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Fansher D, Besna JN, Fendri A, Pelletier JN. Choose Your Own Adventure: A Comprehensive Database of Reactions Catalyzed by Cytochrome P450 BM3 Variants. ACS Catal 2024; 14:5560-5592. [PMID: 38660610 PMCID: PMC11036407 DOI: 10.1021/acscatal.4c00086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 04/26/2024]
Abstract
Cytochrome P450 BM3 monooxygenase is the topic of extensive research as many researchers have evolved this enzyme to generate a variety of products. However, the abundance of information on increasingly diversified variants of P450 BM3 that catalyze a broad array of chemistry is not in a format that enables easy extraction and interpretation. We present a database that categorizes variants by their catalyzed reactions and includes details about substrates to provide reaction context. This database of >1500 P450 BM3 variants is downloadable and machine-readable and includes instructions to maximize ease of gathering information. The database allows rapid identification of commonly reported substitutions, aiding researchers who are unfamiliar with the enzyme in identifying starting points for enzyme engineering. For those actively engaged in engineering P450 BM3, the database, along with this review, provides a powerful and user-friendly platform to understand, predict, and identify the attributes of P450 BM3 variants, encouraging the further engineering of this enzyme.
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Affiliation(s)
- Douglas
J. Fansher
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
| | - Jonathan N. Besna
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
- Department
of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada H3T 1J4
| | - Ali Fendri
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
| | - Joelle N. Pelletier
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
- Department
of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada H3T 1J4
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Ariga K. Materials nanoarchitectonics in a two-dimensional world within a nanoscale distance from the liquid phase. NANOSCALE 2022; 14:10610-10629. [PMID: 35838591 DOI: 10.1039/d2nr02513b] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Promoted understanding of nanotechnology has enabled the construction of functional materials with nanoscale-regulated structures. Accordingly, materials science requires one-step further innovation by coupling nanotechnology with the other materials sciences. As a post-nanotechnology concept, nanoarchitectonics has recently been proposed. It is a methodology to architect functional material systems using atomic, molecular, and nanomaterial unit-components. One of the attractive methodologies would be to develop nanoarchitectonics in a defined dimensional environment with certain dynamism, such as liquid interfaces. However, nanoarchitectonics at liquid interfaces has not been fully explored because of difficulties in direct observations and evaluations with high-resolutions. This unsatisfied situation in the nanoscale understanding of liquid interfaces may keep liquid interfaces as unexplored and attractive frontiers in nanotechnology and nanoarchitectonics. Research efforts related to materials nanoarchitectonics on liquid interfaces have been continuously made. As exemplified in this review paper, a wide range of materials can be organized and functionalized on liquid interfaces, including organic molecules, inorganic nanomaterials, hybrids, organic semiconductor thin films, proteins, and stem cells. Two-dimensional nanocarbon sheets have been fabricated by molecular reactions at dynamically moving interfaces, and metal-organic frameworks and covalent organic frameworks have been fabricated by specific interactions and reactions at liquid interfaces. Therefore, functions such as sensors, devices, energy-related applications, and cell control are being explored. In fact, the potential for the nanoarchitectonics of functional materials in two-dimensional nanospaces at liquid surfaces is sufficiently high. On the basis of these backgrounds, this short review article describes recent approaches to materials nanoarchitectonics in a liquid-based two-dimensional world, i.e., interfacial regions within a nanoscale distance from the liquid phase.
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Affiliation(s)
- Katsuhiko Ariga
- WPI Research Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
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3
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Biomimetic and Biological Nanoarchitectonics. Int J Mol Sci 2022; 23:ijms23073577. [PMID: 35408937 PMCID: PMC8998553 DOI: 10.3390/ijms23073577] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 03/21/2022] [Accepted: 03/24/2022] [Indexed: 12/13/2022] Open
Abstract
A post-nanotechnology concept has been assigned to an emerging concept, nanoarchitectonics. Nanoarchitectonics aims to establish a discipline in which functional materials are fabricated from nano-scale components such as atoms, molecules, and nanomaterials using various techniques. Nanoarchitectonics opens ways to form a more unified paradigm by integrating nanotechnology with organic chemistry, supramolecular chemistry, material chemistry, microfabrication technology, and biotechnology. On the other hand, biological systems consist of rational organization of constituent molecules. Their structures have highly asymmetric and hierarchical features that allow for chained functional coordination, signal amplification, and vector-like energy and signal flow. The process of nanoarchitectonics is based on the premise of combining several different processes, which makes it easier to obtain a hierarchical structure. Therefore, nanoarchitectonics is a more suitable methodology for creating highly functional systems based on structural asymmetry and hierarchy like biosystems. The creation of functional materials by nanoarchitectonics is somewhat similar to the creation of functional systems in biological systems. It can be said that the goal of nanoarchitectonics is to create highly functional systems similar to those found in biological systems. This review article summarizes the synthesis of biomimetic and biological molecules and their functional structure formation from various viewpoints, from the molecular level to the cellular level. Several recent examples are arranged and categorized to illustrate such a trend with sections of (i) synthetic nanoarchitectonics for bio-related units, (ii) self-assembly nanoarchitectonics with bio-related units, (iii) nanoarchitectonics with nucleic acids, (iv) nanoarchitectonics with peptides, (v) nanoarchitectonics with proteins, and (vi) bio-related nanoarchitectonics in conjugation with materials.
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Hu W, Shi J, Lv W, Jia X, Ariga K. Regulation of stem cell fate and function by using bioactive materials with nanoarchitectonics for regenerative medicine. SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS 2022; 23:393-412. [PMID: 35783540 PMCID: PMC9246028 DOI: 10.1080/14686996.2022.2082260] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Nanoarchitectonics has emerged as a post-nanotechnology concept. As one of the applications of nanoarchitectonics, this review paper discusses the control of stem cell fate and function as an important issue. For hybrid nanoarchitectonics involving living cells, it is crucial to understand how biomaterials and their nanoarchitected structures regulate behaviours and fates of stem cells. In this review, biomaterials for the regulation of stem cell fate are firstly discussed. Besides multipotent differentiation, immunomodulation is an important biological function of mesenchymal stem cells (MSCs). MSCs can modulate immune cells to treat multiple immune- and inflammation-mediated diseases. The following sections summarize the recent advances of the regulation of the immunomodulatory functions of MSCs by biophysical signals. In the third part, we discussed how biomaterials direct the self-organization of pluripotent stem cells for organoid. Bioactive materials are constructed which mimic the biophysical cues of in vivo microenvironment such as elasticity, viscoelasticity, biodegradation, fluidity, topography, cell geometry, and etc. Stem cells interpret these biophysical cues by different cytoskeletal forces. The different cytoskeletal forces lead to substantial transcription and protein expression, which affect stem cell fate and function. Regulations of stem cells could not be utilized only for tissue repair and regenerative medicine but also potentially for production of advanced materials systems. Materials nanoarchitectonics with integration of stem cells and related biological substances would have high impacts in science and technology of advanced materials.
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Affiliation(s)
- Wei Hu
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, ShenzhenP. R. China
| | - Jiaming Shi
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, ShenzhenP. R. China
| | - Wenyan Lv
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, ShenzhenP. R. China
| | - Xiaofang Jia
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, ShenzhenP. R. China
- CONTACT Xiaofang Jia School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen518107, P. R. China
| | - Katsuhiko Ariga
- International Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), Ibaraki, Japan
- Department of Advanced Materials Science, Graduate School of Frontier Sciences, the University of Tokyo, KashiwaJapan
- Katsuhiko Ariga International Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), Ibaraki305-0044, Japan
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Nie J, Tian F, Zheng B, Wang Z, Zheng P. Exploration of Metal-Ligand Coordination Bonds in Proteins by Single-molecule Force Spectroscopy. CHEM LETT 2021. [DOI: 10.1246/cl.210307] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jingyuan Nie
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Fang Tian
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Bin Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Ziyi Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
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Maji S, Shrestha LK, Ariga K. Nanoarchitectonics for Hierarchical Fullerene Nanomaterials. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:2146. [PMID: 34443975 PMCID: PMC8400563 DOI: 10.3390/nano11082146] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 08/19/2021] [Accepted: 08/19/2021] [Indexed: 12/12/2022]
Abstract
Nanoarchitectonics is a universal concept to fabricate functional materials from nanoscale building units. Based on this concept, fabrications of functional materials with hierarchical structural motifs from simple nano units of fullerenes (C60 and C70 molecules) are described in this review article. Because fullerenes can be regarded as simple and fundamental building blocks with mono-elemental and zero-dimensional natures, these demonstrations for hierarchical functional structures impress the high capability of the nanoarchitectonics approaches. In fact, various hierarchical structures such as cubes with nanorods, hole-in-cube assemblies, face-selectively etched assemblies, and microstructures with mesoporous frameworks are fabricated by easy fabrication protocols. The fabricated fullerene assemblies have been used for various applications including volatile organic compound sensing, microparticle catching, supercapacitors, and photoluminescence systems.
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Affiliation(s)
- Subrata Maji
- Center for Functional Sensor & Actuator (CFSN), Research Center for Functional Materials, National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba 305-0044, Japan;
| | - Lok Kumar Shrestha
- International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba 305-0044, Japan;
| | - Katsuhiko Ariga
- International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba 305-0044, Japan;
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-0827, Japan
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7
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Chen G, Shrestha LK, Ariga K. Zero-to-Two Nanoarchitectonics: Fabrication of Two-Dimensional Materials from Zero-Dimensional Fullerene. Molecules 2021; 26:molecules26154636. [PMID: 34361787 PMCID: PMC8348140 DOI: 10.3390/molecules26154636] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 11/16/2022] Open
Abstract
Nanoarchitectonics of two-dimensional materials from zero-dimensional fullerenes is mainly introduced in this short review. Fullerenes are simple objects with mono-elemental (carbon) composition and zero-dimensional structure. However, fullerenes and their derivatives can create various types of two-dimensional materials. The exemplified approaches demonstrated fabrications of various two-dimensional materials including size-tunable hexagonal fullerene nanosheet, two-dimensional fullerene nano-mesh, van der Waals two-dimensional fullerene solid, fullerene/ferrocene hybrid hexagonal nanosheet, fullerene/cobalt porphyrin hybrid nanosheet, two-dimensional fullerene array in the supramolecular template, two-dimensional van der Waals supramolecular framework, supramolecular fullerene liquid crystal, frustrated layered self-assembly from two-dimensional nanosheet, and hierarchical zero-to-one-to-two dimensional fullerene assembly for cell culture.
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Affiliation(s)
- Guoping Chen
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan;
| | - Lok Kumar Shrestha
- WPI Research Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Ibaraki, Tsukuba 305-0044, Japan;
| | - Katsuhiko Ariga
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan;
- WPI Research Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Ibaraki, Tsukuba 305-0044, Japan;
- Correspondence:
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Ariga K, Shionoya M. Nanoarchitectonics for Coordination Asymmetry and Related Chemistry. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200362] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Katsuhiko Ariga
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
- Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Ariga K. Progress in Molecular Nanoarchitectonics and Materials Nanoarchitectonics. Molecules 2021; 26:1621. [PMID: 33804013 PMCID: PMC7998694 DOI: 10.3390/molecules26061621] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/12/2021] [Accepted: 03/12/2021] [Indexed: 11/24/2022] Open
Abstract
Although various synthetic methodologies including organic synthesis, polymer chemistry, and materials science are the main contributors to the production of functional materials, the importance of regulation of nanoscale structures for better performance has become clear with recent science and technology developments. Therefore, a new research paradigm to produce functional material systems from nanoscale units has to be created as an advancement of nanoscale science. This task is assigned to an emerging concept, nanoarchitectonics, which aims to produce functional materials and functional structures from nanoscale unit components. This can be done through combining nanotechnology with the other research fields such as organic chemistry, supramolecular chemistry, materials science, and bio-related science. In this review article, the basic-level of nanoarchitectonics is first presented with atom/molecular-level structure formations and conversions from molecular units to functional materials. Then, two typical application-oriented nanoarchitectonics efforts in energy-oriented applications and bio-related applications are discussed. Finally, future directions of the molecular and materials nanoarchitectonics concepts for advancement of functional nanomaterials are briefly discussed.
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Affiliation(s)
- Katsuhiko Ariga
- WPI Research Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan;
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
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Ariga K. Nanoarchitectonics Revolution and Evolution: From Small Science to Big Technology. SMALL SCIENCE 2020. [DOI: 10.1002/smsc.202000032] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Katsuhiko Ariga
- World Premier International (WPI) Research Center for Materials Nanoarchitectonics (MANA) National Institute for Materials Science (NIMS) 1-1 Namiki Tsukuba 305-0044 Japan
- Department of Advanced Materials Science Graduate School of Frontier Sciences The University of Tokyo 5-1-5 Kashiwanoha Kashiwa Chiba 277-8561 Japan
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Ariyasu S, Stanfield JK, Aiba Y, Shoji O. Expanding the applicability of cytochrome P450s and other haemoproteins. Curr Opin Chem Biol 2020; 59:155-163. [PMID: 32781431 DOI: 10.1016/j.cbpa.2020.06.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/15/2020] [Accepted: 06/22/2020] [Indexed: 12/20/2022]
Abstract
Cytochrome P450BM3 has long been regarded as a promising candidate for use as a biocatalyst, owing to its excellent efficiency for the hydroxylation of unactivated C-H bonds. However, because of its high substrate specificity, its possible applications have been severely limited. Consequently, various approaches have been proposed to overcome the enzyme's natural limitations, thereby expanding its substrate scope to encompass non-native substrates, evoking chemoselectivity, regioselectivity and stereoselectivity and enabling previously inaccessible chemical conversions. Herein, these approaches will be classified into three categories: (1) mutagenesis including directed evolution, (2) haem substitution with artificial cofactors and (3) use of substrate mimics, 'decoy molecules'. Herein, we highlight the representative work that has been conducted in above three categories for discussion of the future outlook of P450BM3 in green chemistry.
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Affiliation(s)
- Shinya Ariyasu
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Joshua Kyle Stanfield
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Yuichiro Aiba
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Osami Shoji
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan; JST-CREST, Japan.
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Ravishankar S, Suzuki S, Sawada T, Lim S, Serizawa T. Preparation and Dynamic Behavior of Protein-Polymer Complexes Formed with Polymer-Binding Peptides. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2020. [DOI: 10.1246/bcsj.20200021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Samyukta Ravishankar
- School of Chemical & Biomedical Engineering, 70 Nanyang Drive, Block N1.3, Nanyang Technological University, Singapore 637457
| | - Seigo Suzuki
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 2-12-1-H121 Ookayama, Meguro-ku, Tokyo 152-8550
| | - Toshiki Sawada
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 2-12-1-H121 Ookayama, Meguro-ku, Tokyo 152-8550
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, 4-17 Honcho, Kawaguchi, Saitama 332-0012
| | - Sierin Lim
- School of Chemical & Biomedical Engineering, 70 Nanyang Drive, Block N1.3, Nanyang Technological University, Singapore 637457
| | - Takeshi Serizawa
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 2-12-1-H121 Ookayama, Meguro-ku, Tokyo 152-8550
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