1
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Gaza JT, Nellas RB. Reparameterization of Non-Bonded Parameters for Copper Ions in Plastocyanin: An Adaptive Force Matching Study. J Chem Inf Model 2023; 63:4654-4663. [PMID: 37459569 DOI: 10.1021/acs.jcim.3c00559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Molecular mechanics rely on existing experimental and theoretical inputs to confidently calculate the trajectories of molecular systems. These calculations, however, are often hindered by missing force field parameters. A notable subject of this problem is metal centers of proteins. This study parameterized, through an adaptive force matching (AFM) workflow, the copper cofactor of plastocyanin in its two oxidation states. New 12-6 Lennard-Jones (LJ) parameters and atomic partial charges were generated to complete the non-bonded description of the copper site. Our models show uniform distorted tetrahedral structures for reduced plastocyanin, Cu(I), and oxidized plastocyanin, Cu(II). These structures align with the QM/MM MD results and existing crystallography studies. TD-DFT calculations, meanwhile, showed that conformations with elongated axial Cu-SMet and shortened equatorial Cu-SCys bonds retain the experimental UV-Vis profile of blue copper (BC) proteins, thus signifying the importance of Cu-S interactions on BC proteins' unique spectroscopic properties.
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Affiliation(s)
- Jokent T Gaza
- Institute of Chemistry, College of Science, University of the Philippines Diliman, 1101 Quezon City, Philippines
| | - Ricky B Nellas
- Institute of Chemistry, College of Science, University of the Philippines Diliman, 1101 Quezon City, Philippines
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2
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Barreiro DS, Oliveira RNS, Pauleta SR. Biochemical Characterization of the Copper Nitrite Reductase from Neisseria gonorrhoeae. Biomolecules 2023; 13:1215. [PMID: 37627281 PMCID: PMC10452240 DOI: 10.3390/biom13081215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 07/16/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
The copper-containing nitrite reductase from Neisseria gonorrhoeae has been shown to play a critical role in the infection mechanism of this microorganism by producing NO and abolishing epithelial exfoliation. This enzyme is a trimer with a type 1 copper center per subunit and a type 2 copper center in the subunits interface, with the latter being the catalytic site. The two centers were characterized for the first time by EPR and CD spectroscopy, showing that the type 1 copper center has a high rhombicity due to its lower symmetry and more tetragonal structure, while the type 2 copper center has the usual properties, but with a smaller hyperfine coupling constant (A// = 10.5 mT). The thermostability of the enzyme was analyzed by differential scanning calorimetry, which shows a single endothermic transition in the thermogram, with a maximum at 94 °C, while the CD spectra in the visible region indicate the presence of the type 1 copper center up to 80 °C. The reoxidation of the N. gonorrhoeae copper-containing nitrite reductase in the presence of nitrite were analyzed by visible spectroscopy and showed a pH dependence, being higher at pH 5.5-6.0. The high thermostability of this enzyme may be important to maintaining a high activity in the extracellular space and to making it less susceptible to denaturation and proteolysis, contributing to the proliferation of N. gonorrhoeae.
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Affiliation(s)
- Daniela S. Barreiro
- Microbial Stress Lab, UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Ricardo N. S. Oliveira
- Microbial Stress Lab, UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Sofia R. Pauleta
- Microbial Stress Lab, UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
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3
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Guo J, Fisher OS. Orchestrating copper binding: structure and variations on the cupredoxin fold. J Biol Inorg Chem 2022; 27:529-540. [PMID: 35994119 DOI: 10.1007/s00775-022-01955-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/07/2022] [Indexed: 11/26/2022]
Abstract
A large number of copper binding proteins coordinate metal ions using a shared three-dimensional fold called the cupredoxin domain. This domain was originally identified in Type 1 "blue copper" centers but has since proven to be a common domain architecture within an increasingly large and diverse group of copper binding domains. The cupredoxin fold has a number of qualities that make it ideal for coordinating Cu ions for purposes including electron transfer, enzyme catalysis, assembly of other copper sites, and copper sequestration. The structural core does not undergo major conformational changes upon metal binding, but variations within the coordination environment of the metal site confer a range of Cu-binding affinities, reduction potentials, and spectroscopic properties. Here, we discuss these proteins from a structural perspective, examining how variations within the overall cupredoxin fold and metal binding sites are linked to distinct spectroscopic properties and biological functions. Expanding far beyond the blue copper proteins, cupredoxin domains are used by a growing number of proteins and enzymes as a means of binding copper ions, with many more likely remaining to be identified.
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Affiliation(s)
- Jing Guo
- Department of Chemistry, Lehigh University, Bethlehem, PA, USA
| | - Oriana S Fisher
- Department of Chemistry, Lehigh University, Bethlehem, PA, USA.
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4
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Electrochemical Characterization of an Engineered Red Copper Protein Featuring an Unprecedented Entropic Control of the Reduction Potential. Bioelectrochemistry 2022; 146:108095. [DOI: 10.1016/j.bioelechem.2022.108095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/04/2022] [Accepted: 03/10/2022] [Indexed: 12/12/2022]
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5
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Solomon EI, Jose A. Spiers Memorial Lecture: Activating Metal Sites for Biological Electron Transfer. Faraday Discuss 2022; 234:9-30. [DOI: 10.1039/d2fd00001f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Metal sites in biology often exhibit unique spectroscopic features that reflect novel geometric and electronic structures imposed by the protein that are key to reactivity. The Blue copper active site...
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6
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Bím D, Alexandrova AN. Electrostatic regulation of blue copper sites. Chem Sci 2021; 12:11406-11413. [PMID: 34667549 PMCID: PMC8447924 DOI: 10.1039/d1sc02233d] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 07/26/2021] [Indexed: 01/06/2023] Open
Abstract
In the last 50 years, the blue copper proteins became central targets of investigation. Extensive experiments focused on the Cu coordination to probe the effect of local perturbations on its properties. We found that local electric fields, generated by charged residues evolutionarily placed throughout the protein edifice, mainly second sphere, but also more remotely, constitute an additional significant factor regulating blue copper proteins. These fields are not random, but exhibit a highly specific directionality, negative with respect to the and vectors in the Cu first shell. The field magnitude contributes to fine-tuning of the geometric and electronic properties of Cu sites in individual blue copper proteins. Specifically, the local electric fields evidently control the Cu–SMet bond distance, Cu(ii)–SCys bond covalency, and the energies of the frontier molecular orbitals, which, in turn, govern the Cu(ii/i) reduction potential and the relative absorption intensities at 450 nm and 600 nm. Intramolecular electric fields in blue copper proteins are oriented in a fixed way to modulate properties of their copper sites: they control the first-shell copper interactions to influence geometric, spectroscopic, and redox behavior.![]()
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Affiliation(s)
- Daniel Bím
- Department of Chemistry and Biochemistry, University of California, Los Angeles 607 Charles E. Young Drive East Los Angeles CA 90095-1569 USA
| | - Anastassia N Alexandrova
- Department of Chemistry and Biochemistry, University of California, Los Angeles 607 Charles E. Young Drive East Los Angeles CA 90095-1569 USA .,California NanoSystems Institute, University of California, Los Angeles 570 Westwood Plaza Los Angeles California 90095-1569 USA
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7
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Zhang L, Bill E, Kroneck PMH, Einsle O. A [3Cu:2S] cluster provides insight into the assembly and function of the Cu Z site of nitrous oxide reductase. Chem Sci 2021; 12:3239-3244. [PMID: 34164092 PMCID: PMC8179356 DOI: 10.1039/d0sc05204c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Nitrous oxide reductase (N2OR) is the only known enzyme reducing environmentally critical nitrous oxide (N2O) to dinitrogen (N2) as the final step of bacterial denitrification. The assembly process of its unique catalytic [4Cu:2S] cluster CuZ remains scarcely understood. Here we report on a mutagenesis study of all seven histidine ligands coordinating this copper center, followed by spectroscopic and structural characterization and based on an established, functional expression system for Pseudomonas stutzeri N2OR in Escherichia coli. While no copper ion was found in the CuZ binding site of variants H129A, H130A, H178A, H326A, H433A and H494A, the H382A variant carried a catalytically inactive [3Cu:2S] center, in which one sulfur ligand, SZ2, had relocated to form a weak hydrogen bond to the sidechain of the nearby lysine residue K454. This link provides sufficient stability to avoid the loss of the sulfide anion. The UV-vis spectra of this cluster are strikingly similar to those of the active enzyme, implying that the flexibility of SZ2 may have been observed before, but not recognized. The sulfide shift changes the metal coordination in CuZ and is thus of high mechanistic interest. Variants of all seven histidine ligands of the [4Cu:2S] active site of nitrous oxide reductase mostly result in loss of the metal site. However, a H382A variant retains a [3Cu:2S] cluster that hints towards a structural flexibility also present in the intact site.![]()
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Affiliation(s)
- Lin Zhang
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg Albertstrasse 21 79104 Freiburg im Breisgau Germany
| | - Eckhard Bill
- Max-Planck-Institut für Chemische Energiekonversion Stiftstr. 34-36 D-45470 Mülheim an der Ruhr Germany
| | | | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg Albertstrasse 21 79104 Freiburg im Breisgau Germany
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8
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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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9
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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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10
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Lv P, Zhu L, Yu Y, Wang W, Liu G, Lu H. Effect of NaOH concentration on antibacterial activities of Cu nanoparticles and the antibacterial mechanism. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2020; 110:110669. [PMID: 32204097 DOI: 10.1016/j.msec.2020.110669] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/17/2019] [Accepted: 01/13/2020] [Indexed: 12/15/2022]
Abstract
A series of Cu nanoparticles (NPs) have been prepared by a facile hydrothermal method at 180 °C using different concentrations of NaOH solutions and characterized by XRD, SEM, TEM and FT-IR spectra. Their antibacterial activities were assessed by means of Gram-positive S. aureus and Gram-negative E. coli bacteria, where various dosages (3, 5, 7, 10 mg) of the antibacterial agents were applied, and compared with that of the commercial CuSO4 salt. The antibacterial mechanism was explored based on series of control experiments. The results show that the NaOH concentration affects the crystallinity, crystal size and surface hydroxyl content of the Cu NPs, which significantly influence the antibacterial activities. Compared to the commercial CuSO4 salt, the four Cu samples prepared using no <4 mol L-1 of NaOH display excellent antibacterial activities with low concentrations of copper leachates, which is great beneficial to the practical applications. The experimental results support that the highly reactive and soluble copper species in the antibacterial system of the Cu NPs is a Cu (II)-peptide complex, but not free Cu2+ ions.
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Affiliation(s)
- Pengzhao Lv
- School of Chemistry & Chemical Engineering, Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, Tianjin University of Technology, Tianjin 300384, PR China
| | - Lianjie Zhu
- School of Chemistry & Chemical Engineering, Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, Tianjin University of Technology, Tianjin 300384, PR China.
| | - Yanmiao Yu
- School of Chemistry & Chemical Engineering, Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, Tianjin University of Technology, Tianjin 300384, PR China
| | - Wenwen Wang
- School of Chemistry & Chemical Engineering, Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, Tianjin University of Technology, Tianjin 300384, PR China
| | - Guokai Liu
- School of Chemistry & Chemical Engineering, Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, Tianjin University of Technology, Tianjin 300384, PR China
| | - Hongguang Lu
- School of Chemistry & Chemical Engineering, Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, Tianjin University of Technology, Tianjin 300384, PR China.
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11
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Olloqui-Sariego JL, Díaz-Quintana A, De la Rosa MÁ, Calvente JJ, Márquez I, Díaz-Moreno I, Andreu R. Protein crosslinking improves the thermal resistance of plastocyanin immobilized on a modified gold electrode. Bioelectrochemistry 2018; 124:127-132. [DOI: 10.1016/j.bioelechem.2018.07.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 07/13/2018] [Accepted: 07/13/2018] [Indexed: 10/28/2022]
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12
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Espinoza-Cara A, Zitare U, Alvarez-Paggi D, Klinke S, Otero LH, Murgida DH, Vila AJ. Engineering a bifunctional copper site in the cupredoxin fold by loop-directed mutagenesis. Chem Sci 2018; 9:6692-6702. [PMID: 30310603 PMCID: PMC6115626 DOI: 10.1039/c8sc01444b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/27/2018] [Indexed: 12/30/2022] Open
Abstract
Copper sites in proteins are designed to perform either electron transfer or redox catalysis. Type 1 and CuA sites are electron transfer hubs bound to a rigid protein fold that prevents binding of exogenous ligands and side reactions. Here we report the engineering of two Type 1 sites by loop-directed mutagenesis within a CuA scaffold with unique electronic structures and functional features. A copper-thioether axial bond shorter than the copper-thiolate bond is responsible for the electronic structure features, in contrast to all other natural or chimeric sites where the copper thiolate bond is short. These sites display highly unusual features, such as: (1) a high reduction potential despite a strong interaction with the axial ligand, which we attribute to changes in the hydrogen bond network and (2) the ability to bind exogenous ligands such as imidazole and azide. This strategy widens the possibility of using natural protein scaffolds with functional features not present in nature.
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Affiliation(s)
- Andrés Espinoza-Cara
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) , Rosario , Argentina .
- Área Biofísica , Departamento de Química Biológica , Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario , Rosario , Argentina
| | - Ulises Zitare
- Departamento de Química Inorgánica , Analítica y Química Física-INQUIMAE , Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires-CONICET , Buenos Aires , Argentina
| | - Damián Alvarez-Paggi
- Departamento de Química Inorgánica , Analítica y Química Física-INQUIMAE , Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires-CONICET , Buenos Aires , Argentina
- Fundación Instituto Leloir , IIBBA-CONICET , Buenos Aires , Argentina
| | - Sebastián Klinke
- Fundación Instituto Leloir , IIBBA-CONICET , Buenos Aires , Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica PLABEM. , Buenos Aires , Argentina
| | - Lisandro H Otero
- Fundación Instituto Leloir , IIBBA-CONICET , Buenos Aires , Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica PLABEM. , Buenos Aires , Argentina
| | - Daniel H Murgida
- Departamento de Química Inorgánica , Analítica y Química Física-INQUIMAE , Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires-CONICET , Buenos Aires , Argentina
| | - Alejandro J Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) , Rosario , Argentina .
- Área Biofísica , Departamento de Química Biológica , Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario , Rosario , Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica PLABEM. , Buenos Aires , Argentina
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13
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Hurd CA, Besley NA, Robinson D. A QM/MM study of the nature of the entatic state in plastocyanin. J Comput Chem 2016; 38:1431-1437. [PMID: 27859435 PMCID: PMC5434870 DOI: 10.1002/jcc.24666] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/23/2016] [Accepted: 10/27/2016] [Indexed: 11/27/2022]
Abstract
Plastocyanin is a copper containing protein that is involved in the electron transfer process in photosynthetic organisms. The active site of plastocyanin is described as an entatic state whereby its structure represents a compromise between the structures favored by the oxidized and reduced forms. In this study, the nature of the entatic state is investigated through density functional theory‐based hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations. The strain energy is computed to be 12.8 kcal/mol and 14.5 kcal/mol for the oxidized and reduced forms of the protein, indicating that the active site has an intermediate structure. It is shown that the energy gap between the oxidized and reduced forms varies significantly with the fluctuations in the structure of the active site at room temperature. An accurate determination of the reorganization energy requires averaging over conformation and a large region of the protein around the active site to be treated at the quantum mechanical level. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Catherine A Hurd
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
| | - Nicholas A Besley
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
| | - David Robinson
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
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14
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Abstract
This review focuses on the unique spectroscopic features of the blue copper active sites. These reflect a novel electronic structure that activates the site for rapid long-range electron transfer in its biological function. The role of the protein in determining the geometric and electronic structure of this site is defined, as is its contribution to function. This has been referred to as the entatic/rack-induced state. These concepts are then extended to cytochrome c, which is also determined to be in an entatic state.
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Affiliation(s)
- Edward I Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Ryan G Hadt
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Benjamin E R Snyder
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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15
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Mann SI, Heinisch T, Weitz AC, Hendrich MP, Ward TR, Borovik AS. Modular Artificial Cupredoxins. J Am Chem Soc 2016; 138:9073-6. [PMID: 27385206 DOI: 10.1021/jacs.6b05428] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Cupredoxins are electron-transfer proteins that have active sites containing a mononuclear Cu center with an unusual trigonal monopyramidal structure (Type 1 Cu). A single Cu-Scys bond is present within the trigonal plane that is responsible for its unique physical properties. We demonstrate that a cysteine-containing variant of streptavidin (Sav) can serve as a protein host to model the structure and properties of Type 1 Cu sites. A series of artificial Cu proteins are described that rely on Sav and a series of biotinylated synthetic Cu complexes. Optical and EPR measurements highlight the presence of a Cu-Scys bond, and XRD analysis provides structural evidence. We further provide evidence that changes in the linker between the biotin and Cu complex within the synthetic constructs allows for small changes in the placement of Cu centers within Sav that have dramatic effects on the structural and physical properties of the resulting artificial metalloproteins. These findings highlight the utility of the biotin-Sav technology as an approach for simulating active sites of metalloproteins.
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Affiliation(s)
- Samuel I Mann
- Department of Chemistry, University of California-Irvine , 1102 Natural Sciences II, Irvine, California 92697, United States
| | - Tillmann Heinisch
- Department of Chemistry, University of Basel , Spitalstrasse 51, CH-4056 Basel, Switzerland
| | - Andrew C Weitz
- Department of Chemistry, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Michael P Hendrich
- Department of Chemistry, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Thomas R Ward
- Department of Chemistry, University of Basel , Spitalstrasse 51, CH-4056 Basel, Switzerland
| | - A S Borovik
- Department of Chemistry, University of California-Irvine , 1102 Natural Sciences II, Irvine, California 92697, United States
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16
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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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17
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Jones SM, Solomon EI. Electron transfer and reaction mechanism of laccases. Cell Mol Life Sci 2015; 72:869-83. [PMID: 25572295 DOI: 10.1007/s00018-014-1826-6] [Citation(s) in RCA: 280] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 12/30/2014] [Indexed: 11/25/2022]
Abstract
Laccases are part of the family of multicopper oxidases (MCOs), which couple the oxidation of substrates to the four electron reduction of O2 to H2O. MCOs contain a minimum of four Cu's divided into Type 1 (T1), Type 2 (T2), and binuclear Type 3 (T3) Cu sites that are distinguished based on unique spectroscopic features. Substrate oxidation occurs near the T1, and electrons are transferred approximately 13 Å through the protein via the Cys-His pathway to the T2/T3 trinuclear copper cluster (TNC), where dioxygen reduction occurs. This review outlines the electron transfer (ET) process in laccases, and the mechanism of O2 reduction as elucidated through spectroscopic, kinetic, and computational data. Marcus theory is used to describe the relevant factors which impact ET rates including the driving force, reorganization energy, and electronic coupling matrix element. Then, the mechanism of O2 reaction is detailed with particular focus on the intermediates formed during the two 2e(-) reduction steps. The first 2e(-) step forms the peroxide intermediate, followed by the second 2e(-) step to form the native intermediate, which has been shown to be the catalytically relevant fully oxidized form of the enzyme.
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Affiliation(s)
- Stephen M Jones
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, CA, 94305, USA
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18
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Caruso F, Rossi M, Caruso A. Correlation between DFT calculated and X-ray structures from CSD, for Cu(II) and Cu(I) coordination spheres when coordinated to four acyclic amine ligands. A reconsideration of copper(II) planarity. J COORD CHEM 2014. [DOI: 10.1080/00958972.2014.964222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
| | - Miriam Rossi
- Department of Chemistry, Vassar College, Poughkeepsie, NY, USA
| | - Alessio Caruso
- Department of Chemistry, Vassar College, Poughkeepsie, NY, USA
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19
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King JD, Harrington L, Lada BM, He G, Cooley JW, Blankenship RE. Site-directed mutagenesis of the highly perturbed copper site of auracyanin D. Arch Biochem Biophys 2014; 564:237-43. [DOI: 10.1016/j.abb.2014.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 10/01/2014] [Accepted: 10/07/2014] [Indexed: 10/24/2022]
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20
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Hadt RG, Gorelsky S, Solomon EI. Anisotropic covalency contributions to superexchange pathways in type one copper active sites. J Am Chem Soc 2014; 136:15034-45. [PMID: 25310460 PMCID: PMC4210080 DOI: 10.1021/ja508361h] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Indexed: 01/29/2023]
Abstract
Type one (T1) Cu sites deliver electrons to catalytic Cu active sites: the mononuclear type two (T2) Cu site in nitrite reductases (NiRs) and the trinuclear Cu cluster in the multicopper oxidases (MCOs). The T1 Cu and the remote catalytic sites are connected via a Cys-His intramolecular electron-transfer (ET) bridge, which contains two potential ET pathways: P1 through the protein backbone and P2 through the H-bond between the Cys and the His. The high covalency of the T1 Cu-S(Cys) bond is shown here to activate the T1 Cu site for hole superexchange via occupied valence orbitals of the bridge. This covalency-activated electronic coupling (H(DA)) facilitates long-range ET through both pathways. These pathways can be selectively activated depending on the geometric and electronic structure of the T1 Cu site and thus the anisotropic covalency of the T1 Cu-S(Cys) bond. In NiRs, blue (π-type) T1 sites utilize P1 and green (σ-type) T1 sites utilize P2, with P2 being more efficient. Comparing the MCOs to NiRs, the second-sphere environment changes the conformation of the Cys-His pathway, which selectively activates HDA for superexchange by blue π sites for efficient turnover in catalysis. These studies show that a given protein bridge, here Cys-His, provides different superexchange pathways and electronic couplings depending on the anisotropic covalencies of the donor and acceptor metal sites.
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Affiliation(s)
- Ryan G. Hadt
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Serge
I. Gorelsky
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- Centre
for Catalysis Research and Innovation, Department of Chemistry, University of Ottawa, Ottawa, Ontario K1N 6N6, Canada
| | - Edward I. Solomon
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
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21
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Gast P, Broeren FG, Sottini S, Aoki R, Takashina A, Yamaguchi T, Kohzuma T, Groenen EJ. The type 1 copper site of pseudoazurin: Axial and rhombic. J Inorg Biochem 2014; 137:57-63. [DOI: 10.1016/j.jinorgbio.2014.03.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 03/25/2014] [Accepted: 03/28/2014] [Indexed: 11/29/2022]
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22
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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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23
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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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24
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King JD, McIntosh CL, Halsey CM, Lada BM, Niedzwiedzki DM, Cooley JW, Blankenship RE. Metalloproteins diversified: the auracyanins are a family of cupredoxins that stretch the spectral and redox limits of blue copper proteins. Biochemistry 2013; 52:8267-75. [PMID: 24147561 DOI: 10.1021/bi401163g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The metal sites of electron transfer proteins are tuned for function. The type 1 copper site is one of the most utilized metal sites in electron transfer reactions. This site can be tuned by the protein environment from +80 mV to +680 mV in typical type 1 sites. Accompanying this huge variation in midpoint potentials are large changes in electronic structure, resulting in proteins that are blue, green, or even red. Here, we report a family of blue copper proteins, the auracyanins, from the filamentous anoxygenic phototroph Chloroflexus aurantiacus that display the entire known spectral and redox variations known in the type 1 copper site. C. aurantiacus encodes four auracyanins, labeled A-D. The midpoint potentials vary from +83 mV (auracyanin D) to +423 mV (auracyanin C). The electronic structures vary from classical blue copper UV-vis absorption spectra (auracyanin B) to highly perturbed spectra (auracyanins C and D). The spectrum of auracyanin C is temperature-dependent. The expansion and divergent nature of the auracyanins is a previously unseen phenomenon.
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Affiliation(s)
- Jeremy D King
- Graduate Program in Plant Biology, Departments of ‡Biology and §Chemistry, and ⊥Photosynthetic Antenna Research Center (PARC), Washington University in St. Louis , St. Louis, Missouri 63130, United States
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25
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Do H, Deeth RJ, Besley NA. Computational study of the structure and electronic circular dichroism spectroscopy of blue copper proteins. J Phys Chem B 2013; 117:8105-12. [PMID: 23773120 DOI: 10.1021/jp404107j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The calculation of the electronic circular dichroism (CD) spectra of the oxidized form of the blue copper proteins plastocyanin and cucumber basic protein and the relationship between the observed spectral features and the structure of the active site of the protein is investigated. Excitation energies and transition strengths are computed using multireference configuration interaction, and it is shown that computed spectra based on coordinates from the crystal structure or a single structure optimized in quantum mechanics/molecular mechanics (QM/MM) or ligand field molecular mechanics (LFMM) are qualitatively incorrect. In particular, the rotational strength of the ligand to metal charge transfer band is predicted to be too small or have the incorrect sign. By considering calculations on active site models with modified structures, it is shown that the intensity of this band is sensitive to the nonplanarity of the histidine and cysteine ligands coordinated to copper. Calculation of the ultraviolet absorption and CD spectra based upon averaging over many structures drawn from a LFMM molecular dynamics simulation are in good agreement with experiment, and superior to analogous calculations based upon structures from a classical molecular dynamics simulation. This provides evidence that the LFMM force field provides an accurate description of the molecular dynamics of these proteins.
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Affiliation(s)
- Hainam Do
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
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26
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Sousa SF, Pinto GRP, Ribeiro AJM, Coimbra JTS, Fernandes PA, Ramos MJ. Comparative analysis of the performance of commonly available density functionals in the determination of geometrical parameters for copper complexes. J Comput Chem 2013; 34:2079-90. [PMID: 23798313 DOI: 10.1002/jcc.23349] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 05/16/2013] [Accepted: 05/19/2013] [Indexed: 12/26/2022]
Abstract
In this study, a set of 50 transition-metal complexes of Cu(I) and Cu(II), were used in the evaluation of 18 density functionals in geometry determination. In addition, 14 different basis sets were considered, including four commonly used Pople's all-electron basis sets; four basis sets including popular types of effective-core potentials: Los Alamos, Steven-Basch-Krauss, and Stuttgart-Dresden; and six triple-ζ basis sets. The results illustrate the performance of different methodological alternatives for the treatment of geometrical properties in relevant copper complexes, pointing out Double-Hybrid (DH) and Long-range Correction (LC) Generalized Gradient Approximation (GGA) methods as better descriptors of the geometry of the evaluated systems. These however, are associated with a computational cost several times higher than some of the other methods employed, such as the M06 functional, which has also demonstrated a comparable performance. Regarding the basis sets, 6-31+G(d) and 6-31+G(d,p) were the best performing approaches. In addition, the results show that the use of effective-core potentials has a limited impact, in terms of the accuracy in the determination of metal-ligand bond-lengths and angles in our dataset of copper complexes. Hence, these could become a good alternative for the geometrical description of these systems, particularly CEP-121G and SDD basis sets, if one is considering larger copper complexes where the computational cost could be an issue.
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Affiliation(s)
- Sérgio F Sousa
- REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
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27
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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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28
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Do H, Besley NA. Theoretical Study of the Electronic Spectra of Small Molecules That Incorporate Analogues of the Copper–Cysteine Bond. J Phys Chem A 2012; 116:8507-14. [DOI: 10.1021/jp305807z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hainam Do
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, U.K
| | - Nicholas A. Besley
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, U.K
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29
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Hadt RG, Xie X, Pauleta SR, Moura I, Solomon EI. Analysis of resonance Raman data on the blue copper site in pseudoazurin: excited state π and σ charge transfer distortions and their relation to ground state reorganization energy. J Inorg Biochem 2012; 115:155-62. [PMID: 22560510 DOI: 10.1016/j.jinorgbio.2012.03.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2012] [Revised: 03/18/2012] [Accepted: 03/21/2012] [Indexed: 10/28/2022]
Abstract
The short Cu(2+)-S(Met) bond in pseudoazurin (PAz) results in the presence of two relatively intense S(p)(π) and S(p)(σ) charge transfer (CT) transitions. This has enabled resonance Raman (rR) data to be obtained for each excited state. The rR data show very different intensity distribution patterns for the vibrations in the 300-500 cm(-1) region. Time-dependent density functional theory (TDDFT) calculations have been used to determine that the change in intensity distribution between the S(p)(π) and S(p)(σ) excited states reflects the differential enhancement of S(Cys) backbone modes with Cu-S(Cys)-C(β) out-of-plane (oop) and in-plane (ip) bend character in their respective potential energy distributions (PEDs). The rR excited state distortions have been related to ground state reorganization energies (λ s) and predict that, in addition to M-L stretches, the Cu-S(Cys)-C(β) oop bend needs to be considered. DFT calculations predict a large distortion in the Cu-S(Cys)-C(β) oop bending coordinate upon reduction of a blue copper (BC) site; however, this distortion is not present in the X-ray crystal structures of reduced BC sites. The lack of Cu-S(Cys)-C(β) oop distortion upon reduction corresponds to a previously unconsidered constraint on the thiolate ligand orientation in the reduced state of BC proteins and can be considered as a contribution to the entatic/rack nature of BC sites.
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Affiliation(s)
- Ryan G Hadt
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
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30
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Gunawan C, Teoh WY, Marquis CP, Amal R. Cytotoxic origin of copper(II) oxide nanoparticles: comparative studies with micron-sized particles, leachate, and metal salts. ACS NANO 2011; 5:7214-25. [PMID: 21812479 DOI: 10.1021/nn2020248] [Citation(s) in RCA: 204] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The work investigates the source of toxicity of copper oxide nanoparticles (CuO NPs) with respect to its leaching characteristic and speciation. Complexation-mediated leaching of CuO NPs by amino acids was identified as the source of toxicity toward Escherichia coli, the model microorganism used in the current study. The leached copper-peptide complex induces a multiple-fold increase in intracellular reactive oxygen species generation and reduces the fractions of viable cells, resulting in the overall inhibition of biomass growth. The cytotoxicity of the complex leachate is however different from that of equivalent soluble copper salts (nitrates and sulfates). A pH-dependent copper speciation during the addition of copper salts gives rise to uncoordinated copper ions, which in turn result in greater toxicity and cell lysis, the latter of which was not observed for CuO NPs even at comparable pH. Since leaching did not occur with micrometer-sized CuO, no cytotoxicty effect was observed, thus highlighting the prominence of materials toxicity at the nanoscale.
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Affiliation(s)
- Cindy Gunawan
- ARC Centre of Excellence for Functional Nanomaterials, School of Chemical Engineering, The University of New South Wales, Sydney, NSW 2052, Australia
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31
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Folding and unfolding in the blue copper protein rusticyanin: role of the oxidation state. Bioinorg Chem Appl 2011:54232. [PMID: 18354738 PMCID: PMC2267886 DOI: 10.1155/2007/54232] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2007] [Revised: 05/02/2007] [Accepted: 06/27/2007] [Indexed: 11/17/2022] Open
Abstract
The unfolding process of the blue copper protein rusticyanin has been studied from the structural and the thermodynamic points of view at two pH values (pH 2.5 and 7.0). When Rc unfolds, copper ion remains bound to the polypeptide chain. Nuclear magnetic resonance data suggest that three of the copper ligands in the folded state are bound to the metal ion in the unfolded form, while the other native ligand is detached. These structural changes are reflected in the redox potentials of the protein in both folded and unfolded forms. The affinities of the copper ion in both redox states have been also determined at the two specified pH values. The results indicate that the presence of two histidine ligands in the folded protein can compensate the change in the net charge that the copper ion receives from their ligands, while, in the unfolded protein, charges of aminoacids are completely transferred to the copper ion, altering decisively the relative stability of its two-redox states.
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32
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Incorporation of the red copper nitrosocyanin binding loop into blue copper azurin. J Biol Inorg Chem 2010; 16:473-80. [DOI: 10.1007/s00775-010-0746-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Accepted: 11/24/2010] [Indexed: 10/18/2022]
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33
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Zhekova HR, Seth M, Ziegler T. A Magnetic and Electronic Circular Dichroism Study of Azurin, Plastocyanin, Cucumber Basic Protein, and Nitrite Reductase Based on Time-Dependent Density Functional Theory Calculations. J Phys Chem A 2010; 114:6308-21. [PMID: 20450218 DOI: 10.1021/jp101372s] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hristina R. Zhekova
- Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada, T2N 1N4
| | - Michael Seth
- Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada, T2N 1N4
| | - Tom Ziegler
- Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada, T2N 1N4
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34
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de Almeida K, Cesar A, Rinkevicius Z, Vahtras O, Ågren H. Modelling the visible absorption spectra of copper(II) acetylacetonate by Density Functional Theory. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.04.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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35
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Robinson D, Besley NA. Modelling the spectroscopy and dynamics of plastocyanin. Phys Chem Chem Phys 2010; 12:9667-76. [DOI: 10.1039/c001805h] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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36
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Calculation of Magnetic Circular Dichroism Spectra With Time-Dependent Density Functional Theory. ADVANCES IN INORGANIC CHEMISTRY 2010. [DOI: 10.1016/s0898-8838(10)62002-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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37
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A variable temperature spectroscopic study on Paracoccus pantotrophus pseudoazurin: Protein constraints on the blue Cu site. J Inorg Biochem 2009; 103:1307-13. [DOI: 10.1016/j.jinorgbio.2009.04.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2009] [Revised: 03/20/2009] [Accepted: 04/24/2009] [Indexed: 11/19/2022]
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38
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Thermodynamic equilibrium between blue and green copper sites and the role of the protein in controlling function. Proc Natl Acad Sci U S A 2009; 106:4969-74. [PMID: 19282479 DOI: 10.1073/pnas.0900995106] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A combination of spectroscopies and density functional theory calculations indicate that there are large temperature-dependent absorption spectral changes present in green nitrite reductases (NiRs) due to a thermodynamic equilibrium between a green and a blue type 1 (T1) copper site. The axial methionine (Met) ligand is unconstrained in the oxidized NiRs, which results in an enthalpically favored (DeltaH approximately 4.6 kcal/mol) Met-bound green copper site at low temperatures, and an entropically favored (TDeltaS approximately 4.5 kcal/mol, at room temperature) Met-elongated blue copper site at elevated temperatures. In contrast to the NiRs, the classic blue copper sites in plastocyanin and azurin show no temperature-dependent behavior, indicating that a single species is present at all temperatures. For these blue copper proteins, the polypeptide matrix opposes the gain in entropy that would be associated with the loss of the weak axial Met ligand at physiological temperatures by constraining its coordination to copper. The potential energy surfaces of Met binding indicate that it stabilizes the oxidized state more than the reduced state. This provides a mechanism to tune down the reduction potential of blue copper sites by >200 mV.
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39
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de Almeida KJ, Murugan NA, Rinkevicius Z, Hugosson HW, Vahtras O, Ågren H, Cesar A. Conformations, structural transitions and visible near-infrared absorption spectra of four-, five- and six-coordinated Cu(ii) aqua complexes. Phys Chem Chem Phys 2009; 11:508-19. [DOI: 10.1039/b806423g] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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40
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Unique Spectroscopic Features and Electronic Structures of Copper Proteins: Relation to Reactivity. HIGH RESOLUTION EPR 2009. [DOI: 10.1007/978-0-387-84856-3_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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41
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Pavelka M, Burda JV. Computational study of redox active centres of blue copper proteins: a computational DFT study. Mol Phys 2008. [DOI: 10.1080/00268970802672684] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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42
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Vancoillie S, Pierloot K. Multiconfigurational g tensor calculations as a probe for the covalency of the copper-ligand bonds in copper(II) complexes: [CuCl4]2-, [Cu(NH3)4]2+, and plastocyanin. J Phys Chem A 2008; 112:4011-9. [PMID: 18386853 DOI: 10.1021/jp711345n] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Calculations of the g tensor of three copper(II) complexes [Cu(NH3)4]2+, [CuCl4]2-, and plastocyanin are presented. Two different sum-over-states-based approaches are considered, making use of the multistate CASPT2 method for excitation energies and PMCAS (perturbation modified CAS) wave functions for the computation of the angular momentum and spin-orbit coupling matrix elements. Test calculations on [Cu(NH3)4]2+ and [CuCl4]2- point to the need of including in the MS-CASPT2 treatment the specific charge-transfer state with an electron excited out of the bonding counterpart of the ground-state SOMO. The computed g shifts for these two molecules present a considerable improvement with respect to the results obtained from our previous g tensor calculations based instead on CASSCF/CASPT2. This is shown to be related to an improved description of the covalency of the Cu-L bonds. For the calculations on plastocyanin, different models are used, taken from a recent (QM/MM) DFT study by Sinnecker and Neese. The effect of the surrounding protein is taken into account by surrounding the central cluster either with a dielectric continuum (epsilon = 4) or with a set of point charges. The second approach is found to be indispensable for an accurate description of environmental effects. With this approach, the calculated g values compare to within 30 ppt with the experimental data of plastocyanin.
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Affiliation(s)
- Steven Vancoillie
- Department of Chemistry, University of Leuven Celestijnenlaan, 200F B-3001 Heverlee-Leuven, Belgium
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43
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Zhang Y, Oldfield E. NMR hyperfine shifts in blue copper proteins: a quantum chemical investigation. J Am Chem Soc 2008; 130:3814-23. [PMID: 18314973 DOI: 10.1021/ja075978b] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present the results of the first quantum chemical investigations of 1H NMR hyperfine shifts in the blue copper proteins (BCPs): amicyanin, azurin, pseudoazurin, plastocyanin, stellacyanin, and rusticyanin. We find that very large structural models that incorporate extensive hydrogen bond networks, as well as geometry optimization, are required to reproduce the experimental NMR hyperfine shift results, the best theory vs experiment predictions having R2 = 0.94, a slope = 1.01, and a SD = 40.5 ppm (or approximately 4.7% of the overall approximately 860 ppm shift range). We also find interesting correlations between the hyperfine shifts and the bond and ring critical point properties computed using atoms-in-molecules theory, in addition to finding that hyperfine shifts can be well-predicted by using an empirical model, based on the geometry-optimized structures, which in the future should be of use in structure refinement.
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Affiliation(s)
- Yong Zhang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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44
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Augustine AJ, Kragh ME, Sarangi R, Fujii S, Liboiron BD, Stoj CS, Kosman DJ, Hodgson KO, Hedman B, Solomon EI. Spectroscopic Studies of Perturbed T1 Cu Sites in the Multicopper Oxidases Saccharomyces cerevisiae Fet3p and Rhus vernicifera Laccase: Allosteric Coupling between the T1 and Trinuclear Cu Sites. Biochemistry 2008; 47:2036-45. [DOI: 10.1021/bi7020052] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anthony J. Augustine
- Department of Chemistry, Stanford University, Stanford, California 94305, Faculty of Life Sciences, Department of Natural Sciences, University of Copenhagen, Denmark, Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, Stanford, California 94309, and Department of Biochemistry, School of Medicine and Biomedical Science, State University of New York, Buffalo, New York 14214
| | - Mads Emil Kragh
- Department of Chemistry, Stanford University, Stanford, California 94305, Faculty of Life Sciences, Department of Natural Sciences, University of Copenhagen, Denmark, Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, Stanford, California 94309, and Department of Biochemistry, School of Medicine and Biomedical Science, State University of New York, Buffalo, New York 14214
| | - Ritimukta Sarangi
- Department of Chemistry, Stanford University, Stanford, California 94305, Faculty of Life Sciences, Department of Natural Sciences, University of Copenhagen, Denmark, Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, Stanford, California 94309, and Department of Biochemistry, School of Medicine and Biomedical Science, State University of New York, Buffalo, New York 14214
| | - Satoshi Fujii
- Department of Chemistry, Stanford University, Stanford, California 94305, Faculty of Life Sciences, Department of Natural Sciences, University of Copenhagen, Denmark, Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, Stanford, California 94309, and Department of Biochemistry, School of Medicine and Biomedical Science, State University of New York, Buffalo, New York 14214
| | - Barry D. Liboiron
- Department of Chemistry, Stanford University, Stanford, California 94305, Faculty of Life Sciences, Department of Natural Sciences, University of Copenhagen, Denmark, Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, Stanford, California 94309, and Department of Biochemistry, School of Medicine and Biomedical Science, State University of New York, Buffalo, New York 14214
| | - Christopher S. Stoj
- Department of Chemistry, Stanford University, Stanford, California 94305, Faculty of Life Sciences, Department of Natural Sciences, University of Copenhagen, Denmark, Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, Stanford, California 94309, and Department of Biochemistry, School of Medicine and Biomedical Science, State University of New York, Buffalo, New York 14214
| | - Daniel J. Kosman
- Department of Chemistry, Stanford University, Stanford, California 94305, Faculty of Life Sciences, Department of Natural Sciences, University of Copenhagen, Denmark, Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, Stanford, California 94309, and Department of Biochemistry, School of Medicine and Biomedical Science, State University of New York, Buffalo, New York 14214
| | - Keith O. Hodgson
- Department of Chemistry, Stanford University, Stanford, California 94305, Faculty of Life Sciences, Department of Natural Sciences, University of Copenhagen, Denmark, Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, Stanford, California 94309, and Department of Biochemistry, School of Medicine and Biomedical Science, State University of New York, Buffalo, New York 14214
| | - Britt Hedman
- Department of Chemistry, Stanford University, Stanford, California 94305, Faculty of Life Sciences, Department of Natural Sciences, University of Copenhagen, Denmark, Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, Stanford, California 94309, and Department of Biochemistry, School of Medicine and Biomedical Science, State University of New York, Buffalo, New York 14214
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, Faculty of Life Sciences, Department of Natural Sciences, University of Copenhagen, Denmark, Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, Stanford, California 94309, and Department of Biochemistry, School of Medicine and Biomedical Science, State University of New York, Buffalo, New York 14214
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45
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Brines LM, Shearer J, Fender JK, Schweitzer D, Shoner SC, Barnhart D, Kaminsky W, Lovell S, Kovacs JA. Periodic trends within a series of five-coordinate thiolate-ligated [MII(SMe2N4(tren))]+ (M = Mn, Fe, Co, Ni, Cu, Zn) complexes, including a rare example of a stable CuII-thiolate. Inorg Chem 2007; 46:9267-77. [PMID: 17867686 PMCID: PMC2532082 DOI: 10.1021/ic701433p] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A series of five-coordinate thiolate-ligated complexes [M(II)(tren)N4S(Me2)]+ (M = Mn, Fe, Co, Ni, Cu, Zn; tren = tris(2-aminoethyl)amine) are reported, and their structural, electronic, and magnetic properties are compared. Isolation of dimeric [Ni(II)(SN4(tren)-RS(dang))]2 ("dang"= dangling, uncoordinated thiolate supported by H bonds), using the less bulky [(tren)N4S](1-) ligand, pointed to the need for gem-dimethyls adjacent to the sulfur to sterically prevent dimerization. All of the gem-dimethyl derivatized complexes are monomeric and, with the exception of [Ni(II)(S(Me2)N4(tren)]+, are isostructural and adopt a tetragonally distorted trigonal bipyramidal geometry favored by ligand constraints. The nickel complex uniquely adopts an approximately ideal square pyramidal geometry and resembles the active site of Ni-superoxide dismutase (Ni-SOD). Even in coordinating solvents such as MeCN, only five-coordinate structures are observed. The MII-S thiolate bonds systematically decrease in length across the series (Mn-S > Fe-S > Co-S > Ni-S approximately Cu-S < Zn-S) with exceptions occurring upon the occupation of sigma* orbitals. The copper complex, [Cu(II)(S(Me2)N4(tren)]+, represents a rare example of a stable CuII-thiolate, and models the perturbed "green" copper site of nitrite reductase. In contrast to the intensely colored, low-spin Fe(III)-thiolates, the M(II)-thiolates described herein are colorless to moderately colored and high-spin (in cases where more than one spin-state is possible), reflecting the poorer energy match between the metal d- and sulfur orbitals upon reduction of the metal ion. As the d-orbitals drop in energy proceeding across the across the series M(2+) (M= Mn, Fe, Co, Ni, Cu), the sulfur-to-metal charge-transfer transition moves into the visible region, and the redox potentials cathodically shift. The reduced M(+1) oxidation state is only accessible with copper, and the more oxidized M(+4) oxidation state is only accessible for manganese.
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Affiliation(s)
- Lisa M. Brines
- The Department of Chemistry, University of Washington: Box 351700 Seattle, WA 98195-1700
| | - Jason Shearer
- The Department of Chemistry, University of Washington: Box 351700 Seattle, WA 98195-1700
| | - Jessica K. Fender
- The Department of Chemistry, University of Washington: Box 351700 Seattle, WA 98195-1700
| | - Dirk Schweitzer
- The Department of Chemistry, University of Washington: Box 351700 Seattle, WA 98195-1700
| | - Steven C. Shoner
- The Department of Chemistry, University of Washington: Box 351700 Seattle, WA 98195-1700
| | | | | | | | - Julie A. Kovacs
- The Department of Chemistry, University of Washington: Box 351700 Seattle, WA 98195-1700
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46
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Worrall JAR, Machczynski MC, Keijser BJF, di Rocco G, Ceola S, Ubbink M, Vijgenboom E, Canters GW. Spectroscopic characterization of a high-potential lipo-cupredoxin found in Streptomyces coelicolor. J Am Chem Soc 2007; 128:14579-89. [PMID: 17090042 DOI: 10.1021/ja064112n] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
For many streptomycetes, a distinct dependence on the "bioavailability" of copper ions for their morphological development has been reported. Analysis of the Streptomyces coelicolor genome reveals a number of gene products encoding for putative copper-binding proteins. One of these appears as an unusual copper-binding protein with a lipoprotein signal sequence and a cupredoxin-like domain harboring a putative Type-1 copper-binding motif. Cloning of this gene from S. coelicolor and subsequent heterologous expression in Escherichia coli has allowed for a thorough spectroscopic interrogation of this putative copper-binding protein. Optical and electron paramagnetic resonance spectroscopies have confirmed the presence of a "classic" Type-1 copper site with the axial ligand to the copper a methionine. Paramagnetic NMR spectroscopy on both the native Cu(II) form and Co(II)-substituted protein has yielded active-site structural information, which on comparison with that of other cupredoxin active sites reveals metal-ligand interactions most similar to the "classic" Type-1 copper site found in the amicyanin family of cupredoxins. Despite this high structural similarity, the Cu(II)/(I) midpoint potential of the S. coelicolor protein is an unprecedented +605 mV vs normal hydrogen electrode at neutral pH (amicyanin approximately +250 mV), with no active-site protonation of the N-terminal His ligand observed. Suggestions for the physiological role/function of this high-potential cupredoxin are discussed.
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Affiliation(s)
- Jonathan A R Worrall
- Contribution from the Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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47
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Gradinaru C, Crane BR. Comparison of intra- vs intermolecular long-range electron transfer in crystals of ruthenium-modified azurin. J Phys Chem B 2007; 110:20073-6. [PMID: 17034174 DOI: 10.1021/jp0644309] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Selective metal-ion incorporation and ligand substitution are employed to control whether electrons tunnel over intra- or intermolecular separations in crystals of P. aeruginosa azurin modified with Ru-polypyridine complexes. Cu(1+)-to-Ru3+ electron transfer (ET) across a specific protein-protein interface in the crystal lattice has a time constant 5-10 times longer than ET between the same donor and acceptor within a single protein (tauET = 5 vs 0.5-1.0 micros). Slower intermolecular ET agrees well with a longer distance between redox centers across the inter-protein (18.9 A) compared to the intra-protein separation (17.0 A) and indicates that the closest donor/acceptor pair dominates crystal ET. Lowering the crystal pH accelerates inter-protein ET (tauET = 1.0 micros) but not intra-protein ET. Faster inter-protein ET likely results from a pH-induced peptide bond flip that perturbs hydrogen bonding in the path between Ru and Cu centers on adjacent molecules.
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48
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Abstract
Copper-containing nitrite reductases (NiRs) possess type 1 (T1) and type 2 (T2) copper sites and can be either green or blue in color owing to differences at their T1 centers. The active sites of a green and a blue NiR were studied by utilizing their T1CuI/T2CoII and T1CoII/T2CoII-substituted forms. The UV/Vis spectra of these derivatives highlight the similarity of the T2 centers in these enzymes and that T1 site differences are also present in the CoII forms. The paramagnetic NMR spectra of T1CuI/T2CoII enzymes allow hyperfine shifted resonances from the three T2 His ligands to be assigned: these exhibit remarkably similar positions in the spectra of both NiRs, emphasizing the homology of the T2 centers. The addition of nitrite results in subtle alterations in the paramagnetic NMR spectra of the T1CuI/T2CoII forms at pH<7, which indicate a geometry change upon the binding of substrate. Shifted resonances from all of the T1 site ligands have been assigned and the CoII--N(His) interactions are alike, whereas the CbetaH proton resonances of the Cys ligand exhibit subtle chemical shift differences in the blue and green NiRs. The strength of the axial CoII--S(Met) interaction is similar in the two NiRs studied, but the altered conformation of the side chain of this ligand results in a dramatically different chemical shift pattern for the CgammaH protons. This indicates an alteration in the bonding of the axial ligand in these derivatives, which could be influential in the CuII proteins.
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Affiliation(s)
- Katsuko Sato
- Institute for Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne, NE2 4HH, UK
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49
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Deeth RJ. Comprehensive Molecular Mechanics Model for Oxidized Type I Copper Proteins: Active Site Structures, Strain Energies, and Entatic Bulging. Inorg Chem 2007; 46:4492-503. [PMID: 17461575 DOI: 10.1021/ic062399j] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ligand field molecular mechanics (LFMM) model has been applied to the oxidized Type 1 copper center. In conjunction with the AMBER94 force field implemented in DommiMOE, the ligand field extension of the molecular operating environment (MOE), LFMM parameters for Cu-N(imidazole), Cu-S(thiolate), Cu-S(thioether), and Cu-O(carbonyl) interactions were developed on the basis of experimental and theoretical data for homoleptic model systems. Subsequent LFMM optimizations of the active site model complex [Cu(imidazole)2(SMe)(SMe2]+ agree with high level quantum results both structurally and energetically. Stable trigonal and tetragonal structures are located with the latter about 1.5 kcal mol-1 lower in energy. Fully optimized unconstrained structures were computed for 24 complete proteins containing T1 centers spanning four-coordinate, plastocyanin-like CuN2SS' and stellacyanin-like CuN2SO sites, plus the five-coordinate CuN2SS'O sites of the azurins. The initial structures were based on PDB coordinates augmented by a 10 A layer of water molecules. Agreement between theory and experiment is well within the experimental uncertainties. Moreover, the LFMM results for plastocyanin (Pc), cucumber basic protein (CBP) and azurin (Az) are at least as good as previously reported QM/MM structures and are achieved several orders of magnitude faster. The LFMM calculations suggest the protein provides an entatic strain of about 10 kcal mol-1. However, when combined with the intrinsic 'plasticity' of d9 Cu(II), different starting protein/solvent configurations can have a significant effect on the final optimized structure. This 'entatic bulging' results in relatively large fluctuations in the calculated metal-ligand bond lengths. For example, simply on the basis of 25 different starting configurations of the solvent molecules, the optimized Cu-S(thiolate) bond lengths in Pc vary by 0.04 A while the Cu-S(thioether) distance spans over 0.3 A. These variations are the same order of magnitude as the differences often quoted to correlate the spectroscopic properties from a set of proteins. Isolated optimizations starting from PDB coordinates (or indeed, the PDB structures themselves) may only accidentally correlate with spectroscopic measurements. The present calculations support the work of Warshel who contends that adequate configurational averaging is necessary to make proper contact with experimental properties measured in solution. The LFMM is both sufficiently accurate and fast to make this practical.
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Affiliation(s)
- Robert J Deeth
- Inorganic Computational Chemistry Group, Department of Chemistry, University of Warwick, Coventry, CV4 7AL UK.
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50
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Garner DK, Vaughan MD, Hwang HJ, Savelieff MG, Berry SM, Honek JF, Lu Y. Reduction potential tuning of the blue copper center in Pseudomonas aeruginosa azurin by the axial methionine as probed by unnatural amino acids. J Am Chem Soc 2007; 128:15608-17. [PMID: 17147368 DOI: 10.1021/ja062732i] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The conserved axial ligand methionine 121 from Pseudomonas aeruginosa azurin (Az) has been replaced by isostructural unnatural amino acid analogues, oxomethionine (OxM), difluoromethionine (DFM), trifluoromethionine (TFM), selenomethionine (SeM), and norleucine (Nle) using expressed protein ligation. The replacements resulted in < 6 nm shifts in the S(Cys)-Cu charge transfer (CT) band in the electronic absorption spectra and < 8 gauss changes in the copper hyperfine coupling constants (AII) in the X-band electron paramagnetic resonance spectra, suggesting that isostructural replacement of Met resulted in minimal structural perturbation of the copper center. The slight blue shifts of the CT band follow the trend of stronger electronegativity of the ligands. This trend is supported by 19F NMR studies of the fluorinated methionine analogues. However, the order of AII differs, suggesting additional factors influencing AII. In contrast to the small changes in the UV-vis and EPR spectra, a large variation of > 227 mV in reduction potential was observed for the series of variants reported here. Additionally, a linear correlation was established between the reduction potentials and hydrophobicity of the variants. Extension of this analysis to other type 1 copper-containing proteins reveals a linear correlation between change in hydrophobicity and change in reduction potential, independent of the protein scaffold, experimental conditions, measurement techniques, and steric modifications. This analysis has also revealed for the first time high and low potential states for type 1 centers, and the difference may be attributable to destabilization of the protein fold by disruption of hydrophobic or hydrogen bonding interactions that stabilize the type 1 center.
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Affiliation(s)
- Dewain K Garner
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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