1
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Lam Q, Van Stappen C, Lu Y, Dikanov SA. HYSCORE and QM/MM Studies of Second Sphere Variants of the Type 1 Copper Site in Azurin: Influence of Mutations on the Hyperfine Couplings of Remote Nitrogens. J Phys Chem B 2024; 128:3350-3359. [PMID: 38564809 DOI: 10.1021/acs.jpcb.3c08194] [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: 04/04/2024]
Abstract
Secondary coordination sphere (SCS) interactions have been shown to play important roles in tuning reduction potentials and electron transfer (ET) properties of the Type 1 copper proteins, but the precise roles of these interactions are not fully understood. In this work, we examined the influence of F114P, F114N, and N47S mutations in the SCS on the electronic structure of the T1 copper center in azurin (Az) by studying the hyperfine couplings of (i) histidine remote Nε nitrogens and (ii) the amide Np using the two-dimensional (2D) pulsed electron paramagnetic resonance (EPR) technique HYSCORE (hyperfine sublevel correlation) combined with quantum mechanics/molecular mechanics (QM/MM) and DLPNO-CCSD calculations. Our data show that some components of hyperfine tensor and isotropic coupling in N47SAz and F114PAz (but not F114NAz) deviate by up to ∼±20% from WTAz, indicating that these mutations significantly influence the spin density distribution between the CuII site and coordinating ligands. Furthermore, our calculations support the assignment of Np to the backbone amide of residue 47 (both in Asn and Ser variants). Since the spin density distributions play an important role in tuning the covalency of the Cu-Scys bond of Type 1 copper center that has been shown to be crucial in controlling the reduction potentials, this study provides additional insights into the electron spin factor in tuning the reduction potentials and ET properties.
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Affiliation(s)
- Quan Lam
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Casey Van Stappen
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Sergei A Dikanov
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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2
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Mishima K, Kano N. Contribution Factors of the First Kind Calculated for the Marcus Electron-Transfer Rate and Their Applications. J Phys Chem B 2023; 127:8509-8524. [PMID: 37782079 DOI: 10.1021/acs.jpcb.3c03420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
In this study, we applied the concept of the "contribution factor of the first kind (CFFK)" to the original electron-transfer (ET) rate theory proposed by Marcus. Mathematical derivations provided simple and convenient formulas for estimating the relative contributions of ten physical and chemical parameters involved in the Marcus ET rate formula: (1) the maximum strength of the electronic coupling energy between two molecules, (2) the exponential decay rate of the electronic coupling energy versus the distance between both molecules, (3) the distance between both molecules, (4) the equilibrium distance between both molecules, (5) the Gibbs free energy, (6) reorganization free energy in the prefactor of the Marcus ET rate equation, (7) reorganization free energy in the denominator of the exponential term, (8) reorganization free energy in the argument of the exponential term, (9) Boltzmann constant times absolute temperature in the prefactor of the rate equation, and (10) Boltzmann constant times absolute temperature in the denominator of the exponential term. We applied our theories to (i) ET reactions at bacterial photosynthesis reaction centers, PSI and PSII, and soluble ferredoxins (Fd); (ii) intraprotein ET reactions for designed azurin mutants; and (iii) ET reactions in flavodoxin (Fld). The formulas and calculations suggest that the theory behind the CFFK is useful for quantitatively identifying major and minor physical and chemical factors and corresponding trade-offs, all of which affect the magnitude of the Marcus ET rate.
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Affiliation(s)
- Kenji Mishima
- Independent Researcher, Bunkyo-ku, Tokyo 113-0024, Japan
| | - Naoki Kano
- Department of Chemistry and Chemical Engineering, Faculty of Engineering, Niigata University, 8050 Ikarashi 2-Nocho, Nishi-ku, Niigata 950-2181, Japan
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3
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Palmieri EM, Holewinski R, McGinity CL, Pierri CL, Maio N, Weiss JM, Tragni V, Miranda KM, Rouault TA, Andresson T, Wink DA, McVicar DW. Pyruvate dehydrogenase operates as an intramolecular nitroxyl generator during macrophage metabolic reprogramming. Nat Commun 2023; 14:5114. [PMID: 37607904 PMCID: PMC10444860 DOI: 10.1038/s41467-023-40738-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 08/04/2023] [Indexed: 08/24/2023] Open
Abstract
M1 macrophages enter a glycolytic state when endogenous nitric oxide (NO) reprograms mitochondrial metabolism by limiting aconitase 2 and pyruvate dehydrogenase (PDH) activity. Here, we provide evidence that NO targets the PDH complex by using lipoate to generate nitroxyl (HNO). PDH E2-associated lipoate is modified in NO-rich macrophages while the PDH E3 enzyme, also known as dihydrolipoamide dehydrogenase (DLD), is irreversibly inhibited. Mechanistically, we show that lipoate facilitates NO-mediated production of HNO, which interacts with thiols forming irreversible modifications including sulfinamide. In addition, we reveal a macrophage signature of proteins with reduction-resistant modifications, including in DLD, and identify potential HNO targets. Consistently, DLD enzyme is modified in an HNO-dependent manner at Cys477 and Cys484, and molecular modeling and mutagenesis show these modifications impair the formation of DLD homodimers. In conclusion, our work demonstrates that HNO is produced physiologically. Moreover, the production of HNO is dependent on the lipoate-rich PDH complex facilitating irreversible modifications that are critical to NO-dependent metabolic rewiring.
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Affiliation(s)
- Erika M Palmieri
- Cancer Innovation Laboratory, NCI-Frederick, Frederick, MD, 21702, USA
| | - Ronald Holewinski
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
| | | | - Ciro L Pierri
- Laboratory of Biochemistry, Molecular and Structural Biology, Department of Pharmacy-Pharmaceutical Sciences, University of Bari, Via E. Orabona, 4, Bari, 70125, Italy
| | - Nunziata Maio
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 9000 Rockville Pike, Bethesda, MD, 20892, USA
| | - Jonathan M Weiss
- Cancer Innovation Laboratory, NCI-Frederick, Frederick, MD, 21702, USA
| | - Vincenzo Tragni
- Laboratory of Biochemistry, Molecular and Structural Biology, Department of Pharmacy-Pharmaceutical Sciences, University of Bari, Via E. Orabona, 4, Bari, 70125, Italy
| | - Katrina M Miranda
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA
| | - Tracey A Rouault
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 9000 Rockville Pike, Bethesda, MD, 20892, USA
| | - Thorkell Andresson
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
| | - David A Wink
- Cancer Innovation Laboratory, NCI-Frederick, Frederick, MD, 21702, USA
| | - Daniel W McVicar
- Cancer Innovation Laboratory, NCI-Frederick, Frederick, MD, 21702, USA.
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4
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Ahn S, Zor C, Yang S, Lagnoni M, Dewar D, Nimmo T, Chau C, Jenkins M, Kibler AJ, Pateman A, Rees GJ, Gao X, Adamson P, Grobert N, Bertei A, Johnson LR, Bruce PG. Why charging Li-air batteries with current low-voltage mediators is slow and singlet oxygen does not explain degradation. Nat Chem 2023:10.1038/s41557-023-01203-3. [PMID: 37264102 DOI: 10.1038/s41557-023-01203-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/14/2023] [Indexed: 06/03/2023]
Abstract
Although Li-air rechargeable batteries offer higher energy densities than lithium-ion batteries, the insulating Li2O2 formed during discharge hinders rapid, efficient re-charging. Redox mediators are used to facilitate Li2O2 oxidation; however, fast kinetics at a low charging voltage are necessary for practical applications and are yet to be achieved. We investigate the mechanism of Li2O2 oxidation by redox mediators. The rate-limiting step is the outer-sphere one-electron oxidation of Li2O2 to LiO2, which follows Marcus theory. The second step is dominated by LiO2 disproportionation, forming mostly triplet-state O2. The yield of singlet-state O2 depends on the redox potential of the mediator in a way that does not correlate with electrolyte degradation, in contrast to earlier views. Our mechanistic understanding explains why current low-voltage mediators (<+3.3 V) fail to deliver high rates (the maximum rate is at +3.74 V) and suggests important mediator design strategies to deliver sufficiently high rates for fast charging at potentials closer to the thermodynamic potential of Li2O2 oxidation (+2.96 V).
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Affiliation(s)
- Sunyhik Ahn
- Department of Materials, University of Oxford, Oxford, UK
| | - Ceren Zor
- Department of Materials, University of Oxford, Oxford, UK
| | - Sixie Yang
- Department of Materials, University of Oxford, Oxford, UK
| | - Marco Lagnoni
- Department of Civil and Industrial Engineering, University of Pisa, Pisa, Italy
| | - Daniel Dewar
- Department of Materials, University of Oxford, Oxford, UK
| | - Tammy Nimmo
- Department of Materials, University of Oxford, Oxford, UK
| | - Chloe Chau
- Department of Materials, University of Oxford, Oxford, UK
| | - Max Jenkins
- Department of Materials, University of Oxford, Oxford, UK
| | - Alexander J Kibler
- Nottingham Applied Materials and Interfaces Group, School of Chemistry, University of Nottingham, Nottingham, UK
| | | | - Gregory J Rees
- Department of Materials, University of Oxford, Oxford, UK
| | - Xiangwen Gao
- Department of Materials, University of Oxford, Oxford, UK
| | - Paul Adamson
- Department of Materials, University of Oxford, Oxford, UK
| | - Nicole Grobert
- Department of Materials, University of Oxford, Oxford, UK
| | - Antonio Bertei
- Department of Civil and Industrial Engineering, University of Pisa, Pisa, Italy
| | - Lee R Johnson
- Nottingham Applied Materials and Interfaces Group, School of Chemistry, University of Nottingham, Nottingham, UK
| | - Peter G Bruce
- Department of Materials, University of Oxford, Oxford, UK.
- Department of Chemistry, University of Oxford, Oxford, UK.
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5
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Kontkanen OV, Biriukov D, Futera Z. Applicability of perturbed matrix method for charge transfer studies at bio/metallic interfaces: a case of azurin. Phys Chem Chem Phys 2023; 25:12479-12489. [PMID: 37097130 DOI: 10.1039/d3cp00197k] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
As the field of nanoelectronics based on biomolecules such as peptides and proteins rapidly grows, there is a need for robust computational methods able to reliably predict charge transfer properties at bio/metallic interfaces. Traditionally, hybrid quantum-mechanical/molecular-mechanical techniques are employed for systems where the electron hopping transfer mechanism is applicable to determine physical parameters controlling the thermodynamics and kinetics of charge transfer processes. However, these approaches are limited by a relatively high computational cost when extensive sampling of a configurational space is required, like in the case of soft biomatter. For these applications, semi-empirical approaches such as the perturbed matrix method (PMM) have been developed and successfully used to study charge-transfer processes in biomolecules. Here, we explore the performance of PMM on prototypical redox-active protein azurin in various environments, from solution to vacuum interfaces with gold surfaces and protein junction. We systematically benchmarked the robustness and convergence of the method with respect to the quantum-centre size, size of the Hamiltonian, number of samples, and level of theory. We show that PMM can adequately capture all the trends associated with the structural and electronic changes related to azurin oxidation at bio/metallic interfaces.
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Affiliation(s)
- Outi Vilhelmiina Kontkanen
- Faculty of Science, University of South Bohemia, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic.
| | - Denys Biriukov
- Faculty of Science, University of South Bohemia, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic.
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 16610 Prague 6, Czech Republic
| | - Zdenek Futera
- Faculty of Science, University of South Bohemia, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic.
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6
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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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7
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Kontkanen OV, Biriukov D, Futera Z. Reorganization Free Energy of Copper Proteins in Solution, in Vacuum, and on Metal Surfaces. J Chem Phys 2022; 156:175101. [DOI: 10.1063/5.0085141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Metalloproteins, known to efficiently transfer electronic charge in biological systems, recently found their utilization in nanobiotechnological devices where the protein is placed into direct contact with metal surfaces. The feasibility of oxidation/reduction of the protein redox sites is affected by the reorganization free energies, one of the key parameters determining the transfer rates. While their values have been measured and computed for proteins in their native environments, i.e., in aqueous solution, the reorganization free energies of dry proteins or proteins adsorbed to metal surfaces remain unknown. Here, we investigate the redox properties of blue copper protein azurin, a prototypical redox-active metalloprotein previously probed by various experimental techniques both in solution and on metal/vacuum interfaces. We used a hybrid QM/MM computational technique based on DFT to explore protein dynamics, flexibility, and corresponding reorganization free energies in aqueous solution, vacuum, and on vacuum gold interfaces. Somewhat surprisingly, the reorganization free energy only slightly decreases when azurin is dried because the loss of the hydration shell leads to larger flexibility of the protein near its redox site. At the vacuum gold surfaces, the energetics of the structure relaxation depends on the adsorption geometry, however, significant reduction of the reorganization free energy was not observed. These findings have important consequences for the charge transport mechanism in vacuum devices, showing that the free energy barriers for protein oxidation remain significant even under ultra-high vacuum conditions.
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Affiliation(s)
| | - Denys Biriukov
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences, Czech Republic
| | - Zdenek Futera
- University of South Bohemia in Ceske Budejovice Faculty of Science, Czech Republic
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8
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Yamaguchi T, Akatsu M, Taborosi A, Kohzuma T. Unusual Protein Stability of the Met16Leu Pseudoazurin Variant. CHEM LETT 2020. [DOI: 10.1246/cl.200578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Miyu Akatsu
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - Attila Taborosi
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki 310-8512, 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, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
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9
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Yu SS, Li JJ, Cui C, Tian S, Chen JJ, Yu HQ, Hou C, Nilges MJ, Lu Y. Structural Basis for a Quadratic Relationship between Electronic Absorption and Electronic Paramagnetic Resonance Parameters of Type 1 Copper Proteins. Inorg Chem 2020; 59:10620-10627. [PMID: 32689800 DOI: 10.1021/acs.inorgchem.0c01065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Type 1 copper (T1Cu) proteins play important roles in electron transfer in biology, largely due to the unique structure of the T1Cu center, which is reflected by its spectroscopic properties. Previous reports have suggested a correlation between a high ratio of electronic absorbance at ∼450 nm to that at ∼600 nm (R = A450/A600) and a large copper(II) hyperfine coupling in the z direction (Az) in electron paramagnetic resonance (EPR). However, this correlation does not have a clear physical meaning, nor does it hold for many proteins with a perturbed T1Cu center. To address this issue, a new parameter of R' [A450/(A450 + A600)] with a better physical meaning of a fractional SCys pseudo-σ to Cu(II) charge transfer transition intensity is defined and a quadratic relationship between R' and Az is found on the basis of a comprehensive analysis of ultraviolet-visible absorption, EPR, and structural parameters of T1Cu proteins. We are able to find good correlations between R' and the displacement of copper from the trigonal plane defined by the His2Cys ligands and the angle between the NHis1-Cu-NHis2 plane and the SCys-Cu-axial ligand plane, providing a structural basis for the observed correlation. These findings and analyses provide a new framework for a deeper understanding of the spectroscopic and electronic properties of T1Cu proteins, which may allow better design and applications of this important class of proteins for redox and electron transfer functions.
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Affiliation(s)
- Sheng-Song Yu
- Department of Applied Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, P. R. China.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jun-Jie Li
- Key Laboratory of Biorheology Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, P. R. China.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Chang Cui
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shiliang Tian
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jie-Jie Chen
- Department of Applied Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, P. R. China
| | - Han-Qing Yu
- Department of Applied Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, P. R. China
| | - Changjun Hou
- Key Laboratory of Biorheology Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, P. R. China
| | - Mark J Nilges
- School of Chemical Sciences Electron Paramagnetic Resonance Lab, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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10
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Szuster J, Zitare UA, Castro MA, Leguto AJ, Morgada MN, Vila AJ, Murgida DH. Cu A-based chimeric T1 copper sites allow for independent modulation of reorganization energy and reduction potential. Chem Sci 2020; 11:6193-6201. [PMID: 32953013 PMCID: PMC7480511 DOI: 10.1039/d0sc01620a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 06/01/2020] [Indexed: 01/19/2023] Open
Abstract
Attaining rational modulation of thermodynamic and kinetic redox parameters of metalloproteins is a key milestone towards the (re)design of proteins with new or improved redox functions. Here we report that implantation of ligand loops from natural T1 proteins into the scaffold of a CuA protein leads to a series of distorted T1-like sites that allow for independent modulation of reduction potentials (E°') and electron transfer reorganization energies (λ). On the one hand E°' values could be fine-tuned over 120 mV without affecting λ. On the other, λ values could be modulated by more than a factor of two while affecting E°' only by a few millivolts. These results are in sharp contrast to previous studies that used T1 cupredoxin folds, thus highlighting the importance of the protein scaffold in determining such parameters.
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Affiliation(s)
- Jonathan Szuster
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE, CONICET-UBA) , Argentina .
- Departamento de Química Inorgánica, Analítica y Química-Física , Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , Buenos Aires , Argentina
| | - Ulises A Zitare
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE, CONICET-UBA) , Argentina .
- Departamento de Química Inorgánica, Analítica y Química-Física , Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , Buenos Aires , Argentina
| | - María A Castro
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE, CONICET-UBA) , Argentina .
- Departamento de Química Inorgánica, Analítica y Química-Física , Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , Buenos Aires , Argentina
| | - Alcides J Leguto
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) , Argentina
- Departamento de Química Biológica , Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario , Rosario , Argentina
| | - Marcos N Morgada
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) , Argentina
- Departamento de Química Biológica , Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario , Rosario , Argentina
| | - Alejandro J Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) , Argentina
- Departamento de Química Biológica , Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario , Rosario , Argentina
| | - Daniel H Murgida
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE, CONICET-UBA) , Argentina .
- Departamento de Química Inorgánica, Analítica y Química-Física , Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , Buenos Aires , Argentina
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11
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Romero-Muñiz C, Ortega M, Vilhena JG, Diéz-Pérez I, Cuevas JC, Pérez R, Zotti LA. Mechanical Deformation and Electronic Structure of a Blue Copper Azurin in a Solid-State Junction. Biomolecules 2019; 9:biom9090506. [PMID: 31546917 PMCID: PMC6769874 DOI: 10.3390/biom9090506] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 09/14/2019] [Accepted: 09/16/2019] [Indexed: 01/26/2023] Open
Abstract
Protein-based electronics is an emerging field which has attracted considerable attention over the past decade. Here, we present a theoretical study of the formation and electronic structure of a metal-protein-metal junction based on the blue-copper azurin from pseudomonas aeruginosa. We focus on the case in which the protein is adsorbed on a gold surface and is contacted, at the opposite side, to an STM (Scanning Tunneling Microscopy) tip by spontaneous attachment. This has been simulated through a combination of molecular dynamics and density functional theory. We find that the attachment to the tip induces structural changes in the protein which, however, do not affect the overall electronic properties of the protein. Indeed, only changes in certain residues are observed, whereas the electronic structure of the Cu-centered complex remains unaltered, as does the total density of states of the whole protein.
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Affiliation(s)
- Carlos Romero-Muñiz
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
| | - María Ortega
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
| | - J G Vilhena
- Department of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel, Switzerland.
| | - Ismael Diéz-Pérez
- Department of Chemistry, Faculty of Natural & Mathematical Sciences, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK.
| | - Juan Carlos Cuevas
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
| | - Rubén Pérez
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
| | - Linda A Zotti
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
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12
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Photoinduced electron transfer within supramolecular hemoprotein co-assemblies and heterodimers containing Fe and Zn porphyrins. J Inorg Biochem 2019; 193:42-51. [DOI: 10.1016/j.jinorgbio.2019.01.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 01/03/2019] [Indexed: 12/11/2022]
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13
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Takematsu K, Pospíšil P, Pižl M, Towrie M, Heyda J, Záliš S, Kaiser JT, Winkler JR, Gray HB, Vlček A. Hole Hopping Across a Protein-Protein Interface. J Phys Chem B 2019; 123:1578-1591. [PMID: 30673250 PMCID: PMC6384139 DOI: 10.1021/acs.jpcb.8b11982] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have investigated photoinduced hole hopping in a Pseudomonas aeruginosa azurin mutant Re126WWCuI, where two adjacent tryptophan residues (W124 and W122) are inserted between the CuI center and a Re photosensitizer coordinated to a H126 imidazole (Re = ReI(H126)(CO)3(dmp)+, dmp = 4,7-dimethyl-1,10-phenanthroline). Optical excitation of this mutant in aqueous media (≤40 μM) triggers 70 ns electron transport over 23 Å, yielding a long-lived (120 μs) ReI(H126)(CO)3(dmp•-)WWCuII product. The Re126FWCuI mutant (F124, W122) is not redox-active under these conditions. Upon increasing the concentration to 0.2-2 mM, {Re126WWCuI}2 and {Re126FWCuI}2 are formed with the dmp ligand of the Re photooxidant of one molecule in close contact (3.8 Å) with the W122' indole on the neighboring chain. In addition, {Re126WWCuI}2 contains an interfacial tryptophan quadruplex of four indoles (3.3-3.7 Å apart). In both mutants, dimerization opens an intermolecular W122' → //*Re ET channel (// denotes the protein interface, *Re is the optically excited sensitizer). Excited-state relaxation and ET occur together in two steps (time constants of ∼600 ps and ∼8 ns) that lead to a charge-separated state containing a Re(H126)(CO)3(dmp•-)//(W122•+)' unit; then (CuI)' is oxidized intramolecularly (60-90 ns) by (W122•+)', forming ReI(H126)(CO)3(dmp•-)WWCuI//(CuII)'. The photocycle is closed by ∼1.6 μs ReI(H126)(CO)3(dmp•-) → //(CuII)' back ET that occurs over 12 Å, in contrast to the 23 Å, 120 μs step in Re126WWCuI. Importantly, dimerization makes Re126FWCuI photoreactive and, as in the case of {Re126WWCuI}2, channels the photoproduced "hole" to the molecule that was not initially photoexcited, thereby shortening the lifetime of ReI(H126)(CO)3(dmp•-)//CuII. Although two adjacent W124 and W122 indoles dramatically enhance CuI → *Re intramolecular multistep ET, the tryptophan quadruplex in {Re126WWCuI}2 does not accelerate intermolecular electron transport; instead, it acts as a hole storage and crossover unit between inter- and intramolecular ET pathways. Irradiation of {Re126WWCuII}2 or {Re126FWCuII}2 also triggers intermolecular W122' → //*Re ET, and the Re(H126)(CO)3(dmp•-)//(W122•+)' charge-separated state decays to the ground state by ∼50 ns ReI(H126)(CO)3(dmp•-)+ → //(W122•+)' intermolecular charge recombination. Our findings shed light on the factors that control interfacial hole/electron hopping in protein complexes and on the role of aromatic amino acids in accelerating long-range electron transport.
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Affiliation(s)
- Kana Takematsu
- Department of Chemistry, Bowdoin College, Brunswick, ME 04011, USA
| | - Petr Pospíšil
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, CZ-182 23 Prague, Czech Republic
| | - Martin Pižl
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, CZ-182 23 Prague, Czech Republic
- University of Chemistry and Technology, Prague, Technická 5, CZ-166 28 Prague, Czech Republic
| | - Michael Towrie
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxfordshire, OX11 0FA, UK
| | - Jan Heyda
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, CZ-182 23 Prague, Czech Republic
- University of Chemistry and Technology, Prague, Technická 5, CZ-166 28 Prague, Czech Republic
| | - Stanislav Záliš
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, CZ-182 23 Prague, Czech Republic
| | - Jens T. Kaiser
- Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jay R. Winkler
- Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Harry B. Gray
- Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Antonín Vlček
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, CZ-182 23 Prague, Czech Republic
- Queen Mary University of London, School of Biological and Chemical Sciences, Mile End Road, London E1 4NS, United Kingdom
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14
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Affiliation(s)
- Kazuo Kobayashi
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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15
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Bhagi-Damodaran A, Lu Y. The Periodic Table's Impact on Bioinorganic Chemistry and Biology's Selective Use of Metal Ions. STRUCTURE AND BONDING 2019; 182:153-173. [PMID: 36567794 PMCID: PMC9788643 DOI: 10.1007/430_2019_45] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Despite the availability of a vast variety of metal ions in the periodic table, biology uses only a selective few metal ions. Most of the redox active metals used belong to the first row of transition metals in the periodic table and include Fe, Co, Ni, Mn and Cu. On the other hand, Ca, Zn and Mg are the most commonly used redox inactive metals in biology. In this chapter, we discuss the periodic table's impact on bio-inorganic chemistry, by exploring reasons behind this selective choice of metals biology. A special focus is placed on the chemical and functional reasons why one metal ion is preferred over another one. We discuss the implications of metal choice in various biological processes including catalysis, electron transfer, redox sensing and signaling. We find that bioavailability of metal ions along with their redox potentials, coordination flexibility, valency and ligand affinity determine the specificity of metals for biological processes. Understanding the implications underlying the selective choice of metals of the periodic table in these biological processes can help design more efficient catalysts, more precise biosensors and more effective drugs.
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Affiliation(s)
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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16
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Fluctuating hydrogen-bond networks govern anomalous electron transfer kinetics in a blue copper protein. Proc Natl Acad Sci U S A 2018; 115:6129-6134. [PMID: 29844178 PMCID: PMC6004490 DOI: 10.1073/pnas.1805719115] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
We combine experimental and computational methods to address the anomalous kinetics of long-range electron transfer (ET) in mutants of Pseudomonas aeruginosa azurin. ET rates and driving forces for wild type (WT) and three N47X mutants (X = L, S, and D) of Ru(2,2'-bipyridine)2 (imidazole)(His83) azurin are reported. An enhanced ET rate for the N47L mutant suggests either an increase of the donor-acceptor (DA) electronic coupling or a decrease in the reorganization energy for the reaction. The underlying atomistic features are investigated using a recently developed nonadiabatic molecular dynamics method to simulate ET in each of the azurin mutants, revealing unexpected aspects of DA electronic coupling. In particular, WT azurin and all studied mutants exhibit more DA compression during ET (>2 Å) than previously recognized. Moreover, it is found that DA compression involves an extended network of hydrogen bonds, the fluctuations of which gate the ET reaction, such that DA compression is facilitated by transiently rupturing hydrogen bonds. It is found that the N47L mutant intrinsically disrupts this hydrogen-bond network, enabling particularly facile DA compression. This work, which reveals the surprisingly fluctional nature of ET in azurin, suggests that hydrogen-bond networks can modulate the efficiency of long-range biological ET.
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17
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Wherland S, Pecht I. Radiation chemists look at damage in redox proteins induced by X-rays. Proteins 2018; 86:817-826. [DOI: 10.1002/prot.25521] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 03/26/2018] [Accepted: 04/25/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Scot Wherland
- Department of Chemistry; Washington State University; Pullman Washington
| | - Israel Pecht
- Department of Immunology; The Weizmann Institute of Science; Rehovot 76100 Israel
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18
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Bostick CD, Mukhopadhyay S, Pecht I, Sheves M, Cahen D, Lederman D. Protein bioelectronics: a review of what we do and do not know. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2018; 81:026601. [PMID: 29303117 DOI: 10.1088/1361-6633/aa85f2] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We review the status of protein-based molecular electronics. First, we define and discuss fundamental concepts of electron transfer and transport in and across proteins and proposed mechanisms for these processes. We then describe the immobilization of proteins to solid-state surfaces in both nanoscale and macroscopic approaches, and highlight how different methodologies can alter protein electronic properties. Because immobilizing proteins while retaining biological activity is crucial to the successful development of bioelectronic devices, we discuss this process at length. We briefly discuss computational predictions and their connection to experimental results. We then summarize how the biological activity of immobilized proteins is beneficial for bioelectronic devices, and how conductance measurements can shed light on protein properties. Finally, we consider how the research to date could influence the development of future bioelectronic devices.
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Affiliation(s)
- Christopher D Bostick
- Department of Pharmaceutical Sciences, West Virginia University, Morgantown, WV 26506, United States of America. Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, United States of America
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19
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Sinicropi A. DFT modeling of structures and redox potentials of wild-type, Nickel-substituted and mutated (N47S/M121L, HPAz) Azurin. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2017.08.041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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20
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Ruiz MP, Aragonès AC, Camarero N, Vilhena JG, Ortega M, Zotti LA, Pérez R, Cuevas JC, Gorostiza P, Díez-Pérez I. Bioengineering a Single-Protein Junction. J Am Chem Soc 2017; 139:15337-15346. [DOI: 10.1021/jacs.7b06130] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Marta P. Ruiz
- Departament of Materials Science and Physical Chemistry & Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, Martí i Franquès, 1, Barcelona 08028, Spain
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona
Institute of Science and Technology (BIST), Baldiri Reixac 15-21, Barcelona 08028, Spain
- Centro Investigación Biomédica en Red (CIBER-BBN), Campus Río Ebro-Edificio
I+D, Poeta Mariano Esquillor s/n, 50018 Zaragoza, Spain
| | - Albert C. Aragonès
- Departament of Materials Science and Physical Chemistry & Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, Martí i Franquès, 1, Barcelona 08028, Spain
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona
Institute of Science and Technology (BIST), Baldiri Reixac 15-21, Barcelona 08028, Spain
- Centro Investigación Biomédica en Red (CIBER-BBN), Campus Río Ebro-Edificio
I+D, Poeta Mariano Esquillor s/n, 50018 Zaragoza, Spain
| | - Nuria Camarero
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona
Institute of Science and Technology (BIST), Baldiri Reixac 15-21, Barcelona 08028, Spain
- Centro Investigación Biomédica en Red (CIBER-BBN), Campus Río Ebro-Edificio
I+D, Poeta Mariano Esquillor s/n, 50018 Zaragoza, Spain
| | - J. G. Vilhena
- Departamento
de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
- Department
of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain
| | - Maria Ortega
- Departamento
de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Linda A. Zotti
- Departamento
de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Rubén Pérez
- Departamento
de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
- Condensed
Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Juan Carlos Cuevas
- Departamento
de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
- Condensed
Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Pau Gorostiza
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona
Institute of Science and Technology (BIST), Baldiri Reixac 15-21, Barcelona 08028, Spain
- Centro Investigación Biomédica en Red (CIBER-BBN), Campus Río Ebro-Edificio
I+D, Poeta Mariano Esquillor s/n, 50018 Zaragoza, Spain
- Catalan Institution for Research and Advanced Studies (ICREA)
| | - Ismael Díez-Pérez
- Departament of Materials Science and Physical Chemistry & Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, Martí i Franquès, 1, Barcelona 08028, Spain
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona
Institute of Science and Technology (BIST), Baldiri Reixac 15-21, Barcelona 08028, Spain
- Centro Investigación Biomédica en Red (CIBER-BBN), Campus Río Ebro-Edificio
I+D, Poeta Mariano Esquillor s/n, 50018 Zaragoza, Spain
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21
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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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22
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Bizzarri AR, Baldacchini C, Cannistraro S. Structure, Dynamics, and Electron Transfer of Azurin Bound to a Gold Electrode. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:9190-9200. [PMID: 28789529 DOI: 10.1021/acs.langmuir.7b01102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Blue copper redox protein azurin (AZ) constitutes an ideal active element for building bionano-optoelectronic devices based on the intriguing interplay among its electron transfer (ET), vibrational, and optical properties. A full comprehension of its dynamical and functional behavior is required for efficient applications. Here, AZ bound to gold electrode via its disulfide bridge was investigated by a molecular dynamics simulation approach taking into account for gold electron polarization which provides a more realistic description of the protein-gold interaction. Upon binding to gold, AZ undergoes slight changes in its secondary structure with the preservation of the copper-containing active site structure. Binding of AZ to gold promotes new collective motions, with respect to free AZ, as evidenced by essential dynamics. Analysis of the ET from the AZ copper ion to the gold substrate, performed by the Pathways model, put into evidence the main residues and structural motifs of AZ involved in the ET paths. During the dynamical evolution of the bionanosystem, transient contacts between some lateral protein atoms and the gold substrate occurred; concomitantly, the opening of additional ET channels with much higher rates was registered. These results provide new and detailed insights on the dynamics and ET properties of the AZ-gold system, by also helping to rationalize some imaging and conductive experimental evidences and also to design new bionanodevices with tailored features.
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Affiliation(s)
- Anna Rita Bizzarri
- Biophysics & Nanoscience Centre, DEB, Università della Tuscia , Viterbo 01100, Italy
| | - Chiara Baldacchini
- Biophysics & Nanoscience Centre, DEB, Università della Tuscia , Viterbo 01100, Italy
- IBAF-CNR , Porano 05010, Italy
| | - Salvatore Cannistraro
- Biophysics & Nanoscience Centre, DEB, Università della Tuscia , Viterbo 01100, Italy
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23
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Computational evidence support the hypothesis of neuroglobin also acting as an electron transfer species. J Biol Inorg Chem 2017; 22:615-623. [DOI: 10.1007/s00775-017-1455-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 03/28/2017] [Indexed: 12/31/2022]
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24
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Zanetti-Polzi L, Corni S, Daidone I, Amadei A. Extending the essential dynamics analysis to investigate molecular properties: application to the redox potential of proteins. Phys Chem Chem Phys 2016; 18:18450-9. [PMID: 27339768 DOI: 10.1039/c6cp03394f] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Here, a methodology is proposed to investigate the collective fluctuation modes of an arbitrary set of observables, maximally contributing to the fluctuation of another functionally relevant observable. The methodology, based on the analysis of fully classical molecular dynamics (MD) simulations, exploits the essential dynamics (ED) method, originally developed to analyse the collective motions in proteins. We apply this methodology to identify the residues that are more relevant for determining the reduction potential (E(0)) of a redox-active protein. To this aim, the fluctuation modes of the single-residue electrostatic potentials mostly contributing to the fluctuations of the total electrostatic potential (the main determinant of E(0)) are investigated for wild-type azurin and two of its mutants with a higher E(0). By comparing the results here obtained with a previous study on the same systems [Zanetti-Polzi et al., Org. Biomol. Chem., 2015, 13, 11003] we show that the proposed methodology is able to identify the key sites that determine E(0). This information can be used for a general deeper understanding of the molecular mechanisms on the basis of the redox properties of the proteins under investigation, as well as for the rational design of mutants with a higher or lower E(0). From the results of the present analysis we propose a new azurin mutant that, according to our calculations, shows a further increase of E(0).
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Affiliation(s)
- Laura Zanetti-Polzi
- Department of Physical and Chemical Sciences, University of L'Aquila, via Vetoio (Coppito 1), 67010, L'Aquila, Italy.
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25
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Sadhu B, Sundararajan M. Asn47 and Phe114 modulate the inner sphere reorganization energies of type zero copper proteins. Phys Chem Chem Phys 2016; 18:16748-56. [PMID: 27271560 DOI: 10.1039/c6cp00747c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The geometric structures and electron transfer properties of type 1 Cu proteins are reasonably understood at the molecular level (E. I. Solomon and R. G. Hadt, Coord. Chem. Rev., 2011, 255, 774-789, J. J. Warren, K. M. Lancaster, J. H. Richards and H. B. Gray, J. Inorg. Biochem., 2012, 115, 119-126). Much understanding of type 1 copper electron transfer reactivity has come from site directed mutagenesis studies. For example, artificial "type zero" Cu-centres constructed in cupredoxin-azurin have showcased the capacity of outer-sphere hydrogen bonding networks to enhance Cu II/I electron transfer reactivity. In this paper, we have elaborated on earlier kinetics and electronic structural studies of type zero Cu by calculating the inner sphere reorganization energies of type 1, type 2, and type zero Cu proteins using density functional theory (DFT). Although the choice of density functionals for copper systems is not straightforward, we have benchmarked the density functionals against the recently reported ESI-PES data for two synthetic copper models (S. Niu, D.-L. Huang, P. D. Dau, H.-T. Liu, L.-S. Wang and T. J. Ichiye, Chem. Theory Comput., 2014, 10, 1283). For the Cu proteins, our calculations predict that changes in the coordination number upon metal reduction lead to large inner sphere reorganization energies for type 2 Cu sites, whereas retention in the coordination number is observed for type zero Cu sites. These variations in the coordination number are modulated by the outer-sphere coordinating residues Asn47 and Phe114, which are involved in hydrogen bonding with the Asp112 side chain.
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Affiliation(s)
- Biswajit Sadhu
- Radiation Safety Systems Division, Bhabha Atomic Research Centre, Mumbai - 400 085, India
| | - Mahesh Sundararajan
- Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai - 400 094, India.
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26
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Hosseinzadeh P, Tian S, Marshall NM, Hemp J, Mullen T, Nilges MJ, Gao YG, Robinson H, Stahl DA, Gennis RB, Lu Y. A Purple Cupredoxin from Nitrosopumilus maritimus Containing a Mononuclear Type 1 Copper Center with an Open Binding Site. J Am Chem Soc 2016; 138:6324-7. [DOI: 10.1021/jacs.5b13128] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
| | | | | | | | | | | | | | - Howard Robinson
- Biology
Department, Brookhaven National Laboratory, Upton, New York 11973-5000, United States
| | - David A. Stahl
- Department
of Civil and Environmental Engineering, University of Washington, Seattle, Washington 98195, United States
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27
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Hosseinzadeh P, Lu Y. Design and fine-tuning redox potentials of metalloproteins involved in electron transfer in bioenergetics. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1857:557-581. [PMID: 26301482 PMCID: PMC4761536 DOI: 10.1016/j.bbabio.2015.08.006] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 08/20/2015] [Indexed: 12/25/2022]
Abstract
Redox potentials are a major contributor in controlling the electron transfer (ET) rates and thus regulating the ET processes in the bioenergetics. To maximize the efficiency of the ET process, one needs to master the art of tuning the redox potential, especially in metalloproteins, as they represent major classes of ET proteins. In this review, we first describe the importance of tuning the redox potential of ET centers and its role in regulating the ET in bioenergetic processes including photosynthesis and respiration. The main focus of this review is to summarize recent work in designing the ET centers, namely cupredoxins, cytochromes, and iron-sulfur proteins, and examples in design of protein networks involved these ET centers. We then discuss the factors that affect redox potentials of these ET centers including metal ion, the ligands to metal center and interactions beyond the primary ligand, especially non-covalent secondary coordination sphere interactions. We provide examples of strategies to fine-tune the redox potential using both natural and unnatural amino acids and native and nonnative cofactors. Several case studies are used to illustrate recent successes in this area. Outlooks for future endeavors are also provided. This article is part of a Special Issue entitled Biodesign for Bioenergetics--the design and engineering of electronic transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.
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Affiliation(s)
- Parisa Hosseinzadeh
- Department of Chemistry and Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews St., Urbana, IL, 61801, USA
| | - Yi Lu
- Department of Chemistry and Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews St., Urbana, IL, 61801, USA.
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28
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Zanetti-Polzi L, Corni S. A dynamical approach to non-adiabatic electron transfers at the bio-inorganic interface. Phys Chem Chem Phys 2016; 18:10538-49. [DOI: 10.1039/c6cp00044d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A methodology is proposed to investigate the role of the energy fluctuations, determined by the dynamical evolution of a system, and the role of non-adiabaticity in affecting the kinetic rate of electron transfer reactions at the bio-inorganic interface.
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29
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Blumberger J. Recent Advances in the Theory and Molecular Simulation of Biological Electron Transfer Reactions. Chem Rev 2015; 115:11191-238. [DOI: 10.1021/acs.chemrev.5b00298] [Citation(s) in RCA: 238] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Jochen Blumberger
- Department of Physics and
Astronomy, University College London, Gower Street, London WC1E 6BT, U.K
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30
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Pérez-Henarejos SA, Alcaraz LA, Donaire A. Blue Copper Proteins: A rigid machine for efficient electron transfer, a flexible device for metal uptake. Arch Biochem Biophys 2015; 584:134-48. [DOI: 10.1016/j.abb.2015.08.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 08/24/2015] [Accepted: 08/28/2015] [Indexed: 10/23/2022]
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31
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Zanetti-Polzi L, Bortolotti CA, Daidone I, Aschi M, Amadei A, Corni S. A few key residues determine the high redox potential shift in azurin mutants. Org Biomol Chem 2015; 13:11003-13. [PMID: 26381463 DOI: 10.1039/c5ob01819f] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The wide range of variability of the reduction potential (E(0)) of blue-copper proteins has been the subject of a large number of studies in the past several years. In particular, a series of azurin mutants have been recently rationally designed tuning E(0) over a very broad range (700 mV) without significantly altering the redox-active site [Marshall et al., Nature, 2009, 462, 113]. This clearly suggests that interactions outside the primary coordination sphere are relevant to determine E(0) in cupredoxins. However, the molecular determinants of the redox potential variability are still undisclosed. Here, by means of atomistic molecular dynamics simulations and hybrid quantum/classical calculations, the mechanisms that determine the E(0) shift of two azurin mutants with high potential shifts are unravelled. The reduction potentials of native azurin and of the mutants are calculated obtaining results in good agreement with the experiments. The analysis of the simulations reveals that only a small number of residues (including non-mutated ones) are relevant in determining the experimentally observed E(0) variation via site-specific, but diverse, mechanisms. These findings open the path to the rational design of new azurin mutants with different E(0).
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Affiliation(s)
- Laura Zanetti-Polzi
- Center S3, CNR-Institute of Nanoscience, Via Campi 213/A, 41125, Modena, Italy.
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32
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Lau N, Ziller JW, Borovik AS. Sulfonamido tripods: tuning redox potentials via ligand modifications. Polyhedron 2015; 85:777-782. [PMID: 25419035 DOI: 10.1016/j.poly.2014.09.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
A series of FeII-OH2 complexes were synthesized with ligands based on the tetradentate sulfonamido tripod N,N',N"-[2,2',2"-nitrilotris(ethane-2,1-diyl)]-tris-({R-Ph}-sulfonamido). These complexes differ by the substituent on the aryl rings and were fully characterized, including their molecular structures via X-ray diffraction methods. All the complexes were five-coordinate with trigonal bipyramidal geometry. A linear correlation was observed between the electronic effects of each ligand, given by the Hammett constants of the para-substituents, and the potential of the FeII/FeIII redox couple, which were determined using cyclic voltammetry. It was found that the range of redox potentials for the complexes spanned approximately 160 mV.
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Affiliation(s)
- Nathanael Lau
- Department of Chemistry, University of California - Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Joseph W Ziller
- Department of Chemistry, University of California - Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - A S Borovik
- Department of Chemistry, University of California - Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
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33
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Farver O, Hosseinzadeh P, Marshall NM, Wherland S, Lu Y, Pecht I. Long-Range Electron Transfer in Engineered Azurins Exhibits Marcus Inverted Region Behavior. J Phys Chem Lett 2015; 6:100-105. [PMID: 26263097 DOI: 10.1021/jz5022685] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The Marcus theory of electron transfer (ET) predicts that while the ET rate constants increase with rising driving force until it equals a reaction's reorganization energy, at higher driving force the ET rate decreases, having reached the Marcus inverted region. While experimental evidence of the inverted region has been reported for organic and inorganic ET reactions as well as for proteins conjugated with ancillary redox moieties, evidence of the inverted region in a "protein-only" system has remained elusive. We herein provide such evidence in a series of nonderivatized proteins. These results may facilitate the design of ET centers for future applications such as advanced energy conversions.
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Affiliation(s)
- Ole Farver
- †Department of Analytical and Bioinorganic Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen 2100, Denmark
| | | | | | - Scot Wherland
- ∥Department of Chemistry, Washington State University, PO Box 644630, Pullman, Washington 99164, United States
| | | | - Israel Pecht
- §Department of Immunology, Weizmann Institute of Science, Wolfson Building, Rehovot 76100, Israel
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34
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Liu J, Chakraborty S, Hosseinzadeh P, Yu Y, Tian S, Petrik I, Bhagi A, Lu Y. Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. Chem Rev 2014; 114:4366-469. [PMID: 24758379 PMCID: PMC4002152 DOI: 10.1021/cr400479b] [Citation(s) in RCA: 559] [Impact Index Per Article: 55.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Jing Liu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Saumen Chakraborty
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Parisa Hosseinzadeh
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yang Yu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shiliang Tian
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Igor Petrik
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ambika Bhagi
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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35
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Yu F, Cangelosi VM, Zastrow ML, Tegoni M, Plegaria JS, Tebo AG, Mocny CS, Ruckthong L, Qayyum H, Pecoraro VL. Protein design: toward functional metalloenzymes. Chem Rev 2014; 114:3495-578. [PMID: 24661096 PMCID: PMC4300145 DOI: 10.1021/cr400458x] [Citation(s) in RCA: 340] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Fangting Yu
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | | | | | | | - Alison G. Tebo
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Leela Ruckthong
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hira Qayyum
- University of Michigan, Ann Arbor, Michigan 48109, United States
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