101
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Warren JJ, Lancaster KM, Richards JH, Gray HB. Inner- and outer-sphere metal coordination in blue copper proteins. J Inorg Biochem 2012; 115:119-26. [PMID: 22658756 PMCID: PMC3434318 DOI: 10.1016/j.jinorgbio.2012.05.002] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2012] [Revised: 04/30/2012] [Accepted: 05/01/2012] [Indexed: 10/28/2022]
Abstract
Blue copper proteins (BCPs) comprise classic cases of Nature's profound control over the electronic structures and chemical reactivity of transition metal ions. Early studies of BCPs focused on their inner coordination spheres, that is, residues that directly coordinate Cu. Equally important are the electronic and geometric perturbations to these ligands provided by the outer coordination sphere. In this tribute to Hans Freeman, we review investigations that have advanced the understanding of how inner-sphere and outer-sphere coordination affects biological Cu properties.
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Affiliation(s)
- Jeffrey J Warren
- Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
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102
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Swart M, Johansson MP. Density Functional Study on UV/VIS Spectra of Copper-Protein Active Sites: The Effect of Mutations. Chem Biodivers 2012; 9:1728-38. [DOI: 10.1002/cbdv.201200058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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103
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Takeuchi H. Raman spectral marker of tryptophan conformation: Theoretical basis and extension to a wider range of torsional angle. J Mol Struct 2012. [DOI: 10.1016/j.molstruc.2012.03.075] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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104
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Monari S, Battistuzzi G, Bortolotti CA, Yanagisawa S, Sato K, Li C, Salard I, Kostrz D, Borsari M, Ranieri A, Dennison C, Sola M. Understanding the Mechanism of Short-Range Electron Transfer Using an Immobilized Cupredoxin. J Am Chem Soc 2012; 134:11848-51. [DOI: 10.1021/ja303425b] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stefano Monari
- Department of Chemistry, University of Modena and Reggio Emilia, Via Campi 183,
41125 Modena, Italy
| | - Gianantonio Battistuzzi
- Department of Chemistry, University of Modena and Reggio Emilia, Via Campi 183,
41125 Modena, Italy
| | - Carlo A. Bortolotti
- Department of Chemistry, University of Modena and Reggio Emilia, Via Campi 183,
41125 Modena, Italy
- CNR-NANO Institute of Nanoscience, Via Campi 213/A, I-41125 Modena, Italy
| | - Sachiko Yanagisawa
- Institute for Cell and Molecular
Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K
| | - Katsuko Sato
- Institute for Cell and Molecular
Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K
| | - Chan Li
- Institute for Cell and Molecular
Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K
| | - Isabelle Salard
- Institute for Cell and Molecular
Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K
| | - Dorota Kostrz
- Institute for Cell and Molecular
Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K
| | - Marco Borsari
- Department of Chemistry, University of Modena and Reggio Emilia, Via Campi 183,
41125 Modena, Italy
| | - Antonio Ranieri
- Department of Chemistry, University of Modena and Reggio Emilia, Via Campi 183,
41125 Modena, Italy
| | - Christopher Dennison
- Institute for Cell and Molecular
Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K
| | - Marco Sola
- Department of Chemistry, University of Modena and Reggio Emilia, Via Campi 183,
41125 Modena, Italy
- CNR-NANO Institute of Nanoscience, Via Campi 213/A, I-41125 Modena, Italy
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105
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Shiga D, Hamano Y, Kamei M, Funahashi Y, Masuda H, Sakaguchi M, Ogura T, Tanaka T. Tuning the geometries of a de novo blue copper protein by axial interactions. J Biol Inorg Chem 2012; 17:1025-31. [DOI: 10.1007/s00775-012-0916-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 06/14/2012] [Indexed: 10/27/2022]
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106
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Steiner D, Oostenbrink C, van Gunsteren WF. Calculation of the relative free energy of oxidation of azurin at pH 5 and pH 9. J Comput Chem 2012; 33:1467-77. [DOI: 10.1002/jcc.22972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 02/29/2012] [Indexed: 11/10/2022]
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107
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Abstract
Protein-mediated electron transfer is an essential event in many biochemical processes. Efficient electron transfer requires the reorganization energy of the redox event to be minimized, which is ensured by the presence of rigid donor and acceptor sites. Electron transfer copper sites are present in the ubiquitous cupredoxin fold, able to bind one or two copper ions. The low reorganization energy in these metal centers has been accounted for by assuming that the protein scaffold creates an entatic/rack-induced state, which gives rise to a rigid environment by means of a preformed metal chelating site. However, this notion is incompatible with the need for an exposed metal-binding site and protein-protein interactions enabling metallochaperone-mediated assembly of the copper site. Here we report an NMR study that reveals a high degree of structural heterogeneity in the metal-binding region of the nonmetallated Cu(A)-binding cupredoxin domain, arising from microsecond to second dynamics that are quenched upon metal binding. We also report similar dynamic features in apo-azurin, a paradigmatic blue copper protein, suggesting a general behavior. These findings reveal that the entatic/rack-induced state, governing the features of the metal center in the copper-loaded protein, does not require a preformed metal-binding site. Instead, metal binding is a major contributor to the rigidity of electron transfer copper centers. These results reconcile the seemingly contradictory requirements of a rigid, occluded center for electron transfer, and an accessible, dynamic site required for in vivo copper uptake.
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108
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Lancaster KM, Zaballa ME, Sproules S, Sundararajan M, DeBeer S, Richards JH, Vila AJ, Neese F, Gray HB. Outer-sphere contributions to the electronic structure of type zero copper proteins. J Am Chem Soc 2012; 134:8241-53. [PMID: 22563915 PMCID: PMC4794991 DOI: 10.1021/ja302190r] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Bioinorganic canon states that active-site thiolate coordination promotes rapid electron transfer (ET) to and from type 1 copper proteins. In recent work, we have found that copper ET sites in proteins also can be constructed without thiolate ligation (called "type zero" sites). Here we report multifrequency electron paramagnetic resonance (EPR), magnetic circular dichroism (MCD), and nuclear magnetic resonance (NMR) spectroscopic data together with density functional theory (DFT) and spectroscopy-oriented configuration interaction (SORCI) calculations for type zero Pseudomonas aeruginosa azurin variants. Wild-type (type 1) and type zero copper centers experience virtually identical ligand fields. Moreover, O-donor covalency is enhanced in type zero centers relative that in the C112D (type 2) protein. At the same time, N-donor covalency is reduced in a similar fashion to type 1 centers. QM/MM and SORCI calculations show that the electronic structures of type zero and type 2 are intimately linked to the orientation and coordination mode of the carboxylate ligand, which in turn is influenced by outer-sphere hydrogen bonding.
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Affiliation(s)
- Kyle M. Lancaster
- Beckman Institute, California Institute of Technology, Pasadena CA 91125, United States
- Department of Chemistry and Chemical Biology, Cornell University, Baker Laboratory, Ithaca, NY 14853, United States
| | - María-Eugenia Zaballa
- Instituto de Biología Molecular y Celular de Rosario, (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, (S2002LRK), Rosario, Argentina
| | - Stephen Sproules
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
- EPSRC National UK EPR Facility and Service, Photon Science Institute, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Mahesh Sundararajan
- Theoretical Chemistry Section, Chemistry Group, Bhabha Atomic Research Centre, Mumbai - 400 085, India
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Serena DeBeer
- Department of Chemistry and Chemical Biology, Cornell University, Baker Laboratory, Ithaca, NY 14853, United States
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - John H. Richards
- Beckman Institute, California Institute of Technology, Pasadena CA 91125, United States
| | - Alejandro J. Vila
- Instituto de Biología Molecular y Celular de Rosario, (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, (S2002LRK), Rosario, Argentina
| | - Frank Neese
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
- Institute for Physical and Theoretical Chemistry, University of Bonn, Wegelerstrasse 12, Bonn-53115, Germany
| | - Harry B. Gray
- Beckman Institute, California Institute of Technology, Pasadena CA 91125, United States
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109
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Biological applications of hybrid quantum mechanics/molecular mechanics calculation. J Biomed Biotechnol 2012; 2012:236157. [PMID: 22536015 PMCID: PMC3321478 DOI: 10.1155/2012/236157] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Revised: 10/27/2011] [Accepted: 11/11/2011] [Indexed: 12/17/2022] Open
Abstract
Since in most cases biological macromolecular systems including solvent water molecules are remarkably large, the computational costs of performing ab initio calculations for the entire structures are prohibitive. Accordingly, QM calculations that are jointed with MM calculations are crucial to evaluate the long-range electrostatic interactions, which significantly affect the electronic structures of biological macromolecules. A UNIX-shell-based interface program connecting the quantum mechanics (QMs) and molecular mechanics (MMs) calculation engines, GAMESS and AMBER, was developed in our lab. The system was applied to a metalloenzyme, azurin, and PU.1-DNA complex; thereby, the significance of the environmental effects on the electronic structures of the site of interest was elucidated. Subsequently, hybrid QM/MM molecular dynamics (MD) simulation using the calculation system was employed for investigation of mechanisms of hydrolysis (editing reaction) in leucyl-tRNA synthetase complexed with the misaminoacylated tRNA(Leu), and a novel mechanism of the enzymatic reaction was revealed. Thus, our interface program can play a critical role as a powerful tool for state-of-the-art sophisticated hybrid ab initio QM/MM MD simulations of large systems, such as biological macromolecules.
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110
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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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111
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Potapov A, Lancaster KM, Richards JH, Gray HB, Goldfarb D. Spin delocalization over type zero copper. Inorg Chem 2012; 51:4066-75. [PMID: 22432748 DOI: 10.1021/ic202336m] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hard-ligand, high-potential copper sites have been characterized in double mutants of Pseudomonas aeruginosa azurin (C112D/M121X (X = L, F, I)). These sites feature a small A(zz)(Cu) splitting in the EPR spectrum together with enhanced electron transfer activity. Due to these unique properties, these constructs have been called "type zero" copper sites. In contrast, the single mutant, C112D, features a large A(zz)(Cu) value characteristic of the typical type 2 Cu(II). In general, A(zz)(Cu) comprises contributions from Fermi contact, spin dipolar, and orbital dipolar terms. In order to understand the origin of the low A(zz)(Cu) value of type zero Cu(II), we explored in detail its degree of covalency, as manifested by spin delocalization over its ligands, which affects A(zz)(Cu) through the Fermi contact and spin dipolar contributions. This was achieved by the application of several complementary EPR hyperfine spectroscopic techniques at X- and W-band (∼9.5 and 95 GHz, respectively) frequencies to map the ligand hyperfine couplings. Our results show that spin delocalization over the ligands in type zero Cu(II) is different from that of type 2 Cu(II) in the single C112D mutant. The (14)N hyperfine couplings of the coordinated histidine nitrogens are smaller by about 25-40%, whereas that of the (13)C carboxylate of D112 is about 50% larger. From this comparison, we concluded that the spin delocalization of type zero copper over its ligands is not dramatically larger than in type 2 C112D. Therefore, the reduced A(zz)(Cu) value of type zero Cu(II) is largely attributable to an increased orbital dipolar contribution that is related to its larger g(zz) value, as a consequence of the distorted tetrahedral geometry. The increased spin delocalization over the D112 carboxylate in type zero mutants compared to type 2 C112D suggests that electron transfer paths involving this residue are enhanced.
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Affiliation(s)
- Alexey Potapov
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
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112
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Coordination chemistry of copper proteins: How nature handles a toxic cargo for essential function. J Inorg Biochem 2012; 107:129-43. [DOI: 10.1016/j.jinorgbio.2011.11.024] [Citation(s) in RCA: 232] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 10/25/2011] [Accepted: 11/15/2011] [Indexed: 01/16/2023]
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113
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Role of metal in folding and stability of copper proteins in vitro. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1823:1594-603. [PMID: 22306006 DOI: 10.1016/j.bbamcr.2012.01.013] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Revised: 01/09/2012] [Accepted: 01/18/2012] [Indexed: 01/04/2023]
Abstract
Metal coordination is required for function of many proteins. For biosynthesis of proteins coordinating a metal, the question arises if the metal binds before, during or after folding of the polypeptide. Moreover, when the metal is bound to the protein, how does its coordination affect biophysical properties such as stability and dynamics? Understanding how metals are utilized by proteins in cells on a molecular level requires accurate descriptions of the thermodynamic and kinetic parameters involved in protein-metal complexes. Copper is one of the essential transition metals found in the active sites of many key proteins. To avoid toxicity of free copper ions, living systems have developed elaborate copper-transport systems that involve dedicated proteins that facilitate efficient and specific delivery of copper to target proteins. This review describes in vitro and in silico biophysical work assessing the role of copper in folding and stability of copper-binding proteins. Examples of proteins discussed are: a blue-copper protein (Pseudomonas aeruginosa azurin), members of copper-transport systems (bacterial CopZ, human Atox1 and ATP7B domains) and multi-copper ferroxidases (yeast Fet3p and human ceruloplasmin). The consequences of interactions between copper proteins and platinum-complexes are also discussed. This article is part of a Special Issue entitled: Cell Biology of Metals.
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114
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Zhang Z, Wang L, Gao Y, Zhang J, Zhenirovskyy M, Alexov E. Predicting folding free energy changes upon single point mutations. ACTA ACUST UNITED AC 2012; 28:664-71. [PMID: 22238268 DOI: 10.1093/bioinformatics/bts005] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
MOTIVATION The folding free energy is an important characteristic of proteins stability and is directly related to protein's wild-type function. The changes of protein's stability due to naturally occurring mutations, missense mutations, are typically causing diseases. Single point mutations made in vitro are frequently used to assess the contribution of given amino acid to the stability of the protein. In both cases, it is desirable to predict the change of the folding free energy upon single point mutations in order to either provide insights of the molecular mechanism of the change or to design new experimental studies. RESULTS We report an approach that predicts the free energy change upon single point mutation by utilizing the 3D structure of the wild-type protein. It is based on variation of the molecular mechanics Generalized Born (MMGB) method, scaled with optimized parameters (sMMGB) and utilizing specific model of unfolded state. The corresponding mutations are built in silico and the predictions are tested against large dataset of 1109 mutations with experimentally measured changes of the folding free energy. Benchmarking resulted in root mean square deviation = 1.78 kcal/mol and slope of the linear regression fit between the experimental data and the calculations was 1.04. The sMMGB is compared with other leading methods of predicting folding free energy changes upon single mutations and results discussed with respect to various parameters. AVAILABILITY All the pdb files we used in this article can be downloaded from http://compbio.clemson.edu/downloadDir/mentaldisorders/sMMGB_pdb.rar. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zhe Zhang
- Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, SC 29634, USA
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115
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New SY, Marshall NM, Hor TSA, Xue F, Lu Y. Redox tuning of two biological copper centers through non-covalent interactions: same trend but different magnitude. Chem Commun (Camb) 2012; 48:4217-9. [DOI: 10.1039/c2cc30901g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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116
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Does azurin bind to the transactivation domain of p53? A Trp phosphorescence study. Biophys Chem 2011; 159:287-93. [DOI: 10.1016/j.bpc.2011.07.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Revised: 07/26/2011] [Accepted: 07/27/2011] [Indexed: 11/19/2022]
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117
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Santini S, Bizzarri AR, Cannistraro S. Modelling the interaction between the p53 DNA-binding domain and the p28 peptide fragment of Azurin. J Mol Recognit 2011; 24:1043-55. [DOI: 10.1002/jmr.1153] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Simona Santini
- Biophysics and Nanoscience Centre; CNISM; Facoltà di Scienze; Università della Tuscia; 01100; Viterbo; Italy
| | - Anna Rita Bizzarri
- Biophysics and Nanoscience Centre; CNISM; Facoltà di Scienze; Università della Tuscia; 01100; Viterbo; Italy
| | - Salvatore Cannistraro
- Biophysics and Nanoscience Centre; CNISM; Facoltà di Scienze; Università della Tuscia; 01100; Viterbo; Italy
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118
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Ullmann RT, Ullmann GM. Coupling of Protonation, Reduction, and Conformational Change in azurin from Pseudomonas aeruginosa Investigated with Free Energy Measures of Cooperativity. J Phys Chem B 2011; 115:10346-59. [DOI: 10.1021/jp204644h] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- R. Thomas Ullmann
- Structural Biology/Bioinformatics, University of Bayreuth, Universitätsstrasse 30, BGI, 95447 Bayreuth, Germany
| | - G. Matthias Ullmann
- Structural Biology/Bioinformatics, University of Bayreuth, Universitätsstrasse 30, BGI, 95447 Bayreuth, Germany
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119
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Lancaster KM, Farver O, Wherland S, Crane EJ, Richards JH, Pecht I, Gray HB. Electron transfer reactivity of type zero Pseudomonas aeruginosa azurin. J Am Chem Soc 2011; 133:4865-73. [PMID: 21405124 PMCID: PMC3607328 DOI: 10.1021/ja1093919] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Type zero copper is a hard-ligand analogue of the classical type 1 or blue site in copper proteins that function as electron transfer (ET) agents in photosynthesis and other biological processes. The EPR spectroscopic features of type zero Cu(II) are very similar to those of blue copper, although lacking the deep blue color, due to the absence of thiolate ligation. We have measured the rates of intramolecular ET from the pulse radiolytically generated C3-C26 disulfide radical anion to the Cu(II) in both type zero C112D/M121L and type 2 C112D Pseudomonas aeruginosa azurins in pH 7.0 aqueous solutions between 8 and 45 °C. We also have obtained rate/temperature (10-30 °C) profiles for ET reactions between these mutants and the wild-type azurin. Analysis of the rates and activation parameters for both intramolecular and intermolecular ET reactions indicates that the type zero copper reorganization energy falls in a range (0.9-1.1 eV) slightly above that for type 1 (0.7-0.8 eV), but substantially smaller than that for type 2 (>2 eV), consistent with XAS and EXAFS data that reveal minimal type zero site reorientation during redox cycling.
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Affiliation(s)
- Kyle M. Lancaster
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
| | - Ole Farver
- Institute of Analytical Chemistry, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Scot Wherland
- Department of Chemistry, Washington State University, Pullman, WA 99164-4630
| | - Edward J. Crane
- Department of Chemistry, Pomona College, Claremont CA 91711-6338
| | - John H. Richards
- Beckman Institute, California Institute of Technology, Pasadena CA 91125
| | - Israel Pecht
- Department of Immunology, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Harry B. Gray
- Beckman Institute, California Institute of Technology, Pasadena CA 91125
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120
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Sokolová L, Williamson H, Sýkora J, Hof M, Gray HB, Brutschy B, Vlcek A. Mass spectrometric characterization of oligomers in Pseudomonas aeruginosa azurin solutions. J Phys Chem B 2011; 115:4790-800. [PMID: 21452827 DOI: 10.1021/jp110460k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have employed laser-induced liquid bead ion desorption mass spectroscopy (LILBID MS) to study the solution behavior of Pseudomonas aeruginosa azurin as well as two mutants and corresponding Re-labeled derivatives containing a Re(CO)(3)(4,7-dimethyl-1,10-phenanthroline)(+) chromophore appended to a surface histidine. LILBID spectra show broad oligomer distributions whose particular patterns depend on the solution composition (pure H(2)O, 20-30 mM NaCl, 20 and 50 mM NaP(i) or NH(4)P(i) at pH = 7). The distribution maximum shifts to smaller oligomers upon decreasing the azurin concentration and increasing the buffer concentration. Oligomerization is less extensive for native azurin than its mutants. The oligomerization propensities of unlabeled and Re-labeled proteins are generally comparable, and only Re126 shows some preference for the dimer that persists even in highly diluted solutions. Peak shifts to higher masses and broadening in 20-50 mM NaP(i) confirm strong azurin association with buffer ions and solvation. We have found that LILBID MS reveals the solution behavior of weakly bound nonspecific protein oligomers, clearly distinguishing individual components of the oligomer distribution. Independently, average data on oligomerization and the dependence on solution composition were obtained by time-resolved anisotropy of the Re-label photoluminescence that confirmed relatively long rotation correlation times, 6-30 ns, depending on Re-azurin and solution composition. Labeling proteins with Re-chromophores that have long-lived phosphorescence extends the time scale of anisotropy measurements to hundreds of nanoseconds, thereby opening the way for investigations of large oligomers with long rotation times.
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Affiliation(s)
- Lucie Sokolová
- Institute of Physical and Theoretical Chemistry, Goethe University, Frankfurt am Main, Germany
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121
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Alagaratnam S, Meeuwenoord NJ, Navarro JA, Hervás M, De la Rosa MA, Hoffmann M, Einsle O, Ubbink M, Canters GW. Probing the reactivity of different forms of azurin by flavin photoreduction. FEBS J 2011; 278:1506-21. [DOI: 10.1111/j.1742-4658.2011.08067.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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122
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Choi M, Davidson VL. Cupredoxins--a study of how proteins may evolve to use metals for bioenergetic processes. Metallomics 2011; 3:140-51. [PMID: 21258692 DOI: 10.1039/c0mt00061b] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cupredoxins are small proteins that contain type I copper centers, which are ubiquitous in nature. They function as electron transfer shuttles between proteins. This review of the structure and properties of native cupredoxins, and those modified by site-directed mutagenesis, illustrates how these proteins may have evolved to specifically bind copper, develop recognition sites for specific redox partners, tune redox potential for a particular function, and allow for efficient electron transfer through the protein matrix. This is relevant to the general understanding of the roles of metals in energy metabolism, respiration and photosynthesis.
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Affiliation(s)
- Moonsung Choi
- Department of Biochemistry, University of Mississippi Medical Center, 2500 N. State St., Jackson, MS 39216-4505, USA
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123
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Lancaster KM, Sproules S, Palmer JH, Richards JH, Gray HB. Outer-sphere effects on reduction potentials of copper sites in proteins: the curious case of high potential type 2 C112D/M121E Pseudomonas aeruginosa azurin. J Am Chem Soc 2011; 132:14590-5. [PMID: 20879734 DOI: 10.1021/ja105731x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Redox and spectroscopic (electronic absorption, multifrequency electron paramagnetic resonance (EPR), and X-ray absorption) properties together with X-ray crystal structures are reported for the type 2 Cu(II) C112D/M121E variant of Pseudomonas aeruginosa azurin. The results suggest that Cu(II) is constrained from interaction with the proximal glutamate; this structural frustration implies a "rack" mechanism for the 290 mV (vs NHE) reduction potential measured at neutral pH. At high pH (∼9), hydrogen bonding in the outer coordination sphere is perturbed to allow axial glutamate ligation to Cu(II), with a decrease in potential to 119 mV. These results highlight the role played by outer-sphere interactions, and the structural constraints they impose, in determining the redox behavior of transition metal protein cofactors.
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Affiliation(s)
- Kyle M Lancaster
- Beckman Institute, California Institute of Technology, Pasadena, California 91125, USA.
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124
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Bizzarri AR. Steered Molecular Dynamics Simulations of the Electron Transfer Complex between Azurin and Cytochrome c551. J Phys Chem B 2011; 115:1211-9. [DOI: 10.1021/jp107933k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Anna Rita Bizzarri
- Biophysics and Nanoscience Centre, CNISM, Facolta’ di Scienze, Università della Tuscia, Largo dell’Università, I-01100 Viterbo, Italy
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125
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Waldeck DH, Khoshtariya DE. Fundamental Studies of Long- and Short-Range Electron Exchange Mechanisms between Electrodes and Proteins. MODERN ASPECTS OF ELECTROCHEMISTRY 2011. [DOI: 10.1007/978-1-4614-0347-0_2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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126
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Biological Outer-Sphere Coordination. MOLECULAR ELECTRONIC STRUCTURES OF TRANSITION METAL COMPLEXES I 2011. [DOI: 10.1007/430_2011_49] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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127
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Ullmann RT, Ullmann GM. A Generalized Free Energy Perturbation Theory Accounting for End States with Differing Configuration Space Volume. J Phys Chem B 2010; 115:507-21. [DOI: 10.1021/jp1093838] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- R. Thomas Ullmann
- Structural Biology/Bioinformatics, University of Bayreuth, Universitätsstrasse 30, BGI, 95447 Bayreuth, Germany
| | - G. Matthias Ullmann
- Structural Biology/Bioinformatics, University of Bayreuth, Universitätsstrasse 30, BGI, 95447 Bayreuth, Germany
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128
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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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129
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Li C, Sato K, Monari S, Salard I, Sola M, Banfield MJ, Dennison C. Metal-Binding Loop Length Is a Determinant of the pKa of a Histidine Ligand at a Type 1 Copper Site. Inorg Chem 2010; 50:482-8. [DOI: 10.1021/ic101413e] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Chan Li
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Katsuko Sato
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Stefano Monari
- Department of Chemistry, University of Modena and Reggio Emilia, Via Campi 183, 41125 Modena, Italy
| | - Isabelle Salard
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Marco Sola
- Department of Chemistry, University of Modena and Reggio Emilia, Via Campi 183, 41125 Modena, Italy
| | - Mark J. Banfield
- Department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH, U.K
| | - Christopher Dennison
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
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130
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Clark KM, Yu Y, Marshall NM, Sieracki NA, Nilges MJ, Blackburn NJ, van der Donk WA, Lu Y. Transforming a blue copper into a red copper protein: engineering cysteine and homocysteine into the axial position of azurin using site-directed mutagenesis and expressed protein ligation. J Am Chem Soc 2010; 132:10093-101. [PMID: 20608676 DOI: 10.1021/ja102632p] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Interactions of the axial ligand with its blue copper center are known to be important in tuning spectroscopic and redox properties of cupredoxins. While conversion of the blue copper center with a weak axial ligand to a green copper center containing a medium strength axial ligand has been demonstrated in cupredoxins, converting the blue copper center to a red copper center with a strong axial ligand has not been reported. Here we show that replacing Met121 in azurin from Pseudomonas aeruginosa with Cys caused an increased ratio (R(L)) of absorption at 447 nm over that at 621 nm. Whereas no axial Cu-S(Cys121) interaction in Met121Cys was detectable by extended X-ray absorption fine structure (EXAFS) spectroscopy at pH 5, similar to what was observed in native azurin with Met121 as the axial ligand, the Cu-S(Cys121) interaction at 2.74 A is clearly visible at higher pH. Despite the higher R(L) and stronger axial Cys121 interaction with Cu(II) ion, the Met121Cys variant remains largely a type 1 copper protein at low pH (with hyperfine coupling constant A( parallel) = 54 x 10(-4) cm(-1) at pH 4 and 5), or distorted type 1 or green copper protein at high pH (A(parallel) = 87 x 10(-4) cm(-1) at pH 8 and 9), attributable to the relatively long distance between the axial ligand and copper and the constraint placed by the protein scaffold. To shorten the distance between axial ligand and copper, we replaced Met121 with a nonproteinogenic amino acid homocysteine that contains an extra methylene group, resulting in a variant whose spectra (R(L)= 1.5, and A(parallel) = 180 x 10(-4) cm(-1)) and Cu-S(Cys) distance (2.22 A) are very similar to those of the red copper protein nitrosocyanin. Replacing Met121 with Cys or homocysteine resulted in lowering of the reduction potential from 222 mV in the native azurin to 95 +/- 3 mV for Met121Cys azurin and 113 +/- 6 mV for Met121Hcy azurin at pH 7. The results strongly support the "coupled distortion" model that helps explain axial ligand tuning of spectroscopic properties in cupredoxins, and demonstrate the power of using unnatural amino acids to address critical chemical biological questions.
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Affiliation(s)
- Kevin M Clark
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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131
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Patil AV, Davis JJ. Visualizing and Tuning Thermodynamic Dispersion in Metalloprotein Monolayers. J Am Chem Soc 2010; 132:16938-44. [DOI: 10.1021/ja1065448] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Amol Virendra Patil
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Jason John Davis
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
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132
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Hagiwara Y, Tateno M. Recent advances in jointed quantum mechanics and molecular mechanics calculations of biological macromolecules: schemes and applications coupled to ab initio calculations. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2010; 22:413101. [PMID: 21386583 DOI: 10.1088/0953-8984/22/41/413101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We review the recent research on the functional mechanisms of biological macromolecules using theoretical methodologies coupled to ab initio quantum mechanical (QM) treatments of reaction centers in proteins and nucleic acids. Since in most cases such biological molecules are large, the computational costs of performing ab initio calculations for the entire structures are prohibitive. Instead, simulations that are jointed with molecular mechanics (MM) calculations are crucial to evaluate the long-range electrostatic interactions, which significantly affect the electronic structures of biological macromolecules. Thus, we focus our attention on the methodologies/schemes and applications of jointed QM/MM calculations, and discuss the critical issues to be elucidated in biological macromolecular systems.
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Affiliation(s)
- Yohsuke Hagiwara
- Graduate School of Pure and Applied Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba Science City, Ibaraki 305-8571, Japan
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133
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Structural characteristics of the hydrophobic patch of azurin and its interaction with p53: a site-directed spin labeling study. SCIENCE CHINA-LIFE SCIENCES 2010; 53:1181-8. [PMID: 20953940 DOI: 10.1007/s11427-010-4069-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Accepted: 05/25/2010] [Indexed: 10/18/2022]
Abstract
Site-directed spin labeling (SDSL) is a powerful tool for monitoring protein structure, dynamics and conformational changes. In this study, the domain-specific properties of azurin and its interaction with p53 were studied using this technique. Mutations of six residues, that are located in the hydrophobic patch of azurin, were prepared and spin labeled. Spectra of the six azurin mutants in solution showed that spin labeled residues 45 and 63 are in a very restricted environment, residues 59 and 65 are in a spacious environment and have free movement, and residues 49 and 51 are located in a relatively closed pocket. Polarity experiments confirmed these results. The changes observed in the spectra of spin labeled azurin upon interaction with p53 indicate that the hydrophobic patch is involved in this interaction. Our results provide valuable insight into the topographic structure of the hydrophobic domain of azurin, as well as direct evidence of its interaction with p53 in solution via the hydrophobic patch. Cytotoxicity studies of azurin mutants showed that residues along the hydrophobic patch are important for its cytotoxicity.
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134
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Cioni P, Gabellieri E. Protein dynamics and pressure: what can high pressure tell us about protein structural flexibility? BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:934-41. [PMID: 20934540 DOI: 10.1016/j.bbapap.2010.09.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Revised: 09/22/2010] [Accepted: 09/30/2010] [Indexed: 11/25/2022]
Abstract
After a brief overview of NMR and X-ray crystallography studies on protein flexibility under pressure, we summarize the effects of hydrostatic pressure on the native fold of azurin from Pseudomonas aeruginosa as inferred from the variation of the intrinsic phosphorescence lifetime and the acrylamide bimolecular quenching rate constants of the buried Trp residue. The pressure/temperature response of the globular fold and modulation of its dynamical structure is analyzed both in terms of a reduction of internal cavities and of the hydration of the polypeptide. The study of the effect of two single point cavity forming mutations, F110S and I7S, on the unfolding volume change (ΔV(0)) of azurin and on the internal dynamics of the protein fold under pressure demonstrate that the creation of an internal cavity will enhance the plasticity and lower the stability of the globular structure. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
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Affiliation(s)
- Patrizia Cioni
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Area della Ricerca di Pisa, Via Moruzzi 1, 56100-Pisa, Italy.
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135
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Salverda J, Patil A, Mizzon G, Kuznetsova S, Zauner G, Akkilic N, Canters G, Davis J, Heering H, Aartsma T. Fluorescent Cyclic Voltammetry of Immobilized Azurin: Direct Observation of Thermodynamic and Kinetic Heterogeneity. Angew Chem Int Ed Engl 2010; 49:5776-9. [DOI: 10.1002/anie.201001298] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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136
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Salverda J, Patil A, Mizzon G, Kuznetsova S, Zauner G, Akkilic N, Canters G, Davis J, Heering H, Aartsma T. Fluorescent Cyclic Voltammetry of Immobilized Azurin: Direct Observation of Thermodynamic and Kinetic Heterogeneity. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201001298] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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137
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Shafaat HS, Leigh BS, Tauber MJ, Kim JE. Spectroscopic Comparison of Photogenerated Tryptophan Radicals in Azurin: Effects of Local Environment and Structure. J Am Chem Soc 2010; 132:9030-9. [DOI: 10.1021/ja101322g] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hannah S. Shafaat
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093
| | - Brian S. Leigh
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093
| | - Michael J. Tauber
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093
| | - Judy E. Kim
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093
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138
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Rajapandian V, Hakkim V, Subramanian V. Molecular Dynamics Studies on Native, Loop-Contracted, and Metal Ion-Substituted Azurins. J Phys Chem B 2010; 114:8474-86. [DOI: 10.1021/jp911301v] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- V. Rajapandian
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
| | - V. Hakkim
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
| | - V. Subramanian
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
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139
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Najmudin S, Pauleta SR, Moura I, Romão MJ. The 1.4 A resolution structure of Paracoccus pantotrophus pseudoazurin. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:627-35. [PMID: 20516588 PMCID: PMC2882758 DOI: 10.1107/s1744309110013989] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2010] [Accepted: 04/15/2010] [Indexed: 11/10/2022]
Abstract
Pseudoazurins are small type 1 copper proteins that are involved in the flow of electrons between various electron donors and acceptors in the bacterial periplasm, mostly under denitrifying conditions. The previously determined structure of Paracoccus pantotrophus pseudoazurin in the oxidized form was improved to a nominal resolution of 1.4 A, with R and R(free) values of 0.188 and 0.206, respectively. This high-resolution structure makes it possible to analyze the interactions between the monomers and the solvent structure in detail. Analysis of the high-resolution structure revealed the structural regions that are responsible for monomer-monomer recognition during dimer formation and for protein-protein interaction and that are important for partner recognition. The pseudoazurin structure was compared with other structures of various type 1 copper proteins and these were grouped into families according to similarities in their secondary structure; this may be useful in the annotation of copper proteins in newly sequenced genomes and in the identification of novel copper proteins.
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Affiliation(s)
- Shabir Najmudin
- REQUIMTE, Centro de Química Fina e Biotecnologia, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Sofia R. Pauleta
- REQUIMTE, Centro de Química Fina e Biotecnologia, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Isabel Moura
- REQUIMTE, Centro de Química Fina e Biotecnologia, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Maria J. Romão
- REQUIMTE, Centro de Química Fina e Biotecnologia, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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140
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Bizzarri AR, Di Agostino S, Andolfi L, Cannistraro S. A combined atomic force microscopy imaging and docking study to investigate the complex between p53 DNA binding domain and Azurin. J Mol Recognit 2010; 22:506-15. [PMID: 19642109 DOI: 10.1002/jmr.975] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The tumor suppressor p53 interacts with the redox copper protein Azurin (AZ) forming a complex which is of some relevance in biomedicine and cancer therapy. To obtain information on the spatial organization of this complex when it is immobilized on a substrate, we have used tapping mode-atomic force microscopy (TM-AFM) imaging combined with computational docking. The vertical dimension and the bearing volume of the DNA binding domain (DBD) of p53, anchored to functionalized gold substrate through exposed lysine residues, alone and after deposing AZ, have been measured by TM-AFM. By a computational docking approach, a three-dimensional model for the DBD of p53, before and after addition of AZ, have been predicted. Then we have calculated the possible arrangements of these biomolecular systems on gold substrate by finding a good agreement with the related experimental distribution of the height. The potentiality of the approach combining TM-AFM imaging and computational docking for the study of biomolecular complexes immobilized on substrates is briefly discussed.
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Affiliation(s)
- Anna Rita Bizzarri
- Biophysics & Nanoscience Centre, CNISM, Facolta' di Scienze, Università della Tuscia, I-01100 Viterbo, Italy.
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141
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Potapov A, Pecht I, Goldfarb D. Resolving ligand hyperfine couplings of type 1 and 2 Cu(ii) in ascorbate oxidase by high field pulse EPRcorrelation spectroscopy. Phys Chem Chem Phys 2010; 12:62-5. [DOI: 10.1039/b919069d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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142
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Sottini S, Gast P, Blok A, Canters GW, Cavazzini D, Rossi GL, Groenen EJJ. A Proton ENDOR Study of Azurin. APPLIED MAGNETIC RESONANCE 2010; 37:219-227. [PMID: 19960067 PMCID: PMC2784076 DOI: 10.1007/s00723-009-0048-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Revised: 06/23/2009] [Indexed: 05/15/2023]
Abstract
As part of our ongoing project that aims at the optimum characterization of the electronic structure of the blue-copper site of azurin from Pseudomonas aeruginosa, we present the complete hyperfine tensors of the protons bound to the Cbeta atom of the copper-bound cysteine 112. These tensors have been obtained from a 95 GHz pulsed electron-nuclear double resonance study of a single crystal of the protein.
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Affiliation(s)
- Silvia Sottini
- Huygens Laboratory, Leiden University, P.O. Box 9504, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands
| | - Peter Gast
- Huygens Laboratory, Leiden University, P.O. Box 9504, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands
| | - Anneloes Blok
- Gorlaeus Laboratories, Metallo Protein Group, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Gerard W. Canters
- Gorlaeus Laboratories, Metallo Protein Group, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Davide Cavazzini
- Department of Biochemistry and Molecular Biology, University of Parma, Parco Area delle Scienze 23 A, 43100 Parma, Italy
| | - Gian Luigi Rossi
- Department of Biochemistry and Molecular Biology, University of Parma, Parco Area delle Scienze 23 A, 43100 Parma, Italy
| | - Edgar J. J. Groenen
- Huygens Laboratory, Leiden University, P.O. Box 9504, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands
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143
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Frank P, Benfatto M, Hedman B, Hodgson KO. The XAS model of dissolved Cu(II) and its significance to biological electron transfer. ACTA ACUST UNITED AC 2009. [DOI: 10.1088/1742-6596/190/1/012059] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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144
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Abstract
Electron transfers in photosynthesis and respiration commonly occur between metal-containing cofactors that are separated by large molecular distances. Employing laser flash-quench triggering methods, we have shown that 20-Å, coupling-limited Fe(II) to Ru(III) and Cu(I) to Ru(III) electron tunneling in Ru-modified cytochromes and blue copper proteins can occur on the microsecond timescale both in solutions and crystals. Redox equivalents can be transferred even longer distances by multistep tunneling, often called hopping, through intervening amino acid side chains. Our work has established that 20-Å hole hopping through an intervening tryptophan is two orders of magnitude faster than single-step electron tunneling in a Re-modified blue copper protein.
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Affiliation(s)
- Harry B Gray
- Beckman Institute, California Institute of Technology, Pasadena, California 91125
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145
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Koteishi H, Nojiri M, Nakagami T, Yamaguchi K, Suzuki S. Cytochromec551Is a Mediator of Electron Transfer between Copper-Containing Nitrite Reductase and Azurin in a Denitrifying Bacterium,Achromobacter xylosoxidans. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2009. [DOI: 10.1246/bcsj.82.1003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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146
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Rajapandian V, Raman SS, Hakkim V, Parthasarathi R, Subramanian V. Molecular mechanics and molecular dynamics study on azurin using extensible and systematic force field (ESFF). ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.04.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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147
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Taranta M, Bizzarri AR, Cannistraro S. Modeling the interaction between the N-terminal domain of the tumor suppressor p53 and azurin. J Mol Recognit 2009; 22:215-22. [PMID: 19140135 DOI: 10.1002/jmr.934] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
It is known that the half life of the tumor suppressor p53 can be increased by the interaction with the bacterial protein azurin, resulting in an enhanced anti-tumoral activity. The understanding of the molecular mechanisms on the basis of this phenomenon can open the way to new anti-cancer strategies. Some experimental works have given evidence of an interaction between p53 and azurin (AZ); however the binding regions of the proteins are still unknown. Recently, fluorescence studies have shown that p53 partakes in the binding with the bacterial protein by its N-terminal (NT) domain. Here we have used a computational method to get insight into this interacting mode. The model that we propose for the best complex between AZ and p53 has been obtained from a rigid-body docking, coupled with a molecular dynamics (MD) simulation, a free energy calculation, and validated by mutagenesis analysis. We have found a high degree of geometric fit between the two proteins that are kept together by several hydrophobic interactions and numerous hydrogen bonds. Interestingly, it has emerged that AZ binds essentially to the helices H(I) and H(III) of the p53 NT domain, which are also interacting regions for the foremost inhibitor of p53, MDM2.
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Affiliation(s)
- Monia Taranta
- Biophysics and Nanoscience Centre, CNISM, Facoltà di Scienze, Università della Tuscia, Largo dell'Università 01100, Viterbo, Italy
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148
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Rajapandian V, Hakkim V, Subramanian V. ONIOM Calculation on Azurin: Effect of Metal Ion Substitutions. J Phys Chem A 2009; 113:8615-25. [DOI: 10.1021/jp900451f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- V. Rajapandian
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
| | - V. Hakkim
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
| | - V. Subramanian
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
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149
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Abstract
The C-terminal copper-binding loop in the beta-barrel fold of the cupredoxin azurin has been replaced with a range of sequences containing alanine, glycine, and valine residues to assess the importance of amino acid composition and the length of this region. The introduction of 2 and 4 alanines between the coordinating Cys, His, and Met results in loop structures matching those in naturally occurring proteins with the same loop lengths. A loop with 4 alanines between the Cys and His and 3 between the His and Met ligands has a structure identical to that of the WT protein, whose loop is the same length. Loop structure is dictated by length and not sequence allowing the properties of the main surface patch for interactions with partners, to which the loop is a major contributor, to be optimized. Loops with 2 amino acids between the ligands using glycine, alanine, and valine residues have been compared. An empirical relationship is found between copper site protection by the loop and reduction potential. A loop adorned with 4 methyl groups is sufficient to protect the copper ion, enabling most sequences to adequately perform this task. The mutant with 3 alanine residues between the ligands forms a strand-swapped dimer in the crystal structure, an arrangement that has not, to our knowledge, been seen previously for this family of proteins. Cupredoxins function as redox shuttles and are required to be monomeric; therefore, none have evolved with a metal-binding loop of this length.
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150
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Active site loop dictates the thermodynamics of reduction and ligand protonation in cupredoxins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:995-1000. [PMID: 19230853 DOI: 10.1016/j.bbapap.2009.02.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2008] [Revised: 01/28/2009] [Accepted: 02/03/2009] [Indexed: 11/21/2022]
Abstract
The thermodynamics of reduction and His ligand protonation have been determined for a range of loop-contraction variants of the electron transferring type 1 copper protein azurin (AZ). For AZPC, in which the native C-terminal loop containing the Cys, His and Met ligands has been replaced with the shorter sequence from plastocyanin (PC) and AZAMI, in which the even shorter amicyanin (AMI) loop has been inserted, the thermodynamics of reduction match those of the protein whose loop has been introduced which are different to the values for AZ. The enthalpic contribution to His ligand protonation, which is not observed in AZ, is similar in AZAMI and AMI. The thermodynamics of this process in AZPC are more dissimilar to those for PC. In the case of AZAMI-F, a variant possessing the (non natural) minimal loop that can bind a type 1 copper site, the reduction thermodynamics are intermediate between those of AZPC and AZAMI, whilst the thermodynamic data for His ligand protonation are very similar to those for AMI. The results for AZAMI and AZPC are primarily due to protein based enthalpic effects related to the interaction of the metal with permanent protein dipoles from the loop, and to the decreased loop length which favors His ligand protonation in the cuprous proteins. Entropic factors related to loop flexibility have little influence because of constraints imposed by metal coordination and the fact that the introduced loops pack well against the AZ scaffold. Thus, the host scaffold in general plays a minor thermodynamic role in both processes, although for AZAMI-F differences in the first and second coordination spheres influence the thermodynamics of reduction.
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