1
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Wilson LA, Melville JN, Pedroso MM, Krco S, Hoelzle R, Zaugg J, Southam G, Virdis B, Evans P, Supper J, Harmer JR, Tyson G, Clark A, Schenk G, Bernhardt PV. Kinetic, electrochemical and spectral characterization of bacterial and archaeal rusticyanins; unexpected stability issues and consequences for applications in biotechnology. J Inorg Biochem 2024; 256:112539. [PMID: 38593609 DOI: 10.1016/j.jinorgbio.2024.112539] [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: 01/24/2024] [Revised: 03/21/2024] [Accepted: 03/21/2024] [Indexed: 04/11/2024]
Abstract
Motivated by the ambition to establish an enzyme-driven bioleaching pathway for copper extraction, properties of the Type-1 copper protein rusticyanin from Acidithiobacillus ferrooxidans (AfR) were compared with those from an ancestral form of this enzyme (N0) and an archaeal enzyme identified in Ferroplasma acidiphilum (FaR). While both N0 and FaR show redox potentials similar to that of AfR their electron transport rates were significantly slower. The lack of a correlation between the redox potentials and electron transfer rates indicates that AfR and its associated electron transfer chain evolved to specifically facilitate the efficient conversion of the energy of iron oxidation to ATP formation. In F. acidiphilum this pathway is not as efficient unless it is up-regulated by an as of yet unknown mechanism. In addition, while the electrochemical properties of AfR were consistent with previous data, previously unreported behavior was found leading to a form that is associated with a partially unfolded form of the protein. The cyclic voltammetry (CV) response of AfR immobilized onto an electrode showed limited stability, which may be connected to the presence of the partially unfolded state of this protein. Insights gained in this study may thus inform the engineering of optimized rusticyanin variants for bioleaching processes as well as enzyme-catalyzed solubilization of copper-containing ores such as chalcopyrite.
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Affiliation(s)
- Liam A Wilson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jamie N Melville
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Marcelo M Pedroso
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Stefan Krco
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Robert Hoelzle
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Julian Zaugg
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Gordon Southam
- School of the Environment, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Bernardino Virdis
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Paul Evans
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jenna Supper
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jeffrey R Harmer
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Gene Tyson
- Centre for Microbiome Research, Queensland University of Technology, Woolloongabba, QLD 4102, Australia
| | - Alice Clark
- Sustainable Minerals Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD 4072, Australia; Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia; Sustainable Minerals Institute, The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Paul V Bernhardt
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia.
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2
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Di Rocco G, Battistuzzi G, Borsari M, Bortolotti CA, Ranieri A, Sola M. The enthalpic and entropic terms of the reduction potential of metalloproteins: Determinants and interplay. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214071] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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3
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Osella S. Artificial Photosynthesis: Is Computation Ready for the Challenge Ahead? NANOMATERIALS 2021; 11:nano11020299. [PMID: 33498961 PMCID: PMC7911014 DOI: 10.3390/nano11020299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 12/13/2022]
Abstract
A tremendous effort is currently devoted to the generation of novel hybrid materials with enhanced electronic properties for the creation of artificial photosynthetic systems. This compelling and challenging problem is well-defined from an experimental point of view, as the design of such materials relies on combining organic materials or metals with biological systems like light harvesting and redox-active proteins. Such hybrid systems can be used, e.g., as bio-sensors, bio-fuel cells, biohybrid photoelectrochemical cells, and nanostructured photoelectronic devices. Despite these efforts, the main bottleneck is the formation of efficient interfaces between the biological and the organic/metal counterparts for efficient electron transfer (ET). It is within this aspect that computation can make the difference and improve the current understanding of the mechanisms underneath the interface formation and the charge transfer efficiency. Yet, the systems considered (i.e., light harvesting protein, self-assembly monolayer and surface assembly) are more and more complex, reaching (and often passing) the limit of current computation power. In this review, recent developments in computational methods for studying complex interfaces for artificial photosynthesis will be provided and selected cases discussed, to assess the inherent ability of computation to leave a mark in this field of research.
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Affiliation(s)
- Silvio Osella
- Chemical and Biological Systems Simulation Lab, Center of New Technologies, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland
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4
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North ML, Wilcox DE. Shift from Entropic Cu 2+ Binding to Enthalpic Cu + Binding Determines the Reduction Thermodynamics of Blue Copper Proteins. J Am Chem Soc 2019; 141:14329-14339. [PMID: 31433629 DOI: 10.1021/jacs.9b06836] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The enthalpic and entropic components of Cu2+ and Cu+ binding to the blue copper protein azurin have been quantified with isothermal titration calorimetry (ITC) measurements and analysis, providing the first such experimental values for Cu+ binding to a protein. The high affinity of azurin for Cu2+ is entirely due to a very favorable binding entropy, while its even higher affinity for Cu+ is due to a favorable binding enthalpy and entropy. The binding thermodynamics provide insight into bond enthalpies at the blue copper site and entropic contributions from desolvation and proton displacement. These values were used in thermodynamic cycles to determine the enthalpic and entropic contributions to the free energy of reduction and thus the reduction potential. The reduction thermodynamics obtained with this method are in good agreement with previous results from temperature-dependent electrochemical measurements. The calorimetry method, however, provides new insight into contributions from the initial (oxidized) and final (reduced) states of the reduction. Since ITC measurements quantify the protons that are displaced upon metal binding, the proton transfer that is coupled with electron transfer is also determined with this method. Preliminary results for Cu2+ and Cu+ binding to the Phe114Pro variant of azurin demonstrate the insight about protein tuning of the reduction potential that is provided by the binding thermodynamics of each metal oxidation state.
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Affiliation(s)
- Molly L North
- Department of Chemistry , Dartmouth College , Hanover , New Hampshire 03755 , United States
| | - Dean E Wilcox
- Department of Chemistry , Dartmouth College , Hanover , New Hampshire 03755 , United States
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5
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Shen L, Zeng X, Hu H, Hu X, Yang W. Accurate Quantum Mechanical/Molecular Mechanical Calculations of Reduction Potentials in Azurin Variants. J Chem Theory Comput 2018; 14:4948-4957. [PMID: 30040901 DOI: 10.1021/acs.jctc.8b00403] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Understanding the regulation mechanism and molecular determinants of the reduction potential of metalloprotein is a major challenge. An ab initio quantum mechanical/molecular mechanical (QM/MM) method combining the minimum free energy path (MFEP) and fractional number of electron (FNE) approaches has been developed in our group to simulate the redox processes of large systems. The FNE scheme provides an efficient unique description for the redox process, while the MFEP method provides improved conformational sampling on complex environments such as protein in the QM/MM calculations. The reduction potentials of wild-type and seven mutants of azurin, a type 1 copper metalloprotein, were simulated with the QM/MM-MFEP+FNE approach in this paper. A range of 350 mV for the variations of the reduction potentials of these azurin proteins was reproduced faithfully with relative errors around 20 mV. The correlation between structural interactions and reduction potentials observed in simulations provides in-depth insight into the regulation of reduction potentials, which potentially can also be very useful to the engineering of metalloprotein-based electrocatalysts in artificial photosynthesis. The excellent accuracy and efficiency of the QM/MM-MFEP+FNE approach demonstrate the potential for simulations of many electron transfer processes in condensed phases and biochemical systems.
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Affiliation(s)
- Lin Shen
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , United States
| | - Xiancheng Zeng
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , United States
| | - Hao Hu
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , United States
| | - Xiangqian Hu
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , United States
| | - Weitao Yang
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , United States
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6
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Fowler NJ, Blanford CF, Warwicker J, de Visser SP. Prediction of Reduction Potentials of Copper Proteins with Continuum Electrostatics and Density Functional Theory. Chemistry 2017; 23:15436-15445. [PMID: 28815759 PMCID: PMC5698706 DOI: 10.1002/chem.201702901] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Indexed: 12/20/2022]
Abstract
Blue copper proteins, such as azurin, show dramatic changes in Cu2+/Cu+ reduction potential upon mutation over the full physiological range. Hence, they have important functions in electron transfer and oxidation chemistry and have applications in industrial biotechnology. The details of what determines these reduction potential changes upon mutation are still unclear. Moreover, it has been difficult to model and predict the reduction potential of azurin mutants and currently no unique procedure or workflow pattern exists. Furthermore, high‐level computational methods can be accurate but are too time consuming for practical use. In this work, a novel approach for calculating reduction potentials of azurin mutants is shown, based on a combination of continuum electrostatics, density functional theory and empirical hydrophobicity factors. Our method accurately reproduces experimental reduction potential changes of 30 mutants with respect to wildtype within experimental error and highlights the factors contributing to the reduction potential change. Finally, reduction potentials are predicted for a series of 124 new mutants that have not yet been investigated experimentally. Several mutants are identified that are located well over 10 Å from the copper center that change the reduction potential by more than 85 mV. The work shows that secondary coordination sphere mutations mostly lead to long‐range electrostatic changes and hence can be modeled accurately with continuum electrostatics.
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Affiliation(s)
- Nicholas J Fowler
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Christopher F Blanford
- Manchester Institute of Biotechnology and School of Materials, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Jim Warwicker
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Sam P de Visser
- Manchester Institute of Biotechnology, and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
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7
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Terasaka E, Okada N, Sato N, Sako Y, Shiro Y, Tosha T. Characterization of quinol-dependent nitric oxide reductase from Geobacillus stearothermophilus: enzymatic activity and active site structure. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:1019-26. [PMID: 24569054 DOI: 10.1016/j.bbabio.2014.02.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 02/10/2014] [Accepted: 02/15/2014] [Indexed: 10/25/2022]
Abstract
Nitric oxide reductase (NOR) catalyzes the reduction of nitric oxide to generate nitrous oxide. We recently reported on the crystal structure of a quinol-dependent NOR (qNOR) from Geobacillus stearothermophilus [Y. Matsumoto, T. Tosha, A.V. Pisliakov, T. Hino, H. Sugimoto, S. Nagano, Y. Sugita and Y. Shiro, Nat. Struct. Mol. Biol. 19 (2012) 238-246], and suggested that a water channel from the cytoplasm, which is not observed in cytochrome c-dependent NOR (cNOR), functions as a pathway transferring catalytic protons. Here, we further investigated the functional and structural properties of qNOR, and compared the findings with those for cNOR. The pH optimum for the enzymatic reaction of qNOR was in the alkaline range, whereas Pseudomonas aeruginosa cNOR showed a higher activity at an acidic pH. The considerably slower reduction rate, and a correlation of the pH dependence for enzymatic activity and the reduction rate suggest that the reduction process is the rate-determining step for the NO reduction by qNOR, while the reduction rate for cNOR was very fast and therefore is unlikely to be the rate-determining step. A close examination of the heme/non-heme iron binuclear center by resonance Raman spectroscopy indicated that qNOR has a more polar environment at the binuclear center compared with cNOR. It is plausible that a water channel enhances the accessibility of the active site to solvent water, creating a more polar environment in qNOR. This structural feature could control certain properties of the active site, such as redox potential, which could explain the different catalytic properties of the two NORs. This article is part of a Special Issue entitled: 18th European Bioenergetic Conference.
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Affiliation(s)
- Erina Terasaka
- RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan; Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Norihiro Okada
- RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan; Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Nozomi Sato
- RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan; Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Yoshihiko Sako
- Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Yoshitsugu Shiro
- RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan; Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan.
| | - Takehiko Tosha
- RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan.
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8
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De March M, Di Rocco G, Hickey N, Geremia S. High-resolution crystal structure of the recombinant diheme cytochrome c fromShewanella baltica(OS155). J Biomol Struct Dyn 2014; 33:395-403. [DOI: 10.1080/07391102.2014.880657] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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9
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Wilson TD, Yu Y, Lu Y. Understanding copper-thiolate containing electron transfer centers by incorporation of unnatural amino acids and the CuA center into the type 1 copper protein azurin. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.06.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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10
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Ivanova E, Pang J, Jowitt TA, Yan G, Warwicker J, Sutcliffe MJ, Lu H. Temperature-dependent study reveals that dynamics of hydrophobic residues plays an important functional role in the mitochondrial Tim9-Tim10 complex. Proteins 2011; 80:602-15. [DOI: 10.1002/prot.23224] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Revised: 09/20/2011] [Accepted: 10/12/2011] [Indexed: 11/11/2022]
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11
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Ullmann RT, Ullmann GM. Coupling of Protonation, Reduction, and Conformational Change in azurin from Pseudomonas aeruginosa Investigated with Free Energy Measures of Cooperativity. J Phys Chem B 2011; 115:10346-59. [DOI: 10.1021/jp204644h] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- R. Thomas Ullmann
- Structural Biology/Bioinformatics, University of Bayreuth, Universitätsstrasse 30, BGI, 95447 Bayreuth, Germany
| | - G. Matthias Ullmann
- Structural Biology/Bioinformatics, University of Bayreuth, Universitätsstrasse 30, BGI, 95447 Bayreuth, Germany
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12
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Monari S, Ranieri A, Bortolotti CA, Peressini S, Tavagnacco C, Borsari M. Unfolding of cytochrome c immobilized on self-assembled monolayers. An electrochemical study. Electrochim Acta 2011. [DOI: 10.1016/j.electacta.2011.06.022] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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13
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The impact of urea-induced unfolding on the redox process of immobilised cytochrome c. J Biol Inorg Chem 2010; 15:1233-42. [DOI: 10.1007/s00775-010-0681-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Accepted: 06/02/2010] [Indexed: 11/25/2022]
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14
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Tian Y, Ran Q, Xu J, Xian Y, Peng R, Jin L. High-Quality Covalently Grafting Hemoglobin on Gold Electrodes: Characterization, Redox Thermodynamics and Bio-electrocatalysis. Chemphyschem 2009; 10:3105-11. [DOI: 10.1002/cphc.200900588] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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15
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Active site loop dictates the thermodynamics of reduction and ligand protonation in cupredoxins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:995-1000. [PMID: 19230853 DOI: 10.1016/j.bbapap.2009.02.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2008] [Revised: 01/28/2009] [Accepted: 02/03/2009] [Indexed: 11/21/2022]
Abstract
The thermodynamics of reduction and His ligand protonation have been determined for a range of loop-contraction variants of the electron transferring type 1 copper protein azurin (AZ). For AZPC, in which the native C-terminal loop containing the Cys, His and Met ligands has been replaced with the shorter sequence from plastocyanin (PC) and AZAMI, in which the even shorter amicyanin (AMI) loop has been inserted, the thermodynamics of reduction match those of the protein whose loop has been introduced which are different to the values for AZ. The enthalpic contribution to His ligand protonation, which is not observed in AZ, is similar in AZAMI and AMI. The thermodynamics of this process in AZPC are more dissimilar to those for PC. In the case of AZAMI-F, a variant possessing the (non natural) minimal loop that can bind a type 1 copper site, the reduction thermodynamics are intermediate between those of AZPC and AZAMI, whilst the thermodynamic data for His ligand protonation are very similar to those for AMI. The results for AZAMI and AZPC are primarily due to protein based enthalpic effects related to the interaction of the metal with permanent protein dipoles from the loop, and to the decreased loop length which favors His ligand protonation in the cuprous proteins. Entropic factors related to loop flexibility have little influence because of constraints imposed by metal coordination and the fact that the introduced loops pack well against the AZ scaffold. Thus, the host scaffold in general plays a minor thermodynamic role in both processes, although for AZAMI-F differences in the first and second coordination spheres influence the thermodynamics of reduction.
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16
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Manetto GD, Grasso DM, Milardi D, Pappalardo M, Guzzi R, Sportelli L, Verbeet MP, Canters GW, La Rosa C. The role played by the alpha-helix in the unfolding pathway and stability of azurin: switching between hierarchic and nonhierarchic folding. Chembiochem 2008; 8:1941-9. [PMID: 17868155 DOI: 10.1002/cbic.200700214] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The role played by the alpha-helix in determining the structure, the stability and the unfolding mechanism of azurin was addressed by studying a helix-depleted azurin variant produced by site-directed mutagenesis. The protein structure was investigated by CD, 1D (1)H NMR, fluorescence spectroscopy measurements and MD simulations, whilst EPR, UV-visible and cyclic voltammetry experiments were carried out to investigate the geometry and the properties of the Cu(II) site. The effects of the alpha-helix depletion on the thermal stability and the unfolding pathway of the protein were determined by DSC, UV/visible and fluorescence measurements at increasing temperature. The results show that, in the absence of the alpha-helix segment, the overall protein structure is maintained, and that only the Cu site is slightly modified. In contrast, the protein stability is diminished by about 60% with respect to the wild-type azurin. Moreover, the unfolding pathway of the mutant azurin involves the presence of detectable intermediates. In comparison with previous studies concerning other small beta-sheet cupredoxins, the results as a whole support the hypothesis that the presence of the alpha-helix can switch the folding of azurin from a hierarchic to a nonhierarchic mechanism in which the highly conserved beta-sheet core provides a scaffold for cooperative folding of the wild-type protein.
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Affiliation(s)
- Gaetano D Manetto
- Dipartimento di Scienze Chimiche, Università di Catania, Viale A. Doria 6, 95125 (CT), Italy
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17
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Battistuzzi G, Bellei M, Dennison C, Di Rocco G, Sato K, Sola M, Yanagisawa S. Thermodynamics of the alkaline transition in phytocyanins. J Biol Inorg Chem 2007; 12:895-900. [PMID: 17569996 DOI: 10.1007/s00775-007-0245-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2007] [Accepted: 04/29/2007] [Indexed: 10/23/2022]
Abstract
The thermodynamics of the alkaline transition which influences the spectral and redox properties of the type 1 copper center in phytocyanins has been determined spectroscopically. The proteins investigated include Rhus vernicifera stellacyanin, cucumber basic protein and its Met89Gln variant, and umecyanin, the stellacyanin from horseradish roots, along with its Gln95Met variant. The changes in reaction enthalpy and entropy within the protein series show partial compensatory behavior. Thus, the reaction free energy change (hence the pK (a) value) is rather variable. This indicates that species-dependent differences in reaction thermodynamics, although containing an important contribution from changes in the hydrogen-bonding network of water molecules in the hydration sphere of the protein (which feature enthalpy-entropy compensation), are to a large extent protein-based. The data for axial ligand variants are consistent with the hypothesis of a copper-binding His as the deprotonating residue responsible for this transition.
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Affiliation(s)
- Gianantonio Battistuzzi
- Department of Chemistry, University of Modena and Reggio Emilia, Via Campi 183, 41100 Modena, Italy
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18
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Kamitaka Y, Tsujimura S, Kataoka K, Sakurai T, Ikeda T, Kano K. Effects of axial ligand mutation of the type I copper site in bilirubin oxidase on direct electron transfer-type bioelectrocatalytic reduction of dioxygen. J Electroanal Chem (Lausanne) 2007. [DOI: 10.1016/j.jelechem.2006.10.035] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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19
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Battistuzzi G, Bellei M, De Rienzo F, Sola M. Redox properties of the Fe3+/Fe2+ couple in Arthromyces ramosus class II peroxidase and its cyanide adduct. J Biol Inorg Chem 2006; 11:586-92. [PMID: 16791642 DOI: 10.1007/s00775-006-0108-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2006] [Accepted: 04/10/2006] [Indexed: 10/24/2022]
Abstract
The thermodynamics of the one-electron reduction of the ferric heme in free and cyanide-bound Arthromyces ramosus peroxidase (ARP), a class II plant peroxidase, were determined through spectro-electrochemical experiments. The data were compared with those for class III horseradish peroxidase C (HRP) and its cyanide adduct, and were interpreted in terms of ligand binding features, electrostatic effects and solvent accessible surface area of the heme group and of catalytically relevant residues in the heme distal site. The E(o)' values for free and cyanide-bound ARP (-0.183 and -0.390 V, respectively, at 25 degrees C and pH 7) are higher than those for HRP and HRP-CN. ARP features an enthalpic stabilization of the ferrous state and a remarkably negative reduction entropy, which are both unprecedented for heme peroxidases. Once the compensatory contributions of solvent reorganization are partitioned from the measured reduction enthalpy, the resulting protein-based deltaH(o)'(rc(int)) value for ARP turns out to be less positive than that for HRP by +10 kJ mol(-1). The smaller stabilization of the oxidized heme in ARP most probably results from the less pronounced anionic character of the proximal histidine, and the decreased polarity in the heme distal site as compared with HRP, as indicated by the X-ray structures. The surprisingly negative deltaS(o)'(rc) value for ARP is the result of peculiar reduction-induced solvent reorganization effects.
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Affiliation(s)
- Gianantonio Battistuzzi
- Department of Chemistry and Centro SCS, University of Modena and Reggio Emilia, Via Campi 183, 41100, Modena, Italy
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20
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Barone V, De Rienzo F, Langella E, Menziani MC, Rega N, Sola M. A computational protocol to probe the role of solvation effects on the reduction potential of azurin mutants. Proteins 2005; 62:262-9. [PMID: 16287118 DOI: 10.1002/prot.20772] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Semiquantitative relationships between thermodynamic parameters of Cu2+ reduction experimentally measured for a series of azurin mutants and the solvation free energy of the oxidized state of the proteins were derived. Solvation free energy calculations were carried out within an ONIOM/PCM scheme specifically adapted to this protein series. The method proved to be able to capture the main determinants of the measured reduction parameters, providing satisfactory predictions of the E degrees '.
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Affiliation(s)
- Vincenzo Barone
- Dipartimento di Chimica, Università Federico II di Napoli, Complesso Universitario Monte S. Angelo, Naples, Italy
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Battistuzzi G, Bellei M, Borsari M, Di Rocco G, Ranieri A, Sola M. Axial ligation and polypeptide matrix effects on the reduction potential of heme proteins probed on their cyanide adducts. J Biol Inorg Chem 2005; 10:643-51. [PMID: 16133205 DOI: 10.1007/s00775-005-0014-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2005] [Accepted: 07/25/2005] [Indexed: 10/25/2022]
Abstract
The enthalpic and entropic changes accompanying the reduction reaction of the six-coordinate cyanide adducts of cytochrome c, microperoxidase-11 and a few plant peroxidases were measured electrochemically. Once the compensating changes in reduction enthalpy and entropy due to solvent reorganization effects are factorized out, it is found that cyanide binding stabilizes enthalpically the ferriheme following the order: cyochrome c > peroxidase > microperoxidase-11. The effect is inversely correlated to the solvent accessibility of the heme. Comparison of the reduction thermodynamics for the cyanide adducts of cytochrome c and plant peroxidases with those for microperoxidase-11 and myoglobin, respectively, yielded an estimate of the consequences of protein encapsulation and of the anionic character of the proximal histidine on the reduction potential of the heme-cyanide group. Insertion of the heme-CN group into the folded peptide chain of cyt c induces an enthalpy-based decrease in E degrees ' of approximately 100 mV, consistent with the lower net charge of the oxidized as compared to the reduced iron center, whereas a full imidazolate character of the proximal histidine stabilizes enthalpically the ferriheme by approximately 400 mV. The latter value should be best considered as an upper limit since it also includes some solvation effects arising from the nature of the protein systems being compared.
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Affiliation(s)
- G Battistuzzi
- Department of Chemistry and Centro SCS, University of Modena and Reggio Emilia, via Campi 183, 41100, Modena, Italy
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Battistuzzi G, Bellei M, Leonardi A, Pierattelli R, De Candia A, Vila AJ, Sola M. Reduction thermodynamics of the T1 Cu site in plant and fungal laccases. J Biol Inorg Chem 2005; 10:867-73. [PMID: 16231129 DOI: 10.1007/s00775-005-0035-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2005] [Accepted: 09/19/2005] [Indexed: 10/25/2022]
Abstract
The thermodynamic parameters for reduction of the type-1 (T1) copper site in Rhus vernicifera and Trametes versicolor laccases and for the derivative of the former protein from which the type-2 copper has been selectively removed (T2D) have been determined with UV-vis spectroelectrochemistry. In all cases, the enthalpic term turns out to be the main determinant of the Eo' of the T1 site. Also the difference between the reduction potentials of the two laccases is enthalpy-based and reflects differences in the coordination features of the T1 sites and their protein environment. The T1 sites in native R. vernicifera laccase and its T2D derivative show the same Eo', as a result of compensatory differences in the reduction thermodynamics. This suggests that removal of the type-2 (T2) copper results in modification of the reduction-induced solvent reorganization effects, with no influence in the structure of the multicopper protein site. This conclusion is supported by NMR data recorded on the native, the T2D, and Hg-substituted T1 derivatives of R. vernicifera laccase, which show that the T1 and T2/T3 sites are largely noninteracting.
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Affiliation(s)
- Gianantonio Battistuzzi
- Department of Chemistry-Centro SCS, University of Modena and Reggio Emilia, Via Campi 183, 41100, Modena, Italy.
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Battistuzzi G, Borsari M, Ranieri A, Sola M. Solvent-based deuterium isotope effects on the redox thermodynamics of cytochrome c. J Biol Inorg Chem 2004; 9:781-7. [PMID: 15278784 DOI: 10.1007/s00775-004-0580-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2004] [Accepted: 06/29/2004] [Indexed: 10/26/2022]
Abstract
The reduction thermodynamics of cytochrome c (cytc), determined electrochemically, are found to be sensitive to solvent H/D isotope effects. Reduction of cytochrome c is enthalpically more favored in D(2)O with respect to H(2)O, but is disfavored on entropic grounds. This is consistent with a reduction-induced strengthening of the H-bonding network within the hydration sphere of the protein. No significant changes in E degrees ' occur, since the above variations are compensative. As a main result, this work shows that the oxidation-state-dependent differences in protein solvation, including electrostatics and solvent reorganization effects, play an important role in determining the individual enthalpy and entropy changes of the reduction process. It is conceivable that this is a common thermodynamic feature of all electron transport metalloproteins. The isotope effects turn out to be sensitive to buffer anions which specifically bind to cytc. Evidence is gained that the solvation thermodynamics of both redox forms of cytc are sensibly affected by strongly hydrated anions.
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Affiliation(s)
- G Battistuzzi
- Department of Chemistry and Centro SCS, University of Modena and Reggio Emilia, Via Campi 183, 41100 Modena, Italy
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