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Silveira CM, Zuccarello L, Barbosa C, Caserta G, Zebger I, Hildebrandt P, Todorovic S. Molecular Details on Multiple Cofactor Containing Redox Metalloproteins Revealed by Infrared and Resonance Raman Spectroscopies. Molecules 2021; 26:4852. [PMID: 34443440 PMCID: PMC8398457 DOI: 10.3390/molecules26164852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/06/2021] [Accepted: 08/07/2021] [Indexed: 12/12/2022] Open
Abstract
Vibrational spectroscopy and in particular, resonance Raman (RR) spectroscopy, can provide molecular details on metalloproteins containing multiple cofactors, which are often challenging for other spectroscopies. Due to distinct spectroscopic fingerprints, RR spectroscopy has a unique capacity to monitor simultaneously and independently different metal cofactors that can have particular roles in metalloproteins. These include e.g., (i) different types of hemes, for instance hemes c, a and a3 in caa3-type oxygen reductases, (ii) distinct spin populations, such as electron transfer (ET) low-spin (LS) and catalytic high-spin (HS) hemes in nitrite reductases, (iii) different types of Fe-S clusters, such as 3Fe-4S and 4Fe-4S centers in di-cluster ferredoxins, and (iv) bi-metallic center and ET Fe-S clusters in hydrogenases. IR spectroscopy can provide unmatched molecular details on specific enzymes like hydrogenases that possess catalytic centers coordinated by CO and CN- ligands, which exhibit spectrally well separated IR bands. This article reviews the work on metalloproteins for which vibrational spectroscopy has ensured advances in understanding structural and mechanistic properties, including multiple heme-containing proteins, such as nitrite reductases that house a notable total of 28 hemes in a functional unit, respiratory chain complexes, and hydrogenases that carry out the most fundamental functions in cells.
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Affiliation(s)
- Célia M. Silveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (C.M.S.); (L.Z.); (C.B.)
| | - Lidia Zuccarello
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (C.M.S.); (L.Z.); (C.B.)
| | - Catarina Barbosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (C.M.S.); (L.Z.); (C.B.)
| | - Giorgio Caserta
- Institut fur Chemie, Sekr. PC14, Technische Universitat Berlin, Strasse des 17. Juni 135, D-10623 Berlin, Germany; (G.C.); (I.Z.); (P.H.)
| | - Ingo Zebger
- Institut fur Chemie, Sekr. PC14, Technische Universitat Berlin, Strasse des 17. Juni 135, D-10623 Berlin, Germany; (G.C.); (I.Z.); (P.H.)
| | - Peter Hildebrandt
- Institut fur Chemie, Sekr. PC14, Technische Universitat Berlin, Strasse des 17. Juni 135, D-10623 Berlin, Germany; (G.C.); (I.Z.); (P.H.)
| | - Smilja Todorovic
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (C.M.S.); (L.Z.); (C.B.)
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2
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The Role of Metal Ions in the Electron Transport through Azurin-Based Junctions. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11093732] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We studied the coherent electron transport through metal–protein–metal junctions based on a blue copper azurin, in which the copper ion was replaced by three different metal ions (Co, Ni and Zn). Our results show that neither the protein structure nor the transmission at the Fermi level change significantly upon metal replacement. The discrepancy with previous experimental observations suggests that the transport mechanism taking place in these types of junctions is probably not fully coherent.
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3
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Manesis AC, Musselman BW, Keegan BC, Shearer J, Lehnert N, Shafaat HS. A Biochemical Nickel(I) State Supports Nucleophilic Alkyl Addition: A Roadmap for Methyl Reactivity in Acetyl Coenzyme A Synthase. Inorg Chem 2019; 58:8969-8982. [PMID: 30788970 PMCID: PMC6635881 DOI: 10.1021/acs.inorgchem.8b03546] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
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Nickel-containing
enzymes such as methyl coenzyme M reductase (MCR) and carbon monoxide
dehydrogenase/acetyl coenzyme A synthase (CODH/ACS) play a critical
role in global energy conversion reactions, with significant contributions
to carbon-centered processes. These enzymes are implied to cycle through
a series of nickel-based organometallic intermediates during catalysis,
though identification of these intermediates remains challenging.
In this work, we have developed and characterized a nickel-containing
metalloprotein that models the methyl-bound organometallic intermediates
proposed in the native enzymes. Using a nickel(I)-substituted azurin
mutant, we demonstrate that alkyl binding occurs via nucleophilic
addition of methyl iodide as a methyl donor. The paramagnetic NiIII-CH3 species initially generated can be rapidly
reduced to a high-spin NiII-CH3 species in the
presence of exogenous reducing agent, following a reaction sequence
analogous to that proposed for ACS. These two distinct bioorganometallic
species have been characterized by optical, EPR, XAS, and MCD spectroscopy,
and the overall mechanism describing methyl reactivity with nickel
azurin has been quantitatively modeled using global kinetic simulations.
A comparison between the nickel azurin protein system and existing
ACS model compounds is presented. NiIII-CH3 Az
is only the second example of two-electron addition of methyl iodide
to a NiI center to give an isolable species and the first
to be formed in a biologically relevant system. These results highlight
the divergent reactivity of nickel across the two intermediates, with
implications for likely reaction mechanisms and catalytically relevant
states in the native ACS enzyme. A bioorganometallic model
for acetyl coenzyme A synthase has been developed. This model protein
is able to bind a cationic methyl group via direct addition to the
nickel(I) center. The resultant nickel(III)-methyl species has been
characterized via optical and electron paramagnetic resonance spectroscopy,
and the reduced nickel(II)-methyl state has been characterized using
magnetic circular dichroism and X-ray spectroscopy. Implications for
further reactivity with CO are gleaned from electronic structure analysis
of the nickel-methyl species.
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Affiliation(s)
- Anastasia C Manesis
- Department of Chemistry and Biochemistry , The Ohio State University , 100 W. 18th Avenue , Columbus , Ohio 43210 , United States
| | - Bradley W Musselman
- Department of Chemistry , University of Michigan , 930 N. University Avenue , Ann Arbor , Michigan 48109 , United States
| | - Brenna C Keegan
- Department of Chemistry , Trinity University , One Trinity Place , San Antonio , Texas 78212 , United States
| | - Jason Shearer
- Department of Chemistry , Trinity University , One Trinity Place , San Antonio , Texas 78212 , United States
| | - Nicolai Lehnert
- Department of Chemistry , University of Michigan , 930 N. University Avenue , Ann Arbor , Michigan 48109 , United States
| | - Hannah S Shafaat
- Department of Chemistry and Biochemistry , The Ohio State University , 100 W. 18th Avenue , Columbus , Ohio 43210 , United States
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4
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Kradolfer S, Lipiec E, Baldacchini C, Bizzarri AR, Cannistraro S, Zenobi R. Vibrational Changes Induced by Electron Transfer in Surface Bound Azurin Metalloprotein Studied by Tip-Enhanced Raman Spectroscopy and Scanning Tunneling Microscopy. ACS NANO 2017; 11:12824-12831. [PMID: 29202236 DOI: 10.1021/acsnano.7b07768] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The copper protein azurin, due to the peculiar coupling of its optical and vibronic properties with electron transfer (ET) and its biorecognition capabilities, is a very promising candidate for bioelectronic, bio-optoelectronic and biosensor applications. However, a complete understanding of the fundamental processes relating azurin ET and its optical and vibronic characteristics with the charge transport mechanisms occurring in proteins bound to a conductive surface, the typical scenario for a biosensor or bioelectronic component, is still lacking. We studied azurin proteins bound to a gold electrode surface by scanning tunneling microscopy combined with tip-enhanced Raman spectroscopy (STM-TERS). Robust TER spectra were obtained, and the protein's vibronic response under optical excitation in resonance with its ligand-to-metal charge transfer band was found to be affected by the tunneling parameters, indicating a direct involvement of the active site vibrations in the electron transport process.
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Affiliation(s)
- Stefan Kradolfer
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich , 8093 Zurich, Switzerland
| | - Ewelina Lipiec
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich , 8093 Zurich, Switzerland
- The Henryk Niewodniczanski Institute of Nuclear Physics, Polish Academy of Sciences 31-342 Krakow, Poland
| | - Chiara Baldacchini
- Biophysics and Nanoscience Centre, DEB, Università della Tuscia , I-01100 Viterbo, Italy
- Institute of Agro-Environmental and Forest Biology, CNR , I-05010 Porano, Italy
| | - Anna Rita Bizzarri
- Biophysics and Nanoscience Centre, DEB, Università della Tuscia , I-01100 Viterbo, Italy
| | - Salvatore Cannistraro
- Biophysics and Nanoscience Centre, DEB, Università della Tuscia , I-01100 Viterbo, Italy
| | - Renato Zenobi
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich , 8093 Zurich, Switzerland
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5
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Design of a single protein that spans the entire 2-V range of physiological redox potentials. Proc Natl Acad Sci U S A 2015; 113:262-7. [PMID: 26631748 DOI: 10.1073/pnas.1515897112] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The reduction potential (E°') is a critical parameter in determining the efficiency of most biological and chemical reactions. Biology employs three classes of metalloproteins to cover the majority of the 2-V range of physiological E°'s. An ultimate test of our understanding of E°' is to find out the minimal number of proteins and their variants that can cover this entire range and the structural features responsible for the extreme E°'. We report herein the design of the protein azurin to cover a range from +970 mV to -954 mV vs. standard hydrogen electrode (SHE) by mutating only five residues and using two metal ions. Spectroscopic methods have revealed geometric parameters important for the high E°'. The knowledge gained and the resulting water-soluble redox agents with predictable E°'s, in the same scaffold with the same surface properties, will find wide applications in chemical, biochemical, biophysical, and biotechnological fields.
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6
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Manesis AC, Shafaat HS. Electrochemical, Spectroscopic, and Density Functional Theory Characterization of Redox Activity in Nickel-Substituted Azurin: A Model for Acetyl-CoA Synthase. Inorg Chem 2015; 54:7959-67. [PMID: 26234790 DOI: 10.1021/acs.inorgchem.5b01103] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Nickel-containing enzymes are key players in global hydrogen, carbon dioxide, and methane cycles. Many of these enzymes rely on Ni(I) oxidation states in critical catalytic intermediates. However, due to the highly reactive nature of these species, their isolation within metalloenzymes has often proved elusive. In this report, we describe and characterize a model biological Ni(I) species that has been generated within the electron transfer protein, azurin. Replacement of the native copper cofactor with nickel is shown to preserve the redox activity of the protein. The Ni(II/I) couple is observed at -590 mV versus NHE, with an interfacial electron transfer rate of 70 s(-1). Chemical reduction of Ni(II)Az generates a stable species with strong absorption features at 350 nm and a highly anisotropic, axial EPR signal with principal g-values of 2.56 and 2.10. Density functional theory calculations provide insight into the electronic and geometric structure of the Ni(I) species, suggesting a trigonal planar coordination environment. The predicted spectroscopic features of this low-coordinate nickel site are in good agreement with the experimental data. Molecular orbital analysis suggests potential for both metal-centered and ligand-centered reactivity, highlighting the covalency of the metal-thiolate bond. Characterization of a stable Ni(I) species within a model protein has implications for understanding the mechanisms of complex enzymes, including acetyl coenzyme A synthase, and developing scaffolds for unique reactivity.
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Vita N, Brubach JB, Hienerwadel R, Bremond N, Berthomieu D, Roy P, Berthomieu C. Electrochemically Induced Far-Infrared Difference Spectroscopy on Metalloproteins Using Advanced Synchrotron Technology. Anal Chem 2013; 85:2891-8. [DOI: 10.1021/ac303511g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Nicolas Vita
- Lab Interactions Protein Metal, Commissariat à l’Energie Atomique (CEA), DSV, IBEB, Saint-Paul-lez-Durance,
F-13108, France
- Centre National de la Recherche Scientifique, UMR Biol Veget et Microbiol
Environ, Saint-Paul-lez-Durance, F-13108, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, F-13108, France
- Société Civile Synchrotron SOLEIL, L’Orme des Merisiers,
St-Aubin BP48, 91192 Gif-sur-Yvette Cedex, France
| | - Jean-Blaise Brubach
- Société Civile Synchrotron SOLEIL, L’Orme des Merisiers,
St-Aubin BP48, 91192 Gif-sur-Yvette Cedex, France
| | - Rainer Hienerwadel
- Centre National de la Recherche Scientifique, UMR Biol Veget et Microbiol
Environ, Saint-Paul-lez-Durance, F-13108, France
- Lab Genet Biophys Plantes, Aix-Marseille Université, Marseille, F-13009,
France
- Commissariat à l’Energie Atomique (CEA), DSV, IBEB, Marseille,
F-13009, France
| | - Nicolas Bremond
- Lab Interactions Protein Metal, Commissariat à l’Energie Atomique (CEA), DSV, IBEB, Saint-Paul-lez-Durance,
F-13108, France
- Centre National de la Recherche Scientifique, UMR Biol Veget et Microbiol
Environ, Saint-Paul-lez-Durance, F-13108, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, F-13108, France
| | - Dorothée Berthomieu
- Institut Charles Gerhardt, MACS, UMR 5253 CNRS-ENSCM-UM1-UM2, 8, rue
de l’Ecole Normale, 34296 Montpellier Cedex 5, France
| | - Pascale Roy
- Société Civile Synchrotron SOLEIL, L’Orme des Merisiers,
St-Aubin BP48, 91192 Gif-sur-Yvette Cedex, France
| | - Catherine Berthomieu
- Lab Interactions Protein Metal, Commissariat à l’Energie Atomique (CEA), DSV, IBEB, Saint-Paul-lez-Durance,
F-13108, France
- Centre National de la Recherche Scientifique, UMR Biol Veget et Microbiol
Environ, Saint-Paul-lez-Durance, F-13108, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, F-13108, France
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8
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McLaughlin MP, Retegan M, Bill E, Payne TM, Shafaat HS, Peña S, Sudhamsu J, Ensign AA, Crane BR, Neese F, Holland PL. Azurin as a protein scaffold for a low-coordinate nonheme iron site with a small-molecule binding pocket. J Am Chem Soc 2012; 134:19746-57. [PMID: 23167247 PMCID: PMC3515693 DOI: 10.1021/ja308346b] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The apoprotein of Pseudomonas aeruginosa azurin binds iron(II) to give a 1:1 complex, which has been characterized by electronic absorption, Mössbauer, and NMR spectroscopies, as well as X-ray crystallography and quantum-chemical computations. Despite potential competition by water and other coordinating residues, iron(II) binds tightly to the low-coordinate site. The iron(II) complex does not react with chemical redox agents to undergo oxidation or reduction. Spectroscopically calibrated quantum-chemical computations show that the complex has high-spin iron(II) in a pseudotetrahedral coordination environment, which features interactions with side chains of two histidines and a cysteine as well as the C═O of Gly45. In the (5)A(1) ground state, the d(z(2)) orbital is doubly occupied. Mutation of Met121 to Ala leaves the metal site in a similar environment but creates a pocket for reversible binding of small anions to the iron(II) center. Specifically, azide forms a high-spin iron(II) complex and cyanide forms a low-spin iron(II) complex.
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Affiliation(s)
| | - Marius Retegan
- Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany
| | - Eckhard Bill
- Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany
| | - Thomas M. Payne
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853
| | - Hannah S. Shafaat
- Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany
| | - Salvador Peña
- Department of Chemistry, University of Rochester, Rochester, New York 14618
| | - Jawahar Sudhamsu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853
| | - Amy A. Ensign
- Department of Chemistry, University of Rochester, Rochester, New York 14618
| | - Brian R. Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853
| | - Frank Neese
- Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany
| | - Patrick L. Holland
- Department of Chemistry, University of Rochester, Rochester, New York 14618
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Lee T, Min J, Kim SU, Choi JW. Multifunctional 4-bit biomemory chip consisting of recombinant azurin variants. Biomaterials 2011; 32:3815-21. [DOI: 10.1016/j.biomaterials.2011.01.072] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 01/30/2011] [Indexed: 10/18/2022]
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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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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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12
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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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Nickel(II)-substituted azurin I from Alcaligenes xylosoxidans as characterized by resonance Raman spectroscopy at cryogenic temperature. J Biol Inorg Chem 2009; 14:611-20. [DOI: 10.1007/s00775-009-0475-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Accepted: 01/28/2009] [Indexed: 10/21/2022]
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Direct immobilization of cupredoxin azurin modified by site-directed mutagenesis on gold surface. Ultramicroscopy 2008; 108:1390-5. [DOI: 10.1016/j.ultramic.2008.04.048] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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