 28029, Spain
| | - Modesto Torcuato Lopez-Lopez
- Departamento
de Física Aplicada, Facultad de Ciencias, Universidad de Granada, 18002 Granada, Spain
- Instituto
de Investigación Biosanitaria ibs, Granada 18012, Spain
| | - Alejandro Rodriguez-Navarro
- Departamento
de Mineralogía y Petrología, Facultad de Ciencias, Universidad de Granada, 18002 Granada, Spain
| | - Luis Alvarez De Cienfuegos
- Departamento
de Química Orgánica, Facultad de Ciencias, Unidad de
Excelencia de Química Aplicada a Biomedicina y Medioambiente
(UEQ), Universidad de Granada, 18002 Granada, Spain
- Instituto
de Investigación Biosanitaria ibs, Granada 18012, Spain
| | - Concepcion Jimenez-Lopez
- Departamento
de Microbiología, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18002 Granada, Spain
| | - José Antonio Gavira
- Laboratorio
de Estudios Cristalográficos, Instituto
Andaluz de Ciencias de la Tierra (Consejo Superior de Investigaciones
Científicas-Universidad de Granada), Avenida de las Palmeras 4, 18100 Armilla, Granada, Spain
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3
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Chen T, Peng Y, Qiu M, Yi C, Xu Z. Protein-supported transition metal catalysts: Preparation, catalytic applications, and prospects. Int J Biol Macromol 2023; 230:123206. [PMID: 36638614 DOI: 10.1016/j.ijbiomac.2023.123206] [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: 10/09/2022] [Revised: 12/26/2022] [Accepted: 01/05/2023] [Indexed: 01/12/2023]
Abstract
The immobilization of transition metal catalysts onto supports enables their easier recycling and improves catalytic performance. Protein supports not only support and stabilize transition metal catalysts but also enable the incorporation of biocompatibility and enzymatic catalysis into these catalysts. Consequently, the engineering of protein-supported transition metal catalysts (PTMCs) has emerged as an effective approach to improving their catalytic performance and widening their catalytic applications. Here, we review the recent development of the preparation and applications of PTMCs. The preparation of PTMCs will be summarized and discussed in terms of the types of protein supports, including proteins, protein assemblies, protein-polymer conjugates, and cross-linked proteins. Then, their catalytic applications including organic synthesis, photocatalysis, polymerization, and biomedicine, will be surveyed and compared. Meanwhile, the established catalytic structures-function relationships will be summarized. Lastly, the remaining issues and prospects will be discussed. By surveying a wide range of PTMCs, we believe that this review will attract a broad readership and stimulate the development of PTMCs.
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Affiliation(s)
- Tianyou Chen
- Ministry of Education Key Laboratory for the Green Preparation and Application of Functional Materials, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, China.
| | - Yan Peng
- Ministry of Education Key Laboratory for the Green Preparation and Application of Functional Materials, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, China
| | - Meishuang Qiu
- Ministry of Education Key Laboratory for the Green Preparation and Application of Functional Materials, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, China
| | - Changfeng Yi
- Ministry of Education Key Laboratory for the Green Preparation and Application of Functional Materials, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, China
| | - Zushun Xu
- Ministry of Education Key Laboratory for the Green Preparation and Application of Functional Materials, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, China.
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4
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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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5
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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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6
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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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7
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Ramberg KO, Engilberge S, Skorek T, Crowley PB. Facile Fabrication of Protein-Macrocycle Frameworks. J Am Chem Soc 2021; 143:1896-1907. [PMID: 33470808 PMCID: PMC8154523 DOI: 10.1021/jacs.0c10697] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
Precisely defined protein aggregates,
as exemplified by crystals,
have applications in functional materials. Consequently, engineered
protein assembly is a rapidly growing field. Anionic calix[n]arenes
are useful scaffolds that can mold to cationic proteins and induce
oligomerization and assembly. Here, we describe protein-calixarene
composites obtained via cocrystallization of commercially available
sulfonato-calix[8]arene (sclx8) with the symmetric and “neutral” protein RSL. Cocrystallization
occurred across a wide range of conditions and protein charge states,
from pH 2.2–9.5, resulting in three crystal forms. Cationization
of the protein surface at pH ∼ 4 drives calixarene complexation
and yielded two types of porous frameworks with pore diameters >3
nm. Both types of framework provide evidence of protein encapsulation
by the calixarene. Calixarene-masked proteins act as nodes within
the frameworks, displaying octahedral-type coordination in one case.
The other framework formed millimeter-scale crystals within hours,
without the need for precipitants or specialized equipment. NMR experiments
revealed macrocycle-modulated side chain pKa values and suggested a mechanism for pH-triggered assembly.
The same low pH framework was generated at high pH with a permanently
cationic arginine-enriched RSL variant. Finally, in addition to protein
framework fabrication, sclx8 enables de novo structure determination.
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Affiliation(s)
- Kiefer O Ramberg
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
| | - Sylvain Engilberge
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland.,Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Tomasz Skorek
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
| | - Peter B Crowley
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
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8
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Abstract
Recent advances in structural studies unveiling the basis of the metal compounds/protein recognition process are discussed.
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Affiliation(s)
- Antonello Merlino
- Department of Chemical Sciences
- University of Naples Federico II
- Complesso Universitario di Monte Sant’Angelo
- Napoli
- Italy
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9
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Uwada T, Kouno K, Ishikawa M. In Situ Absorption and Fluorescence Microspectroscopy Investigation of the Molecular Incorporation Process into Single Nanoporous Protein Crystals. ACS OMEGA 2020; 5:9605-9613. [PMID: 32363313 PMCID: PMC7191835 DOI: 10.1021/acsomega.0c01038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 04/02/2020] [Indexed: 05/27/2023]
Abstract
Protein crystals exhibit distinct three-dimensional structures, which contain well-ordered nanoporous solvent channels, providing a chemically heterogeneous environment. In this paper, the incorporation of various molecules into the solvent channels of native hen egg-white lysozyme crystals was demonstrated using fluorescent dyes, including acridine yellow G, rhodamine 6G, and eosin Y. The process was evaluated on the basis of absorption and fluorescence microspectroscopy at a single-crystal level. The molecular loading process was clearly visualized as a function of time, and it was determined that the protein crystals could act as nanoporous materials. It was found that the incorporation process is strongly dependent on the molecular charge, leading to heterogeneous molecular aggregation, which suggests host-guest interaction of protein crystals from the viewpoint of nanoporous materials.
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10
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Minamihata K, Tsukamoto K, Adachi M, Shimizu R, Mishina M, Kuroki R, Nagamune T. Genetically fused charged peptides induce rapid crystallization of proteins. Chem Commun (Camb) 2020; 56:3891-3894. [PMID: 32134050 DOI: 10.1039/c9cc09529b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We utilized electrostatic interaction to induce rapid crystallization of streptavidin. Simply mixing streptavidins possessing either a positively or negatively charged peptide at their C-terminus generated diffraction-quality crystals in a few hours. We modified the streptavidin crystals with fluorescent molecules using biotin, demonstrating the concept of protein crystals as functional biomaterials.
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Affiliation(s)
- K Minamihata
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Fukuoka, 819-0395, Japan.
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11
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Guagnini F, Engilberge S, Ramberg KO, Pérez J, Crowley PB. Engineered assembly of a protein–cucurbituril biohybrid. Chem Commun (Camb) 2020; 56:360-363. [DOI: 10.1039/c9cc07198a] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Additional Q7 binding sites drive protein aggregation in solution and statistical disorder in the crystalline biohybrid suggest new possibilities for protein-based materials.
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Affiliation(s)
| | | | - Kiefer O. Ramberg
- School of Chemistry
- National University of Ireland Galway
- Galway
- Ireland
| | - Javier Pérez
- Synchrotron SOLEIL
- L’Orme des Merisiers
- 91192 Gif-sur-Yvette Cedex
- France
| | - Peter B. Crowley
- School of Chemistry
- National University of Ireland Galway
- Galway
- Ireland
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12
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Marchenkova MA, Kuranova IP, Timofeev VI, Boikova AS, Dorovatovskii PV, Dyakova YA, Ilina KB, Pisarevskiy YV, Kovalchuk MV. The binding of precipitant ions in the tetragonal crystals of hen egg white lysozyme. J Biomol Struct Dyn 2019; 38:5159-5172. [PMID: 31760865 DOI: 10.1080/07391102.2019.1696706] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The bonds between lysozyme molecules and precipitant ions in single crystals grown with chlorides of several metals are analysed on the basis of crystal structure data. Crystals of tetragonal hen egg lysozyme (HEWL) were grown with chlorides of several alkali and transition metals (LiCl, NaCl, KCl, NiCl2 and CuCl2) as precipitants and the three-dimensional structures were determined at 1.35 Å resolution by X-ray diffraction method. The positions of metal and chloride ions attached to the protein were located, divided into three groups and analysed. Some of them, in accordance with the recently proposed and experimentally confirmed crystal growth model, provide connections in protein dimers and octamers that are precursor clusters in the crystallization lysozyme solution. The first group, including Cu+2, Ni+2 and Na+1 cations, binds specifically to the protein molecule. The second group consists of metal and chloride ions bound inside the dimers and octamers. The third group of ions can participate in connections between the octamers that are suggested as building units during the crystal growth. The arrangement of chloride and metal ions associated with lysozyme molecule at all stages of the crystallization solution formation and crystal growth is discussed.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Margarita A Marchenkova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre "Kurchatov Institute", Moscow, Russian Federation
| | - Inna P Kuranova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre "Kurchatov Institute", Moscow, Russian Federation
| | - Vladimir I Timofeev
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre "Kurchatov Institute", Moscow, Russian Federation
| | - Anastasiia S Boikova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre "Kurchatov Institute", Moscow, Russian Federation
| | | | - Yulia A Dyakova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre "Kurchatov Institute", Moscow, Russian Federation
| | - Kseniia B Ilina
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre "Kurchatov Institute", Moscow, Russian Federation
| | - Yury V Pisarevskiy
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre "Kurchatov Institute", Moscow, Russian Federation
| | - Mikhail V Kovalchuk
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre "Kurchatov Institute", Moscow, Russian Federation.,The Faculty of Physics, St. Petersburg State University, St. Petersburg, Russian Federation
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13
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Nguyen TK, Negishi H, Abe S, Ueno T. Construction of supramolecular nanotubes from protein crystals. Chem Sci 2019; 10:1046-1051. [PMID: 30774900 PMCID: PMC6346403 DOI: 10.1039/c8sc04167a] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 10/26/2018] [Indexed: 01/26/2023] Open
Abstract
Investigations involving the design of protein assemblies for the development of biomaterials are receiving significant attention. In nature, proteins can be driven into assemblies frequently by various non-covalent interactions. Assembly of proteins into supramolecules can be conducted under limited conditions in solution. These factors force the assembly process into an equilibrium state with low stability. Here, we report a new method for preparing assemblies using protein crystals as non-equilibrium molecular scaffolds. Protein crystals provide an ideal environment with a highly ordered packing of subunits in which the supramolecular assembled structures are formed in the crystalline matrix. Based on this feature, we demonstrate the self-assembly of supramolecular nanotubes constructed from protein crystals triggered by co-oxidation with cross-linkers. The assembly of tubes is driven by the formation of disulfide bonds to retain the intermolecular interactions within each assembly in the crystalline matrix after dissolution of the crystals.
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Affiliation(s)
- Tien Khanh Nguyen
- School of Life Science and Technology , Tokyo Institute of Technology , Nagatsuta-cho , Midori-ku , Yokohama 226-8501 , Japan .
| | - Hashiru Negishi
- School of Life Science and Technology , Tokyo Institute of Technology , Nagatsuta-cho , Midori-ku , Yokohama 226-8501 , Japan .
| | - Satoshi Abe
- School of Life Science and Technology , Tokyo Institute of Technology , Nagatsuta-cho , Midori-ku , Yokohama 226-8501 , Japan .
| | - Takafumi Ueno
- School of Life Science and Technology , Tokyo Institute of Technology , Nagatsuta-cho , Midori-ku , Yokohama 226-8501 , Japan .
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14
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Russo Krauss I, Ferraro G, Pica A, Márquez JA, Helliwell JR, Merlino A. Principles and methods used to grow and optimize crystals of protein-metallodrug adducts, to determine metal binding sites and to assign metal ligands. Metallomics 2018; 9:1534-1547. [PMID: 28967006 DOI: 10.1039/c7mt00219j] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The characterization of the interactions between biological macromolecules (proteins and nucleic acids) and metal-based drugs is a fundamental prerequisite for understanding their mechanisms of action. X-ray crystallography enables the structural analysis of such complexes with atomic level detail. However, this approach requires the preparation of highly diffracting single crystals, the measurement of diffraction patterns and the structural analysis and interpretation of macromolecule-metal interactions from electron density maps. In this review, we describe principles and methods used to grow and optimize crystals of protein-metallodrug adducts, to determine metal binding sites and to assign and validate metal ligands. Examples from the literature and experience in our own laboratory are provided and key challenges are described, notably crystallization and molecular model refinement against the X-ray diffraction data.
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Affiliation(s)
- Irene Russo Krauss
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, I-80126, Napoli, Italy.
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15
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Negishi H, Abe S, Yamashita K, Hirata K, Niwase K, Boudes M, Coulibaly F, Mori H, Ueno T. Supramolecular protein cages constructed from a crystalline protein matrix. Chem Commun (Camb) 2018; 54:1988-1991. [PMID: 29405208 DOI: 10.1039/c7cc08689j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Protein crystals are formed via ordered arrangements of proteins, which assemble to form supramolecular structures. Here, we show a method for the assembly of supramolecular protein cages within a crystalline environment. The cages are stabilized by covalent cross-linking allowing their release via dissolution of the crystal. The high stability of the desiccated protein crystals allows cages to be constructed.
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Affiliation(s)
- Hashiru Negishi
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
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16
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Abe S, Atsumi K, Yamashita K, Hirata K, Mori H, Ueno T. Structure of in cell protein crystals containing organometallic complexes. Phys Chem Chem Phys 2018; 20:2986-2989. [PMID: 29138769 DOI: 10.1039/c7cp06651a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The molecular structures of in cell protein crystals containing organometallic Pd(allyl) complexes were determined by performing microfocus X-ray diffraction experiments. The coordination sites in a polyhedrin mutant with deletion of selected amino acid residues located at the interface of the polyhedrin trimer are dramatically altered compared to those of the wild-type composite.
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Affiliation(s)
- Satoshi Abe
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
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17
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Abe S, Maity B, Ueno T. Design of a confined environment using protein cages and crystals for the development of biohybrid materials. Chem Commun (Camb) 2018; 52:6496-512. [PMID: 27032539 DOI: 10.1039/c6cc01355d] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
There is growing interest in the design of protein assemblies for use in materials science and bionanotechnology. Protein assemblies, such as cages and crystalline protein structures, provide confined chemical environments that allow immobilization of metal complexes, nanomaterials, and proteins by metal coordination, assembly/disassembly reactions, genetic manipulation and crystallization methods. Protein assembly composites can be used to prepare hybrid materials with catalytic, magnetic and optical properties for cellular applications due to their high stability, solubility and biocompatibility. In this feature article, we focus on the recent development of ferritin as the most promising molecular template protein cage and in vivo and in vitro engineering of protein crystals as solid protein materials with functional properties.
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Affiliation(s)
- Satoshi Abe
- Department of Biomolecular Engineering, Graduate School of Bioscience and Biotechonology, Tokyo Institute of Techonology, B-55, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
| | - Basudev Maity
- Department of Biomolecular Engineering, Graduate School of Bioscience and Biotechonology, Tokyo Institute of Techonology, B-55, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
| | - Takafumi Ueno
- Department of Biomolecular Engineering, Graduate School of Bioscience and Biotechonology, Tokyo Institute of Techonology, B-55, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
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18
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Huber TR, McPherson EC, Keating CE, Snow CD. Installing Guest Molecules at Specific Sites within Scaffold Protein Crystals. Bioconjug Chem 2017; 29:17-22. [DOI: 10.1021/acs.bioconjchem.7b00668] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Thaddaus R. Huber
- Department of Chemical and
Biological Engineering, Colorado State University, 1301 Campus Delivery Fort Collins, Colorado 80523, United States
| | - Eli C. McPherson
- Department of Chemical and
Biological Engineering, Colorado State University, 1301 Campus Delivery Fort Collins, Colorado 80523, United States
| | - Carolyn E. Keating
- Department of Chemical and
Biological Engineering, Colorado State University, 1301 Campus Delivery Fort Collins, Colorado 80523, United States
| | - Christopher D. Snow
- Department of Chemical and
Biological Engineering, Colorado State University, 1301 Campus Delivery Fort Collins, Colorado 80523, United States
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19
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Functionalization of protein crystals with metal ions, complexes and nanoparticles. Curr Opin Chem Biol 2017; 43:68-76. [PMID: 29245143 DOI: 10.1016/j.cbpa.2017.11.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 11/09/2017] [Accepted: 11/26/2017] [Indexed: 01/08/2023]
Abstract
Self-assembled proteins have specific functions in biology. With inspiration provided by natural protein systems, several artificial protein assemblies have been constructed via site-specific mutations or metal coordination, which have important applications in catalysis, material and bio-supramolecular chemistry. Similar to natural protein assemblies, protein crystals have been recognized as protein assemblies formed of densely-packed monomeric proteins. Protein crystals can be functionalized with metal ions, metal complexes or nanoparticles via soaking, co-crystallization, creating new metal binding sites by site-specific mutations. The field of protein crystal engineering with metal coordination is relatively new and has gained considerable attention for developing solid biomaterials as well as structural investigations of enzymatic reactions, growth of nanoparticles and catalysis. This review highlights recent and significant research on functionalization of protein crystals with metal coordination and future prospects.
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20
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Hartje LF, Munsky B, Ni TW, Ackerson CJ, Snow CD. Adsorption-Coupled Diffusion of Gold Nanoclusters within a Large-Pore Protein Crystal Scaffold. J Phys Chem B 2017; 121:7652-7659. [DOI: 10.1021/acs.jpcb.7b03999] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Luke F. Hartje
- Department
of Biochemistry and Molecular Biology, ‡Department of Chemical and Biological
Engineering, and §Department of Chemistry, Colorado State University, Fort Collins, Colorado 80521, United States
| | - Brian Munsky
- Department
of Biochemistry and Molecular Biology, ‡Department of Chemical and Biological
Engineering, and §Department of Chemistry, Colorado State University, Fort Collins, Colorado 80521, United States
| | - Thomas W. Ni
- Department
of Biochemistry and Molecular Biology, ‡Department of Chemical and Biological
Engineering, and §Department of Chemistry, Colorado State University, Fort Collins, Colorado 80521, United States
| | - Christopher J. Ackerson
- Department
of Biochemistry and Molecular Biology, ‡Department of Chemical and Biological
Engineering, and §Department of Chemistry, Colorado State University, Fort Collins, Colorado 80521, United States
| | - Christopher D. Snow
- Department
of Biochemistry and Molecular Biology, ‡Department of Chemical and Biological
Engineering, and §Department of Chemistry, Colorado State University, Fort Collins, Colorado 80521, United States
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21
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Abe S, Ueno T. Development of Bio-Hybrid Materials by Design of Supramolecular Protein Assemblies. J SYN ORG CHEM JPN 2017. [DOI: 10.5059/yukigoseikyokaishi.75.1264] [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)
- Satoshi Abe
- School of Life Science and Technology, Tokyo Institute of Technology
| | - Takafumi Ueno
- School of Life Science and Technology, Tokyo Institute of Technology
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22
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Interactions between proteins and Ru compounds of medicinal interest: A structural perspective. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.08.001] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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23
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Kowalski AE, Huber TR, Ni TW, Hartje LF, Appel KL, Yost JW, Ackerson CJ, Snow CD. Gold nanoparticle capture within protein crystal scaffolds. NANOSCALE 2016; 8:12693-12696. [PMID: 27264210 DOI: 10.1039/c6nr03096c] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
DNA assemblies have been used to organize inorganic nanoparticles into 3D arrays, with emergent properties arising as a result of nanoparticle spacing and geometry. We report here the use of engineered protein crystals as an alternative approach to biologically mediated assembly of inorganic nanoparticles. The protein crystal's 13 nm diameter pores result in an 80% solvent content and display hexahistidine sequences on their interior. The hexahistidine sequence captures Au25(glutathione)∼17 (nitrilotriacetic acid)∼1 nanoclusters throughout a chemically crosslinked crystal via the coordination of Ni(ii) to both the cluster and the protein. Nanoparticle loading was validated by confocal microscopy and elemental analysis. The nanoparticles may be released from the crystal by exposure to EDTA, which chelates the Ni(ii) and breaks the specific protein/nanoparticle interaction. The integrity of the protein crystals after crosslinking and nanoparticle capture was confirmed by single crystal X-ray crystallography.
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Affiliation(s)
- Ann E Kowalski
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80521, USA.
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24
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Ferraro G, Massai L, Messori L, Merlino A. Cisplatin binding to human serum albumin: a structural study. Chem Commun (Camb) 2016; 51:9436-9. [PMID: 25873085 DOI: 10.1039/c5cc01751c] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The reaction between cisplatin and human serum albumin (HSA) was investigated by X-ray crystallography and crystal structures of the cisplatin/HSA adduct were eventually solved for the first time. Structural data unambiguously prove that cisplatin mainly binds to His105 and Met329 side chains; additional binding sites are detected at His288, Met298, and Met548 and at His535, His67 and His247.
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Affiliation(s)
- Giarita Ferraro
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, I-80126, Napoli, Italy.
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25
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England MW, Patil AJ, Mann S. Synthesis and Confinement of Carbon Dots in Lysozyme Single Crystals Produces Ordered Hybrid Materials with Tuneable Luminescence. Chemistry 2015; 21:9008-13. [DOI: 10.1002/chem.201501429] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Indexed: 11/06/2022]
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26
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Tabe H, Shimoi T, Fujita K, Abe S, Ijiri H, Tsujimoto M, Kuchimaru T, Kizaka-Kondo S, Mori H, Kitagawa S, Ueno T. Design of a CO-releasing Extracellular Scaffold Using in Vivo Protein Crystals. CHEM LETT 2015. [DOI: 10.1246/cl.141035] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Hiroyasu Tabe
- Graduate School of Engineering, Kyoto University
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University
| | - Takuya Shimoi
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology
| | - Kenta Fujita
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology
| | - Satoshi Abe
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology
| | - Hiroshi Ijiri
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology
| | - Masahiko Tsujimoto
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University
| | - Takahiro Kuchimaru
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology
| | - Shinae Kizaka-Kondo
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology
| | - Hajime Mori
- Insect Biomedical Research Center, Kyoto Institute of Technology
| | - Susumu Kitagawa
- Graduate School of Engineering, Kyoto University
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University
| | - Takafumi Ueno
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology
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27
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Abe S, Tokura Y, Pal R, Komura N, Imamura A, Matsumoto K, Ijiri H, Sanghamitra NJM, Tabe H, Ando H, Kiso M, Mori H, Kitagawa S, Ueno T. Surface Functionalization of Protein Crystals with Carbohydrate Using Site-selective Bioconjugation. CHEM LETT 2015. [DOI: 10.1246/cl.140865] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Satoshi Abe
- Department of Biomolecular Engineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology
| | - Yu Tokura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University
| | - Rita Pal
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University
- Department of Applied Bioorganic Chemistry, Gifu University
| | - Naoko Komura
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University
- Department of Applied Bioorganic Chemistry, Gifu University
| | | | | | - Hiroshi Ijiri
- Department of Biomolecular Engineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology
| | | | - Hiroyasu Tabe
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University
| | - Hiromune Ando
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University
- Department of Applied Bioorganic Chemistry, Gifu University
| | - Makoto Kiso
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University
- Department of Applied Bioorganic Chemistry, Gifu University
| | - Hajime Mori
- Insect Biomedical Research Center, Kyoto Institute of Technology
| | - Susumu Kitagawa
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University
| | - Takafumi Ueno
- Department of Biomolecular Engineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology
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28
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Abstract
Protein crystals have been functionalized for applications in preparation of inorganic materials, asymmetric catalysis and accumulation of functional compounds.
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Affiliation(s)
- Satoshi Abe
- Department of Biomolecular Engineering
- Graduate School of Bioscience and Biotechnology
- Tokyo Institute of Technology
- Midori-ku
- Japan
| | - Takafumi Ueno
- Department of Biomolecular Engineering
- Graduate School of Bioscience and Biotechnology
- Tokyo Institute of Technology
- Midori-ku
- Japan
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29
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Yan EK, Cao HL, Zhang CY, Lu QQ, Ye YJ, He J, Huang LJ, Yin DC. Cross-linked protein crystals by glutaraldehyde and their applications. RSC Adv 2015. [DOI: 10.1039/c5ra01722j] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The mechanism of cross-linked protein crystals using glutaraldehyde, and their properties and applications are discussed in detail.
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Affiliation(s)
- Er-Kai Yan
- Institute for Special Environmental Biophysics
- Key Laboratory for Space Bioscience and Space Biotechnology
- School of Life Sciences
- Northwestern Polytechnical University
- Xi'an 710072
| | - Hui-Ling Cao
- Institute for Special Environmental Biophysics
- Key Laboratory for Space Bioscience and Space Biotechnology
- School of Life Sciences
- Northwestern Polytechnical University
- Xi'an 710072
| | - Chen-Yan Zhang
- Institute for Special Environmental Biophysics
- Key Laboratory for Space Bioscience and Space Biotechnology
- School of Life Sciences
- Northwestern Polytechnical University
- Xi'an 710072
| | - Qin-Qin Lu
- Institute for Special Environmental Biophysics
- Key Laboratory for Space Bioscience and Space Biotechnology
- School of Life Sciences
- Northwestern Polytechnical University
- Xi'an 710072
| | - Ya-Jing Ye
- Institute for Special Environmental Biophysics
- Key Laboratory for Space Bioscience and Space Biotechnology
- School of Life Sciences
- Northwestern Polytechnical University
- Xi'an 710072
| | - Jin He
- Institute for Special Environmental Biophysics
- Key Laboratory for Space Bioscience and Space Biotechnology
- School of Life Sciences
- Northwestern Polytechnical University
- Xi'an 710072
| | - Lin-Jun Huang
- Institute for Special Environmental Biophysics
- Key Laboratory for Space Bioscience and Space Biotechnology
- School of Life Sciences
- Northwestern Polytechnical University
- Xi'an 710072
| | - Da-Chuan Yin
- Institute for Special Environmental Biophysics
- Key Laboratory for Space Bioscience and Space Biotechnology
- School of Life Sciences
- Northwestern Polytechnical University
- Xi'an 710072
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30
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Tabe H, Fujita K, Abe S, Tsujimoto M, Kuchimaru T, Kizaka-Kondoh S, Takano M, Kitagawa S, Ueno T. Preparation of a cross-linked porous protein crystal containing Ru carbonyl complexes as a CO-releasing extracellular scaffold. Inorg Chem 2014; 54:215-20. [PMID: 25494847 DOI: 10.1021/ic502159x] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Protein crystals generally are stable solid protein assemblies. Certain protein crystals are suitable for use as nanovessels for immobilizing metal complexes. Here we report the preparation of ruthenium carbonyl-incorporated cross-linked hen egg white lysozyme crystals (Ru·CL-HEWL). Ru·CL-HEWL retains a Ru carbonyl moiety that can release CO, although a composite of Ru carbonyl-HEWL dissolved in buffer solution (Ru·HEWL) does not release CO. We found that treatment of cells with Ru·CL-HEWL significantly increased nuclear factor kappa B (NF-κB) activity as a cellular response to CO. These results demonstrate that Ru·CL-HEWL has potential for use as an artificial extracellular scaffold suitable for transport and release of a gas molecule.
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Affiliation(s)
- Hiroyasu Tabe
- Graduate School of Engineering, Kyoto University, Katsura , Nishikyo-ku, Kyoto 615-8510, Japan
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31
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Abstract
The construction of crystalline arrays allows proteins to be presented in a dense, oriented and functional way that also facilitates determination of their structure. Rational design of these supramolecular structures is becoming increasingly tractable with recent successes exploiting both innate protein symmetry and advances in protein–protein interface design. Pre-existing symmetry minimizes the number of non-native interfaces that must be produced, and the use of symmetric interfaces facilitates protein alignment. Arrays in which metal coordination or peptide binding are responsible for the inter-particle associations show particular promise due to the malleable and reversible nature of these interactions. Cross-pollination of the principles that underlie successful strategies is likely to produce rapid advances in this field and consequent benefits to both nanotechnology and structural biology.
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32
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Messori L, Scaletti F, Massai L, Cinellu MA, Gabbiani C, Vergara A, Merlino A. The mode of action of anticancer gold-based drugs: a structural perspective. Chem Commun (Camb) 2014; 49:10100-2. [PMID: 24045294 DOI: 10.1039/c3cc46400h] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The interactions between a few representative gold-based drugs and hen egg white lysozyme were studied by X-ray crystallography. High resolution crystal structures solved for three metallodrug-protein adducts provide valuable insight into the molecular mechanism of these promising metal compounds and the inherent protein metalation processes.
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Affiliation(s)
- Luigi Messori
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
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33
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Tabe H, Abe S, Hikage T, Kitagawa S, Ueno T. Porous Protein Crystals as Catalytic Vessels for Organometallic Complexes. Chem Asian J 2014; 9:1373-8. [DOI: 10.1002/asia.201301347] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 12/26/2013] [Indexed: 01/19/2023]
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34
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Ding Y, Shi L, Wei H. Protein-directed approaches to functional nanomaterials: a case study of lysozyme. J Mater Chem B 2014; 2:8268-8291. [DOI: 10.1039/c4tb01235f] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Using lysozyme as a model, protein-directed approaches to functional nanomaterials were reviewed, making rational materials design possible in the future.
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Affiliation(s)
- Yubin Ding
- Department of Biomedical Engineering
- Aerosol Bioeffects and Health Research Center
- College of Engineering and Applied Sciences
- Nanjing National Laboratory of Microstructures
- Nanjing University
| | - Leilei Shi
- Department of Biomedical Engineering
- Aerosol Bioeffects and Health Research Center
- College of Engineering and Applied Sciences
- Nanjing National Laboratory of Microstructures
- Nanjing University
| | - Hui Wei
- Department of Biomedical Engineering
- Aerosol Bioeffects and Health Research Center
- College of Engineering and Applied Sciences
- Nanjing National Laboratory of Microstructures
- Nanjing University
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35
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Liang M, Wang L, Liu X, Qi W, Su R, Huang R, Yu Y, He Z. Cross-linked lysozyme crystal templated synthesis of Au nanoparticles as high-performance recyclable catalysts. NANOTECHNOLOGY 2013; 24:245601. [PMID: 23680924 DOI: 10.1088/0957-4484/24/24/245601] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Bio-nanomaterials fabricated using a bioinspired templating technique represent a novel class of composite materials with diverse applications in biomedical, electronic devices, drug delivery, and catalysis. In this study, Au nanoparticles (NPs) are synthesized within the solvent channels of cross-linked lysozyme crystals (CLLCs) in situ without the introduction of extra chemical reagents or physical treatments. The as-prepared AuNPs-in-protein crystal hybrid materials are characterized by light microscopy, transmission electron microscopy, x-ray diffraction, and Fourier-transform infrared spectroscopy analyses. Small AuNPs with narrow size distribution reveal the restriction effects of the porous structure in the lysozyme crystals. These composite materials are proven to be active heterogeneous catalysts for the reduction of 4-nitrophenol to 4-aminophenol. These catalysts can be easily recovered and reused at least 20 times because of the physical stability and macro-dimension of CLLCs. This work is the first to use CLLCs as a solid biotemplate for the preparation of recyclable high-performance catalysts.
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Affiliation(s)
- Miao Liang
- State Key Laboratory of Chemical Engineering, Tianjin Key Laboratory of Membrane Science and Desalination Technology, School of Chemical Engineering and Technology, Tianjin University, Nankai District, Tianjin, People's Republic of China
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36
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Abstract
Porous protein crystals have the potential to provide new porous materials due to their unique chemical environments composed of amino acid residues periodically exposed at the surface of the solvent channels in the crystal lattice. This enables accumulation of external compounds in special arrangements by metal coordination interactions or by chemical modifications. This article presents a review of advances in the recently established field of porous protein crystals.
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Affiliation(s)
- Takafumi Ueno
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta-cho 4259-B55, Midori-ku, Yokohama 226-8501, Japan.
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37
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Artificial Metalloenzymes Constructed From Hierarchically-Assembled Proteins. Chem Asian J 2013; 8:1646-60. [DOI: 10.1002/asia.201300347] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Indexed: 01/20/2023]
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38
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Liang M, Wang L, Su R, Qi W, Wang M, Yu Y, He Z. Synthesis of silver nanoparticles within cross-linked lysozyme crystals as recyclable catalysts for 4-nitrophenol reduction. Catal Sci Technol 2013. [DOI: 10.1039/c3cy00157a] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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39
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Sanghamitra NJM, Ueno T. Expanding coordination chemistry from protein to protein assembly. Chem Commun (Camb) 2013; 49:4114-26. [DOI: 10.1039/c2cc36935d] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Tian J, Liu G, Chen X, Lu J, Zhou Z, Huang R. Unique pressure-crystallized structures in ternary bisphenol-a polycarbonate/dioctyl phthalate/fullerene C60 composites. J Appl Polym Sci 2012. [DOI: 10.1002/app.38822] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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