1
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Riegerová P, Horváth M, Šebesta F, Sýkora J, Šulc M, Vlček A. Single-step purification and characterization of Pseudomonas aeruginosa azurin. Protein Expr Purif 2024; 224:106566. [PMID: 39128594 DOI: 10.1016/j.pep.2024.106566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 07/30/2024] [Accepted: 08/06/2024] [Indexed: 08/13/2024]
Abstract
Azurin is a small periplasmic blue copper protein found in bacterial strains such as Pseudomonas and Alcaligenes where it facilitates denitrification. Azurin is extensively studied for its ability to mediate electron-transfer processes, but it has also sparked interest of the pharmaceutical community as a potential antimicrobial or anticancer agent. Here we offer a novel approach for expression and single-step purification of azurin in Escherichia coli with high yields and optimal metalation. A fusion tag strategy using an N-terminal GST tag was employed to obtain pure protein without requiring any additional purification steps. After the on-column cleavage by HRV 3C Protease, azurin is collected and additionally incubated with copper sulphate to ensure sufficient metalation. UV-VIS absorption, mass spectroscopy, and circular dichroism analysis all validated the effective production of azurin, appropriate protein folding and the development of an active site with an associated cofactor. MD simulations verified that incorporation of the N-terminal GPLGS segment does not affect azurin structure. In addition, the biological activity of azurin was tested in HeLa cells.
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Affiliation(s)
- Petra Riegerová
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 2155/3, 182 23, Prague, Czech Republic.
| | - Matej Horváth
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 2155/3, 182 23, Prague, Czech Republic; Department of Cell Biology, Charles University, BIOCEV, Průmyslová 595, 252 50, Vestec, Czech Republic
| | - Filip Šebesta
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 2155/3, 182 23, Prague, Czech Republic; Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16, Prague 2, Czech Republic
| | - Jan Sýkora
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 2155/3, 182 23, Prague, Czech Republic
| | - Miroslav Šulc
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030, 128 43, Prague 2, Czech Republic
| | - Antonín Vlček
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 2155/3, 182 23, Prague, Czech Republic; Queen Mary University of London, Department of Chemistry, Mile End Road, London, E1 4NS, United Kingdom.
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2
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Wei Y, Li P. Theoretical insights into the reduction of Azurin metal site with unnatural amino acid substitutions. J Inorg Biochem 2024; 259:112651. [PMID: 38968926 DOI: 10.1016/j.jinorgbio.2024.112651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/10/2024] [Accepted: 06/21/2024] [Indexed: 07/07/2024]
Abstract
Copper-containing proteins play crucial roles in biological systems. Azurin is a copper-containing protein which has a Type 1 copper site that facilitates electron transfer in the cytochrome chain. Previous research has highlighted the significant impact of mutations in the axial Met121 of the copper site on the reduction potential. However, the mechanism of this regulation has not been fully established. In this study, we employed theoretical modeling to investigate the reduction of the Type 1 copper site, focusing on how unnatural amino acid substitutions at Met121 influence its behavior. Our findings demonstrated a strong linear correlation between electrostatic interactions and the reduction potential of the copper site, which indicates that the perturbation of the reduction potential is primarily influenced by electrostatic interactions between the metal ion and the ligating atom. Furthermore, we found that CF/π and CF…H interactions could induce subtle changes in geometry and hence impact the electronic properties of the systems under study. In addition, our calculations suggest the coordination mode and ion-ligand distance could significantly impact the reduction potential of a copper site. Overall, this study offers valuable insights into the structural and electronic properties of the Type 1 copper site, which could potentially guide the design of future artificial catalysts.
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Affiliation(s)
- Yang Wei
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL 60660, United States
| | - Pengfei Li
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL 60660, United States.
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3
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Kaur S, Das A, Velasco L, Sauvan M, Bera M, Ugale A, Charisiadis A, Moonshiram D, Paria S. Spectroscopic characterization and reactivity studies of a copper(II) iminoxyl radical complex. Chem Commun (Camb) 2024; 60:9934-9937. [PMID: 39072688 DOI: 10.1039/d4cc02922d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
A CuII complex (1) of a bis-pyridine-dioxime ligand and its one-electron oxidized analog (1-ox) were thoroughly characterized by various spectroscopic techniques, including X-ray absorption spectroscopy. 1-ox was found to be a CuII complex of a ligand iminoxyl radical and represents the first example of such a type. Reorganization energy (λ) of 2.12 eV was determined for the 1-ox/1 couple, which is considerably higher than the type 1 protein and synthetic CuIII/II(OH) complexes.
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Affiliation(s)
- Simarjeet Kaur
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
| | - Avijit Das
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
| | - Lucia Velasco
- Instituto de Ciencia de Materiales de Madrid, Consejo Superior de Investigaciones Científicas, Sor Juana Inés de la Cruz, 3, 28049, Madrid, Spain.
| | - Maxime Sauvan
- Instituto de Ciencia de Materiales de Madrid, Consejo Superior de Investigaciones Científicas, Sor Juana Inés de la Cruz, 3, 28049, Madrid, Spain.
| | - Moumita Bera
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
| | - Ashok Ugale
- Instituto de Ciencia de Materiales de Madrid, Consejo Superior de Investigaciones Científicas, Sor Juana Inés de la Cruz, 3, 28049, Madrid, Spain.
| | - Asterios Charisiadis
- Instituto de Ciencia de Materiales de Madrid, Consejo Superior de Investigaciones Científicas, Sor Juana Inés de la Cruz, 3, 28049, Madrid, Spain.
| | - Dooshaye Moonshiram
- Instituto de Ciencia de Materiales de Madrid, Consejo Superior de Investigaciones Científicas, Sor Juana Inés de la Cruz, 3, 28049, Madrid, Spain.
| | - Sayantan Paria
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
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4
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Li JY, Si DH, Mi FQ, Xu WL, Zhang T, Cao R. A Bioinspired Copper-Pair Catalyst in Metal-Organic Frameworks for Molecular Dioxygen Activation and Aerobic Oxidative C-N Coupling. J Am Chem Soc 2024; 146:12444-12453. [PMID: 38680118 DOI: 10.1021/jacs.3c14794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Open Cu sites were loaded to the UiO-67 metal-organic framework (MOF) skeleton by introduction of flexible Cu-binding pyridylmethylamine (pyma) side chains to the biphenyldicarboxylate linkers. Distance between Cu centers in the MOF pores was tuned by controlling the density of metal-binding side chains. "Interacted" Cu-pair or "isolated" monomeric Cu sites were achieved with high and low (pyma)Cu side chain loading, respectively. Spectroscopic and theoretical studies indicate that "interacted" Cu pairs can effectively bind and activate molecular dioxygen to form Cu2O2 clusters, which showed high catalytic activity for aerobic oxidative C-N coupling. On the contrary, MOF catalyst bearing isolated monomeric Cu sites only showed modest catalytic activity. Enhancement in catalytic performance for the Cu-pair catalyst is attributed to the remote synergistic effect of the paired Cu site, which binds molecular dioxygen and cleaves the O═O bond in a collaborative manner. This work demonstrates that noncovalently interacted metal-pair sites can effectively activate inert small molecules and promote heterogeneous catalytic processes.
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Affiliation(s)
- Jun-Yu Li
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Duan-Hui Si
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
- Fujian Science and Technology Innovation Laboratory for Optoelectronic Information of China, Fuzhou, Fujian 350108, China
| | - Fu-Qi Mi
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Wang-Lan Xu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
- Fujian College, University of the Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, Fujian 350007, China
| | - Teng Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
- Fujian College, University of the Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
| | - Rong Cao
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
- Fujian Science and Technology Innovation Laboratory for Optoelectronic Information of China, Fuzhou, Fujian 350108, China
- Fujian College, University of the Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
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5
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Bols ML, Ma J, Rammal F, Plessers D, Wu X, Navarro-Jaén S, Heyer AJ, Sels BF, Solomon EI, Schoonheydt RA. In Situ UV-Vis-NIR Absorption Spectroscopy and Catalysis. Chem Rev 2024; 124:2352-2418. [PMID: 38408190 DOI: 10.1021/acs.chemrev.3c00602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
This review highlights in situ UV-vis-NIR range absorption spectroscopy in catalysis. A variety of experimental techniques identifying reaction mechanisms, kinetics, and structural properties are discussed. Stopped flow techniques, use of laser pulses, and use of experimental perturbations are demonstrated for in situ studies of enzymatic, homogeneous, heterogeneous, and photocatalysis. They access different time scales and are applicable to different reaction systems and catalyst types. In photocatalysis, femto- and nanosecond resolved measurements through transient absorption are discussed for tracking excited states. UV-vis-NIR absorption spectroscopies for structural characterization are demonstrated especially for Cu and Fe exchanged zeolites and metalloenzymes. This requires combining different spectroscopies. Combining magnetic circular dichroism and resonance Raman spectroscopy is especially powerful. A multitude of phenomena can be tracked on transition metal catalysts on various supports, including changes in oxidation state, adsorptions, reactions, support interactions, surface plasmon resonances, and band gaps. Measurements of oxidation states, oxygen vacancies, and band gaps are shown on heterogeneous catalysts, especially for electrocatalysis. UV-vis-NIR absorption is burdened by broad absorption bands. Advanced analysis techniques enable the tracking of coking reactions on acid zeolites despite convoluted spectra. The value of UV-vis-NIR absorption spectroscopy to catalyst characterization and mechanistic investigation is clear but could be expanded.
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Affiliation(s)
- Max L Bols
- Laboratory for Chemical Technology (LCT), University of Ghent, Technologiepark Zwijnaarde 125, 9052 Ghent, Belgium
| | - Jing Ma
- Department of Microbial and Molecular Systems, Center for Sustainable Catalysis and Engineering, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Fatima Rammal
- Department of Microbial and Molecular Systems, Center for Sustainable Catalysis and Engineering, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Dieter Plessers
- Department of Microbial and Molecular Systems, Center for Sustainable Catalysis and Engineering, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Xuejiao Wu
- Department of Microbial and Molecular Systems, Center for Sustainable Catalysis and Engineering, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Sara Navarro-Jaén
- Department of Microbial and Molecular Systems, Center for Sustainable Catalysis and Engineering, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Alexander J Heyer
- Department of Microbial and Molecular Systems, Center for Sustainable Catalysis and Engineering, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Bert F Sels
- Department of Microbial and Molecular Systems, Center for Sustainable Catalysis and Engineering, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Edward I Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Robert A Schoonheydt
- Department of Microbial and Molecular Systems, Center for Sustainable Catalysis and Engineering, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
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6
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Fukuda Y, Lintuluoto M, Kurihara K, Hasegawa K, Inoue T, Tamada T. Overlooked Hydrogen Bond in a Blue Copper Protein Uncovered by Neutron and Sub-Ångström Resolution X-ray Crystallography. Biochemistry 2024; 63:339-347. [PMID: 38232298 DOI: 10.1021/acs.biochem.3c00517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Metalloproteins play fundamental roles in organisms and are utilized as starting points for the directed evolution of artificial enzymes. Knowing the strategies of metalloproteins, by which they exquisitely tune their activities, will not only lead to an understanding of biochemical phenomena but also contribute to various applications. The blue copper protein (BCP) has been a renowned model system to understand the biology, chemistry, and physics of metalloproteins. Pseudoazurin (Paz), a blue copper protein, mediates electron transfer in the bacterial anaerobic respiratory chain. Its redox potential is finely tuned by hydrogen (H) bond networks; however, difficulty in visualizing H atom positions in the protein hinders the detailed understanding of the protein's structure-function relationship. We here used neutron and sub-ångström resolution X-ray crystallography to directly observe H atoms in Paz. The 0.86-Å-resolution X-ray structure shows that the peptide bond between Pro80 and the His81 Cu ligand deviates from the ideal planar structure. The 1.9-Å-resolution neutron structure confirms a long-overlooked H bond formed by the amide of His81 and the S atom of another Cu ligand Cys78. Quantum mechanics/molecular mechanics calculations show that this H bond increases the redox potential of the Cu site and explains the experimental results well. Our study demonstrates the potential of neutron and sub-ångström resolution X-ray crystallography to understand the chemistry of metalloproteins at atomic and quantum levels.
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Affiliation(s)
- Yohta Fukuda
- Graduate School of Pharmaceutical Science, Osaka University, Suita 565-0871, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita 565-0871, Osaka, Japan
| | - Masami Lintuluoto
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan
| | - Kazuo Kurihara
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Tokai 319-1106, Ibaraki, Japan
| | - Kazuya Hasegawa
- Structural Biology Division, Japan Synchrotron Radiation Research Institute, Sayo 679-5198, Hyogo, Japan
| | - Tsuyoshi Inoue
- Graduate School of Pharmaceutical Science, Osaka University, Suita 565-0871, Osaka, Japan
| | - Taro Tamada
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, Chiba 263-8555, Chiba, Japan
- Graduate School of Science and Engineering, Chiba University, Chiba 263-8552, Chiba, Japan
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7
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Sarkar A, Das S, Mondal P, Maiti B, Sen Gupta S. Synthesis, Characterization, and Reactivity of High-Valent Carbene Dicarboxamide-Based Nickel Pincer Complexes. Inorg Chem 2023. [PMID: 38001041 DOI: 10.1021/acs.inorgchem.3c03465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2023]
Abstract
High-valent metal-fluoride complexes are currently being explored for concerted proton-electron transfer (CPET) reactions, the driving force being the high bond dissociation energy of H-F (BDEH-F = 135 kcal/mol) that is formed after the reaction. Ni(III)-fluoride-based complexes on the pyridine dicarboxamide pincer ligand framework have been utilized for CPET reactions toward phenols and hydrocarbons. We have replaced the central pyridine ligand with an N-heterocyclic carbene carbene to probe its effect in both stabilizing the high-valent Ni(III) state and its ability to initiate CPET reactions. We report a monomeric carbene-diamide-based Ni(II)-fluoride pincer complex that was characterized through 1H/19F NMR, mass spectrometry, UV-vis, and X-ray crystallography analysis. Although carbenes and deprotonated carboxamides in the Ni(II)-fluoride complex are expected to stabilize the Ni(III) state upon oxidation, the Ni(III)/Ni(II) redox process occurred at very high potential (0.87 V vs Fc+/Fc, dichloromethane) and was irreversible. Structural studies indicate significant distortion in the imidazolium "NCN" carbene plane of Ni(II)-fluoride caused by the formation of six-membered metallacycles. The high-valent NiIII-fluoride analogue was synthesized by the addition of 1.0 equiv CTAN (ceric tetrabutylammonium nitrate) in dichloromethane at -20 °C which was characterized by UV-vis, mass spectrometry, and EPR spectroscopy. Density functional theory studies indicate that the Ni-carbene bond elongated, while the Ni-F bond shortened upon oxidation to the Ni(III) species. The high-valent Ni(III)-fluoride was found to react with the substituted phenols. Analysis of the KIE and linear free energy relationship correlates well with the CPET nature of the reaction. Preliminary analysis indicates that the CPET is asynchronous and is primarily driven by the E0' of the Ni(III)-fluoride complex.
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Affiliation(s)
- Aniruddha Sarkar
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
| | - Soumadip Das
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
| | - Prasenjit Mondal
- Department of Chemistry, Indian Institute of Technology Tirupati (IIT Tirupati), Tirupati, AP 517619, India
| | - Biswajit Maiti
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Sayam Sen Gupta
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
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8
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Ding Q, Sun Z, Ma W. Probing conformational kinetics of catalase with and without magnetic field by single-entity collision electrochemistry. Sci Bull (Beijing) 2023; 68:2564-2573. [PMID: 37718236 DOI: 10.1016/j.scib.2023.08.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/12/2023] [Accepted: 08/23/2023] [Indexed: 09/19/2023]
Abstract
The conformational motions of enzymes are crucial for their catalytic activities, but these fluctuations are usually spontaneous and unsynchronized and thus difficult to obtain from ensemble-averaged measurements. Here, we employ label-free single-entity electrochemical measurements to monitor in real time the fluctuating enzymatic behavior of single catalase molecules toward the degradation of hydrogen peroxide. By probing the electrochemical signals of single catalase molecules at a carbon nanoelectrode, we were able to observe three distinct current traces that could be attributed to conformational changes on the sub-millisecond timescale. Whereas, nearly uniform single long peaks were observed for single catalase molecules under a moderate magnetic field due to the restricted conformational changes of catalase. By combining high-resolution current signals with a multiphysics simulation model, we studied the catalytic kinetics of catalase with and without a magnetic field, and further estimated the maximum catalytic rate and conformational transition rate. This work introduces a new complementary approach to existing single-molecule enzymology, giving further insight into the enzymatic reaction mechanism.
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Affiliation(s)
- Qingdan Ding
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Zehui Sun
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Wei Ma
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China.
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9
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Mohammed TP, George A, Sivaramakrishnan MP, Vadivelu P, Balasubramanian S, Sankaralingam M. Deciphering the effect of amine versus imine ligands of copper(II) complexes in 2-aminophenol oxidation. J Inorg Biochem 2023; 247:112309. [PMID: 37451084 DOI: 10.1016/j.jinorgbio.2023.112309] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/19/2023] [Accepted: 06/27/2023] [Indexed: 07/18/2023]
Abstract
A series of amine (1-6) and imine (5',6') based copper(II) complexes with tridentate (NNO) ligand donors were synthesized and characterized using modern analytical techniques. All the complexes were subjected to 2-aminophenol (OAP) oxidation to form 2-aminophenoxazin-3-one, as a functional analogue of an enzyme, phenoxazinone synthase. In addition, a critical comparison of the reactivity using the amine-based complexes with their respective imine counterparts was achieved in both experimental as well as theoretical studies. For instance, the kinetic measurement revealed that the imine-based copper(II) complexes (kcat, 2.4 × 105-6.2 × 106 h-1) are better than amine-based (kcat, 6.3 × 104-3.9 × 105 h-1) complexes. The complex-substrate adducts [Cu(L3)(OAP)] (7) and [Cu(L3')(OAP)] (7') were characterized for both systems by mass spectrometry. Further, the DFT study was performed with amine- (3) and imine- (3') based copper(II) complexes, to compare their efficacy in the oxidation of OAP. The mechanistic investigations reveal that the key elementary step to determine the reactivity of 3 and 3' is the proton-coupled electron transfer (PCET) step occurring from the intermediates 7/7'. Further, the computed HOMO-LUMO energy gap of 7' was smaller than 7 by 0.8 eV, which indicates the facile PCET compared to that of 7. Moreover, the coupling of the OAP moiety using imine-complexes (ΔGR.E = -5.8 kcal/mol) was found to be thermodynamically more favorable than amine complexes (ΔGR.E = +3.3 kcal/mol). Overall, the theoretical findings are in good agreement with the experimental results.
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Affiliation(s)
- Thasnim P Mohammed
- Bioinspired & Biomimetic Inorganic Chemistry Lab, Department of Chemistry, National Institute of Technology Calicut, Kozhikode, Kerala 673601, India
| | - Akhila George
- Bioinspired & Biomimetic Inorganic Chemistry Lab, Department of Chemistry, National Institute of Technology Calicut, Kozhikode, Kerala 673601, India
| | | | - Prabha Vadivelu
- Department of Chemistry, Central University of Tamil Nadu, Thiruvarur 610 005, India
| | - Sridhar Balasubramanian
- Centre for X-ray Crystallography, CSIR-Indian Institute of Chemical Technology, Hyderabad, Telangana 500007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Muniyandi Sankaralingam
- Bioinspired & Biomimetic Inorganic Chemistry Lab, Department of Chemistry, National Institute of Technology Calicut, Kozhikode, Kerala 673601, India.
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10
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Griffin PJ, Olshansky L. Rapid Electron Transfer Self-Exchange in Conformationally Dynamic Copper Coordination Complexes. J Am Chem Soc 2023; 145:20158-20162. [PMID: 37683290 DOI: 10.1021/jacs.3c05935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/10/2023]
Abstract
We report the electron transfer (ET) self-exchange rate constants (k11) for a pair of CuII/I complexes utilizing dpaR (dpa = dipicolylaniline, R = OMe, SMe) ligands assessed by NMR line broadening experiments. These ligands afford copper complexes that are conformationally dynamic in one oxidation state. With R = OMe, the CuI complex is dynamic, while with R = SMe, the CuII complex is dynamic. Both complexes exhibit unexpectedly large k11 values of 2.48(6) × 105 and 2.21(9) × 106 M-1 s-1 for [CuCl(dpaOMe)]+/0 and [CuCl(dpaSMe)]+/0, respectively. Among the fastest reported molecular copper coordination complexes to date, that of [CuCl(dpaSMe)]+/0 exceeds all others by an order of magnitude and compares only with those observed in type 1 blue copper proteins. The dynamicity of these complexes establishes pre-steady-state conformational equilibria that minimize the inner-sphere reorganization energies to 0.71 and 0.62 eV for R = OMe and SMe, respectively. In contrast to the emphasis on rigidity in the formulation of entatic states applied to blue copper proteins, the success of these two systems highlights the relevance of conformational dynamicity in mediating rapid ET.
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Affiliation(s)
- Paul J Griffin
- Department of Chemistry, Center for Biophysics and Quantitative Biology, and Materials Research Laboratory, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Lisa Olshansky
- Department of Chemistry, Center for Biophysics and Quantitative Biology, and Materials Research Laboratory, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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11
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Hess SS, Coppola F, Dang VT, Tran PN, Mickel PJ, Oktawiec J, Ren Z, Král P, Nguyen AI. Noncovalent Peptide Assembly Enables Crystalline, Permutable, and Reactive Thiol Frameworks. J Am Chem Soc 2023; 145:19588-19600. [PMID: 37639365 DOI: 10.1021/jacs.3c03645] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Though thiols are exceptionally versatile, their high reactivity has also hindered the synthesis and characterization of well-defined thiol-containing porous materials. Leveraging the mild conditions of the noncovalent peptide assembly, we readily synthesized and characterized a number of frameworks with thiols displayed at many unique positions and in several permutations. Importantly, nearly all assemblies were structurally determined using single-crystal X-ray diffraction to reveal their rich sequence-structure landscape and the cooperative noncovalent interactions underlying their assembly. These observations and supporting molecular dynamics calculations enabled rational engineering by the positive and negative design of noncovalent interactions. Furthermore, the thiol-containing frameworks undergo diverse single-crystal-to-single-crystal reactions, including toxic metal ion coordination (e.g., Cd2+, Pb2+, and Hg2+), selective uptake of Hg2+ ions, and redox transformations. Notably, we find a framework that supports thiol-nitrosothiol interconversion, which is applicable for biocompatible nitric oxide delivery. The modularity, ease of synthesis, functionality, and well-defined nature of these peptide-based thiol frameworks are expected to accelerate the design of complex materials with reactive active sites.
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Affiliation(s)
- Selina S Hess
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
| | - Francesco Coppola
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
| | - Viet Thuc Dang
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
| | - Phuong Nguyen Tran
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
| | - Philip J Mickel
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
| | - Julia Oktawiec
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Zhong Ren
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
| | - Petr Král
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
| | - Andy I Nguyen
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
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12
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Mammoser CC, LeMasters BE, Edwards SG, McRae EM, Mullins MH, Wang Y, Garcia NM, Edmonds KA, Giedroc DP, Thielges MC. The structure of plastocyanin tunes the midpoint potential by restricting axial ligation of the reduced copper ion. Commun Chem 2023; 6:175. [PMID: 37612467 PMCID: PMC10447441 DOI: 10.1038/s42004-023-00977-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/07/2023] [Indexed: 08/25/2023] Open
Abstract
Blue copper proteins are models for illustrating how proteins tune metal properties. Nevertheless, the mechanisms by which the protein controls the metal site remain to be fully elucidated. A hindrance is that the closed shell Cu(I) site is inaccessible to most spectroscopic analyses. Carbon deuterium (C-D) bonds used as vibrational probes afford nonperturbative, selective characterization of the key cysteine and methionine copper ligands in both redox states. The structural integrity of Nostoc plastocyanin was perturbed by disrupting potential hydrogen bonds between loops of the cupredoxin fold via mutagenesis (S9A, N33A, N34A), variably raising the midpoint potential. The C-D vibrations show little change to suggest substantial alteration to the Cu(II) coordination in the oxidized state or in the Cu(I) interaction with the cysteine ligand. They rather indicate, along with visible and NMR spectroscopy, that the methionine ligand distinctly interacts more strongly with the Cu(I) ion, in line with the increases in midpoint potential. Here we show that the protein structure determines the redox properties by restricting the interaction between the methionine ligand and Cu(I) in the reduced state.
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Affiliation(s)
- Claire C Mammoser
- Indiana University Department of Chemistry, 800 E. Kirkwood Ave., Bloomington, IN, 47405, USA
| | - Brynn E LeMasters
- Indiana University Department of Chemistry, 800 E. Kirkwood Ave., Bloomington, IN, 47405, USA
- Department of Chemistry, University of Wisconsin, Madison, WI, 53706, USA
| | - Sydney G Edwards
- Indiana University Department of Chemistry, 800 E. Kirkwood Ave., Bloomington, IN, 47405, USA
| | - Emma M McRae
- Indiana University Department of Chemistry, 800 E. Kirkwood Ave., Bloomington, IN, 47405, USA
| | - M Hunter Mullins
- Indiana University Department of Chemistry, 800 E. Kirkwood Ave., Bloomington, IN, 47405, USA
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Yiqi Wang
- Indiana University Department of Chemistry, 800 E. Kirkwood Ave., Bloomington, IN, 47405, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Nicholas M Garcia
- Indiana University Department of Chemistry, 800 E. Kirkwood Ave., Bloomington, IN, 47405, USA
- University of Wisconsin School of Medicine and Public Health, Madison, WI, 53726, USA
| | - Katherine A Edmonds
- Indiana University Department of Chemistry, 800 E. Kirkwood Ave., Bloomington, IN, 47405, USA
| | - David P Giedroc
- Indiana University Department of Chemistry, 800 E. Kirkwood Ave., Bloomington, IN, 47405, USA
| | - Megan C Thielges
- Indiana University Department of Chemistry, 800 E. Kirkwood Ave., Bloomington, IN, 47405, USA.
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13
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Chowdhury SN, Biswas S, Das S, Biswas AN. Kinetic and mechanistic investigations of dioxygen reduction by a molecular Cu(II) catalyst bearing a pentadentate amidate ligand. Dalton Trans 2023; 52:11581-11590. [PMID: 37548356 DOI: 10.1039/d3dt02194g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
A pentadentate Cu(II) complex, [CuII(dpaq)](ClO4) (1), featuring a redox active ligand, H-dpaq (H-dpaq = 2-[bis(pyridine-2-ylmethyl)]amino-N-quinolin-8-yl-acetamidate), catalyses four-electron reduction of dioxygen by decamethylferrocene (Fc*) in the presence of trifluoroacetic acid (CF3COOH) in acetone at 298 K. No catalytic oxygen reduction was observed in the presence of stronger Brønsted acids than CF3COOH, such as perchloric acid (HClO4) or trifluoromethanesulphonic acid (HOTf). In contrast, facile catalytic reduction of O2 occurs by Fc* with 1 and HClO4 or HOTf in dimethylformamide (DMF). The use of CF3COOH as the proton source in DMF results in the suppression of O2 reduction under otherwise identical reaction conditions. While the O2 reduction reactions in DMF are linearly dependent on the pKa of Brønsted acids, the acid dependence on catalytic O2-reduction reactivity by 1 in acetone showed complete reversal. Cyclic voltammetry studies using p-chloranil as the probe substrates in the presence of acids in the solvents reveal that the strengths of the protonic acids increase significantly in acetone compared to that in DMF. The amidate-N in [CuII(dpaq)](ClO4) (1) undergoes protonation in the presence of HClO4 or HOTf in DMF to form [CuII(H-dpaq)]2+ (1-H+), but not in the presence of CF3COOH. Enhanced acid strength of CF3COOH in acetone, however, effectively protonates 1 and triggers O2 reduction. Protonation of 1 with HClO4 or HOTf in acetone results in the change of its coordination environment, and this protonated species does not trigger O2 reduction. Detailed kinetic studies indicate that 1-H+ undergoes reduction by two-electrons and the reduced species binds O2 to form a Cu(II)-superoxo intermediate. This is followed by a rate-determining proton-coupled electron-transfer (PCET) reduction to generate the Cu(II)-hydroperoxo intermediate. While catalytic O2 reduction in acetone occurs predominantly via a 4e-/4H+ pathway, product selectivity (H2O vs. H2O2) in DMF depends upon the concentration of the reductant (Fc*). While dioxygen reduction to H2O2 is favoured at low [Fc*], mechanistic studies suggest that O2 reduction with high [Fc*] proceeds via a [2e- + 2e-] mechanism, where the released H2O2 during catalysis is further reduced to water.
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Affiliation(s)
- Srijan Narayan Chowdhury
- Department of Chemistry, National Institute of Technology Sikkim, Ravangla, South Sikkim 737139, India.
| | - Sachidulal Biswas
- Department of Chemistry, National Institute of Technology Sikkim, Ravangla, South Sikkim 737139, India.
| | - Saikat Das
- Department of Chemistry, National Institute of Technology Sikkim, Ravangla, South Sikkim 737139, India.
| | - Achintesh N Biswas
- Department of Chemistry, National Institute of Technology Sikkim, Ravangla, South Sikkim 737139, India.
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14
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Gaza JT, Nellas RB. Reparameterization of Non-Bonded Parameters for Copper Ions in Plastocyanin: An Adaptive Force Matching Study. J Chem Inf Model 2023; 63:4654-4663. [PMID: 37459569 DOI: 10.1021/acs.jcim.3c00559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Molecular mechanics rely on existing experimental and theoretical inputs to confidently calculate the trajectories of molecular systems. These calculations, however, are often hindered by missing force field parameters. A notable subject of this problem is metal centers of proteins. This study parameterized, through an adaptive force matching (AFM) workflow, the copper cofactor of plastocyanin in its two oxidation states. New 12-6 Lennard-Jones (LJ) parameters and atomic partial charges were generated to complete the non-bonded description of the copper site. Our models show uniform distorted tetrahedral structures for reduced plastocyanin, Cu(I), and oxidized plastocyanin, Cu(II). These structures align with the QM/MM MD results and existing crystallography studies. TD-DFT calculations, meanwhile, showed that conformations with elongated axial Cu-SMet and shortened equatorial Cu-SCys bonds retain the experimental UV-Vis profile of blue copper (BC) proteins, thus signifying the importance of Cu-S interactions on BC proteins' unique spectroscopic properties.
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Affiliation(s)
- Jokent T Gaza
- Institute of Chemistry, College of Science, University of the Philippines Diliman, 1101 Quezon City, Philippines
| | - Ricky B Nellas
- Institute of Chemistry, College of Science, University of the Philippines Diliman, 1101 Quezon City, Philippines
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15
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Barreiro DS, Oliveira RNS, Pauleta SR. Biochemical Characterization of the Copper Nitrite Reductase from Neisseria gonorrhoeae. Biomolecules 2023; 13:1215. [PMID: 37627281 PMCID: PMC10452240 DOI: 10.3390/biom13081215] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 07/16/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
The copper-containing nitrite reductase from Neisseria gonorrhoeae has been shown to play a critical role in the infection mechanism of this microorganism by producing NO and abolishing epithelial exfoliation. This enzyme is a trimer with a type 1 copper center per subunit and a type 2 copper center in the subunits interface, with the latter being the catalytic site. The two centers were characterized for the first time by EPR and CD spectroscopy, showing that the type 1 copper center has a high rhombicity due to its lower symmetry and more tetragonal structure, while the type 2 copper center has the usual properties, but with a smaller hyperfine coupling constant (A// = 10.5 mT). The thermostability of the enzyme was analyzed by differential scanning calorimetry, which shows a single endothermic transition in the thermogram, with a maximum at 94 °C, while the CD spectra in the visible region indicate the presence of the type 1 copper center up to 80 °C. The reoxidation of the N. gonorrhoeae copper-containing nitrite reductase in the presence of nitrite were analyzed by visible spectroscopy and showed a pH dependence, being higher at pH 5.5-6.0. The high thermostability of this enzyme may be important to maintaining a high activity in the extracellular space and to making it less susceptible to denaturation and proteolysis, contributing to the proliferation of N. gonorrhoeae.
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Affiliation(s)
- Daniela S. Barreiro
- Microbial Stress Lab, UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Ricardo N. S. Oliveira
- Microbial Stress Lab, UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Sofia R. Pauleta
- Microbial Stress Lab, UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
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16
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Yamaguchi T, Taborosi A, Sakai C, Akao K, Mori S, Kohzuma T. Systematic elucidation of the second coordination sphere effect on the structure and properties of a blue copper protein, pseudoazurin. J Inorg Biochem 2023; 246:112292. [PMID: 37354604 DOI: 10.1016/j.jinorgbio.2023.112292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 06/26/2023]
Abstract
The rational structural and computational studies of a blue copper protein, pseudoazurin (PAz), and its Met16X (X = Phe, Leu, Val, Ile) variants gave clear functional meanings of the noncovalent interaction (NCI) through the second coordination sphere. The high-resolution X-ray crystal structures of Met16X PAz demonstrated that the active site geometry is significantly affected by the substitution of Met16, which is located within the NCI distance from the His81 imidazole ring at the copper active site. The computational chemistry calculations based on the crystal structure analyses confirmed that the NCI of S-π/CH-π (wild-type), π-π (Met16Phe), double CH-π (Met16Leu), and single CH-π (Met16Val and Met16Ile). The estimated interaction energies for the NCI demonstrated that the fine-tuning of the protein stability and Cu site properties form the second coordination sphere of PAz.
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Affiliation(s)
- Takahide Yamaguchi
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki 310-8512, Japan; Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1, Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Attila Taborosi
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki 310-8512, Japan; Research Initiative for Supra-Materials, Faculty of Engineering, Shinshu University, 4-17-1, Wakasato, Nagano, Nagano 380-8553, Japan
| | - Chihiro Sakai
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - Kohei Akao
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - Seiji Mori
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki 310-8512, Japan; Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1, Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Takamitsu Kohzuma
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki 310-8512, Japan; Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1, Shirakata, Tokai, Ibaraki 319-1106, Japan.
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17
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Singha A, Sekretareva A, Tao L, Lim H, Ha Y, Braun A, Jones SM, Hedman B, Hodgson KO, Britt RD, Kosman DJ, Solomon EI. Tuning the Type 1 Reduction Potential of Multicopper Oxidases: Uncoupling the Effects of Electrostatics and H-Bonding to Histidine Ligands. J Am Chem Soc 2023. [PMID: 37294874 PMCID: PMC10392966 DOI: 10.1021/jacs.3c03241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In multicopper oxidases (MCOs), the type 1 (T1) Cu accepts electrons from the substrate and transfers these to the trinuclear Cu cluster (TNC) where O2 is reduced to H2O. The T1 potential in MCOs varies from 340 to 780 mV, a range not explained by the existing literature. This study focused on the ∼350 mV difference in potential of the T1 center in Fet3p and Trametes versicolor laccase (TvL) that have the same 2His1Cys ligand set. A range of spectroscopies performed on the oxidized and reduced T1 sites in these MCOs shows that they have equivalent geometric and electronic structures. However, the two His ligands of the T1 Cu in Fet3p are H-bonded to carboxylate residues, while in TvL they are H-bonded to noncharged groups. Electron spin echo envelope modulation spectroscopy shows that there are significant differences in the second-sphere H-bonding interactions in the two T1 centers. Redox titrations on type 2-depleted derivatives of Fet3p and its D409A and E185A variants reveal that the two carboxylates (D409 and E185) lower the T1 potential by 110 and 255-285 mV, respectively. Density functional theory calculations uncouple the effects of the charge of the carboxylates and their difference in H-bonding interactions with the His ligands on the T1 potential, indicating 90-150 mV for anionic charge and ∼100 mV for a strong H-bond. Finally, this study provides an explanation for the generally low potentials of metallooxidases relative to the wide range of potentials of the organic oxidases in terms of different oxidized states of their TNCs involved in catalytic turnover.
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Affiliation(s)
- Asmita Singha
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Alina Sekretareva
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Lizhi Tao
- Department of Chemistry, University of California at Davis, Davis, California 95616, United States
| | - Hyeongtaek Lim
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Yang Ha
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Augustin Braun
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Stephen M Jones
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Keith O Hodgson
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - R David Britt
- Department of Chemistry, University of California at Davis, Davis, California 95616, United States
| | - Daniel J Kosman
- Department of Biochemistry, The University at Buffalo, Buffalo, New York 14214, United States
| | - Edward I Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
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18
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Kircheva N, Angelova S, Dobrev S, Petkova V, Nikolova V, Dudev T. Cu +/Ag + Competition in Type I Copper Proteins (T1Cu). Biomolecules 2023; 13:biom13040681. [PMID: 37189429 DOI: 10.3390/biom13040681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 05/17/2023] Open
Abstract
Due to the similarity in the basic coordination behavior of their mono-charged cations, silver biochemistry is known to be linked to that of copper in biological systems. Still, Cu+/2+ is an essential micronutrient in many organisms, while no known biological process requires silver. In human cells, copper regulation and trafficking is strictly controlled by complex systems including many cytosolic copper chaperones, whereas some bacteria exploit the so-called "blue copper" proteins. Therefore, evaluating the controlling factors of the competition between these two metal cations is of enormous interest. By employing the tools of computational chemistry, we aim to delineate the extent to which Ag+ might be able to compete with the endogenous copper in its Type I (T1Cu) proteins, and where and if, alternatively, it is handled uniquely. The effect of the surrounding media (dielectric constant) and the type, number, and composition of amino acid residues are taken into account when modelling the reactions in the present study. The obtained results clearly indicate the susceptibility of the T1Cu proteins to a silver attack due to the favorable composition and geometry of the metal-binding centers, along with the similarity between the Ag+/Cu+-containing structures. Furthermore, by exploring intriguing questions of both metals' coordination chemistry, an important background for understanding the metabolism and biotransformation of silver in organisms is provided.
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Affiliation(s)
- Nikoleta Kircheva
- Institute of Optical Materials and Technologies "Acad. J. Malinowski", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Silvia Angelova
- Institute of Optical Materials and Technologies "Acad. J. Malinowski", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Stefan Dobrev
- Institute of Optical Materials and Technologies "Acad. J. Malinowski", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Vladislava Petkova
- Institute of Optical Materials and Technologies "Acad. J. Malinowski", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Valya Nikolova
- Faculty of Chemistry and Pharmacy, Sofia University "St. Kliment Ohridski", 1164 Sofia, Bulgaria
| | - Todor Dudev
- Faculty of Chemistry and Pharmacy, Sofia University "St. Kliment Ohridski", 1164 Sofia, Bulgaria
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19
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Ahmad R, Tyryshkin AM, Xie L, Hansen WA, Yachnin BJ, Emge TJ, Mashrai A, Khare SD, Knapp S. A Bis(imidazole)-based cysteine labeling tool for metalloprotein assembly. J Inorg Biochem 2023; 244:112206. [PMID: 37030124 DOI: 10.1016/j.jinorgbio.2023.112206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 03/24/2023] [Accepted: 03/31/2023] [Indexed: 04/03/2023]
Abstract
Precise metal-protein coordination by design remains a considerable challenge. Polydentate, high-metal-affinity protein modifications, both chemical and recombinant, can enable metal localization. However, these constructs are often bulky, conformationally and stereochemically ill-defined, or coordinately saturated. Here, we expand the biomolecular metal-coordination toolbox with the irreversible attachment to cysteine of bis(1-methylimidazol-2-yl)ethene ("BMIE"), which generates a compact imidazole-based metal-coordinating ligand. Conjugate additions of small-molecule thiols (thiocresol and N-Boc-Cys) with BMIE confirm general thiol reactivity. The BMIE adducts are shown to complex the divalent metal ions Cu++ and Zn++ in bidentate (N2) and tridentate (N2S*) coordination geometries. Cysteine-targeted BMIE modification (>90% yield at pH 8.0) of a model protein, the S203C variant of carboxypeptidase G2 (CPG2), measured with ESI-MS, confirms its utility as a site-selective bioconjugation method. ICP-MS analysis confirms mono-metallation of the BMIE-modified CPG2 protein with Zn++, Cu++, and Co++. EPR characterization of the BMIE-modified CPG2 protein reveals the structural details of the site selective 1:1 BMIE-Cu++ coordination and symmetric tetragonal geometry under physiological conditions and in the presence of various competing and exchangeable ligands (H2O/HO-, tris, and phenanthroline). An X-ray protein crystal structure of BMIE-modified CPG2-S203C demonstrates that the BMIE modification is minimally disruptive to the overall protein structure, including the carboxypeptidase active sites, although Zn++ metalation could not be conclusively discerned at the resolution obtained. The carboxypeptidase catalytic activity of BMIE-modified CPG2-S203C was also assayed and found to be minimally affected. These features, combined with ease of attachment, define the new BMIE-based ligation as a versatile metalloprotein design tool, and enable future catalytic and structural applications.
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Affiliation(s)
- Raheel Ahmad
- Department of Chemistry & Chemical Biology, Rutgers The State University of New Jersey, 123 Bevier Rd, Piscataway, NJ 08854, United States of America
| | - Alexei M Tyryshkin
- Department of Marine and Coastal Sciences, Rutgers The State University of New Jersey, 71 Dudley Road, New Brunswick, NJ 08901, United States of America
| | - Lingjun Xie
- Department of Chemistry & Chemical Biology, Rutgers The State University of New Jersey, 123 Bevier Rd, Piscataway, NJ 08854, United States of America
| | - William A Hansen
- Department of Chemistry & Chemical Biology, Rutgers The State University of New Jersey, 123 Bevier Rd, Piscataway, NJ 08854, United States of America; Rutgers Center for Integrative Proteomics Research, 174 Frelinghuysen Rd, Piscataway, NJ 08854, United States of America
| | - Brahm J Yachnin
- Department of Chemistry & Chemical Biology, Rutgers The State University of New Jersey, 123 Bevier Rd, Piscataway, NJ 08854, United States of America; Rutgers Center for Integrative Proteomics Research, 174 Frelinghuysen Rd, Piscataway, NJ 08854, United States of America
| | - Thomas J Emge
- Department of Chemistry & Chemical Biology, Rutgers The State University of New Jersey, 123 Bevier Rd, Piscataway, NJ 08854, United States of America
| | - Ashraf Mashrai
- Department of Chemistry & Chemical Biology, Rutgers The State University of New Jersey, 123 Bevier Rd, Piscataway, NJ 08854, United States of America; Rutgers Center for Integrative Proteomics Research, 174 Frelinghuysen Rd, Piscataway, NJ 08854, United States of America
| | - Sagar D Khare
- Department of Chemistry & Chemical Biology, Rutgers The State University of New Jersey, 123 Bevier Rd, Piscataway, NJ 08854, United States of America; Rutgers Center for Integrative Proteomics Research, 174 Frelinghuysen Rd, Piscataway, NJ 08854, United States of America
| | - Spencer Knapp
- Department of Chemistry & Chemical Biology, Rutgers The State University of New Jersey, 123 Bevier Rd, Piscataway, NJ 08854, United States of America.
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20
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Maqboul I. Profiling charge transport: A new computational approach. Int J Biol Macromol 2023; 237:124065. [PMID: 36948333 DOI: 10.1016/j.ijbiomac.2023.124065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/12/2023] [Accepted: 03/13/2023] [Indexed: 03/24/2023]
Abstract
To maintain life, charge transfer processes must be efficient to allow electrons to migrate across distances as large as 30-50 Å within a timescale from picoseconds to milliseconds, and the free-energy cost should not exceed one electron volt. By employing local ionization and local affinity energies, we calculated the pathway for electron and electron-hole transport, respectively. The pathway is then used to calculate both the driving force and the activation energy. The electronic coupling is calculated using configuration interaction procedure. When the charge acceptor is not known, as in oxidative stress, the charge transport terminals are found using Monte-Carlo simulation. These parameters were used to calculate the rate described by Marcus theory. Our approach has been elaborately explained using the famous androstane example and then applied to two proteins: electron transport in azurin protein and hole-hopping migration route from the heme center of cytochrome c peroxidase to its surface. This model gives an effective method to calculate the charge transport pathway and the free-energy profile within 0.1 eV from the experimental measurements and electronic coupling within 3 meV.
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Affiliation(s)
- Ibrahim Maqboul
- Computer Chemistry Center (CCC), Department of Chemistry and Pharmacy, Faculty of Sciences, Friedrich-Alexander-University, Erlangen, Germany; Computer Chemistry Center (CCC), Department of Chemistry and Pharmacy, Faculty of Sciences, Friedrich-Alexander-University, Nägelsbachstraße 25, 91052 Erlangen, Germany..
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21
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Interplay of electronic and geometric structure on Cu phenanthroline, bipyridine and derivative complexes, synthesis, characterization, and reactivity towards oxygen. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2022.214943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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22
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Structural Analyses of the Multicopper Site of CopG Support a Role as a Redox Enzyme. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1414:97-121. [PMID: 36637718 DOI: 10.1007/5584_2022_753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Metal ions can be both essential components of cells as well as potential toxins if present in excess. Organisms utilize a variety of protein systems to maintain the concentration of metal ions within the appropriate range for cellular function, and to avoid concentrations where cellular damage can occur. In bacteria, numerous proteins contribute to copper homeostasis, including copper transporters, chelators, and redox enzymes. The genes that encode these proteins are often found in clusters, thus providing modular components that work together to achieve homeostasis. A better understanding of how these components function and cooperate to achieve metal ion resistance is needed, given the extensive use of metal ions, including copper, as broad-spectrum biocides in a variety of clinical and environmental settings. The copG gene is a common component of such copper resistance clusters, but its contribution to copper resistance is not well understood. In this review the available information about the CopG protein encoded by this gene is summarized. Comparison of the recent structure to diverse copper-containing metallochaperones, metalloenzymes, and electron transfer proteins suggests that CopG is a redox enzyme that uses multiple copper ions as active site redox cofactors to act on additional copper ion substrates. Mechanisms for both oxidase and reductase activity are proposed, and the biological advantages that these activities can contribute in conjunction with existing systems are described.
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23
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Kondo HX, Iizuka H, Masumoto G, Kabaya Y, Kanematsu Y, Takano Y. Prediction of Protein Function from Tertiary Structure of the Active Site in Heme Proteins by Convolutional Neural Network. Biomolecules 2023; 13:biom13010137. [PMID: 36671521 PMCID: PMC9855806 DOI: 10.3390/biom13010137] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 01/07/2023] [Indexed: 01/11/2023] Open
Abstract
Structure-function relationships in proteins have been one of the crucial scientific topics in recent research. Heme proteins have diverse and pivotal biological functions. Therefore, clarifying their structure-function correlation is significant to understand their functional mechanism and is informative for various fields of science. In this study, we constructed convolutional neural network models for predicting protein functions from the tertiary structures of heme-binding sites (active sites) of heme proteins to examine the structure-function correlation. As a result, we succeeded in the classification of oxygen-binding protein (OB), oxidoreductase (OR), proteins with both functions (OB-OR), and electron transport protein (ET) with high accuracy. Although the misclassification rate for OR and ET was high, the rates between OB and ET and between OB and OR were almost zero, indicating that the prediction model works well between protein groups with quite different functions. However, predicting the function of proteins modified with amino acid mutation(s) remains a challenge. Our findings indicate a structure-function correlation in the active site of heme proteins. This study is expected to be applied to the prediction of more detailed protein functions such as catalytic reactions.
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Affiliation(s)
- Hiroko X. Kondo
- Faculty of Engineering, Kitami Institute of Technology, 165 Koen-cho, Kitami 090-8507, Japan
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima 731-3194, Japan
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research, 6-2-3 Furuedai, Suita 565-0874, Japan
- Correspondence: (H.X.K.); (Y.T.); Tel.: +81-157-26-9401 (H.X.K.); +81-82-830-1825 (Y.T.)
| | - Hiroyuki Iizuka
- Graduate School of Information Science and Technology, Hokkaido University, Kita 14, Nishi 9, Kitaku, Sapporo 060-0814, Japan
| | - Gen Masumoto
- Information Systems Division, RIKEN Information R&D and Strategy Headquarters, 2-1 Hirosawa, Wako 351-0198, Japan
| | - Yuichi Kabaya
- Faculty of Engineering, Kitami Institute of Technology, 165 Koen-cho, Kitami 090-8507, Japan
| | - Yusuke Kanematsu
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima 731-3194, Japan
- Graduate School of Advanced Science and Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima 739-8527, Japan
| | - Yu Takano
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima 731-3194, Japan
- Correspondence: (H.X.K.); (Y.T.); Tel.: +81-157-26-9401 (H.X.K.); +81-82-830-1825 (Y.T.)
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24
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Gordon JB, Albert T, Yadav S, Thomas J, Siegler MA, Moënne-Loccoz P, Goldberg DP. Oxygen versus Sulfur Coordination in Cobalt Superoxo Complexes: Spectroscopic Properties, O 2 Binding, and H-Atom Abstraction Reactivity. Inorg Chem 2023; 62:392-400. [PMID: 36538786 PMCID: PMC10194424 DOI: 10.1021/acs.inorgchem.2c03484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A five-coordinate, disiloxide-ligated cobalt(II) (S = 3/2) complex (1) was prepared as an oxygen-ligated analogue to the previously reported silanedithiolate-ligated CoII(Me3TACN)(S2SiMe2) (J. Am. Chem. Soc., 2019, 141, 3641-3653). The structural and spectroscopic properties of 1 were analyzed by single-crystal X-ray diffraction, electron paramagnetic resonance (EPR), and NMR spectroscopies. The reactivity of 1 with dioxygen was examined, and it was shown to bind O2 reversibly in a range of solvents at low temperatures. A cobalt(III)-superoxo complex, CoIII(O2·-)(Me3TACN)((OSi2Ph)2O) (2), was generated, and was analyzed by UV-vis, EPR, and resonance Raman spectroscopies. Unlike its sulfur-ligated analogue, complex 2 can thermally release O2 to regenerate 1. Vibrational assignments for selective 18O isotopic labeling of both O2 and disiloxide ligands in 2 are consistent with a 6-coordinate, Co(η1-O2·-)("end-on") complex. Complex 2 reacts with the O-H bond of 4-methoxy-2,2,6,6-tetramethylpiperidin-1-ol (4-MeO-TEMPOH) via H-atom abstraction with a rate of 0.58(2) M-1 s-1 at -105 °C, but it is unable to oxidize phenol substrates. This bracketed reactivity suggests that the O-H bond being formed in the putative CoIII(OOH) product has a relatively weak O-H bond strength (BDFE ∼66-74 kcal mol-1). These thermodynamic and kinetic parameters are similar to those seen for the sulfur-ligated Co(O2)(Me3TACN)(S2SiMe2), indicating that the differences in the electronic structure for O versus S ligation do not have a large impact on H-atom abstraction reactivity.
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Affiliation(s)
- Jesse B Gordon
- Department of Chemistry, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Therese Albert
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Sudha Yadav
- Department of Chemistry, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Jithin Thomas
- Department of Chemistry, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Maxime A Siegler
- Department of Chemistry, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Pierre Moënne-Loccoz
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - David P Goldberg
- Department of Chemistry, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
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25
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Baluta S, Romaniec M, Halicka-Stępień K, Alicka M, Pieła A, Pala K, Cabaj J. A Novel Strategy for Selective Thyroid Hormone Determination Based on an Electrochemical Biosensor with Graphene Nanocomposite. SENSORS (BASEL, SWITZERLAND) 2023; 23:602. [PMID: 36679398 PMCID: PMC9861372 DOI: 10.3390/s23020602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/01/2023] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
This article presents a novel and selective electrochemical bioassay with antibody and laccase for the determination of free thyroid hormone (free triiodothyronine, fT3). The biosensor was based on a glassy carbon electrode modified with a Fe3O4@graphene nanocomposite with semiconducting properties, an antibody (anti-PDIA3) with high affinity for fT3, and laccase, which was responsible for catalyzing the redox reaction of fT3. The electrode modification procedure was investigated using a cyclic voltammetry technique, based on the response of the peak current after modifications. All characteristic working parameters of the developed biosensor were analyzed using differential pulse voltammetry. Obtained experimental results showed that the biosensor revealed a sensitive response to fT3 in a concentration range of 10-200 µM, a detection limit equal to 27 nM, and a limit of quantification equal to 45.9 nM. Additionally, the constructed biosensor was selective towards fT3, even in the presence of interference substances: ascorbic acid, tyrosine, and levothyroxine, and was applied for the analysis of fT3 in synthetic serum samples with excellent recovery results. The designed biosensor also exhibited good stability and can find application in future medical diagnostics.
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Affiliation(s)
- Sylwia Baluta
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Marta Romaniec
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Kinga Halicka-Stępień
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Michalina Alicka
- Food4Future Technologies Sp. z o.o., ul. Tarasa Szewczenki 24, 51-351 Wrocław, Poland
| | - Aleksandra Pieła
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Katarzyna Pala
- Food4Future Technologies Sp. z o.o., ul. Tarasa Szewczenki 24, 51-351 Wrocław, Poland
| | - Joanna Cabaj
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
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26
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Sahoo SR, Bera D, Saha S, Goswami N. Switchable catalysis and CO 2 sensing by reduction resistant, luminescent copper-thiolate complexes. NANOSCALE 2022; 14:18051-18059. [PMID: 36448343 DOI: 10.1039/d2nr05396a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Metal-thiolate complexes have been the focus of research for several years because of their unique photophysical properties and their use as a precursor for synthesizing various well-defined metal nanoclusters. A rational understanding of their structure-property relationship is necessary to realize their full potential in practical applications. Herein, we demonstrate the synthesis of a unique copper-thiolate complex with reversibly switchable catalytic and photoluminescence (PL) properties. The as-synthesized complex at basic pH (Complex B) showed cyan PL with a strong peak at ∼488 nm (cyan) and a small shoulder peak at ∼528 nm (green). When the pH of the complex was changed to acidic (Complex A), the PL was switched to light green. Such pH-responsive PL properties were demonstrated to be useful for pH and CO2 sensing. The switchable properties originate from their two distinct structural states at two different pHs. We found that Complex A was resistant to high concentrations of a strong reducing agent, and had an intermediate oxidation state of copper (Cu+) with good thermodynamic stability. Furthermore, the switchable catalytic property was investigated with a 4-nitrophenol reduction and 3,3',5,5'-tetramethylbenzidine (TMB) oxidation reaction. The reduction kinetics followed pseudo-first-order, where the catalytic activity was enhanced by more than 103 times when Complex B was switched to Complex A. A similar trend was also observed for TMB oxidation. Our design strategy demonstrates that redox switchable metal-thiolate complexes could be a powerful candidate for a plethora of applications.
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Affiliation(s)
- Satya Ranjan Sahoo
- Materials Chemistry Department, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar, Odisha 751013, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Debkumar Bera
- Materials Chemistry Department, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar, Odisha 751013, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Sumit Saha
- Materials Chemistry Department, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar, Odisha 751013, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Nirmal Goswami
- Materials Chemistry Department, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar, Odisha 751013, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
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27
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Sarkar C, Sk S, Majumder A, Haldar S, Vijaykumar G, Bera M. Synthesis, structure, thermal and magnetic properties of new tetranuclear copper(II) complex supported by multidentate ligand and glutarate functionality. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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28
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Walencik PK. The redox-active Cu-FomA complex: the mode that provides coordination of Cu II/Cu I ions during the reduction/oxidation cycle. Dalton Trans 2022; 51:15515-15529. [PMID: 36165635 DOI: 10.1039/d2dt02398a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Colorectal cancer (CRC) is the third most commonly diagnosed form of cancer worldwide. Recent studies have indicated a strong correlation between microbial imbalance and the development of CRC. An abundance of Fusobacterium nucleatum, an anaerobic Gram-negative bacterium, has been considered a biomarker of CRC progression. Several investigations have also proposed that binding copper ions to various bacterial proteins enhances the CuII + e- ⇄ CuI redox cycle, which consequently promotes uncontrolled production of reactive oxygen species (ROS) and propels colorectal carcinogenesis. In this work, a multidisciplinary approach was applied to study the molecular relation of copper with the peptide models of FomA, a protein expressed by Fusobacterium nucleatum. The main goal was to investigate all the factors that tune the CuII + e- ⇄ CuI equilibrium. A linear peptide Fom1 (Ac-KGHGNGEEGTPTVHNE-NH2) and cyclic peptide Fom2 (cyclo-(KGHGNGEEGTPTVHNE)) were used as ligands. The coordination of CuI was deduced from the NMR data. The conditional dissociation constants KcondD defined the stability of CuI complexes. The electrochemical activity of CuII and CuI compounds was analysed using cyclic voltammetry. A quasi-reversible redox conversion CuII-peptide + e- ⇄ CuI-peptide was revealed for all studied systems. In the presence of ascorbic acid (HAsc), CuII complexes were immediately reduced to CuI species; however, their re-oxidation was kinetically sluggish. The HAsc-induced redox cycle provoked the metal-catalyzed oxidation (MCO) effect. That in the end prevented coordination of the re-appearing CuII ion to its initial binding site. The toxicity of the FomA-CuII/CuI complexes and their role in CRC progression were briefly discussed.
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Affiliation(s)
- Paulina K Walencik
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383 Wroclaw, Poland.
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29
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Cu(Proline) 2 Complex: A Model of Bio-Copper Structural Ambivalence. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27185846. [PMID: 36144582 PMCID: PMC9502899 DOI: 10.3390/molecules27185846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/17/2022] [Accepted: 09/05/2022] [Indexed: 11/17/2022]
Abstract
Complexes of Cu2+(d9) with proline may be considered a simple model to address the structural flexibility and electronic properties of copper metalloproteins. To discuss optical electronic spectra and infrared spectral responses, we use quantum chemistry applied to model systems prepared under different geometries and degree of hydration. A comparison of experimental data with calculations indicates that first explicit neighbor water clustering next to the Cu2+(d9) complex is critical for a correct description of the electronic properties of this system. We deduce that the moderately hydrated trans conformer is the main structural form of the complex in water. Further, we suggest that the antisymmetric stretching mode of the carbonyl moieties of the conformer is dominant in the spectrally broadened infrared resonance at 1605 cm−1, where inhomogeneity of the transition at the blue side can be ascribed to a continuum of less optimal interactions with the solvent. Extracted structural properties and hydration features provide information on the structural flexibility/plasticity specific to Cu2+(d9) systems in correlation with the electronic behavior upon photoexcitation. We discuss the role and the nature of the axial ligand in bio-copper structural ambivalence and reactivity.
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30
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Buzzetti PHM, Berezovska A, Nedellec Y, Cosnier S. Hollow Bioelectrodes Based on Buckypaper Assembly. Application to the Electroenzymatic Reduction of O2. NANOMATERIALS 2022; 12:nano12142399. [PMID: 35889624 PMCID: PMC9317853 DOI: 10.3390/nano12142399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/07/2022] [Accepted: 07/11/2022] [Indexed: 01/27/2023]
Abstract
A new concept of hollow electrode based on the assembly of two buckypapers creating a microcavity which contains a biocatalyst is described. To illustrate this innovative concept, hollow bioelectrodes containing 0.16–4 mg bilirubin oxidase in a microcavity were fabricated and applied to electroenzymatic reduction of O2 in aqueous solution. For hemin-modified buckypaper, the bioelectrode shows a direct electron transfer between multi-walled carbon nanotubes and bilirubin oxidase with an onset potential of 0.77 V vs. RHE. The hollow bioelectrodes showed good storage stability in solution with an electroenzymatic activity of 30 and 11% of its initial activity after 3 and 6 months, respectively. The co-entrapment of bilirubin oxidase and 2,2-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) in the microcavity leads to a bioelectrode exhibiting mediated electron transfer. After 23 h of intermittent operation, 5.66 × 10−4 mol of O2 were electroreduced (turnover number of 19,245), the loss of catalytic current being only 54% after 7 days.
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31
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Van Stappen C, Deng Y, Liu Y, Heidari H, Wang JX, Zhou Y, Ledray AP, Lu Y. Designing Artificial Metalloenzymes by Tuning of the Environment beyond the Primary Coordination Sphere. Chem Rev 2022; 122:11974-12045. [PMID: 35816578 DOI: 10.1021/acs.chemrev.2c00106] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes catalyze a variety of reactions using a limited number of natural amino acids and metallocofactors. Therefore, the environment beyond the primary coordination sphere must play an important role in both conferring and tuning their phenomenal catalytic properties, enabling active sites with otherwise similar primary coordination environments to perform a diverse array of biological functions. However, since the interactions beyond the primary coordination sphere are numerous and weak, it has been difficult to pinpoint structural features responsible for the tuning of activities of native enzymes. Designing artificial metalloenzymes (ArMs) offers an excellent basis to elucidate the roles of these interactions and to further develop practical biological catalysts. In this review, we highlight how the secondary coordination spheres of ArMs influence metal binding and catalysis, with particular focus on the use of native protein scaffolds as templates for the design of ArMs by either rational design aided by computational modeling, directed evolution, or a combination of both approaches. In describing successes in designing heme, nonheme Fe, and Cu metalloenzymes, heteronuclear metalloenzymes containing heme, and those ArMs containing other metal centers (including those with non-native metal ions and metallocofactors), we have summarized insights gained on how careful controls of the interactions in the secondary coordination sphere, including hydrophobic and hydrogen bonding interactions, allow the generation and tuning of these respective systems to approach, rival, and, in a few cases, exceed those of native enzymes. We have also provided an outlook on the remaining challenges in the field and future directions that will allow for a deeper understanding of the secondary coordination sphere a deeper understanding of the secondary coordintion sphere to be gained, and in turn to guide the design of a broader and more efficient variety of ArMs.
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Affiliation(s)
- Casey Van Stappen
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yunling Deng
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yiwei Liu
- Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Hirbod Heidari
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Jing-Xiang Wang
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yu Zhou
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Aaron P Ledray
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States.,Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
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32
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Kerns S, Biswas A, Minnetian NM, Borovik AS. Artificial Metalloproteins: At the Interface between Biology and Chemistry. JACS AU 2022; 2:1252-1265. [PMID: 35783165 PMCID: PMC9241007 DOI: 10.1021/jacsau.2c00102] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 05/22/2023]
Abstract
Artificial metalloproteins (ArMs) have recently gained significant interest due to their potential to address issues in a broad scope of applications, including biocatalysis, biotechnology, protein assembly, and model chemistry. ArMs are assembled by the incorporation of a non-native metallocofactor into a protein scaffold. This can be achieved by a number of methods that apply tools of chemical biology, computational de novo design, and synthetic chemistry. In this Perspective, we highlight select systems in the hope of demonstrating the breadth of ArM design strategies and applications and emphasize how these systems address problems that are otherwise difficult to do so with strictly biochemical or synthetic approaches.
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Affiliation(s)
- Spencer
A. Kerns
- Department of Chemistry, University of California, 1102 Natural
Science II, Irvine, California 92797, United States
| | - Ankita Biswas
- Department of Chemistry, University of California, 1102 Natural
Science II, Irvine, California 92797, United States
| | - Natalie M. Minnetian
- Department of Chemistry, University of California, 1102 Natural
Science II, Irvine, California 92797, United States
| | - A. S. Borovik
- Department of Chemistry, University of California, 1102 Natural
Science II, Irvine, California 92797, United States
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33
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Lee YJ, Park S, Kim Y, Kim SH, Seo J. Facile synthetic method for peptoids bearing multiple azoles on side chains. Pept Sci (Hoboken) 2022. [DOI: 10.1002/pep2.24287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yen Jea Lee
- Department of Chemistry Gwangju Institute of Science and Technology Gwangju Republic of Korea
| | - Soyeon Park
- Department of Chemistry Gwangju Institute of Science and Technology Gwangju Republic of Korea
| | - Yujeong Kim
- Western Seoul Center Korea Basic Science Institute Seoul Republic of Korea
| | - Sun Hee Kim
- Western Seoul Center Korea Basic Science Institute Seoul Republic of Korea
- Department of Chemistry and Nano Science Ewha Womans University Seoul Republic of Korea
| | - Jiwon Seo
- Department of Chemistry Gwangju Institute of Science and Technology Gwangju Republic of Korea
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34
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Gamze Sogukomerogullari H, Delidoğan A, Aytar E, Köse A, Sönmez M. Pd(II), Ni(II), Cu(II) and Co(II) complexes bearing “SNS” Pincer Type Ligand: Application as Catalysts for chemical CO2 conversion to obtain cyclic carbonates. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2022.121040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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35
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Eady RR, Samar Hasnain S. New horizons in structure-function studies of copper nitrite reductase. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2022.214463] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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36
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Yu Y, Marshall NM, Garner DK, Nilges MJ, Lu Y. Tuning reduction potentials of type 1 copper center in azurin by replacing a histidine ligand with its isostructural analogues. J Inorg Biochem 2022; 234:111863. [DOI: 10.1016/j.jinorgbio.2022.111863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 05/02/2022] [Accepted: 05/08/2022] [Indexed: 11/16/2022]
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37
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Isaeva VA, Molchanov AS, Shishkin MV, Sharnin VA. Stability of Cobalt(II) Complexes with Glycinate Ion as a Function of Water–Dimethyl Sulfoxide Solvent Composition. RUSS J INORG CHEM+ 2022. [DOI: 10.1134/s0036023622050084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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38
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Sarhangi SM, Matyushov DV. Anomalously Small Reorganization Energy of the Half Redox Reaction of Azurin. J Phys Chem B 2022; 126:3000-3011. [DOI: 10.1021/acs.jpcb.2c00338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Setare M. Sarhangi
- Department of Physics, Arizona State University, P.O. Box 871504, Tempe, Arizona 85287-1504, United States
| | - Dmitry V. Matyushov
- School of Molecular Sciences and Department of Physics, Arizona State University, P.O. Box 871504, Tempe, Arizona 85287-1504, United States
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39
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Fedoretz-Maxwell BP, Shin CH, MacNeil GA, Worrall LJ, Park R, Strynadka NCJ, Walsby CJ, Warren JJ. The Impact of Second Coordination Sphere Methionine-Aromatic Interactions in Copper Proteins. Inorg Chem 2022; 61:5563-5571. [DOI: 10.1021/acs.inorgchem.2c00030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Brooklyn P. Fedoretz-Maxwell
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Catherine H. Shin
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Gregory A. MacNeil
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Liam J. Worrall
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Rachel Park
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Natalie C. J. Strynadka
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Charles J. Walsby
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Jeffrey J. Warren
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
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40
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Li C, Shen J, Wu K, Yang N. Metal Centers and Organic Ligands Determine Electrochemistry of Metal-Organic Frameworks. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2106607. [PMID: 34994066 DOI: 10.1002/smll.202106607] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/08/2021] [Indexed: 06/14/2023]
Abstract
The properties and applications of metal-organic frameworks (MOFs) can be tuned by their metal centers and organic ligands. To reveal experimentally and theoretically the influence of metal centers and ligands on electrochemical performance of MOFs, three MOFs with copper or zinc centers and organic ligands of 2-methylimidazole (2MI) or 1,3,5-benzenetricarboxylic acid (H3 BTC) are synthesized and characterized in this study. 2D and porous Cu-2MI exhibits a larger active area, faster electron transfer capability, and stronger adsorption capacity than bulk Cu-BTC and dodecahedron Zn-2MI. Density functional theory calculations of adsorption ability of three MOFs toward xanthine (XA), hypoxanthine (HXA), and malachite green (MG) prove that 2D Cu-2MI has the strongest adsorption energies to three targets. Rotating disk electrode measurements reveal that 2D Cu-2MI features the biggest intrinsic heterogeneous rate constant toward three analytes. On 2D Cu-2MI sensitive and selective monitoring of XA, HXA, and MG is then achieved using differential pulse voltammetry. Their monitoring in real samples on 2D Cu-2MI is accurate and comparable with that using high-performance liquid chromatography. In summary, regulation of electrochemical sensing features of MOFs is realized through defining selected metal centers and organic ligands.
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Affiliation(s)
- Caoling Li
- Key Laboratory for Material Chemistry of Energy Conversion and Storage, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jian Shen
- Key Laboratory for Material Chemistry of Energy Conversion and Storage, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Kangbing Wu
- Key Laboratory for Material Chemistry of Energy Conversion and Storage, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Nianjun Yang
- Department of Engineering, Institute of Materials Engineering, University of Siegen, 57076, Siegen, Germany
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41
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Electrochemical Characterization of an Engineered Red Copper Protein Featuring an Unprecedented Entropic Control of the Reduction Potential. Bioelectrochemistry 2022; 146:108095. [DOI: 10.1016/j.bioelechem.2022.108095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/04/2022] [Accepted: 03/10/2022] [Indexed: 12/12/2022]
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42
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Chen X, Chen M, Wolynes PG, Wittung-Stafshede P, Gray HB. Frustration Dynamics and Electron-Transfer Reorganization Energies in Wild-Type and Mutant Azurins. J Am Chem Soc 2022; 144:4178-4185. [PMID: 35171591 PMCID: PMC8915257 DOI: 10.1021/jacs.1c13454] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Long-range electron
tunneling through metalloproteins is facilitated
by evolutionary tuning of donor–acceptor electronic couplings,
formal electrochemical potentials, and active-site reorganization
energies. Although the minimal frustration of the folding landscape
enables this tuning, residual frustration in the vicinity of the metallocofactor
can allow conformational fluctuations required for protein function.
We show here that the constrained copper site in wild-type azurin
is governed by an intricate pattern of minimally frustrated local
and distant interactions that together enable rapid electron flow
to and from the protein. In contrast, sluggish electron transfer reactions
(unfavorable reorganization energies) of active-site azurin variants
are attributable to increased frustration near to as well as distant
from the copper site, along with an exaggerated oxidation-state dependence
of both minimally and highly frustrated interaction patterns.
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Affiliation(s)
- Xun Chen
- Center for Theoretical Biological Physics, Houston, Texas 77005, United States.,Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Mingchen Chen
- Center for Theoretical Biological Physics, Houston, Texas 77005, United States
| | - Peter G Wolynes
- Center for Theoretical Biological Physics, Houston, Texas 77005, United States.,Department of Chemistry, Rice University, Houston, Texas 77005, United States.,Department of Biosciences, Rice University, Houston, Texas 77005, United States
| | - Pernilla Wittung-Stafshede
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Harry B Gray
- Beckman Institute and Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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43
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Rivillas‐Acevedo L, Grande‐Aztatzi R, Juaristi E, Vela A, Quintanar L. Reversible Stereoisomer‐Specific Cotton Effect of the Ligand Field Transitions at a Copper(II) Binding Site of the Prion Protein. Eur J Inorg Chem 2022. [DOI: 10.1002/ejic.202100625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Lina Rivillas‐Acevedo
- Centro de Investigación en Dinámica Celular Universidad Autónoma del Estado de Morelos Avenida Universidad #1001 62209 Cuernavaca, México
| | - Rafael Grande‐Aztatzi
- Escuela de Ingeniería y Ciencias Tecnológico de Monterrey Av. Eugenio Garza Sada 2501 64849 Monterrey Nuevo León, México
| | - Eusebio Juaristi
- Departamento de Química Centro de Investigación y de Estudios Avanzados (Cinvestav) Av. IPN #2508, Gustavo A. Madero 07360 Ciudad de México México
- El Colegio Nacional Donceles # 104, Centro Histórico 06020 Ciudad de México Mexico
| | - Alberto Vela
- Departamento de Química Centro de Investigación y de Estudios Avanzados (Cinvestav) Av. IPN #2508, Gustavo A. Madero 07360 Ciudad de México México
| | - Liliana Quintanar
- Departamento de Química Centro de Investigación y de Estudios Avanzados (Cinvestav) Av. IPN #2508, Gustavo A. Madero 07360 Ciudad de México México
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44
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Giraldi V, Marchini M, Di Giosia M, Gualandi A, Cirillo M, Calvaresi M, Ceroni P, Giacomini D, Cozzi PG. Acceleration of oxidation promoted by laccase irradiation with red light. NEW J CHEM 2022. [DOI: 10.1039/d2nj01107g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Irradiation with red light is able to improve yields and shorten the reaction time in enzymatic reactions.
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Affiliation(s)
- Valentina Giraldi
- Dipartimento di Chimica “Giacomo Ciamician”, Alma Mater Studiorum – Università di Bologna, Via Selmi 2, 40126, Bologna, Italy
| | - Marianna Marchini
- Dipartimento di Chimica “Giacomo Ciamician”, Alma Mater Studiorum – Università di Bologna, Via Selmi 2, 40126, Bologna, Italy
| | - Matteo Di Giosia
- Dipartimento di Chimica “Giacomo Ciamician”, Alma Mater Studiorum – Università di Bologna, Via Selmi 2, 40126, Bologna, Italy
- Center for Chemical Catalysis - C3, Alma Mater Studiorum Università di Bologna, Via Selmi 2, 40126, Bologna, Italy
| | - Andrea Gualandi
- Dipartimento di Chimica “Giacomo Ciamician”, Alma Mater Studiorum – Università di Bologna, Via Selmi 2, 40126, Bologna, Italy
- Center for Chemical Catalysis - C3, Alma Mater Studiorum Università di Bologna, Via Selmi 2, 40126, Bologna, Italy
| | - Martina Cirillo
- Dipartimento di Chimica “Giacomo Ciamician”, Alma Mater Studiorum – Università di Bologna, Via Selmi 2, 40126, Bologna, Italy
| | - Matteo Calvaresi
- Dipartimento di Chimica “Giacomo Ciamician”, Alma Mater Studiorum – Università di Bologna, Via Selmi 2, 40126, Bologna, Italy
- Center for Chemical Catalysis - C3, Alma Mater Studiorum Università di Bologna, Via Selmi 2, 40126, Bologna, Italy
| | - Paola Ceroni
- Dipartimento di Chimica “Giacomo Ciamician”, Alma Mater Studiorum – Università di Bologna, Via Selmi 2, 40126, Bologna, Italy
- Center for Chemical Catalysis - C3, Alma Mater Studiorum Università di Bologna, Via Selmi 2, 40126, Bologna, Italy
| | - Daria Giacomini
- Dipartimento di Chimica “Giacomo Ciamician”, Alma Mater Studiorum – Università di Bologna, Via Selmi 2, 40126, Bologna, Italy
- Center for Chemical Catalysis - C3, Alma Mater Studiorum Università di Bologna, Via Selmi 2, 40126, Bologna, Italy
| | - Pier Giorgio Cozzi
- Dipartimento di Chimica “Giacomo Ciamician”, Alma Mater Studiorum – Università di Bologna, Via Selmi 2, 40126, Bologna, Italy
- Center for Chemical Catalysis - C3, Alma Mater Studiorum Università di Bologna, Via Selmi 2, 40126, Bologna, Italy
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45
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Solomon EI, Jose A. Spiers Memorial Lecture: Activating Metal Sites for Biological Electron Transfer. Faraday Discuss 2022; 234:9-30. [DOI: 10.1039/d2fd00001f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Metal sites in biology often exhibit unique spectroscopic features that reflect novel geometric and electronic structures imposed by the protein that are key to reactivity. The Blue copper active site...
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46
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Thennarasu AS, Mohammed TP, Sankaralingam M. Mononuclear copper( ii) Schiff base complexes as effective models for phenoxazinone synthase. NEW J CHEM 2022. [DOI: 10.1039/d2nj03934f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Copper(ii) complexes of tridentate (N2O) Schiff base ligands as efficient catalysts for 2-aminophenol oxidation to 2-aminophenoxazin-3-one with excellent reaction rates.
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Affiliation(s)
- Abinaya Sushana Thennarasu
- Bioinspired & Biomimetic Inorganic Chemistry Lab, Department of Chemistry, National Institute of Technology Calicut, Kozhikode, Kerala 673601, India
| | - Thasnim P Mohammed
- Bioinspired & Biomimetic Inorganic Chemistry Lab, Department of Chemistry, National Institute of Technology Calicut, Kozhikode, Kerala 673601, India
| | - Muniyandi Sankaralingam
- Bioinspired & Biomimetic Inorganic Chemistry Lab, Department of Chemistry, National Institute of Technology Calicut, Kozhikode, Kerala 673601, India
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47
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Mammoser CC, Agh RE, Garcia NM, Wang Y, Thielges M. Altered coordination in a blue copper protein upon association with redox partner revealed by carbon-deuterium vibrational probes. Phys Chem Chem Phys 2022; 24:21588-21592. [DOI: 10.1039/d2cp03314c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Proteins tune the reactivity of metal sites; less understood is the impact of association with a redox partner. We demonstrate the utility of carbon-deuterium labels for selective analysis of delicate...
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48
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Vilbert AC, Liu Y, Dai H, Lu Y. Recent advances in tuning redox properties of electron transfer centers in metalloenzymes catalyzing oxygen reduction reaction and H 2 oxidation important for fuel cells design. CURRENT OPINION IN ELECTROCHEMISTRY 2021; 30:100780. [PMID: 34435160 PMCID: PMC8382256 DOI: 10.1016/j.coelec.2021.100780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Current fuel-cell catalysts for oxygen reduction reaction (ORR) and H2 oxidation use precious metals and, for ORR, require high overpotentials. In contrast, metalloenzymes perform their respective reaction at low overpotentials using earth-abundant metals, making metalloenzymes ideal candidates for inspiring electrocatalytic design. Critical to the success of these enzymes are redox-active metal centers surrounding the enzyme active sites that ensure fast electron transfer (ET) to or away from the active site, by tuning the catalytic potential of the reaction as observed in multicopper oxidases but also in dictating the catalytic bias of the reaction as realized in hydrogenases. This review summarizes recent advances in studying these ET centers in multicopper oxidases and heme-copper oxidases that perform ORR and hydrogenases in carrying out H2 oxidation. Insights gained from understanding how the reduction potential of the ET centers effects reactivity at the active site in both the enzymes and their models are provided.
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Affiliation(s)
| | - Yiwei Liu
- Department of Chemistry and Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Huiguang Dai
- Department of Chemistry and Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yi Lu
- Pacific Northwest National Laboratory, Richland, WA 99352, USA
- Department of Chemistry and Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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49
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Buades AB, Viñas C, Fontrodona X, Teixidor F. 1.3 V Inorganic Sequential Redox Chain with an All-Anionic Couple 1-/2- in a Single Framework. Inorg Chem 2021; 60:16168-16177. [PMID: 34693711 PMCID: PMC9180739 DOI: 10.1021/acs.inorgchem.1c01822] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The relatively low symmetry of [3,3′-Co(1,2-C2B9H11)2]− ([1]−), along with the high number
of available
substitution sites, 18 on the boron atoms and 4 on the carbon atoms,
allows a fairly regioselective and stepwise chlorination of the platform
and therefore a very controlled tuning of the electrochemical potential
tuning. This is not so easily found in other systems, e.g., ferrocene.
In this work, we show how a single platform with boron and carbon
in the ligand, and only cobalt can produce a tuning of potentials
in a stepwise manner in the 1.3 V range. The platform used is made
of two icosahedra sharing one vertex. The E1/2 tuning has been achieved from [1]− by sequential chlorination, which has given potentials whose values
increase sequentially and linearly with the number of chloro groups
in the platform. [Cl8-1]−, [Cl10-1]−, and [Cl12-1]− have been obtained, which
are added to the existing [Cl-1]−,
[Cl2-1]−, [Cl4-1]−, and [Cl6-1]− described earlier to give the 1.3 V range. It is envisaged
to extend this range also sequentially by changing the metal from
cobalt to iron. The last successful synthesis of the highest chlorinated
derivatives of cobaltabis(dicarbollide) dates back to 1982, and since
then, no more advances have occurred toward more substituted metallacarborane
chlorinated compounds. [Cl8-1]−, [Cl10-1]−, and [Cl12-1]− are made
with an easy and fast method. The key point of the reaction is the
use of the protonated form of [Co(C2B9H11)2]−, as a starting material,
and the use of sulfuryl chloride, a less hazardous and easier to use
chlorinating agent. In addition, we present a complete, spectroscopic,
crystallographic, and electrochemical characterization, together with
a study of the influence of the chlorination position in the electrochemical
properties. By sequential halogenation of [Co(C2B9H11)2]− ([1]−) with chlorine, the [Cl8-1]−, [Cl10-1]−, and [Cl12-1]− derivatives
of [1]− have been prepared and isolated.
The E1/2 values increase sequentially
and linearly with the number of chloro groups in the platform. If
these potentials are added to the existing E1/2 values due to [Cl-1]−, [Cl2-1]−, [Cl4-1]−, and [Cl6-1]− described earlier, a 1.3 V range is obtained. This
allows tuning of the desired potentials for the purposes of nature.
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Affiliation(s)
- Ana B Buades
- Institut de Ciència de Materials de Barcelona, Consejo Superior de Investigaciones Científicas, Campus Universitat Autonòma de Barcelona (UAB), 08193 Bellaterra, Spain
| | - Clara Viñas
- Institut de Ciència de Materials de Barcelona, Consejo Superior de Investigaciones Científicas, Campus Universitat Autonòma de Barcelona (UAB), 08193 Bellaterra, Spain
| | - Xavier Fontrodona
- Departamento de Química and Serveis Tècnics de Recerca, Universitat de Girona, Campus de Montilivi, 17071 Girona, Spain
| | - Francesc Teixidor
- Institut de Ciència de Materials de Barcelona, Consejo Superior de Investigaciones Científicas, Campus Universitat Autonòma de Barcelona (UAB), 08193 Bellaterra, Spain
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50
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Ramírez CS, Tolmie C, Opperman DJ, González PJ, Rivas MG, Brondino CD, Ferroni FM. Copper nitrite reductase from Sinorhizobium meliloti 2011: Crystal structure and interaction with the physiological versus a nonmetabolically related cupredoxin-like mediator. Protein Sci 2021; 30:2310-2323. [PMID: 34562300 DOI: 10.1002/pro.4195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 11/08/2022]
Abstract
We report the crystal structure of the copper-containing nitrite reductase (NirK) from the Gram-negative bacterium Sinorhizobium meliloti 2011 (Sm), together with complex structural alignment and docking studies with both non-cognate and the physiologically related pseudoazurins, SmPaz1 and SmPaz2, respectively. S. meliloti is a rhizobacterium used for the formulation of Medicago sativa bionoculants, and SmNirK plays a key role in this symbiosis through the denitrification pathway. The structure of SmNirK, solved at a resolution of 2.5 Å, showed a striking resemblance with the overall structure of the well-known Class I NirKs composed of two Greek key β-barrel domains. The activity of SmNirK is ~12% of the activity reported for classical NirKs, which could be attributed to several factors such as subtle structural differences in the secondary proton channel, solvent accessibility of the substrate channel, and that the denitrifying activity has to be finely regulated within the endosymbiont. In vitro kinetics performed in homogenous and heterogeneous media showed that both SmPaz1 and SmPaz2, which are coded in different regions of the genome, donate electrons to SmNirK with similar performance. Even though the energetics of the interprotein electron transfer (ET) process is not favorable with either electron donors, adduct formation mediated by conserved residues allows minimizing the distance between the copper centers involved in the interprotein ET process.
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Affiliation(s)
- Cintia Soledad Ramírez
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL). CONICET, Ciudad Universitaria, Santa Fe, Argentina
| | - Carmien Tolmie
- Department of Microbiology and Biochemistry, University of the Free State (UFS), Bloemfontein, South Africa
| | - Diederik Johannes Opperman
- Department of Microbiology and Biochemistry, University of the Free State (UFS), Bloemfontein, South Africa
| | - Pablo Javier González
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL). CONICET, Ciudad Universitaria, Santa Fe, Argentina
| | - María Gabriela Rivas
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL). CONICET, Ciudad Universitaria, Santa Fe, Argentina
| | - Carlos Dante Brondino
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL). CONICET, Ciudad Universitaria, Santa Fe, Argentina
| | - Felix Martín Ferroni
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL). CONICET, Ciudad Universitaria, Santa Fe, Argentina
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