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First-principles study on the structure and optical spectroscopy of the redox-active center of blue copper proteins. Chem Phys 2020. [DOI: 10.1016/j.chemphys.2020.110859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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2
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Da-yang TE, Fifen JJ, Malloum A, Lahmar S, Nsangou M, Conradie J. Structures of the solvated copper(ii) ion in ammonia at various temperatures. NEW J CHEM 2020. [DOI: 10.1039/c9nj05169d] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigated theoretically the structures and relative stabilities of the solvated copper(ii) ion in ammonia, Cu2+(NH3)n, n = 1–10.
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Affiliation(s)
| | - Jean Jules Fifen
- Department of Physics
- Faculty of Science
- The University of Ngaoundere
- Ngaoundere
- Cameroon
| | - Alhadji Malloum
- Department of Chemistry
- University of the Free State
- Bloemfontein
- South Africa
- Department of Physics
| | - Souad Lahmar
- Laboratoire de Spectroscopie Atomique Moléculaire et Applications
- Faculté des Sciences de Tunis
- Université de Tunis El Manar
- Tunis
- Tunisia
| | - Mama Nsangou
- University of Maroua
- Maroua
- Cameroon
- Department of Physics
- Faculty of Science
| | - Jeanet Conradie
- Department of Chemistry
- University of the Free State
- Bloemfontein
- South Africa
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3
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Olloqui-Sariego JL, Márquez I, Frutos-Beltrán E, Díaz-Moreno I, De la Rosa MA, Calvente JJ, Andreu R, Díaz-Quintana A. Key Role of the Local Hydrophobicity in the East Patch of Plastocyanins on Their Thermal Stability and Redox Properties. ACS OMEGA 2018; 3:11447-11454. [PMID: 31459248 PMCID: PMC6645426 DOI: 10.1021/acsomega.8b01612] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 09/06/2018] [Indexed: 06/10/2023]
Abstract
Understanding the molecular basis of the thermal stability and functionality of redox proteins has important practical applications. Here, we show a distinct thermal dependence of the spectroscopic and electrochemical properties of two plastocyanins from the thermophilic cyanobacterium Phormidium laminosum and their mesophilic counterpart from Synechocystis sp. PCC 6803, despite the similarity of their molecular structures. To explore the origin of these differences, we have mimicked the local hydrophobicity in the east patch of the thermophilic protein by replacing a valine of the mesophilic plastocyanin by isoleucine. Interestingly, the resulting mutant approaches the thermal stability, redox thermodynamics, and dynamic coupling of the flexible site motions of the thermophilic protein, indicating the existence of a close connection between the hydrophobic packing of the east patch region of plastocyanin and the functional control and stability of the oxidized and reduced forms of the protein.
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Affiliation(s)
- José Luis Olloqui-Sariego
- Departamento
de Química Física, Universidad
de Sevilla, c/ Profesor García González, 1, 41012 Sevilla, Spain
| | - Inmaculada Márquez
- Departamento
de Química Física, Universidad
de Sevilla, c/ Profesor García González, 1, 41012 Sevilla, Spain
| | - Estrella Frutos-Beltrán
- Instituto
de Investigaciones Químicas, cicCartuja, Universidad de Sevilla y CSIC, Avd. Américo Vespucio 49, 41092 Sevilla, Spain
| | - Irene Díaz-Moreno
- Instituto
de Investigaciones Químicas, cicCartuja, Universidad de Sevilla y CSIC, Avd. Américo Vespucio 49, 41092 Sevilla, Spain
| | - Miguel A. De la Rosa
- Instituto
de Investigaciones Químicas, cicCartuja, Universidad de Sevilla y CSIC, Avd. Américo Vespucio 49, 41092 Sevilla, Spain
| | - Juan José Calvente
- Departamento
de Química Física, Universidad
de Sevilla, c/ Profesor García González, 1, 41012 Sevilla, Spain
| | - Rafael Andreu
- Departamento
de Química Física, Universidad
de Sevilla, c/ Profesor García González, 1, 41012 Sevilla, Spain
| | - Antonio Díaz-Quintana
- Instituto
de Investigaciones Químicas, cicCartuja, Universidad de Sevilla y CSIC, Avd. Américo Vespucio 49, 41092 Sevilla, Spain
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4
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Exploration of selected electronic characteristics of half-sandwich organoruthenium(II) β-diketonate complexes. J Mol Model 2018; 24:98. [DOI: 10.1007/s00894-018-3598-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 01/26/2018] [Indexed: 12/11/2022]
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5
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Sabolović J, Ramek M, Marković M. Calculating the geometry and Raman spectrum of physiological bis(l-histidinato)copper(II): an assessment of DFT functionals for aqueous and isolated systems. J Mol Model 2017; 23:290. [DOI: 10.1007/s00894-017-3448-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 08/28/2017] [Indexed: 11/24/2022]
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6
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Study on electronic properties, thermodynamic and kinetic parameters of the selected platinum(II) derivatives interacting with guanine. J Inorg Biochem 2017; 172:100-109. [DOI: 10.1016/j.jinorgbio.2017.04.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 04/06/2017] [Accepted: 04/08/2017] [Indexed: 11/23/2022]
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7
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Hurd CA, Besley NA, Robinson D. A QM/MM study of the nature of the entatic state in plastocyanin. J Comput Chem 2016; 38:1431-1437. [PMID: 27859435 PMCID: PMC5434870 DOI: 10.1002/jcc.24666] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/23/2016] [Accepted: 10/27/2016] [Indexed: 11/27/2022]
Abstract
Plastocyanin is a copper containing protein that is involved in the electron transfer process in photosynthetic organisms. The active site of plastocyanin is described as an entatic state whereby its structure represents a compromise between the structures favored by the oxidized and reduced forms. In this study, the nature of the entatic state is investigated through density functional theory‐based hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations. The strain energy is computed to be 12.8 kcal/mol and 14.5 kcal/mol for the oxidized and reduced forms of the protein, indicating that the active site has an intermediate structure. It is shown that the energy gap between the oxidized and reduced forms varies significantly with the fluctuations in the structure of the active site at room temperature. An accurate determination of the reorganization energy requires averaging over conformation and a large region of the protein around the active site to be treated at the quantum mechanical level. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Catherine A Hurd
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
| | - Nicholas A Besley
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
| | - David Robinson
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
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8
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Tsipis AC. DFT/TDDFT insights into the chemistry, biochemistry and photophysics of copper coordination compounds. RSC Adv 2014. [DOI: 10.1039/c4ra04921g] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Highlighting the recent progress in DFT/TDDFT application to coordination chemistry of copper.
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Affiliation(s)
- Athanassios C. Tsipis
- Laboratory of Inorganic and General Chemistry
- Department of Chemistry
- University of Ioannina
- 451 10 Ioannina
- Greece
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9
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Vázquez-Lima H, Guadarrama P, Martínez-Anaya C. Geometric distortions on a three-coordinated T1 Cu site model as a potential strategy to modulate redox potential. A theoretical study. J Mol Model 2011; 18:455-66. [DOI: 10.1007/s00894-011-1063-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Accepted: 03/22/2011] [Indexed: 10/18/2022]
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10
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Chaboy J, Díaz-Moreno S, Díaz-Moreno I, De la Rosa MA, Díaz-Quintana A. How the local geometry of the Cu-binding site determines the thermal stability of blue copper proteins. ACTA ACUST UNITED AC 2011; 18:25-31. [PMID: 21276936 DOI: 10.1016/j.chembiol.2010.12.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Revised: 12/09/2010] [Accepted: 12/10/2010] [Indexed: 12/16/2022]
Abstract
Identifying the factors that govern the thermal resistance of cupredoxins is essential for understanding their folding and stability, and for improving our ability to design highly stable enzymes with potential biotechnological applications. Here, we show that the thermal unfolding of plastocyanins from two cyanobacteria--the mesophilic Synechocystis and the thermophilic Phormidium--is closely related to the short-range structure around the copper center. Cu K-edge X-ray absorption spectroscopy shows that the bond length between Cu and the S atom from the cysteine ligand is a key structural factor that correlates with the thermal stability of the cupredoxins in both oxidized and reduced states. These findings were confirmed by an additional study of a site-directed mutant of Phormidium plastocyanin showing a reverse effect of the redox state on the thermal stability of the protein.
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Affiliation(s)
- Jesús Chaboy
- Instituto de Ciencia de Materiales de Aragón, Consejo Superior de Investigaciones Científicas-Universidad de Zaragoza, 50009 Zaragoza, Spain.
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Ando K. The axial methionine ligand may control the redox reorganizations in the active site of blue copper proteins. J Chem Phys 2010; 133:175101. [DOI: 10.1063/1.3495983] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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12
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Zhekova HR, Seth M, Ziegler T. A Magnetic and Electronic Circular Dichroism Study of Azurin, Plastocyanin, Cucumber Basic Protein, and Nitrite Reductase Based on Time-Dependent Density Functional Theory Calculations. J Phys Chem A 2010; 114:6308-21. [PMID: 20450218 DOI: 10.1021/jp101372s] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hristina R. Zhekova
- Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada, T2N 1N4
| | - Michael Seth
- Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada, T2N 1N4
| | - Tom Ziegler
- Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada, T2N 1N4
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