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Crittenden CM, Novelli ET, Mehaffey MR, Xu GN, Giles DH, Fies WA, Dalby KN, Webb LJ, Brodbelt JS. Structural Evaluation of Protein/Metal Complexes via Native Electrospray Ultraviolet Photodissociation Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1140-1150. [PMID: 32275426 PMCID: PMC7386362 DOI: 10.1021/jasms.0c00066] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Ultraviolet photodissociation (UVPD) has emerged as a promising tool to characterize proteins with regard to not only their primary sequences and post-translational modifications, but also their tertiary structures. In this study, three metal-binding proteins, Staphylococcal nuclease, azurin, and calmodulin, are used to demonstrate the use of UVPD to elucidate metal-binding regions via comparisons between the fragmentation patterns of apo (metal-free) and holo (metal-bound) proteins. The binding of staphylococcal nuclease to calcium was evaluated, in addition to a series of lanthanide(III) ions which are expected to bind in a similar manner as calcium. On the basis of comparative analysis of the UVPD spectra, the binding region for calcium and the lanthanide ions was determined to extend from residues 40-50, aligning with the known crystal structure. Similar analysis was performed for both azurin (interrogating copper and silver binding) and calmodulin (four calcium binding sites). This work demonstrates the utility of UVPD methods for determining and analyzing the metal binding sites of a variety of classes of proteins.
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Affiliation(s)
| | - Elisa T Novelli
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
| | - M Rachel Mehaffey
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
| | - Gulan N Xu
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
| | - David H Giles
- Division of Chemical Biology and Medicinal Chemistry, University of Texas, Austin, Texas 78712, United States
| | - Whitney A Fies
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
| | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, University of Texas, Austin, Texas 78712, United States
- Graduate Program in Cell and Molecular Biology, University of Texas, Austin, Texas 78712, United States
| | - Lauren J Webb
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
- Institute for Cell and Molecular Biology, University of Texas, Austin, Texas 78712, United States
- Texas Materials Institute, University of Texas, Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
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2
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Leguto AJ, Smith MA, Morgada MN, Zitare UA, Murgida DH, Lancaster KM, Vila AJ. Dramatic Electronic Perturbations of Cu A Centers via Subtle Geometric Changes. J Am Chem Soc 2019; 141:1373-1381. [PMID: 30582893 DOI: 10.1021/jacs.8b12335] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
CuA is a binuclear copper site acting as electron entry port in terminal heme-copper oxidases. In the oxidized form, CuA is a mixed valence pair whose electronic structure can be described using a potential energy surface with two minima, σu* and πu, that are variably populated at room temperature. We report that mutations in the first and second coordination spheres of the binuclear metallocofactor can be combined in an additive manner to tune the energy gap and, thus, the relative populations of the two lowest-lying states. A series of designed mutants span σu*/πu energy gaps ranging from 900 to 13 cm-1. The smallest gap corresponds to a variant with an effectively degenerate ground state. All engineered sites preserve the mixed-valence character of this metal center and the electron transfer functionality. An increase of the Cu-Cu distance less than 0.06 Å modifies the σu*/πu energy gap by almost 2 orders of magnitude, with longer distances eliciting a larger population of the πu state. This scenario offers a stark contrast to synthetic systems, as model compounds require a lengthening of 0.5 Å in the Cu-Cu distance to stabilize the πu state. These findings show that the tight control of the protein environment allows drastic perturbations in the electronic structure of CuA sites with minor geometric changes.
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Affiliation(s)
- Alcides J Leguto
- Instituto de Biología Molecular y Celular de Rosario (IBR), Departamento de Química Biológica, Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario and CONICET , 2000 Rosario , Argentina
| | - Meghan A Smith
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
| | - Marcos N Morgada
- Instituto de Biología Molecular y Celular de Rosario (IBR), Departamento de Química Biológica, Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario and CONICET , 2000 Rosario , Argentina
| | - Ulises A Zitare
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires and CONICET , 1428 Buenos Aires , Argentina
| | - Daniel H Murgida
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires and CONICET , 1428 Buenos Aires , Argentina
| | - Kyle M Lancaster
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
| | - Alejandro J Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR), Departamento de Química Biológica, Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario and CONICET , 2000 Rosario , Argentina
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3
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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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4
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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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5
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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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6
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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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7
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Flemming Hansen D, Gorelsky SI, Sarangi R, Hodgson KO, Hedman B, Christensen HEM, Solomon EI, Led JJ. Reinvestigation of the method used to map the electronic structure of blue copper proteins by NMR relaxation. J Biol Inorg Chem 2006; 11:277-85. [PMID: 16432723 DOI: 10.1007/s00775-005-0070-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2005] [Accepted: 11/29/2005] [Indexed: 10/25/2022]
Abstract
A previous method for mapping the electron spin distribution in blue copper proteins by paramagnetic nuclear magnetic resonance (NMR) relaxation (Hansen DF, Led JJ, 2004, J Am Chem Soc 126:1247-1253) suggested that the blue copper site of plastocyanin from Anabaena variabilis (A.v.) is less covalent than those found for other plastocyanins by other experimental methods, such as X-ray absorption spectroscopy. Here, a detailed spectroscopic study revealed that the electronic structure of A.v. plastocyanin is similar to those of other plastocyanins. Therefore, the NMR approach was reinvestigated using a more accurate geometric structure as the basis for the mapping, in contrast to the previous approach, as well as a more complete spin distribution model including Gaussian-type natural atomic orbitals instead of Slater-type hydrogen-like atomic orbitals. The refinement results in a good agreement between the electron spin density derived from paramagnetic NMR and the electronic structure description obtained by the other experimental methods. The refined approach was evaluated against density functional theory (DFT) calculations on a model complex of the metal site of plastocyanin in the crystal phase. In general, the agreement between the experimental paramagnetic relaxation rates and the corresponding rates obtained by the DFT calculations is good. Small deviations are attributed to minor differences between the solution structure and the crystal structure outside the first coordination sphere. Overall, the refined approach provides a complementary experimental method for determining the electronic structure of paramagnetic metalloproteins, provided that an accurate geometric structure is available.
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Affiliation(s)
- D Flemming Hansen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark
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8
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9
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Monleón D, Ribes F, Jiménez HR, Moratal JM, Celda B. NMR and homology modeling studies of copper(II)-halocyanin from Natronobacterium pharaonis bacteria. Inorganica Chim Acta 2004. [DOI: 10.1016/j.ica.2003.10.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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10
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Battistuzzi G, Bellei M, Borsari M, Canters GW, de Waal E, Jeuken LJC, Ranieri A, Sola M. Control of metalloprotein reduction potential: compensation phenomena in the reduction thermodynamics of blue copper proteins. Biochemistry 2003; 42:9214-20. [PMID: 12885256 DOI: 10.1021/bi034585w] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The reduction thermodynamics (Delta H degrees '(rc) and Delta S degrees '(rc)) for native Paracoccus versutus amicyanin, for Alcaligenes faecalis S-6 pseudoazurin, and for the G45P, M64E, and K27C variants of Pseudomonas aeruginosa azurin were measured electrochemically. Comparison with the data available for other native and mutated blue copper proteins indicates that the features of metal coordination and the electrostatic potential due to the protein matrix and the solvent control the reduction enthalpy in a straightforward way. However, the effects on the reduction potential are rather unpredictable owing to the entropic contribution to E degrees ', which is mainly determined by solvent reorganization effects. Analysis of all the Delta H degrees '(rc) and Delta S degrees '(rc) values available for this protein class indicates that enthalpy-entropy compensation occurs in the reduction thermodynamics of wt cupredoxins from different sources, as well as for mutants of the same species. The findings indicate that the reduction enthalpies and entropies for these species are strongly affected by reduction-induced reorganization of solvent molecules within the solvation sphere of the protein. The absence of a perfect enthalpy-entropy compensation is due to the fact that while the differences between reduction entropies are dominated by solvent reorganization effects, those between reduction enthalpies are significantly controlled by intrinsic molecular factors related to the selective stabilization of the reduced form by coordination features of the copper site and electrostatic effects at the interface with the protein matrix.
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Affiliation(s)
- Gianantonio Battistuzzi
- Department of Chemistry, University of Modena and Reggio Emilia, Via Campi 183, 41100 Modena, Italy
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11
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Berry SM, Ralle M, Low DW, Blackburn NJ, Lu Y. Probing the role of axial methionine in the blue copper center of azurin with unnatural amino acids. J Am Chem Soc 2003; 125:8760-8. [PMID: 12862470 DOI: 10.1021/ja029699u] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Expressed protein ligation was used to replace the axial methionine of the blue copper protein azurin from Pseudomonas aeruginosa with unnatural amino acids. The highly conserved methionine121 residue was replaced with the isostructural amino acids norleucine (Nle) and selenomethionine (SeM). The UV-visible absorption, X- and Q-band EPR, and Cu EXAFS spectra of the variants are slightly perturbed from WT. All variants have a predominant S(Cys) to Cu(II) charge transfer band around 625 nm and narrow EPR hyperfine splittings. The Se EXAFS of the M121SeM variant is also reported. In contrast to the small spectral changes, the reduction potentials of M121SeM, M121Leu, and M121Nle are 25, 135, and 140 mV, respectively, higher than that of WT azurin. The use of unnatural amino acids allowed deconvolution of different factors affecting the reduction potentials of the blue copper center. A careful analysis of the WT azurin and its variants obtained in this work showed the large reduction potential variation was linearly correlated with the hydrophobicity of the axial ligand side chains. Therefore, hydrophobicity is the dominant factor in tuning the reduction potentials of blue copper centers by axial ligands.
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Affiliation(s)
- Steven M Berry
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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12
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Banci L, Pierattelli R, Vila AJ. Nuclear magnetic resonance spectroscopy studies on copper proteins. ADVANCES IN PROTEIN CHEMISTRY 2003; 60:397-449. [PMID: 12418182 DOI: 10.1016/s0065-3233(02)60058-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Affiliation(s)
- Lucia Banci
- CERM, University of Florence, 50019 Sesto Fiorentino, Italy
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13
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Dennison C, Sato K. Paramagnetic 1H NMR spectrum of nickel(II) pseudoazurin: investigation of the active site structure and the acid and alkaline transitions. Inorg Chem 2002; 41:6662-72. [PMID: 12470061 DOI: 10.1021/ic020303p] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The paramagnetic (1)H NMR spectrum of Ni(II) pseudoazurin [(PA)Ni(II)] possesses a number of resonances exhibiting sizable Fermi-contact shifts. These have been assigned to protons associated with the four ligating amino acids, His40, Cys78, His81, and Met86. The shifts experienced by the C(gamma)H protons of the axial Met86 ligand are unprecedented compared to other Ni(II)- and Co(II)-substituted cupredoxins (the C(gamma)(1)H signal is found at 432.5 ppm at 25 degrees C). The large shift of protons of the axial Met86 ligand highlights a strong Ni(II)-S(Met) interaction in (PA)Ni(II). The paramagnetic (1)H NMR spectrum of (PA)Ni(II) is altered by decreasing and increasing the pH value from 8.0. At acidic pH a number of the hyperfine-shifted resonances undergo limited changes in their chemical shift values. This effect is assigned to the surface His6 residue whose protonation results in a structural modification of the active site. Increasing the pH value from 8.0 has a more significant effect on the paramagnetic (1)H NMR spectrum of (PA)Ni(II), and the alkaline transition can now be assigned to two surface lysine residues close to the active site of the protein. The effect of altering pH on the (1)H NMR spectrum of Ni(II) pseudoazurin is smaller than that previously observed in the Cu(II) protein indicating more limited structural rearrangements at the non-native metal site.
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14
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Donaire A, Jiménez B, Fernández CO, Pierattelli R, Niizeki T, Moratal JM, Hall JF, Kohzuma T, Hasnain SS, Vila AJ. Metal-ligand interplay in blue copper proteins studied by 1H NMR spectroscopy: Cu(II)-pseudoazurin and Cu(II)-rusticyanin. J Am Chem Soc 2002; 124:13698-708. [PMID: 12431099 DOI: 10.1021/ja0267019] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The blue copper proteins (BCPs), pseudoazurin from Achromobacter cycloclastes and rusticyanin from Thiobacillus ferrooxidans, have been investigated by (1)H NMR at a magnetic field of 18.8 T. Hyperfine shifts of the protons belonging to the coordinated ligands have been identified by exchange spectroscopy, including the indirect detection for those resonances that cannot be directly observed (the beta-CH(2) of the Cys ligand, and the NH amide hydrogen bonded to the S(gamma)(Cys) atom). These data reveal that the Cu(II)-Cys interaction in pseudoazurin and rusticyanin is weakened compared to that in classic blue sites (plastocyanin and azurin). This weakening is not induced by a stronger interaction with the axial ligand, as found in stellacyanin, but might be determined by the protein folding around the metal site. The average chemical shift of the beta-CH(2) Cys ligand in all BCPs can be correlated to geometric factors of the metal site (the Cu-S(gamma)(Cys) distance and the angle between the CuN(His)N(His) plane and the Cu-S(gamma)(Cys) vector). It is concluded that the degree of tetragonal distortion is not necessarily related to the strength of the Cu(II)-S(gamma)(Cys) bond. The copper-His interaction is similar in all BCPs, even for the solvent-exposed His ligand. It is proposed that the copper xy magnetic axes in blue sites are determined by subtle geometrical differences, particularly the orientation of the His ligands. Finally, the observed chemical shifts for beta-CH(2) Cys and Ser NH protons in rusticyanin suggest that a less negative charge at the sulfur atom could contribute to the high redox potential (680 mV) of this protein.
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Affiliation(s)
- Antonio Donaire
- Biophysics Section and Instituto de Biología Molecular y Celular de Rosario (IBR), University of Rosario, Suipacha 531, S2002LRK Rosario, Argentina
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15
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Sato K, Dennison C. Effect of histidine 6 protonation on the active site structure and electron-transfer capabilities of pseudoazurin from Achromobacter cycloclastes. Biochemistry 2002; 41:120-30. [PMID: 11772009 DOI: 10.1021/bi0117448] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The paramagnetic (1)H NMR spectrum of Cu(II) pseudoazurin [PACu(II)] contains eight directly observed hyperfine-shifted resonances which we have assigned using saturation transfer experiments on a 1:1 mixture of PACu(I) and PACu(II). The spectrum exhibits a number of similarities to those of other cupredoxins, but differences are found concerning the Cu-S(Met) interaction. The spectrum is dependent on pH* in the range 8.5-4.5 (pK(a)* 6.4), and a conformational change involving movement of the copper ion away from the Met toward the equatorial ligands, as a consequence of protonation of the surface His6 residue, is identified. Corresponding changes are also seen in the UV/vis spectrum. The protonation/deprotonation equilibrium of His6 influences the reduction potential of the protein in the same pH range. The self-exchange rate constant of PACu at pH* 6.0 (25 degrees C) is considerably smaller (1.1 x 10(3) M(-1) s(-1)) than the value obtained at pH* 7.6 (3.7 x 10(3) M(-1) s(-1)). The effect on the self-exchange reactivity is mainly due to an alteration in the reorganization energy of the copper site brought about by the structural change resulting from His6 protonation.
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Affiliation(s)
- Katsuko Sato
- Department of Chemistry, University of Newcastle upon Tyne, Newcastle upon Tyne, NE1 7RU, UK
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16
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Battistuzzi G, Borsari M, Canters GW, de Waal E, Loschi L, Warmerdam G, Sola M. Enthalpic and entropic contributions to the mutational changes in the reduction potential of azurin. Biochemistry 2001; 40:6707-12. [PMID: 11389584 DOI: 10.1021/bi010333o] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The changes in the reduction potential of Pseudomonas aeruginosa and Alcaligenes denitrificans azurins following point mutations and residue ionizations were factorized into the enthalpic and entropic contributions through variable temperature direct electrochemistry experiments. The effects on the reduction enthalpy due to changes in the first coordination sphere of the copper ion, as in the Met121Gln and Met121His variants of A. denitrificans azurin, insertion of a net charge and alteration in the solvation properties and electrostatic potential in proximity of the metal site, as in the Met44Lys and His35Leu variants of P. aeruginosa azurin, respectively, and proton uptake/release in wild-type and mutated species could invariably be accounted for on the basis of simple coordination chemistry and/or electrostatic considerations. The concomitant changes in reduction entropy were found in general to contribute to the E degrees ' variation to a lesser extent as compared to the enthalpy changes. However, their effects were by no means negligible and in some instances were found to heavily contribute to (or even become the main determinant of) the observed change in reduction potential. Several lines of evidence indicate that the entropic effects are notably influenced by reduction-induced solvent reorganization effects. In particular, protein reduction tends to be favored on entropic grounds with increasing exposure of the copper site to the solvent. Moreover, enthalpy-entropy compensation phenomena are invariably observed when residue mutation or pH-induced conformational changes modify the solvent accessibility of the metal site or alter the H-bonding network in the hydration shell of the molecule. Therefore, in these cases, caution must be used in making predictions of E degrees ' changes simply based on Coulombic or coordination chemistry arguments.
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Affiliation(s)
- G Battistuzzi
- Department of Chemistry, University of Modena and Reggio Emilia, Via Campi 183, 41100 Modena, Italy
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17
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Farver O, Jeuken LJ, Canters GW, Pecht I. Role of ligand substitution on long-range electron transfer in azurins. EUROPEAN JOURNAL OF BIOCHEMISTRY 2000; 267:3123-9. [PMID: 10824096 DOI: 10.1046/j.1432-1327.2000.01317.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Azurin contains two potential redox sites, a copper centre and, at the opposite end of the molecule, a cystine disulfide (RSSR). Intramolecular electron transfer between a pulse radiolytically produced RSSR- radical anion and the blue Cu(II) ion was studied in a series of azurins in which single-site mutations were introduced into the copper ligand sphere. In the Met121His mutant, the rate constant for intramolecular electron transfer is half that of the corresponding wild-type azurin. In the His46Gly and His117Gly mutants, a water molecule is co-ordinated to the copper ion when no external ligands are added. Both these mutants also exhibit slower intramolecular electron transfer than the corresponding wild-type azurin. However, for the His117Gly mutant in the presence of excess imidazole, an azurin-imidazole complex is formed and the intramolecular electron-transfer rate increases considerably, becoming threefold faster than that observed in the native protein. Activation parameters for all these electron-transfer processes were determined and combined with data from earlier studies on intramolecular electron transfer in wild-type and single-site-mutated azurins. A linear relationship between activation enthalpy and activation entropy was observed. These results are discussed in terms of reorganization energies, driving force and possible electron-transfer pathways.
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Affiliation(s)
- O Farver
- Institute of Analytical and Pharmaceutical Chemistry, The Royal Danish School of Pharmacy, Copenhagen, Denmark.
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18
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Bertini I, Fernández CO, Karlsson BG, Leckner J, Luchinat C, Malmström BG, Nersissian AM, Pierattelli R, Shipp E, Valentine JS, Vila AJ. Structural Information through NMR Hyperfine Shifts in Blue Copper Proteins. J Am Chem Soc 2000. [DOI: 10.1021/ja992674j] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ivano Bertini
- Contribution from the Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy, LANAIS RMN-300, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, 1113 Buenos Aires, Argentina, Department of Molecular Biotechnology, Chalmers University of Technology, P.O. Box 462 SE-405 30 Göteborg, Sweden, Department of Chemistry, Biochemistry and Biophysics, Göteborg University, SE-40530 Göteborg, Sweden, Department of Chemistry and
| | - Claudio O. Fernández
- Contribution from the Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy, LANAIS RMN-300, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, 1113 Buenos Aires, Argentina, Department of Molecular Biotechnology, Chalmers University of Technology, P.O. Box 462 SE-405 30 Göteborg, Sweden, Department of Chemistry, Biochemistry and Biophysics, Göteborg University, SE-40530 Göteborg, Sweden, Department of Chemistry and
| | - B. Göran Karlsson
- Contribution from the Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy, LANAIS RMN-300, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, 1113 Buenos Aires, Argentina, Department of Molecular Biotechnology, Chalmers University of Technology, P.O. Box 462 SE-405 30 Göteborg, Sweden, Department of Chemistry, Biochemistry and Biophysics, Göteborg University, SE-40530 Göteborg, Sweden, Department of Chemistry and
| | - Johan Leckner
- Contribution from the Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy, LANAIS RMN-300, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, 1113 Buenos Aires, Argentina, Department of Molecular Biotechnology, Chalmers University of Technology, P.O. Box 462 SE-405 30 Göteborg, Sweden, Department of Chemistry, Biochemistry and Biophysics, Göteborg University, SE-40530 Göteborg, Sweden, Department of Chemistry and
| | - Claudio Luchinat
- Contribution from the Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy, LANAIS RMN-300, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, 1113 Buenos Aires, Argentina, Department of Molecular Biotechnology, Chalmers University of Technology, P.O. Box 462 SE-405 30 Göteborg, Sweden, Department of Chemistry, Biochemistry and Biophysics, Göteborg University, SE-40530 Göteborg, Sweden, Department of Chemistry and
| | - Bo G. Malmström
- Contribution from the Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy, LANAIS RMN-300, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, 1113 Buenos Aires, Argentina, Department of Molecular Biotechnology, Chalmers University of Technology, P.O. Box 462 SE-405 30 Göteborg, Sweden, Department of Chemistry, Biochemistry and Biophysics, Göteborg University, SE-40530 Göteborg, Sweden, Department of Chemistry and
| | - Aram M. Nersissian
- Contribution from the Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy, LANAIS RMN-300, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, 1113 Buenos Aires, Argentina, Department of Molecular Biotechnology, Chalmers University of Technology, P.O. Box 462 SE-405 30 Göteborg, Sweden, Department of Chemistry, Biochemistry and Biophysics, Göteborg University, SE-40530 Göteborg, Sweden, Department of Chemistry and
| | - Roberta Pierattelli
- Contribution from the Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy, LANAIS RMN-300, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, 1113 Buenos Aires, Argentina, Department of Molecular Biotechnology, Chalmers University of Technology, P.O. Box 462 SE-405 30 Göteborg, Sweden, Department of Chemistry, Biochemistry and Biophysics, Göteborg University, SE-40530 Göteborg, Sweden, Department of Chemistry and
| | - Eric Shipp
- Contribution from the Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy, LANAIS RMN-300, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, 1113 Buenos Aires, Argentina, Department of Molecular Biotechnology, Chalmers University of Technology, P.O. Box 462 SE-405 30 Göteborg, Sweden, Department of Chemistry, Biochemistry and Biophysics, Göteborg University, SE-40530 Göteborg, Sweden, Department of Chemistry and
| | - Joan S. Valentine
- Contribution from the Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy, LANAIS RMN-300, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, 1113 Buenos Aires, Argentina, Department of Molecular Biotechnology, Chalmers University of Technology, P.O. Box 462 SE-405 30 Göteborg, Sweden, Department of Chemistry, Biochemistry and Biophysics, Göteborg University, SE-40530 Göteborg, Sweden, Department of Chemistry and
| | - Alejandro J. Vila
- Contribution from the Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy, LANAIS RMN-300, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, 1113 Buenos Aires, Argentina, Department of Molecular Biotechnology, Chalmers University of Technology, P.O. Box 462 SE-405 30 Göteborg, Sweden, Department of Chemistry, Biochemistry and Biophysics, Göteborg University, SE-40530 Göteborg, Sweden, Department of Chemistry and
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Buning C, Canters GW, Comba P, Dennison C, Jeuken L, Melter M, Sanders-Loehr J. Loop-Directed Mutagenesis of the Blue Copper Protein Amicyanin fromParacoccus versutusand Its Effect on the Structure and the Activity of the Type-1 Copper Site. J Am Chem Soc 2000. [DOI: 10.1021/ja992796b] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Dennison C, Kohzuma T. Alkaline Transition of Pseudoazurin from Achromobacter cycloclastes Studied by Paramagnetic NMR and Its Effect on Electron Transfer. Inorg Chem 1999. [DOI: 10.1021/ic981242r] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Christopher Dennison
- Department of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland, and Department of Chemistry, Ibaraki University, Mito, Ibaraki 310, Japan
| | - Takamitsu Kohzuma
- Department of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland, and Department of Chemistry, Ibaraki University, Mito, Ibaraki 310, Japan
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Bertini I, Ciurli S, Dikiy A, Gasanov R, Luchinat C, Martini G, Safarov N. High-Field NMR Studies of Oxidized Blue Copper Proteins: The Case of Spinach Plastocyanin. J Am Chem Soc 1999. [DOI: 10.1021/ja983833m] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ivano Bertini
- Contribution from the Department of Chemistry, University of Florence, Via Gino Capponi 7/9, 50121 Florence, Italy, Institute of Agricultural Chemistry, University of Bologna, viale Berti Pichat 10, 40120 Bologna, Italy, Institute of Molecular Biology and Biotechnology, Azerbaijan Academy of Sciences, Matbuat pr., 2, 370073, Baku, Azerbaijan, and Department of Soil Science and Plant Nutrition, University of Florence, P.le delle Cascine 28, 50144 Florence, Italy
| | - Stefano Ciurli
- Contribution from the Department of Chemistry, University of Florence, Via Gino Capponi 7/9, 50121 Florence, Italy, Institute of Agricultural Chemistry, University of Bologna, viale Berti Pichat 10, 40120 Bologna, Italy, Institute of Molecular Biology and Biotechnology, Azerbaijan Academy of Sciences, Matbuat pr., 2, 370073, Baku, Azerbaijan, and Department of Soil Science and Plant Nutrition, University of Florence, P.le delle Cascine 28, 50144 Florence, Italy
| | - Alexander Dikiy
- Contribution from the Department of Chemistry, University of Florence, Via Gino Capponi 7/9, 50121 Florence, Italy, Institute of Agricultural Chemistry, University of Bologna, viale Berti Pichat 10, 40120 Bologna, Italy, Institute of Molecular Biology and Biotechnology, Azerbaijan Academy of Sciences, Matbuat pr., 2, 370073, Baku, Azerbaijan, and Department of Soil Science and Plant Nutrition, University of Florence, P.le delle Cascine 28, 50144 Florence, Italy
| | - Ralphreed Gasanov
- Contribution from the Department of Chemistry, University of Florence, Via Gino Capponi 7/9, 50121 Florence, Italy, Institute of Agricultural Chemistry, University of Bologna, viale Berti Pichat 10, 40120 Bologna, Italy, Institute of Molecular Biology and Biotechnology, Azerbaijan Academy of Sciences, Matbuat pr., 2, 370073, Baku, Azerbaijan, and Department of Soil Science and Plant Nutrition, University of Florence, P.le delle Cascine 28, 50144 Florence, Italy
| | - Claudio Luchinat
- Contribution from the Department of Chemistry, University of Florence, Via Gino Capponi 7/9, 50121 Florence, Italy, Institute of Agricultural Chemistry, University of Bologna, viale Berti Pichat 10, 40120 Bologna, Italy, Institute of Molecular Biology and Biotechnology, Azerbaijan Academy of Sciences, Matbuat pr., 2, 370073, Baku, Azerbaijan, and Department of Soil Science and Plant Nutrition, University of Florence, P.le delle Cascine 28, 50144 Florence, Italy
| | - Giacomo Martini
- Contribution from the Department of Chemistry, University of Florence, Via Gino Capponi 7/9, 50121 Florence, Italy, Institute of Agricultural Chemistry, University of Bologna, viale Berti Pichat 10, 40120 Bologna, Italy, Institute of Molecular Biology and Biotechnology, Azerbaijan Academy of Sciences, Matbuat pr., 2, 370073, Baku, Azerbaijan, and Department of Soil Science and Plant Nutrition, University of Florence, P.le delle Cascine 28, 50144 Florence, Italy
| | - Niaz Safarov
- Contribution from the Department of Chemistry, University of Florence, Via Gino Capponi 7/9, 50121 Florence, Italy, Institute of Agricultural Chemistry, University of Bologna, viale Berti Pichat 10, 40120 Bologna, Italy, Institute of Molecular Biology and Biotechnology, Azerbaijan Academy of Sciences, Matbuat pr., 2, 370073, Baku, Azerbaijan, and Department of Soil Science and Plant Nutrition, University of Florence, P.le delle Cascine 28, 50144 Florence, Italy
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Messerschmidt A, Prade L, Kroes SJ, Sanders-Loehr J, Huber R, Canters GW. Rack-induced metal binding vs. flexibility: Met121His azurin crystal structures at different pH. Proc Natl Acad Sci U S A 1998; 95:3443-8. [PMID: 9520385 PMCID: PMC19855 DOI: 10.1073/pnas.95.7.3443] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The rack-induced bonding mechanism of metals to proteins is a useful concept for explaining the generation of metal sites in electron transfer proteins, such as the blue copper proteins, that are designed for rapid electron transfer. The trigonal pyramidal structure imposed by the protein with three strong equatorial ligands (one Cys and two His) provides a favorable geometry for both cuprous and cupric oxidation states. However, the crystal structures of the Met121His mutant of azurin from Alcaligenes denitrificans at pH 6.5 (1.89- and 1.91-A resolutions) and pH 3.5 (2.45-A resolution) show that the preformed metal binding cavity in the protein is more flexible than expected. At high pH (6.5), the Cu site retains the same three equatorial ligands as in the wild-type azurin and adds His121 as a fourth strong ligand, creating a tetrahedral copper site geometry with a green color referred to as 1.5 type. In the low pH (3.5) structure, the protonation of His121 causes a conformational change in residues 117-123, moving His121 away from the copper. The empty coordination site is occupied by an oxygen atom of a nitrate molecule of the buffer solution. This axial ligand is coordinated less strongly, generating a distorted tetrahedral copper geometry with a blue color and spectroscopic properties of a type-1 site. These crystal structures demonstrate that blue copper proteins are flexible enough to permit a range of movement of the Cu atom along the axial direction of the trigonal pyramid.
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Affiliation(s)
- A Messerschmidt
- Max-Planck-Institut für Biochemie, D-82152 Martinsried, Germany.
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