151
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Wołczański G, Cal M, Waliczek M, Lisowski M, Stefanowicz P. Self-Synthesizing Models of Helical Proteins Based on Aromatic Disulfide Chemistry. Chemistry 2018; 24:12869-12878. [DOI: 10.1002/chem.201800187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 06/13/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Grzegorz Wołczański
- Faculty of Chemistry; University of Wrocław; F. Joliot-Curie 14 50-383 Wrocław Poland
| | - Marta Cal
- Faculty of Chemistry; University of Wrocław; F. Joliot-Curie 14 50-383 Wrocław Poland
- Institute of Organic and Biomolecular Chemistry; Georg-August University Göttingen; Tammannstrasse 2 D-37077 Göttingen Germany
| | - Mateusz Waliczek
- Faculty of Chemistry; University of Wrocław; F. Joliot-Curie 14 50-383 Wrocław Poland
| | - Marek Lisowski
- Faculty of Chemistry; University of Wrocław; F. Joliot-Curie 14 50-383 Wrocław Poland
| | - Piotr Stefanowicz
- Faculty of Chemistry; University of Wrocław; F. Joliot-Curie 14 50-383 Wrocław Poland
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152
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Hyodo F, Sho T, Maity B, Fujita K, Tachibana Y, Akashi S, Mano M, Hishikawa Y, Matsuo M, Ueno T. Photoinduced in Vivo Magnetic Resonance Imaging (MRI) with Rapid CO Release from an MnCO‐Protein Needle Composite. Chemistry 2018; 24:11578-11583. [DOI: 10.1002/chem.201802445] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Indexed: 11/07/2022]
Affiliation(s)
- Fuminori Hyodo
- Innovation Center for Medical Redox NavigationKyushu University 3-1-1 Maidashi Higashi-ku Fukuoka 812-8582 Japan
- Department of radiologySchool of MedicineGifu University 1-1 Yanagido Gifu 501-1194 Japan
| | - Takeya Sho
- School of Life Science and TechnologyTokyo Institute of Technology B55-4259 Nagatsuta-cho Midori-ku Yokohama 226-8501 Japan
| | - Basudev Maity
- School of Life Science and TechnologyTokyo Institute of Technology B55-4259 Nagatsuta-cho Midori-ku Yokohama 226-8501 Japan
| | - Kenta Fujita
- School of Life Science and TechnologyTokyo Institute of Technology B55-4259 Nagatsuta-cho Midori-ku Yokohama 226-8501 Japan
| | - Yoko Tachibana
- Innovation Center for Medical Redox NavigationKyushu University 3-1-1 Maidashi Higashi-ku Fukuoka 812-8582 Japan
| | - Satoko Akashi
- Graduate School of Medical Life ScienceYokohama City University 1-7-29 Suehiro-cho, Tsurumi-ku Yokohama Kanagawa 230-0045 Japan
| | - Megumi Mano
- School of Life Science and TechnologyTokyo Institute of Technology B55-4259 Nagatsuta-cho Midori-ku Yokohama 226-8501 Japan
| | - Yuki Hishikawa
- School of Life Science and TechnologyTokyo Institute of Technology B55-4259 Nagatsuta-cho Midori-ku Yokohama 226-8501 Japan
| | - Masayuki Matsuo
- Department of radiologySchool of MedicineGifu University 1-1 Yanagido Gifu 501-1194 Japan
| | - Takafumi Ueno
- School of Life Science and TechnologyTokyo Institute of Technology B55-4259 Nagatsuta-cho Midori-ku Yokohama 226-8501 Japan
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153
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Leurs M, Dorn B, Wilhelm S, Manisegaran M, Tiller JC. Multicore Artificial Metalloenzymes Derived from Acylated Proteins as Catalysts for the Enantioselective Dihydroxylation and Epoxidation of Styrene Derivatives. Chemistry 2018; 24:10859-10867. [DOI: 10.1002/chem.201802185] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Melanie Leurs
- Chair of Biomaterials and Polymer Science, Department of Biochemical and Chemical Engineering; TU Dortmund; Emil-Figge-Str. 66 44227 Dortmund Germany
| | - Bjoern Dorn
- Chair of Biomaterials and Polymer Science, Department of Biochemical and Chemical Engineering; TU Dortmund; Emil-Figge-Str. 66 44227 Dortmund Germany
| | - Sascha Wilhelm
- Chair of Biomaterials and Polymer Science, Department of Biochemical and Chemical Engineering; TU Dortmund; Emil-Figge-Str. 66 44227 Dortmund Germany
| | - Magiliny Manisegaran
- Chair of Biomaterials and Polymer Science, Department of Biochemical and Chemical Engineering; TU Dortmund; Emil-Figge-Str. 66 44227 Dortmund Germany
| | - Joerg. C. Tiller
- Chair of Biomaterials and Polymer Science, Department of Biochemical and Chemical Engineering; TU Dortmund; Emil-Figge-Str. 66 44227 Dortmund Germany
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154
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155
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Heinisch T, Schwizer F, Garabedian B, Csibra E, Jeschek M, Vallapurackal J, Pinheiro VB, Marlière P, Panke S, Ward TR. E. coli surface display of streptavidin for directed evolution of an allylic deallylase. Chem Sci 2018; 9:5383-5388. [PMID: 30079176 PMCID: PMC6048633 DOI: 10.1039/c8sc00484f] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/22/2018] [Indexed: 11/21/2022] Open
Abstract
Artificial metalloenzymes (ArMs hereafter) combine attractive features of both homogeneous catalysts and enzymes and offer the potential to implement new-to-nature reactions in living organisms. Herein we present an E. coli surface display platform for streptavidin (Sav hereafter) relying on an Lpp-OmpA anchor. The system was used for the high throughput screening of a bioorthogonal CpRu-based artificial deallylase (ADAse) that uncages an allylcarbamate-protected aminocoumarin 1. Two rounds of directed evolution afforded the double mutant S112M-K121A that displayed a 36-fold increase in surface activity vs. cellular background and a 5.7-fold increased in vitro activity compared to the wild type enzyme. The crystal structure of the best ADAse reveals the importance of mutation S112M to stabilize the cofactor conformation inside the protein.
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Affiliation(s)
- Tillmann Heinisch
- Department of Chemistry , University of Basel , Mattenstrasse 24a , Basel CH-4002 , Switzerland .
| | - Fabian Schwizer
- Department of Chemistry , University of Basel , Mattenstrasse 24a , Basel CH-4002 , Switzerland .
| | - Brett Garabedian
- Department of Chemistry , University of Basel , Mattenstrasse 24a , Basel CH-4002 , Switzerland .
| | - Eszter Csibra
- Institute of Structural and Molecular Biology , University College London , Gower Street , London , WC1E 6BT , UK
| | - Markus Jeschek
- Department of Biosystems Science and Engineering , ETH Zurich , Mattenstrasse 26 , Basel CH-4058 , Switzerland
| | - Jaicy Vallapurackal
- Department of Chemistry , University of Basel , Mattenstrasse 24a , Basel CH-4002 , Switzerland .
| | - Vitor B Pinheiro
- Institute of Structural and Molecular Biology , University College London , Gower Street , London , WC1E 6BT , UK
| | | | - Sven Panke
- Department of Biosystems Science and Engineering , ETH Zurich , Mattenstrasse 26 , Basel CH-4058 , Switzerland
| | - Thomas R Ward
- Department of Chemistry , University of Basel , Mattenstrasse 24a , Basel CH-4002 , Switzerland .
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156
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Ngo AH, Bose S, Do LH. Intracellular Chemistry: Integrating Molecular Inorganic Catalysts with Living Systems. Chemistry 2018; 24:10584-10594. [DOI: 10.1002/chem.201800504] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/16/2018] [Indexed: 01/09/2023]
Affiliation(s)
- Anh H. Ngo
- Department of Chemistry; University of Houston; 4800 Calhoun Road Houston TX 77004 USA
| | - Sohini Bose
- Department of Chemistry; University of Houston; 4800 Calhoun Road Houston TX 77004 USA
| | - Loi H. Do
- Department of Chemistry; University of Houston; 4800 Calhoun Road Houston TX 77004 USA
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157
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Ang TF, Maiangwa J, Salleh AB, Normi YM, Leow TC. Dehalogenases: From Improved Performance to Potential Microbial Dehalogenation Applications. Molecules 2018; 23:E1100. [PMID: 29735886 PMCID: PMC6100074 DOI: 10.3390/molecules23051100] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/07/2018] [Accepted: 04/09/2018] [Indexed: 11/16/2022] Open
Abstract
The variety of halogenated substances and their derivatives widely used as pesticides, herbicides and other industrial products is of great concern due to the hazardous nature of these compounds owing to their toxicity, and persistent environmental pollution. Therefore, from the viewpoint of environmental technology, the need for environmentally relevant enzymes involved in biodegradation of these pollutants has received a great boost. One result of this great deal of attention has been the identification of environmentally relevant bacteria that produce hydrolytic dehalogenases—key enzymes which are considered cost-effective and eco-friendly in the removal and detoxification of these pollutants. These group of enzymes catalyzing the cleavage of the carbon-halogen bond of organohalogen compounds have potential applications in the chemical industry and bioremediation. The dehalogenases make use of fundamentally different strategies with a common mechanism to cleave carbon-halogen bonds whereby, an active-site carboxylate group attacks the substrate C atom bound to the halogen atom to form an ester intermediate and a halide ion with subsequent hydrolysis of the intermediate. Structurally, these dehalogenases have been characterized and shown to use substitution mechanisms that proceed via a covalent aspartyl intermediate. More so, the widest dehalogenation spectrum of electron acceptors tested with bacterial strains which could dehalogenate recalcitrant organohalides has further proven the versatility of bacterial dehalogenators to be considered when determining the fate of halogenated organics at contaminated sites. In this review, the general features of most widely studied bacterial dehalogenases, their structural properties, basis of the degradation of organohalides and their derivatives and how they have been improved for various applications is discussed.
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Affiliation(s)
- Thiau-Fu Ang
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Jonathan Maiangwa
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Abu Bakar Salleh
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Institute of Bioscience, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Yahaya M Normi
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Thean Chor Leow
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Institute of Bioscience, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
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158
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Schneider CR, Manesis AC, Stevenson MJ, Shafaat HS. A photoactive semisynthetic metalloenzyme exhibits complete selectivity for CO 2 reduction in water. Chem Commun (Camb) 2018; 54:4681-4684. [PMID: 29675518 PMCID: PMC5934327 DOI: 10.1039/c8cc01297k] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A series of artificial metalloenzymes containing a ruthenium chromophore and [NiII(cyclam)]2+, both incorporated site-selectively, have been constructed within an azurin protein scaffold. These light-driven, semisynthetic enzymes do not evolve hydrogen, thus displaying complete selectivity for CO2 reduction to CO. Electrostatic effects rather than direct excited-state electron transfer dominate the ruthenium photophysics, suggesting that intramolecular electron transfer from photogenerated RuI to [NiII(cyclam)]2+ represents the first step in catalysis. Stern-Volmer analyses rationalize the observation that ascorbate is the only sacrificial electron donor that supports turnover. Collectively, these results highlight the important interplay of elements that must be considered when developing and characterizing molecular catalysts.
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Affiliation(s)
- Camille R Schneider
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA.
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159
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Korschelt K, Tahir MN, Tremel W. A Step into the Future: Applications of Nanoparticle Enzyme Mimics. Chemistry 2018; 24:9703-9713. [DOI: 10.1002/chem.201800384] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Karsten Korschelt
- Institut für Anorganische Chemie und Analytische Chemie; Johannes-Gutenberg-Universität; Duesbergweg 10-14 55128 Mainz Germany
| | - Muhammad Nawaz Tahir
- Department of Chemistry; King Fahd University of Petroleum and Minerals; Kingdom of Saudi Arabia
| | - Wolfgang Tremel
- Institut für Anorganische Chemie und Analytische Chemie; Johannes-Gutenberg-Universität; Duesbergweg 10-14 55128 Mainz Germany
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160
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Mann SI, Heinisch T, Ward TR, Borovik AS. Coordination chemistry within a protein host: regulation of the secondary coordination sphere. Chem Commun (Camb) 2018; 54:4413-4416. [PMID: 29645031 PMCID: PMC5942233 DOI: 10.1039/c8cc01931b] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Secondary coordination spheres of metal complexes are instrumental in controlling properties that are linked to function. To study these effects in aqueous solutions artificial Cu proteins have been developed using biotin-streptavidin (Sav) technology and their binding of external azide ions investigated. Parallel binding studies were done in crystallo on single crystals of the artificial Cu proteins. Spectroscopic changes in solution are consistent with azide binding to the Cu centers. Structural studies corroborate that a Cu-N3 unit is present in each Sav subunit and reveal the composition of hydrogen bonding (H-bonding) networks that include the coordinated azido ligand. The networks involve amino acid residues and water molecules within the secondary coordination sphere. Mutation of these residues to ones that cannot form H-bonds caused a measurble change in the equilibrium binding constants that were measured in solution. These findings further demonstrate the utility of biotin-Sav technology to prepare water-stable inorganic complexes whose structures can be controlled within both primary and secondary coordination spheres.
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Affiliation(s)
- Samuel I Mann
- Department of Chemistry, 1102 Natural Science II, University of California, Irvine, CA 92697, USA.
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161
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Setiawan D, Brender J, Zhang Y. Recent advances in automated protein design and its future challenges. Expert Opin Drug Discov 2018; 13:587-604. [PMID: 29695210 DOI: 10.1080/17460441.2018.1465922] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
INTRODUCTION Protein function is determined by protein structure which is in turn determined by the corresponding protein sequence. If the rules that cause a protein to adopt a particular structure are understood, it should be possible to refine or even redefine the function of a protein by working backwards from the desired structure to the sequence. Automated protein design attempts to calculate the effects of mutations computationally with the goal of more radical or complex transformations than are accessible by experimental techniques. Areas covered: The authors give a brief overview of the recent methodological advances in computer-aided protein design, showing how methodological choices affect final design and how automated protein design can be used to address problems considered beyond traditional protein engineering, including the creation of novel protein scaffolds for drug development. Also, the authors address specifically the future challenges in the development of automated protein design. Expert opinion: Automated protein design holds potential as a protein engineering technique, particularly in cases where screening by combinatorial mutagenesis is problematic. Considering solubility and immunogenicity issues, automated protein design is initially more likely to make an impact as a research tool for exploring basic biology in drug discovery than in the design of protein biologics.
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Affiliation(s)
- Dani Setiawan
- a Department of Computational Medicine and Bioinformatics , University of Michigan , Ann Arbor , MI , USA
| | - Jeffrey Brender
- b Radiation Biology Branch , Center for Cancer Research, National Cancer Institute - NIH , Bethesda , MD , USA
| | - Yang Zhang
- a Department of Computational Medicine and Bioinformatics , University of Michigan , Ann Arbor , MI , USA.,c Department of Biological Chemistry , University of Michigan , Ann Arbor , MI , USA
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162
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Tebo AG, Pinter TBJ, García-Serres R, Speelman AL, Tard C, Sénéque O, Blondin G, Latour JM, Penner-Hahn J, Lehnert N, Pecoraro VL. Development of a Rubredoxin-Type Center Embedded in a de Dovo-Designed Three-Helix Bundle. Biochemistry 2018; 57:2308-2316. [PMID: 29561598 DOI: 10.1021/acs.biochem.8b00091] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Protein design is a powerful tool for interrogating the basic requirements for the function of a metal site in a way that allows for the selective incorporation of elements that are important for function. Rubredoxins are small electron transfer proteins with a reduction potential centered near 0 mV (vs normal hydrogen electrode). All previous attempts to design a rubredoxin site have focused on incorporating the canonical CXXC motifs in addition to reproducing the peptide fold or using flexible loop regions to define the morphology of the site. We have produced a rubredoxin site in an utterly different fold, a three-helix bundle. The spectra of this construct mimic the ultraviolet-visible, Mössbauer, electron paramagnetic resonance, and magnetic circular dichroism spectra of native rubredoxin. Furthermore, the measured reduction potential suggests that this rubredoxin analogue could function similarly. Thus, we have shown that an α-helical scaffold sustains a rubredoxin site that can cycle with the desired potential between the Fe(II) and Fe(III) states and reproduces the spectroscopic characteristics of this electron transport protein without requiring the classic rubredoxin protein fold.
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Affiliation(s)
- Alison G Tebo
- Program in Chemical Biology , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Tyler B J Pinter
- Department of Chemistry and Biophysics , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Ricardo García-Serres
- Université Grenoble Alpes, CNRS, CEA, BIG, LCBM (UMR 5249), F-38054 Grenoble , France
| | - Amy L Speelman
- Department of Chemistry and Biophysics , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Cédric Tard
- LCM, CNRS, École Polytechnique, Université Paris-Saclay, 91128 Palaiseau Cedex, France
| | - Olivier Sénéque
- Université Grenoble Alpes, CNRS, CEA, BIG, LCBM (UMR 5249), F-38054 Grenoble , France
| | - Geneviève Blondin
- Université Grenoble Alpes, CNRS, CEA, BIG, LCBM (UMR 5249), F-38054 Grenoble , France
| | - Jean-Marc Latour
- Université Grenoble Alpes, CNRS, CEA, BIG, LCBM (UMR 5249), F-38054 Grenoble , France
| | - James Penner-Hahn
- Department of Chemistry and Biophysics , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Nicolai Lehnert
- Department of Chemistry and Biophysics , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Vincent L Pecoraro
- Program in Chemical Biology , University of Michigan , Ann Arbor , Michigan 48109 , United States.,Department of Chemistry and Biophysics , University of Michigan , Ann Arbor , Michigan 48109 , United States
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163
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Esmieu C, Raleiras P, Berggren G. From protein engineering to artificial enzymes - biological and biomimetic approaches towards sustainable hydrogen production. SUSTAINABLE ENERGY & FUELS 2018; 2:724-750. [PMID: 31497651 PMCID: PMC6695573 DOI: 10.1039/c7se00582b] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 01/31/2018] [Indexed: 06/09/2023]
Abstract
Hydrogen gas is used extensively in industry today and is often put forward as a suitable energy carrier due its high energy density. Currently, the main source of molecular hydrogen is fossil fuels via steam reforming. Consequently, novel production methods are required to improve the sustainability of hydrogen gas for industrial processes, as well as paving the way for its implementation as a future solar fuel. Nature has already developed an elaborate hydrogen economy, where the production and consumption of hydrogen gas is catalysed by hydrogenase enzymes. In this review we summarize efforts on engineering and optimizing these enzymes for biological hydrogen gas production, with an emphasis on their inorganic cofactors. Moreover, we will describe how our understanding of these enzymes has been applied for the preparation of bio-inspired/-mimetic systems for efficient and sustainable hydrogen production.
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Affiliation(s)
- C Esmieu
- Department of Chemistry , Ångström Laboratory , Uppsala University , Box 523 , SE-75120 Uppsala , Sweden .
| | - P Raleiras
- Department of Chemistry , Ångström Laboratory , Uppsala University , Box 523 , SE-75120 Uppsala , Sweden .
| | - G Berggren
- Department of Chemistry , Ångström Laboratory , Uppsala University , Box 523 , SE-75120 Uppsala , Sweden .
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164
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Hirotsu M, Santo K, Tanaka Y, Kinoshita I. Iron carbonyl complexes of N,C,S-pincer ligands with a pendant thioether arm: Synthesis, structures and reactivity. Polyhedron 2018. [DOI: 10.1016/j.poly.2017.10.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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165
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Chino M, Leone L, Zambrano G, Pirro F, D'Alonzo D, Firpo V, Aref D, Lista L, Maglio O, Nastri F, Lombardi A. Oxidation catalysis by iron and manganese porphyrins within enzyme-like cages. Biopolymers 2018; 109:e23107. [DOI: 10.1002/bip.23107] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 01/31/2018] [Accepted: 02/05/2018] [Indexed: 01/03/2023]
Affiliation(s)
- Marco Chino
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
| | - Linda Leone
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
| | - Gerardo Zambrano
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
| | - Fabio Pirro
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
| | - Daniele D'Alonzo
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
| | - Vincenzo Firpo
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
| | - Diaa Aref
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
| | - Liliana Lista
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
| | - Ornella Maglio
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
- Institute of Biostructures and Bioimages-National Research Council, Via Mezzocannone 16; Napoli 80134 Italy
| | - Flavia Nastri
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
| | - Angela Lombardi
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
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166
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Valasatava Y, Rosato A, Furnham N, Thornton JM, Andreini C. To what extent do structural changes in catalytic metal sites affect enzyme function? J Inorg Biochem 2018; 179:40-53. [PMID: 29161638 PMCID: PMC5760197 DOI: 10.1016/j.jinorgbio.2017.11.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 11/02/2017] [Accepted: 11/04/2017] [Indexed: 01/09/2023]
Abstract
About half of known enzymatic reactions involve metals. Enzymes belonging to the same superfamily often evolve to catalyze different reactions on the same structural scaffold. The work presented here investigates how functional differentiation, within superfamilies that contain metalloenzymes, relates to structural changes at the catalytic metal site. In general, when the catalytic metal site is unchanged across the enzymes of a superfamily, the functional differentiation within the superfamily tends to be low and the mechanism conserved. Conversely, all types of structural changes in the metal binding site are observed for superfamilies with high functional differentiation. Overall, the catalytic role of the metal ions appears to be one of the most conserved features of the enzyme mechanism within metalloenzyme superfamilies. In particular, when the catalytic role of the metal ion does not involve a redox reaction (i.e. there is no exchange of electrons with the substrate), this role is almost always maintained even when the site undergoes significant structural changes. In these enzymes, functional diversification is most often associated with modifications in the surrounding protein matrix, which has changed so much that the enzyme chemistry is significantly altered. On the other hand, in more than 50% of the examples where the metal has a redox role in catalysis, changes at the metal site modify its catalytic role. Further, we find that there are no examples in our dataset where metal sites with a redox role are lost during evolution. SYNOPSIS In this paper we investigate how functional diversity within superfamilies of metalloenzymes relates to structural changes at the catalytic metal site. Evolution tends to strictly conserve the metal site. When changes occur, they do not modify the catalytic role of non-redox metals whereas they affect the role of redox-active metals.
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Affiliation(s)
- Yana Valasatava
- Magnetic Resonance Center, University of Florence, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Antonio Rosato
- Magnetic Resonance Center, University of Florence, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Nicholas Furnham
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Janet M Thornton
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Claudia Andreini
- Magnetic Resonance Center, University of Florence, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy.
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167
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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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168
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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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169
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Zhang SQ, Chino M, Liu L, Tang Y, Hu X, DeGrado WF, Lombardi A. De Novo Design of Tetranuclear Transition Metal Clusters Stabilized by Hydrogen-Bonded Networks in Helical Bundles. J Am Chem Soc 2018; 140:1294-1304. [PMID: 29249157 PMCID: PMC5860638 DOI: 10.1021/jacs.7b08261] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
De novo design provides an attractive approach to test the mechanism by which metalloproteins define the geometry and reactivity of their metal ion cofactors. While there has been considerable progress in designing proteins that bind transition metal ions including iron-sulfur clusters, the design of tetranuclear clusters with oxygen-rich environments has not been accomplished. Here, we describe the design of tetranuclear clusters, consisting of four Zn2+ and four carboxylate oxygens situated at the vertices of a distorted cube-like structure. The tetra-Zn2+ clusters are bound at a buried site within a four-helix bundle, with each helix donating a single carboxylate (Glu or Asp) and imidazole (His) ligand, as well as second- and third-shell ligands. Overall, the designed site consists of four Zn2+ and 16 polar side chains in a fully connected hydrogen-bonded network. The designed proteins have apolar cores at the top and bottom of the bundle, which drive the assembly of the liganding residues near the center of the bundle. The steric bulk of the apolar residues surrounding the binding site was varied to determine how subtle changes in helix-helix packing affect the binding site. The crystal structures of two of four proteins synthesized were in good agreement with the overall design; both formed a distorted cuboidal site stabilized by flanking second- and third-shell interactions that stabilize the primary ligands. A third structure bound a single Zn2+ in an unanticipated geometry, and the fourth bound multiple Zn2+ at multiple sites at partial occupancy. The metal-binding and conformational properties of the helical bundles in solution, probed by circular dichroism spectroscopy, analytical ultracentrifugation, and NMR, were consistent with the crystal structures.
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Affiliation(s)
- Shao-Qing Zhang
- Department of Chemistry, University of Pennsylvania, 209 South 33rd Street, Philadelphia, PA 19104-6396, United States
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA 94158-9001, United States
| | - Marco Chino
- Department of Chemical Sciences, University of Napoli “Federico II”, Via Cintia, 46, I-80126 Napoli, Italy
| | - Lijun Liu
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA 94158-9001, United States
- DLX Scientific, Lawrence, KS 66049, United States
| | - Youzhi Tang
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA 94158-9001, United States
- College of Veterinary Medicine, South China Agricultural University, Guangdong 510642, China
| | - Xiaozhen Hu
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA 94158-9001, United States
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA 94158-9001, United States
| | - Angela Lombardi
- Department of Chemical Sciences, University of Napoli “Federico II”, Via Cintia, 46, I-80126 Napoli, Italy
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170
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Yu Y, Hu C, Xia L, Wang J. Artificial Metalloenzyme Design with Unnatural Amino Acids and Non-Native Cofactors. ACS Catal 2018. [DOI: 10.1021/acscatal.7b03754] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Yang Yu
- Tianjin
Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Cheng Hu
- Laboratory
of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Lin Xia
- Center
for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
| | - Jiangyun Wang
- Laboratory
of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
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171
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Koebke KJ, Yu F, Salerno E, Van Stappen C, Tebo AG, Penner-Hahn JE, Pecoraro VL. Modifying the Steric Properties in the Second Coordination Sphere of Designed Peptides Leads to Enhancement of Nitrite Reductase Activity. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712757] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Karl J. Koebke
- Department of Chemistry; University of Michigan; Ann Arbor MI 48109 USA
| | - Fangting Yu
- Department of Chemistry; University of Michigan; Ann Arbor MI 48109 USA
| | - Elvin Salerno
- Department of Chemistry; University of Michigan; Ann Arbor MI 48109 USA
| | - Casey Van Stappen
- Department of Chemistry; University of Michigan; Ann Arbor MI 48109 USA
| | - Alison G. Tebo
- Department of Chemistry; University of Michigan; Ann Arbor MI 48109 USA
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172
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Koebke KJ, Yu F, Salerno E, Van Stappen C, Tebo AG, Penner-Hahn JE, Pecoraro VL. Modifying the Steric Properties in the Second Coordination Sphere of Designed Peptides Leads to Enhancement of Nitrite Reductase Activity. Angew Chem Int Ed Engl 2018; 57:3954-3957. [PMID: 29316146 DOI: 10.1002/anie.201712757] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Indexed: 11/10/2022]
Abstract
Protein design is a useful strategy to interrogate the protein structure-function relationship. We demonstrate using a highly modular 3-stranded coiled coil (TRI-peptide system) that a functional type 2 copper center exhibiting copper nitrite reductase (NiR) activity exhibits the highest homogeneous catalytic efficiency under aqueous conditions for the reduction of nitrite to NO and H2 O. Modification of the amino acids in the second coordination sphere of the copper center increases the nitrite reductase activity up to 75-fold compared to previously reported systems. We find also that steric bulk can be used to enforce a three-coordinate CuI in a site, which tends toward two-coordination with decreased steric bulk. This study demonstrates the importance of the second coordination sphere environment both for controlling metal-center ligation and enhancing the catalytic efficiency of metalloenzymes and their analogues.
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Affiliation(s)
- Karl J Koebke
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Fangting Yu
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Elvin Salerno
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Casey Van Stappen
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alison G Tebo
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Vincent L Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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173
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Nye DB, Preimesberger MR, Majumdar A, Lecomte JTJ. Histidine-Lysine Axial Ligand Switching in a Hemoglobin: A Role for Heme Propionates. Biochemistry 2018; 57:631-644. [PMID: 29271191 DOI: 10.1021/acs.biochem.7b01155] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The hemoglobin of Synechococcus sp. PCC 7002, GlbN, is a monomeric group I truncated protein (TrHb1) that coordinates the heme iron with two histidine ligands at neutral pH. One of these is the distal histidine (His46), a residue that can be displaced by dioxygen and other small molecules. Here, we show with mutagenesis, electronic absorption spectroscopy, and nuclear magnetic resonance (NMR) spectroscopy that at high pH and exclusively in the ferrous state, Lys42 competes with His46 for the iron coordination site. When b heme is originally present, the population of the lysine-bound species remains too small for detailed characterization; however, the population can be increased significantly by using dimethyl-esterified heme. Electronic absorption and NMR spectroscopies showed that the reversible ligand switching process occurs with an apparent pKa of 9.3 and a Lys-ligated population of ∼60% at the basic pH limit in the modified holoprotein. The switching rate, which is slow on the chemical shift time scale, was estimated to be 20-30 s-1 by NMR exchange spectroscopy. Lys42-His46 competition and attendant conformational rearrangement appeared to be related to weakened bis-histidine ligation and enhanced backbone dynamics in the ferrous protein. The pH- and redox-dependent ligand exchange process observed in GlbN illustrates the structural plasticity allowed by the TrHb1 fold and demonstrates the importance of electrostatic interactions at the heme periphery for achieving axial ligand selection. An analogy is drawn to the alkaline transition of cytochrome c, in which Lys-Met competition is detected at alkaline pH, but, in contrast to GlbN, in the ferric state only.
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Affiliation(s)
- Dillon B Nye
- T. C. Jenkins Department of Biophysics, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Matthew R Preimesberger
- T. C. Jenkins Department of Biophysics, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Ananya Majumdar
- Biomolecular NMR Center, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Juliette T J Lecomte
- T. C. Jenkins Department of Biophysics, Johns Hopkins University , Baltimore, Maryland 21218, United States
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174
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Renom-Carrasco M, Lefort L. Ligand libraries for high throughput screening of homogeneous catalysts. Chem Soc Rev 2018; 47:5038-5060. [DOI: 10.1039/c7cs00844a] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
This review describes different approaches to construct ligand libraries towards high throughput screening of homogeneous metal catalysts.
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Affiliation(s)
- Marc Renom-Carrasco
- Institut de Chimie de Lyon
- Laboratory C2P2 UMR 5265-CNRS-Université de Lyon 1-CPE Lyon
- 69616 Villeurbanne
- France
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175
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Facchetti G, Rimoldi I. 8-Amino-5,6,7,8-tetrahydroquinoline in iridium(iii) biotinylated Cp* complex as artificial imine reductase. NEW J CHEM 2018. [DOI: 10.1039/c8nj04558e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The imine reductase formed by the (R)-CAMPY ligand bound to the S112M Sav mutant showed an 83% ee in the asymmetric transfer hydrogenation of 6,7-dimethoxy-1-methyl-3,4-dihydroisoquinoline.
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Affiliation(s)
- Giorgio Facchetti
- Dipartimento di Scienze Farmaceutiche
- Università degli Studi di Milano
- 10033 Milano
- Italy
| | - Isabella Rimoldi
- Dipartimento di Scienze Farmaceutiche
- Università degli Studi di Milano
- 10033 Milano
- Italy
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176
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Johnson NA, Wolfe SR, Kabir H, Andrade GA, Yap GPA, Heiden ZM, Moberly JG, Roll MF, Waynant KV. Deconvoluting the Innocent vs. Non-innocent Behavior of N,N-diethylphenylazothioformamide Ligands with Copper Sources. Eur J Inorg Chem 2017; 2017:5576-5581. [PMID: 30410418 PMCID: PMC6217847 DOI: 10.1002/ejic.201701097] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Indexed: 11/07/2022]
Abstract
Redox-active ligands lead to ambiguity in often clearly defined oxidation states of both the metal centre and the ligand. The arylazothioformamide (ATF) ligand class represents a redox-active ligand with three possible redox states (neutral, singly reduced, and doubly reduced). ATF-metal interactions result in strong colorimetric transitions allowing for the use of ATFs in metal detection and/or separations. While previous reports have discussed dissolution of zerovalent metals, the resulting oxidation states of coordination complexes have proved difficult to interpret through X-ray crystallographic analysis alone. This report describes the X-ray crystallographic analysis combined with computational modelling of the ATF ligand and metal complexes to deconvolute the metal and ligand oxidation state of metal-ATF complexes. Metal(ATF)2 complexes that originated from zerovalent metals were found to exist as dicationic metal centers containing two singly reduced ATF ligands. When employing Cu(I) salts instead of Cu(0) to generate copper-ATF complexes, the resulting complexes remained Cu(I) and the ATF ligand remained "innocent", existing in its neutral state. Although the use of CuX (where X = Br or I) or [Cu(NCMe)4]Y (where Y = BF4 or PF6) generated species of the type: [(ATF)Cu(μ-X)]2 and [Cu(ATF)2]Y, respectively, the ATF ligand remained in its neutral state for each species type.
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Affiliation(s)
- Nicolas A Johnson
- Department of Chemistry, University of Idaho, 875 Perimeter Dr. Moscow, ID 83844
| | - Samuel R Wolfe
- Department of Chemical and Materials Engineering, University of Idaho, 875 Perimeter Dr. Moscow, ID 83844
| | - Humayun Kabir
- Department of Chemistry, University of Idaho, 875 Perimeter Dr. Moscow, ID 83844
| | - Gabriel A Andrade
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716
| | - Glenn P A Yap
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716
| | | | - James G Moberly
- Department of Chemical and Materials Engineering, University of Idaho, 875 Perimeter Dr. Moscow, ID 83844
| | - Mark F Roll
- Department of Chemical and Materials Engineering, University of Idaho, 875 Perimeter Dr. Moscow, ID 83844
| | - Kristopher V Waynant
- Department of Chemistry, University of Idaho, 875 Perimeter Dr. Moscow, ID 83844
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177
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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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178
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Espiritu E, Olson TL, Williams JC, Allen JP. Binding and Energetics of Electron Transfer between an Artificial Four-Helix Mn-Protein and Reaction Centers from Rhodobacter sphaeroides. Biochemistry 2017; 56:6460-6469. [PMID: 29131579 DOI: 10.1021/acs.biochem.7b00978] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ability of an artificial four-helix bundle Mn-protein, P1, to bind and transfer an electron to photosynthetic reaction centers from the purple bacterium Rhodobacter sphaeroides was characterized using optical spectroscopy. Upon illumination of reaction centers, an electron is transferred from P, the bacteriochlorophyll dimer, to QA, the primary electron acceptor. The P1 Mn-protein can bind to the reaction center and reduce the oxidized bacteriochlorophyll dimer, P+, with a dissociation constant of 1.2 μM at pH 9.4, comparable to the binding constant of c-type cytochromes. Amino acid substitutions of surface residues on the Mn-protein resulted in increases in the dissociation constant to 8.3 μM. The extent of reduction of P+ by the P1 Mn-protein was dependent on the P/P+ midpoint potential and the pH. Analysis of the free energy difference yielded a midpoint potential of approximately 635 mV at pH 9.4 for the Mn cofactor of the P1 Mn-protein, a value similar to those found for other Mn cofactors in proteins. The linear dependence of -56 mV/pH is consistent with one proton being released upon Mn oxidation, allowing the complex to maintain overall charge neutrality. These outcomes demonstrate the feasibility of designing four-helix bundles and other artificial metalloproteins to bind and transfer electrons to bacterial reaction centers and establish the usefulness of this system as a platform for designing sites to bind novel metal cofactors capable of performing complex oxidation-reduction reactions.
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Affiliation(s)
- Eduardo Espiritu
- School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287-1604, United States
| | - Tien L Olson
- School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287-1604, United States
| | - JoAnn C Williams
- School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287-1604, United States
| | - James P Allen
- School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287-1604, United States
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179
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Nema A, Pareek R, Rai T, Panda D. The Role of Glutathione and Ethanol in Dictating the Emission Dynamics of Natural Resources-Derived Highly Luminescent Carbon Nanodots. ChemistrySelect 2017. [DOI: 10.1002/slct.201702455] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Akansh Nema
- Rajiv Gandhi Institute of Petroleum Technology; Institute of National Importance; Jais- 229304, Uttar Pradesh INDIA
| | - Rakshit Pareek
- Rajiv Gandhi Institute of Petroleum Technology; Institute of National Importance; Jais- 229304, Uttar Pradesh INDIA
| | - Tripti Rai
- Rajiv Gandhi Institute of Petroleum Technology; Institute of National Importance; Jais- 229304, Uttar Pradesh INDIA
| | - Debashis Panda
- Rajiv Gandhi Institute of Petroleum Technology; Institute of National Importance; Jais- 229304, Uttar Pradesh INDIA
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180
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Design of artificial metalloproteins/metalloenzymes by tuning noncovalent interactions. J Biol Inorg Chem 2017; 23:7-25. [DOI: 10.1007/s00775-017-1506-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 09/20/2017] [Indexed: 12/12/2022]
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181
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Lopez S, Rondot L, Leprêtre C, Marchi-Delapierre C, Ménage S, Cavazza C. Cross-Linked Artificial Enzyme Crystals as Heterogeneous Catalysts for Oxidation Reactions. J Am Chem Soc 2017; 139:17994-18002. [PMID: 29148757 DOI: 10.1021/jacs.7b09343] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Designing systems that merge the advantages of heterogeneous catalysis, enzymology, and molecular catalysis represents the next major goal for sustainable chemistry. Cross-linked enzyme crystals display most of these essential assets (well-designed mesoporous support, protein selectivity, and molecular recognition of substrates). Nevertheless, a lack of reaction diversity, particularly in the field of oxidation, remains a constraint for their increased use in the field. Here, thanks to the design of cross-linked artificial nonheme iron oxygenase crystals, we filled this gap by developing biobased heterogeneous catalysts capable of oxidizing carbon-carbon double bonds. First, reductive O2 activation induces selective oxidative cleavage, revealing the indestructible character of the solid catalyst (at least 30 000 turnover numbers without any loss of activity). Second, the use of 2-electron oxidants allows selective and high-efficiency hydroxychlorination with thousands of turnover numbers. This new technology by far outperforms catalysis using the inorganic complexes alone, or even the artificial enzymes in solution. The combination of easy catalyst synthesis, the improvement of "omic" technologies, and automation of protein crystallization makes this strategy a real opportunity for the future of (bio)catalysis.
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Affiliation(s)
- Sarah Lopez
- Université Grenoble-Alpes , Grenoble F-38000, France.,CEA, BIG, Laboratory of Chemistry and Biology of Metals, BioCE and BioCat group , Grenoble F-38054, France.,CNRS, UMR5249 , Grenoble F-38054, France
| | - Laurianne Rondot
- Université Grenoble-Alpes , Grenoble F-38000, France.,CEA, BIG, Laboratory of Chemistry and Biology of Metals, BioCE and BioCat group , Grenoble F-38054, France.,CNRS, UMR5249 , Grenoble F-38054, France
| | - Chloé Leprêtre
- Université Grenoble-Alpes , Grenoble F-38000, France.,CEA, BIG, Laboratory of Chemistry and Biology of Metals, BioCE and BioCat group , Grenoble F-38054, France.,CNRS, UMR5249 , Grenoble F-38054, France
| | - Caroline Marchi-Delapierre
- Université Grenoble-Alpes , Grenoble F-38000, France.,CEA, BIG, Laboratory of Chemistry and Biology of Metals, BioCE and BioCat group , Grenoble F-38054, France.,CNRS, UMR5249 , Grenoble F-38054, France
| | - Stéphane Ménage
- Université Grenoble-Alpes , Grenoble F-38000, France.,CEA, BIG, Laboratory of Chemistry and Biology of Metals, BioCE and BioCat group , Grenoble F-38054, France.,CNRS, UMR5249 , Grenoble F-38054, France
| | - Christine Cavazza
- Université Grenoble-Alpes , Grenoble F-38000, France.,CEA, BIG, Laboratory of Chemistry and Biology of Metals, BioCE and BioCat group , Grenoble F-38054, France.,CNRS, UMR5249 , Grenoble F-38054, France
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182
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Chino M, Leone L, Maglio O, D'Alonzo D, Pirro F, Pavone V, Nastri F, Lombardi A. A De Novo Heterodimeric Due Ferri Protein Minimizes the Release of Reactive Intermediates in Dioxygen-Dependent Oxidation. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707637] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Marco Chino
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
| | - Linda Leone
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
| | - Ornella Maglio
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
- IBB-National Research Council; Via Mezzocannone 16 80134 Napoli Italy
| | - Daniele D'Alonzo
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
| | - Fabio Pirro
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
| | - Vincenzo Pavone
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
| | - Flavia Nastri
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
| | - Angela Lombardi
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
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183
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Cao-Milán R, He LD, Shorkey S, Tonga GY, Wang LS, Zhang X, Uddin I, Das R, Sulak M, Rotello VM. Modulating the Catalytic Activity of Enzyme-like Nanoparticles Through their Surface Functionalization. MOLECULAR SYSTEMS DESIGN & ENGINEERING 2017; 2:624-628. [PMID: 29430303 PMCID: PMC5805145 DOI: 10.1039/c7me00055c] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The inclusion of transition metal catalysts into nanoparticle scaffolds permits the creation of catalytic nanosystems (nanozymes) able to imitate the behaviour of natural enzymes. Here we report the fabrication of a family of nanozymes comprised of bioorthogonal ruthenium catalysts inserted in the protective monolayer of gold nanoparticles. By introducing simple modifications to the functional groups at the surface of the nanozymes, we have demonstrated control over the kinetic mechanism of our system. Cationic nanozymes with hydrophobic surface functionalities tend to replicate the classical Michaelis Menten model, while those with polar groups display substrate inhibition behaviour, a key mechanism present in 20 % of natural enzymes. The structural parameters described herein can be used for creating artificial nanosystems that mimic the complexity observed in cell machinery.
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Affiliation(s)
- Roberto Cao-Milán
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003, USA
| | - Luke D He
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003, USA
| | - Spencer Shorkey
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003, USA
| | - Gulen Y Tonga
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003, USA
| | - Li-Sheng Wang
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003, USA
| | - Xianzhi Zhang
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003, USA
| | - Imad Uddin
- Department of Chemistry, Hazara University, Mansehra 21120, Pakistan
| | - Riddha Das
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003, USA
| | - Mine Sulak
- School of Applied Science, Pamukkale University, 20600, Çivril, Denizli, Turkey
| | - Vincent M Rotello
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003, USA
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184
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Nangle SN, Sakimoto KK, Silver PA, Nocera DG. Biological-inorganic hybrid systems as a generalized platform for chemical production. Curr Opin Chem Biol 2017; 41:107-113. [DOI: 10.1016/j.cbpa.2017.10.023] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 10/16/2017] [Accepted: 10/20/2017] [Indexed: 12/16/2022]
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185
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Olson TL, Espiritu E, Edwardraja S, Canarie E, Flores M, Williams JC, Ghirlanda G, Allen JP. Biochemical and spectroscopic characterization of dinuclear Mn-sites in artificial four-helix bundle proteins. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2017; 1858:945-954. [PMID: 28882760 DOI: 10.1016/j.bbabio.2017.08.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 08/28/2017] [Accepted: 08/31/2017] [Indexed: 01/18/2023]
Abstract
To better understand metalloproteins with Mn-clusters, we have designed artificial four-helix bundles to have one, two, or three dinuclear metal centers able to bind Mn(II). Circular dichroism measurements showed that the Mn-proteins have substantial α-helix content, and analysis of electron paramagnetic resonance spectra is consistent with the designed number of bound Mn-clusters. The Mn-proteins were shown to catalyze the conversion of hydrogen peroxide into molecular oxygen. The loss of hydrogen peroxide was dependent upon the concentration of protein with bound Mn, with the proteins containing multiple Mn-clusters showing greater activity. Using an oxygen sensor, the oxygen concentration was found to increase with a rate up to 0.4μM/min, which was dependent upon the concentrations of hydrogen peroxide and the Mn-protein. In addition, the Mn-proteins were shown to serve as electron donors to bacterial reaction centers using optical spectroscopy. Similar binding of the Mn-proteins to reaction centers was observed with an average dissociation constant of 2.3μM. The Mn-proteins with three metal centers were more effective at this electron transfer reaction than the Mn-proteins with one or two metal centers. Thus, multiple Mn-clusters can be incorporated into four-helix bundles with the capability of performing catalysis and electron transfer to a natural protein.
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Affiliation(s)
- Tien L Olson
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Eduardo Espiritu
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | | | - Elizabeth Canarie
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Marco Flores
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - JoAnn C Williams
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Giovanna Ghirlanda
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - James P Allen
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.
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186
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Fast CS, Vahidi S, Konermann L. Changes in Enzyme Structural Dynamics Studied by Hydrogen Exchange-Mass Spectrometry: Ligand Binding Effects or Catalytically Relevant Motions? Anal Chem 2017; 89:13326-13333. [DOI: 10.1021/acs.analchem.7b03506] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Courtney S. Fast
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Siavash Vahidi
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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187
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Keller SG, Pannwitz A, Mallin H, Wenger OS, Ward TR. Streptavidin as a Scaffold for Light-Induced Long-Lived Charge Separation. Chemistry 2017; 23:18019-18024. [PMID: 29024136 DOI: 10.1002/chem.201703885] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Indexed: 01/03/2023]
Abstract
Long-lived photo-driven charge separation is demonstrated by assembling a triad on a protein scaffold. For this purpose, a biotinylated triarylamine was added to a RuII -streptavidin conjugate bearing a methyl viologen electron acceptor covalently linked to the N-terminus of streptavidin. To improve the rate and lifetime of the electron transfer, a negative patch consisting of up to three additional negatively charged amino acids was engineered through mutagenesis close to the biotin-binding pocket of streptavidin. Time-resolved laser spectroscopy revealed that the covalent attachment and the negative patch were beneficial for charge separation within the streptavidin hosted triad; the charge separated state was generated within the duration of the excitation laser pulse, and lifetimes up to 3120 ns could be achieved with the optimized supramolecular triad.
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Affiliation(s)
- Sascha G Keller
- Department of Chemistry, University of Basel, Mattenstrasse 24a, CH-4002, Basel, Switzerland
| | - Andrea Pannwitz
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, CH-4056, Basel, Switzerland
| | - Hendrik Mallin
- Department of Chemistry, University of Basel, Mattenstrasse 24a, CH-4002, Basel, Switzerland
| | - Oliver S Wenger
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, CH-4056, Basel, Switzerland
| | - Thomas R Ward
- Department of Chemistry, University of Basel, Mattenstrasse 24a, CH-4002, Basel, Switzerland
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188
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Chino M, Leone L, Maglio O, D'Alonzo D, Pirro F, Pavone V, Nastri F, Lombardi A. A De Novo Heterodimeric Due Ferri Protein Minimizes the Release of Reactive Intermediates in Dioxygen-Dependent Oxidation. Angew Chem Int Ed Engl 2017; 56:15580-15583. [DOI: 10.1002/anie.201707637] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Indexed: 12/29/2022]
Affiliation(s)
- Marco Chino
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
| | - Linda Leone
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
| | - Ornella Maglio
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
- IBB-National Research Council; Via Mezzocannone 16 80134 Napoli Italy
| | - Daniele D'Alonzo
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
| | - Fabio Pirro
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
| | - Vincenzo Pavone
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
| | - Flavia Nastri
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
| | - Angela Lombardi
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
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189
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Song WJ, Yu J, Tezcan FA. Importance of Scaffold Flexibility/Rigidity in the Design and Directed Evolution of Artificial Metallo-β-lactamases. J Am Chem Soc 2017; 139:16772-16779. [PMID: 28992705 DOI: 10.1021/jacs.7b08981] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We describe the design and evolution of catalytic hydrolase activity on a supramolecular protein scaffold, Zn4:C96RIDC14, which was constructed from cytochrome cb562 building blocks via a metal-templating strategy. Previously, we reported that Zn4:C96RIDC14 could be tailored with tripodal (His/His/Glu), unsaturated Zn coordination motifs in its interfaces to generate a variant termed Zn8:A104AB34, which in turn displayed catalytic activity for the hydrolysis of activated esters and β-lactam antibiotics. Zn8:A104AB34 was subsequently subjected to directed evolution via an in vivo selection strategy, leading to a variant Zn8:A104/G57AB34 which displayed enzyme-like Michaelis-Menten behavior for ampicillin hydrolysis. A criterion for the evolutionary utility or designability of a new protein structure is its ability to accommodate different active sites. With this in mind, we examined whether Zn4:C96RIDC14 could be tailored with alternative Zn coordination sites that could similarly display evolvable catalytic activities. We report here a detailed structural and functional characterization of new variant Zn8:AB54, which houses similar, unsaturated Zn coordination sites to those in Zn8:A104/G57AB34, but in completely different microenvironments. Zn8:AB54 displays Michaelis-Menten behavior for ampicillin hydrolysis without any optimization. Yet, the subsequent directed evolution of Zn8:AB54 revealed limited catalytic improvement, which we ascribed to the local protein rigidity surrounding the Zn centers and the lack of evolvable loop structures nearby. The relaxation of local rigidity via the elimination of adjacent disulfide linkages led to a considerable structural transformation with a concomitant improvement in β-lactamase activity. Our findings reaffirm previous observations that the delicate balance between protein flexibility and stability is crucial for enzyme design and evolution.
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Affiliation(s)
- Woon Ju Song
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093-0356, United States.,Department of Chemistry, Seoul National University , Seoul 08826, Korea
| | - Jaeseung Yu
- Department of Chemistry, Seoul National University , Seoul 08826, Korea
| | - F Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093-0356, United States
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190
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Manin NG, Kolker AM. Thermodynamic properties of LiCl solutions in N-methylacetamide at 308.15–328.15 K. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2017. [DOI: 10.1134/s0036024417120184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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191
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Vinogradova EV. Organometallic chemical biology: an organometallic approach to bioconjugation. PURE APPL CHEM 2017. [DOI: 10.1515/pac-2017-0207] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
AbstractThis review summarizes the history and recent developments of the field of organometallic chemical biology with a particular emphasis on the development of novel bioconjugation approaches. Over the years, numerous transformations have emerged for biomolecule modification with the use of organometallic reagents; these include [3+2] cycloadditions, C–C, C–S, C–N, and C–O bond forming processes, as well as metal-mediated deprotection (“decaging”) reactions. These conceptually new additions to the chemical biology toolkit highlight the potential of organometallic chemistry to make a significant impact in the field of chemical biology by providing further opportunities for the development of chemoselective, site-specific and spatially resolved methods for biomolecule structure and function manipulation. Examples of these transformations, as well as existing challenges and future prospects of this rapidly developing field are highlighted in this review.
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192
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Jeschek M, Panke S, Ward TR. Artificial Metalloenzymes on the Verge of New-to-Nature Metabolism. Trends Biotechnol 2017; 36:60-72. [PMID: 29061328 DOI: 10.1016/j.tibtech.2017.10.003] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 09/29/2017] [Accepted: 10/02/2017] [Indexed: 01/13/2023]
Abstract
Residing at the interface of chemistry and biotechnology, artificial metalloenzymes (ArMs) offer an attractive technology to combine the versatile reaction repertoire of transition metal catalysts with the exquisite catalytic features of enzymes. While earlier efforts in this field predominantly comprised studies in well-defined test-tube environments, a trend towards exploiting ArMs in more complex environments has recently emerged. Integration of these artificial biocatalysts in enzymatic cascades and using them in whole-cell biotransformations and in vivo opens up entirely novel prospects for both preparative chemistry and synthetic biology. We highlight selected recent developments with a particular focus on challenges and opportunities in the in vivo application of ArMs.
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Affiliation(s)
- Markus Jeschek
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel, Switzerland.
| | - Sven Panke
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel, Switzerland
| | - Thomas R Ward
- Department of Chemistry, University of Basel, Basel, Switzerland
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193
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Dang B, Wu H, Mulligan VK, Mravic M, Wu Y, Lemmin T, Ford A, Silva DA, Baker D, DeGrado WF. De novo design of covalently constrained mesosize protein scaffolds with unique tertiary structures. Proc Natl Acad Sci U S A 2017; 114:10852-10857. [PMID: 28973862 PMCID: PMC5642715 DOI: 10.1073/pnas.1710695114] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The folding of natural proteins typically relies on hydrophobic packing, metal binding, or disulfide bond formation in the protein core. Alternatively, a 3D structure can be defined by incorporating a multivalent cross-linking agent, and this approach has been successfully developed for the selection of bicyclic peptides from large random-sequence libraries. By contrast, there is no general method for the de novo computational design of multicross-linked proteins with predictable and well-defined folds, including ones not found in nature. Here we use Rosetta and Tertiary Motifs (TERMs) to design small proteins that fold around multivalent cross-linkers. The hydrophobic cross-linkers stabilize the fold by macrocyclic restraints, and they also form an integral part of a small apolar core. The designed CovCore proteins were prepared by chemical synthesis, and their structures were determined by solution NMR or X-ray crystallography. These mesosized proteins, lying between conventional proteins and small peptides, are easily accessible either through biosynthetic precursors or chemical synthesis. The unique tertiary structures and ease of synthesis of CovCore proteins indicate that they should provide versatile templates for developing inhibitors of protein-protein interactions.
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Affiliation(s)
- Bobo Dang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
| | - Haifan Wu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
| | | | - Marco Mravic
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
| | - Yibing Wu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
| | - Thomas Lemmin
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
| | - Alexander Ford
- Department of Biochemistry, University of Washington, Seattle, WA 98195
| | | | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158;
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194
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Lupi F, Marzo T, D'Adamio G, Cretella S, Cardona F, Messori L, Goti A. Diruthenium Diacetate Catalysed Aerobic Oxidation of Hydroxylamines and Improved Chemoselectivity by Immobilisation to Lysozyme. ChemCatChem 2017. [DOI: 10.1002/cctc.201701083] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Flavia Lupi
- Dipartimento di Chimica “Ugo Schiff”; Università di Firenze; Via della Lastruccia 3-13 50019 Sesto Fiorentino (FI) Italy
- LENS; University of Florence; Via Nello Carrara 1 50019 Sesto Fiorentino (FI) Italy
| | - Tiziano Marzo
- Dipartimento di Chimica “Ugo Schiff”; Università di Firenze; Via della Lastruccia 3-13 50019 Sesto Fiorentino (FI) Italy
- Dipartimento di Chimica e Chimica Industriale (DCCI); Università di Pisa; Via Moruzzi, 13 56124 Pisa Italy
| | - Giampiero D'Adamio
- Dipartimento di Chimica “Ugo Schiff”; Università di Firenze; Via della Lastruccia 3-13 50019 Sesto Fiorentino (FI) Italy
| | - Sara Cretella
- Dipartimento di Chimica “Ugo Schiff”; Università di Firenze; Via della Lastruccia 3-13 50019 Sesto Fiorentino (FI) Italy
| | - Francesca Cardona
- Dipartimento di Chimica “Ugo Schiff”; Università di Firenze; Via della Lastruccia 3-13 50019 Sesto Fiorentino (FI) Italy
- Associated with CNR-INO; Via Nello Carrara 1 Sesto Fiorentino (FI) Italy
| | - Luigi Messori
- Dipartimento di Chimica “Ugo Schiff”; Università di Firenze; Via della Lastruccia 3-13 50019 Sesto Fiorentino (FI) Italy
| | - Andrea Goti
- Dipartimento di Chimica “Ugo Schiff”; Università di Firenze; Via della Lastruccia 3-13 50019 Sesto Fiorentino (FI) Italy
- Associated with CNR-INO; Via Nello Carrara 1 Sesto Fiorentino (FI) Italy
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195
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Drienovská I, Alonso-Cotchico L, Vidossich P, Lledós A, Maréchal JD, Roelfes G. Design of an enantioselective artificial metallo-hydratase enzyme containing an unnatural metal-binding amino acid. Chem Sci 2017; 8:7228-7235. [PMID: 29081955 PMCID: PMC5633786 DOI: 10.1039/c7sc03477f] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 09/01/2017] [Indexed: 01/04/2023] Open
Abstract
The design of artificial metalloenzymes is a challenging, yet ultimately highly rewarding objective because of the potential for accessing new-to-nature reactions. One of the main challenges is identifying catalytically active substrate-metal cofactor-host geometries. The advent of expanded genetic code methods for the in vivo incorporation of non-canonical metal-binding amino acids into proteins allow to address an important aspect of this challenge: the creation of a stable, well-defined metal-binding site. Here, we report a designed artificial metallohydratase, based on the transcriptional repressor lactococcal multidrug resistance regulator (LmrR), in which the non-canonical amino acid (2,2'-bipyridin-5yl)alanine is used to bind the catalytic Cu(ii) ion. Starting from a set of empirical pre-conditions, a combination of cluster model calculations (QM), protein-ligand docking and molecular dynamics simulations was used to propose metallohydratase variants, that were experimentally verified. The agreement observed between the computationally predicted and experimentally observed catalysis results demonstrates the power of the artificial metalloenzyme design approach presented here.
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Affiliation(s)
- Ivana Drienovská
- Stratingh Institute for Chemistry , University of Groningen , Nijenborgh 4 , 9747 AG Groningen , Netherlands .
| | - Lur Alonso-Cotchico
- Departament de Química , Universitat Autònoma de Barcelona , Edifici C.n. , 08193 Cerdanyola del Vallés , Barcelona , Spain .
| | - Pietro Vidossich
- Departament de Química , Universitat Autònoma de Barcelona , Edifici C.n. , 08193 Cerdanyola del Vallés , Barcelona , Spain .
| | - Agustí Lledós
- Departament de Química , Universitat Autònoma de Barcelona , Edifici C.n. , 08193 Cerdanyola del Vallés , Barcelona , Spain .
| | - Jean-Didier Maréchal
- Departament de Química , Universitat Autònoma de Barcelona , Edifici C.n. , 08193 Cerdanyola del Vallés , Barcelona , Spain .
| | - Gerard Roelfes
- Stratingh Institute for Chemistry , University of Groningen , Nijenborgh 4 , 9747 AG Groningen , Netherlands .
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196
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Baker EG, Bartlett GJ, Porter Goff KL, Woolfson DN. Miniprotein Design: Past, Present, and Prospects. Acc Chem Res 2017; 50:2085-2092. [PMID: 28832117 DOI: 10.1021/acs.accounts.7b00186] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The design and study of miniproteins, that is, polypeptide chains <40 amino acids in length that adopt defined and stable 3D structures, is resurgent. Miniproteins offer possibilities for reducing the complexity of larger proteins and so present new routes to studying sequence-to-structure and sequence-to-stability relationships in proteins generally. They also provide modules for protein design by pieces and, with this, prospects for building more-complex or even entirely new protein structures. In addition, miniproteins are useful scaffolds for templating functional domains, for example, those involved in protein-protein interactions, catalysis, and biomolecular binding, leading to potential applications in biotechnology and medicine. Here we select examples from almost four decades of miniprotein design, development, and dissection. Simply because of the word limit for this Account, we focus on miniproteins that are cooperatively folded monomers in solution and not stabilized by cross-linking or metal binding. In these cases, the optimization of noncovalent interactions is even more critical for the maintenance of the folded states than in larger proteins. Our chronology and catalogue highlights themes in miniproteins, which we explore further and begin to put on a firmer footing through an analysis of the miniprotein structures that have been deposited in the Protein Data Bank (PDB) thus far. Specifically, and compared with larger proteins, miniproteins generally have a lower proportion of residues in regular secondary structure elements (α helices, β strands, and polyproline-II helices) and, concomitantly, more residues in well-structured loops. This allows distortions of the backbone enabling mini-hydrophobic cores to be made. This also contrasts with larger proteins, which can achieve hydrophobic cores through tertiary contacts between distant regions of sequence. On average, miniproteins have a higher proportion of aromatic residues than larger proteins, and specifically electron-rich Trp and Tyr, which are often found in combination with Pro and Arg to render networks of CH-π or cation-π interactions. Miniproteins also have a higher proportion of the long-chain charged amino acids (Arg, Glu, and Lys), which presumably reflects salt-bridge formation and their greater surface area-to-volume ratio. Together, these amino-acid preferences appear to support greater densities of noncovalent interactions in miniproteins compared with larger proteins. We anticipate that with recent developments such as parametric protein design, it will become increasingly routine to use computation to generate and evaluate models for miniproteins in silico ahead of experimental studies. This could include accessing new structures comprising secondary structure elements linked in previously unseen configurations. The improved understanding of the noncovalent interactions that stabilize the folded states of such miniproteins that we are witnessing through both in-depth bioinformatics analyses and experimental testing will feed these computational protein designs. With this in mind, we can expect a new and exciting era for miniprotein design, study, and application.
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Affiliation(s)
- Emily G. Baker
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Gail J. Bartlett
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | | | - Derek N. Woolfson
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
- School
of Biochemistry, University of Bristol, Biomedical Sciences Building, University
Walk, Bristol BS8 1TD, U.K
- BrisSynBio
and the Bristol BioDesign Institute, University of Bristol, Life Sciences
Building, Tyndall Avenue, Bristol BS8 1TQ, U.K
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197
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Itel F, Schattling PS, Zhang Y, Städler B. Enzymes as key features in therapeutic cell mimicry. Adv Drug Deliv Rev 2017; 118:94-108. [PMID: 28916495 DOI: 10.1016/j.addr.2017.09.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/21/2017] [Accepted: 09/07/2017] [Indexed: 11/19/2022]
Abstract
Cell mimicry is a nature inspired concept that aims to substitute for missing or lost (sub)cellular function. This review focuses on the latest advancements in the use of enzymes in cell mimicry for encapsulated catalysis and artificial motility in synthetic bottom-up assemblies with emphasis on the biological response in cell culture or more rarely in animal models. Entities across the length scale from nano-sized enzyme mimics, sub-micron sized artificial organelles and self-propelled particles (swimmers) to micron-sized artificial cells are discussed. Although the field remains in its infancy, the primary aim of this review is to illustrate the advent of nature-mimicking artificial molecules and assemblies on their way to become a complementary alternative to their role models for diverse biomedical purposes.
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Affiliation(s)
- Fabian Itel
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus 8000, Denmark
| | - Philipp S Schattling
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus 8000, Denmark
| | - Yan Zhang
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus 8000, Denmark
| | - Brigitte Städler
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus 8000, Denmark.
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198
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Du B, Li D, Wang J, Wang E. Designing metal-contained enzyme mimics for prodrug activation. Adv Drug Deliv Rev 2017; 118:78-93. [PMID: 28412325 DOI: 10.1016/j.addr.2017.04.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 03/22/2017] [Accepted: 04/04/2017] [Indexed: 01/09/2023]
Abstract
Enzyme-activated prodrug therapy (EAPT) is a widely-used and effective treatment method for cancer by converting prodrugs into drugs at the demanded time and space, whose key step is prodrug activation. Traditional prodrug activations are mostly dependent on natural enzymes, which are unstable, expensive and hard to be functionalized. The emerging enzyme mimics, especially the metal-contained enzyme mimics (MEMs), provide a potential chance for improving the traditional EAPT because of their high stability, low cost and easiness of preparation and functionalization. The existing MEMs can be classified into three categories: catalytic core-scaffold MEM (csMEM), nanoparticle MEM (npMEMs) and metal-organic framework (MOF) MEM (mofMEM). These MEMs can mimic diverse functions corresponding to natural enzymes, and some of which are potentially used in prodrug activation, such as DNase, RNase, carbonate esterase, etc. In this review, we briefly summarize the MEMs according to their structure and composition, and highlight the successful and potential applications for prodrug activation mediated by hydrolase-like and oxidoreductase-like MEMs.
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199
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Abstract
![]()
The
year 2017 marks the twentieth anniversary of terpenoid cyclase
structural biology: a trio of terpenoid cyclase structures reported
together in 1997 were the first to set the foundation for understanding
the enzymes largely responsible for the exquisite chemodiversity of
more than 80000 terpenoid natural products. Terpenoid cyclases catalyze
the most complex chemical reactions in biology, in that more than
half of the substrate carbon atoms undergo changes in bonding and
hybridization during a single enzyme-catalyzed cyclization reaction.
The past two decades have witnessed structural, functional, and computational
studies illuminating the modes of substrate activation that initiate
the cyclization cascade, the management and manipulation of high-energy
carbocation intermediates that propagate the cyclization cascade,
and the chemical strategies that terminate the cyclization cascade.
The role of the terpenoid cyclase as a template for catalysis is paramount
to its function, and protein engineering can be used to reprogram
the cyclization cascade to generate alternative and commercially important
products. Here, I review key advances in terpenoid cyclase structural
and chemical biology, focusing mainly on terpenoid cyclases and related
prenyltransferases for which X-ray crystal structures have informed
and advanced our understanding of enzyme structure and function.
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Affiliation(s)
- David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania , 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
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Affiliation(s)
- Yasunori Okamoto
- Department of Chemistry; University of Basel; Spitalstrasse 51 4056 Basel Switzerland
| | - Thomas R. Ward
- Department of Chemistry; University of Basel; Spitalstrasse 51 4056 Basel Switzerland
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