51
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Jin H, Zhang Y, Buchko GW, Varnum SM, Robinson H, Squier TC, Long PE. Structure determination and functional analysis of a chromate reductase from Gluconacetobacter hansenii. PLoS One 2012; 7:e42432. [PMID: 22879982 PMCID: PMC3412864 DOI: 10.1371/journal.pone.0042432] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 07/09/2012] [Indexed: 11/19/2022] Open
Abstract
Environmental protection through biological mechanisms that aid in the reductive immobilization of toxic metals (e.g., chromate and uranyl) has been identified to involve specific NADH-dependent flavoproteins that promote cell viability. To understand the enzyme mechanisms responsible for metal reduction, the enzyme kinetics of a putative chromate reductase from Gluconacetobacter hansenii (Gh-ChrR) was measured and the crystal structure of the protein determined at 2.25 Å resolution. Gh-ChrR catalyzes the NADH-dependent reduction of chromate, ferricyanide, and uranyl anions under aerobic conditions. Kinetic measurements indicate that NADH acts as a substrate inhibitor; catalysis requires chromate binding prior to NADH association. The crystal structure of Gh-ChrR shows the protein is a homotetramer with one bound flavin mononucleotide (FMN) per subunit. A bound anion is visualized proximal to the FMN at the interface between adjacent subunits within a cationic pocket, which is positioned at an optimal distance for hydride transfer. Site-directed substitutions of residues proposed to involve in both NADH and metal anion binding (N85A or R101A) result in 90–95% reductions in enzyme efficiencies for NADH-dependent chromate reduction. In comparison site-directed substitution of a residue (S118A) participating in the coordination of FMN in the active site results in only modest (50%) reductions in catalytic efficiencies, consistent with the presence of a multitude of side chains that position the FMN in the active site. The proposed proximity relationships between metal anion binding site and enzyme cofactors is discussed in terms of rational design principles for the use of enzymes in chromate and uranyl bioremediation.
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Affiliation(s)
- Hongjun Jin
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America.
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Pardoux R, Sauge-Merle S, Lemaire D, Delangle P, Guilloreau L, Adriano JM, Berthomieu C. Modulating uranium binding affinity in engineered calmodulin EF-hand peptides: effect of phosphorylation. PLoS One 2012; 7:e41922. [PMID: 22870263 PMCID: PMC3411679 DOI: 10.1371/journal.pone.0041922] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2012] [Accepted: 06/29/2012] [Indexed: 12/21/2022] Open
Abstract
To improve our understanding of uranium toxicity, the determinants of uranyl affinity in proteins must be better characterized. In this work, we analyzed the contribution of a phosphoryl group on uranium binding affinity in a protein binding site, using the site 1 EF-hand motif of calmodulin. The recombinant domain 1 of calmodulin from A. thaliana was engineered to impair metal binding at site 2 and was used as a structured template. Threonine at position 9 of the loop was phosphorylated in vitro, using the recombinant catalytic subunit of protein kinase CK2. Hence, the T9TKE12 sequence was substituted by the CK2 recognition sequence TAAE. A tyrosine was introduced at position 7, so that uranyl and calcium binding affinities could be determined by following tyrosine fluorescence. Phosphorylation was characterized by ESI-MS spectrometry, and the phosphorylated peptide was purified to homogeneity using ion-exchange chromatography. The binding constants for uranyl were determined by competition experiments with iminodiacetate. At pH 6, phosphorylation increased the affinity for uranyl by a factor of ∼5, from Kd = 25±6 nM to Kd = 5±1 nM. The phosphorylated peptide exhibited a much larger affinity at pH 7, with a dissociation constant in the subnanomolar range (Kd = 0.25±0.06 nM). FTIR analyses showed that the phosphothreonine side chain is partly protonated at pH 6, while it is fully deprotonated at pH 7. Moreover, formation of the uranyl-peptide complex at pH 7 resulted in significant frequency shifts of the νas(P-O) and νs(P-O) IR modes of phosphothreonine, supporting its direct interaction with uranyl. Accordingly, a bathochromic shift in νas(UO2)2+ vibration (from 923 cm−1 to 908 cm−1) was observed upon uranyl coordination to the phosphorylated peptide. Together, our data demonstrate that the phosphoryl group plays a determining role in uranyl binding affinity to proteins at physiological pH.
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Affiliation(s)
- Romain Pardoux
- CEA, DSV IBEB, Laboratoire des Interactions Protéine-Métal, Saint-Paul-lez-Durance, France
- CNRS, UMR Biologie Végétale et Microbiologie Environnementale, Saint-Paul-lez-Durance, France
- Université d’Aix-Marseille, Saint-Paul-lez-Durance, France
| | - Sandrine Sauge-Merle
- CEA, DSV IBEB, Laboratoire des Interactions Protéine-Métal, Saint-Paul-lez-Durance, France
- CNRS, UMR Biologie Végétale et Microbiologie Environnementale, Saint-Paul-lez-Durance, France
- Université d’Aix-Marseille, Saint-Paul-lez-Durance, France
| | - David Lemaire
- CEA, DSV IBEB, Laboratoire des Interactions Protéine-Métal, Saint-Paul-lez-Durance, France
- CNRS, UMR Biologie Végétale et Microbiologie Environnementale, Saint-Paul-lez-Durance, France
- Université d’Aix-Marseille, Saint-Paul-lez-Durance, France
| | - Pascale Delangle
- CEA, INAC, Service de Chimie Inorganique et Biologique (UMR_E 3 CEA UJF), Grenoble, France
| | - Luc Guilloreau
- CEA, DSV IBEB, Laboratoire des Interactions Protéine-Métal, Saint-Paul-lez-Durance, France
- CNRS, UMR Biologie Végétale et Microbiologie Environnementale, Saint-Paul-lez-Durance, France
- Université d’Aix-Marseille, Saint-Paul-lez-Durance, France
| | - Jean-Marc Adriano
- CNRS, UMR Biologie Végétale et Microbiologie Environnementale, Saint-Paul-lez-Durance, France
- Université d’Aix-Marseille, Saint-Paul-lez-Durance, France
- CEA, DSV IBEB, Laboratoire de Bioénergétique et Biotechnologie des Bactéries et Microalgues, Saint Paul-lez-Durance, France
| | - Catherine Berthomieu
- CEA, DSV IBEB, Laboratoire des Interactions Protéine-Métal, Saint-Paul-lez-Durance, France
- CNRS, UMR Biologie Végétale et Microbiologie Environnementale, Saint-Paul-lez-Durance, France
- Université d’Aix-Marseille, Saint-Paul-lez-Durance, France
- * E-mail:
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Wan D, Liao LF, Zhao MM, Wu ML, Wu YM, Lin YW. Interactions of uranyl ion with cytochrome b 5 and its His39Ser variant as revealed by molecular simulation in combination with experimental methods. J Mol Model 2011; 18:1009-13. [DOI: 10.1007/s00894-011-1097-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2010] [Accepted: 03/22/2011] [Indexed: 11/24/2022]
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54
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Rao L, Cui Q, Xu X. Electronic Properties and Desolvation Penalties of Metal Ions Plus Protein Electrostatics Dictate the Metal Binding Affinity and Selectivity in the Copper Efflux Regulator. J Am Chem Soc 2010; 132:18092-102. [DOI: 10.1021/ja103742k] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Li Rao
- Department of Chemistry, Xiamen University, Xiamen, P. R. China, and Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Qiang Cui
- Department of Chemistry, Xiamen University, Xiamen, P. R. China, and Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Xin Xu
- Department of Chemistry, Xiamen University, Xiamen, P. R. China, and Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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55
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Köhler V, Wilson YM, Lo C, Sardo A, Ward TR. Protein-based hybrid catalysts—design and evolution. Curr Opin Biotechnol 2010; 21:744-52. [DOI: 10.1016/j.copbio.2010.09.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Revised: 09/07/2010] [Accepted: 09/08/2010] [Indexed: 10/19/2022]
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56
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Pible O, Vidaud C, Plantevin S, Pellequer JL, Quéméneur E. Predicting the disruption by UO2(2+) of a protein-ligand interaction. Protein Sci 2010; 19:2219-30. [PMID: 20842713 PMCID: PMC3005792 DOI: 10.1002/pro.501] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Revised: 08/30/2010] [Accepted: 09/04/2010] [Indexed: 01/27/2023]
Abstract
The uranyl cation (UO(2) (2+)) can be suspected to interfere with the binding of essential metal cations to proteins, underlying some mechanisms of toxicity. A dedicated computational screen was used to identify UO(2) (2+) binding sites within a set of nonredundant protein structures. The list of potential targets was compared to data from a small molecules interaction database to pinpoint specific examples where UO(2) (2+) should be able to bind in the vicinity of an essential cation, and would be likely to affect the function of the corresponding protein. The C-reactive protein appeared as an interesting hit since its structure involves critical calcium ions in the binding of phosphorylcholine. Biochemical experiments confirmed the predicted binding site for UO(2) (2+) and it was demonstrated by surface plasmon resonance assays that UO(2) (2+) binding to CRP prevents the calcium-mediated binding of phosphorylcholine. Strikingly, the apparent affinity of UO(2) (2+) for native CRP was almost 100-fold higher than that of Ca(2+). This result exemplifies in the case of CRP the capability of our computational tool to predict effective binding sites for UO(2) (2+) in proteins and is a first evidence of calcium substitution by the uranyl cation in a native protein.
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Affiliation(s)
- Olivier Pible
- CEA Life Sciences Division, DSV, IBEB, SBTN, Bagnols-sur-Cèze, F-30207, France.
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57
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Brodin JD, Medina-Morales A, Ni T, Salgado EN, Ambroggio XI, Tezcan FA. Evolution of metal selectivity in templated protein interfaces. J Am Chem Soc 2010; 132:8610-7. [PMID: 20515031 PMCID: PMC2896502 DOI: 10.1021/ja910844n] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Selective binding by metalloproteins to their cognate metal ions is essential to cellular survival. How proteins originally acquired the ability to selectively bind metals and evolved a diverse array of metal-centered functions despite the availability of only a few metal-coordinating functionalities remains an open question. Using a rational design approach (Metal-Templated Interface Redesign), we describe the transformation of a monomeric electron transfer protein, cytochrome cb(562), into a tetrameric assembly ((C96)RIDC-1(4)) that stably and selectively binds Zn(2+) and displays a metal-dependent conformational change reminiscent of a signaling protein. A thorough analysis of the metal binding properties of (C96)RIDC-1(4) reveals that it can also stably harbor other divalent metals with affinities that rival (Ni(2+)) or even exceed (Cu(2+)) those of Zn(2+) on a per site basis. Nevertheless, this analysis suggests that our templating strategy simultaneously introduces an increased bias toward binding a higher number of Zn(2+) ions (four high affinity sites) versus Cu(2+) or Ni(2+) (two high affinity sites), ultimately leading to the exclusive selectivity of (C96)RIDC-1(4) for Zn(2+) over those ions. More generally, our results indicate that an initial metal-driven nucleation event followed by the formation of a stable protein architecture around the metal provides a straightforward path for generating structural and functional diversity.
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Affiliation(s)
- Jeffrey D. Brodin
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0356
| | - Annette Medina-Morales
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0356
| | - Thomas Ni
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0356
| | - Eric N. Salgado
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0356
| | | | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0356
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Şahin M, Koca A, Özdemir N, Dinçer M, Büyükgüngör O, Bal-Demirci T, Ülküseven B. Synthesis, X-ray crystal structures, thermal and electrochemical properties of thiosemicarbazidatodioxouranium(vi) complexes. Dalton Trans 2010; 39:10228-37. [DOI: 10.1039/c0dt00265h] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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59
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Abstract
Metalloproteins catalyse some of the most complex and important processes in nature, such as photosynthesis and water oxidation. An ultimate test of our knowledge of how metalloproteins work is to design new metalloproteins. Doing so not only can reveal hidden structural features that may be missing from studies of native metalloproteins and their variants, but also can result in new metalloenzymes for biotechnological and pharmaceutical applications. Although it is much more challenging to design metalloproteins than non-metalloproteins, much progress has been made in this area, particularly in functional design, owing to recent advances in areas such as computational and structural biology.
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Affiliation(s)
- Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
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60
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Dougherty MJ, Arnold FH. Directed evolution: new parts and optimized function. Curr Opin Biotechnol 2009; 20:486-91. [PMID: 19720520 DOI: 10.1016/j.copbio.2009.08.005] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2009] [Revised: 08/07/2009] [Accepted: 08/12/2009] [Indexed: 11/28/2022]
Abstract
Constructing novel biological systems that function in a robust and predictable manner requires better methods for discovering new functional molecules and for optimizing their assembly in novel biological contexts. By enabling functional diversification and optimization in the absence of detailed mechanistic understanding, directed evolution is a powerful complement to 'rational' engineering approaches. Aided by clever selection schemes, directed evolution has generated new parts for genetic circuits, cell-cell communication systems, and non-natural metabolic pathways in bacteria.
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Affiliation(s)
- Michael J Dougherty
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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