1
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Koebke KJ, Pinter TBJ, Pitts WC, Pecoraro VL. Catalysis and Electron Transfer in De Novo Designed Metalloproteins. Chem Rev 2022; 122:12046-12109. [PMID: 35763791 PMCID: PMC10735231 DOI: 10.1021/acs.chemrev.1c01025] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One of the hallmark advances in our understanding of metalloprotein function is showcased in our ability to design new, non-native, catalytically active protein scaffolds. This review highlights progress and milestone achievements in the field of de novo metalloprotein design focused on reports from the past decade with special emphasis on de novo designs couched within common subfields of bioinorganic study: heme binding proteins, monometal- and dimetal-containing catalytic sites, and metal-containing electron transfer sites. Within each subfield, we highlight several of what we have identified as significant and important contributions to either our understanding of that subfield or de novo metalloprotein design as a discipline. These reports are placed in context both historically and scientifically. General suggestions for future directions that we feel will be important to advance our understanding or accelerate discovery are discussed.
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Affiliation(s)
- Karl J. Koebke
- Department of Chemistry, University of Michigan Ann Arbor, MI 48109 USA
| | | | - Winston C. Pitts
- Department of Chemistry, University of Michigan Ann Arbor, MI 48109 USA
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2
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Mitra S, Ainavarapu SRK, Dasgupta J. Long-Range Charge Delocalization Mediates the Ultrafast Ligand-to-Metal Charge Transfer Dynamics at the Cu 2+-Active Site in Azurin. J Phys Chem B 2022; 126:5390-5399. [PMID: 35797135 DOI: 10.1021/acs.jpcb.2c01427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The blue color metalloprotein in azurin has traditionally been attributed to the intense cysteine-to-Cu2+ ligand-to-metal charge transfer transition centered at 628 nm. Although resonance Raman measurements of the Cu2+ active site have implied that the LMCT transition electronically couples to the protein scaffold well beyond its primary metal-ligand coordination shell, the structural extent of this electronic coupling and visualization of the protein-mediated charge transfer dynamics have remained elusive. Here, using femtosecond broadband transient absorption and impulsive Raman spectroscopy, we provide direct evidence for a rapid relaxation between two distinct charge transfer states, having different spatial delocalization, within ∼300 fs followed by recombination of charges in subpicosecond time scales. We invoke the formation of a protein-centered radical cation, possibly Trp48 or a Phe residue, within 100 fs substantiating the long-range electronic coupling for the first time beyond the traditional copper active site. The Raman spectra of the excited CT state show the presence of protein-centric vibrations along with the vibrational modes assigned to the copper active site. Our results demonstrate a large delocalization length scale of the initially populated CT state, thereby highlighting the possibility of exploiting azurin photochemistry for energy conversion techniques.
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Affiliation(s)
- Soumyajit Mitra
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | | | - Jyotishman Dasgupta
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
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3
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Das D, Ainavarapu SRK. Azurin-Derived Peptides: Comparison of Nickel- and Copper-Binding Properties. Inorg Chem 2021; 60:9720-9726. [PMID: 34137603 DOI: 10.1021/acs.inorgchem.1c01007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Metalloproteins are an important class of proteins involved in metal uptake, transport, and electron-transfer reactions. Mimicking the active sites of these proteins through miniaturization is an active area of research with applications in biotechnology and medicine. Azurin is a 128-residue copper-binding cupredoxin protein involved in electron-transfer reactions. Previous studies have reported on the copper-binding-induced spectroscopic and structural properties of peptide loops (11 and 13 residues) from azurin. These azurin peptides exhibited novel stoichiometries. However, the underlying mechanism of fluorescence quenching upon copper binding remains to be understood, whether it is due to electron transfer, energy transfer, or both. Here, we report nickel-binding-associated spectroscopic and structural properties of the azurin peptides. They develop a β-turn upon nickel binding as seen in circular dichroism and exhibit electronic transitions centered at 270 and 450 nm. Unlike copper, which exhibited 1:1 and 1:2 peptide:metal stoichiometries, nickel exhibited only a 1:1 stoichiometry. Tryptophan-containing peptides showed fluorescence quenching upon nickel binding, which is due to electron transfer. These results further suggest that the quenching in copper-bound peptides is also due to electron transfer, which could not be ascertained in previous studies. Overall, azurin peptides provide a platform for studying metal-induced structural and spectroscopic properties using transition-metal ions.
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Affiliation(s)
- Debanjana Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr. Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Sri Rama Koti Ainavarapu
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr. Homi Bhabha Road, Colaba, Mumbai 400005, India
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4
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Mirts EN, Dikanov SA, Jose A, Solomon EI, Lu Y. A Binuclear Cu A Center Designed in an All α-Helical Protein Scaffold. J Am Chem Soc 2020; 142:13779-13794. [PMID: 32662996 DOI: 10.1021/jacs.0c04226] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The primary and secondary coordination spheres of metal binding sites in metalloproteins have been investigated extensively, leading to the creation of high-performing functional metalloproteins; however, the impact of the overall structure of the protein scaffold on the unique properties of metalloproteins has rarely been studied. A primary example is the binuclear CuA center, an electron transfer cupredoxin domain of photosynthetic and respiratory complexes and, recently, a protein coregulated with particulate methane and ammonia monooxygenases. The redox potential, Cu-Cu spectroscopic features, and a valence delocalized state of CuA are difficult to reproduce in synthetic models, and every artificial protein CuA center to-date has used a modified cupredoxin. Here, we present a fully functional CuA center designed in a structurally nonhomologous protein, cytochrome c peroxidase (CcP), by only two mutations (CuACcP). We demonstrate with UV-visible absorption, resonance Raman, and magnetic circular dichroism spectroscopy that CuACcP is valence delocalized. Continuous wave and pulsed (HYSCORE) X-band EPR show it has a highly compact gz area and small Az hyperfine principal value with g and A tensors that resemble axially perturbed CuA. Stopped-flow kinetics found that CuA formation proceeds through a single T2Cu intermediate. The reduction potential of CuACcP is comparable to native CuA and can transfer electrons to a physiological redox partner. We built a structural model of the designed Cu binding site from extended X-ray absorption fine structure spectroscopy and validated it by mutation of coordinating Cys and His residues, revealing that a triad of residues (R48C, W51C, and His52) rigidly arranged on one α-helix is responsible for chelating the first Cu(II) and that His175 stabilizes the binuclear complex by rearrangement of the CcP heme-coordinating helix. This design is a demonstration that a highly conserved protein fold is not uniquely necessary to induce certain characteristic physical and chemical properties in a metal redox center.
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Affiliation(s)
- Evan N Mirts
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Sergei A Dikanov
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Anex Jose
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Edward I Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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5
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Das D, Mitra S, Kumar R, Banerjee S, Koti Ainavarapu SR. Copper-induced spectroscopic and structural changes in short peptides derived from azurin. Arch Biochem Biophys 2020; 687:108388. [PMID: 32343975 DOI: 10.1016/j.abb.2020.108388] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/07/2020] [Accepted: 04/21/2020] [Indexed: 11/26/2022]
Abstract
The active sites of metalloproteins may be mimicked by designing peptides that bind to their respective metal ions. Studying the binding of protein ligands to metal ions along with the associated structural changes is important in understanding metal uptake, transport and electron transfer functions of proteins. Copper-binding metalloprotein azurin is a 128-residue electron transfer protein with a redox-active copper cofactor. Here, we report the copper-binding associated spectroscopic and structural properties of peptide loops (11 and 13 residues) from the copper-binding site of azurin. These peptides develop a β-turn upon copper-binding with a 1:1 Cu2+:peptide stoichiometry as seen in circular dichroism and exhibit electronic transitions centered at 340 nm and 540 nm. Further addition of copper develops a helical feature along with a shift in the absorption maxima to ~360 nm and ~580 nm at 2:1 Cu2+:peptide stoichiometry, indicating stoichiometric dependence of copper-binding geometry. Mass spectrometry indicates the copper-binding to cysteine, histidine and methionine in the peptide with 1:1 stoichiometry, and interestingly, dimerization through a disulfide linkage at 2:1 stoichiometry, as observed previously for denatured azurin. Fluorescence quenching studies on peptides with tryptophan further confirm the copper-binding induced changes in the two peptides are bi-phasic.
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Affiliation(s)
- Debanjana Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr. Homi Bhabha Road, Colaba, Mumbai, 400005, India
| | - Soumyajit Mitra
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr. Homi Bhabha Road, Colaba, Mumbai, 400005, India
| | - Rohit Kumar
- Department of Chemistry, Indian Institute of Science Education and Research Tirupati, Tirupati, 517507, India
| | - Shibdas Banerjee
- Department of Chemistry, Indian Institute of Science Education and Research Tirupati, Tirupati, 517507, India.
| | - Sri Rama Koti Ainavarapu
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr. Homi Bhabha Road, Colaba, Mumbai, 400005, India.
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6
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Lihi N, Sanna D, Bányai I, Várnagy K, Sóvágó I. Unusual binding modes in the copper(ii) and palladium(ii) complexes of peptides containing both histidyl and cysteinyl residues. NEW J CHEM 2017. [DOI: 10.1039/c6nj03735f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The change of the histidine in the peptide chain provides unusual binding behavior of albumin related peptides.
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Affiliation(s)
- Norbert Lihi
- Department of Inorganic and Analytical Chemistry
- University of Debrecen
- Debrecen
- Hungary
| | - Daniele Sanna
- Istituto CNR di Chimica Biomolecolare
- I-07040 Sassari
- Italy
| | - István Bányai
- Department of Physical Chemistry
- University of Debrecen
- Debrecen
- Hungary
| | - Katalin Várnagy
- Department of Inorganic and Analytical Chemistry
- University of Debrecen
- Debrecen
- Hungary
| | - Imre Sóvágó
- Department of Inorganic and Analytical Chemistry
- University of Debrecen
- Debrecen
- Hungary
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7
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Carrasco-Pozo C, Alvarez-Lueje A, Olea-Azar C, López-Alarcón C, Speisky H. In Vitro Interaction Between Homocysteine and Copper Ions: Potential Redox Implications. Exp Biol Med (Maywood) 2016; 231:1569-75. [PMID: 17018882 DOI: 10.1177/153537020623100918] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Homocysteine (Hcys) has been implicated in various oxidative stress-related disorders. The presence of a thiol on its structure allows Hcys to exert a double-edge redox action. Depending on whether Cu2+ ions occur concomitantly, Hcys can either promote or prevent free radical generation and its consequences. We have addressed In vitro the interaction between Hcys and Cu2+ Ions, in terms of the consequences that such interaction may have on the free radical scavenging properties of Hcys and on the redox state and redox activity of the metal. To this end, we investigated the free radical-scavenging, O2--generating, and ascorbate-oxidizing properties of the interacting species by assessing the bleaching of ABTS'+ radicals, the reduction of O2--dependent cytochrome c, and the copper-dependent oxidation of ascorbate, respectively. In addition, electron paramagnetic resonance and Cu(I)-bathocuproine formation were applied to assess the formation of paramagnetic complexes and the metal redox state. Upon a brief incubation, the Hcys/Cu2+ Interaction led to a decrease in the free radical-scavenging properties of Hcys, and to a comparable loss of the thiol density. Both effects were partial and were not modified by increasing the Incubation time, despite the presence of Cu2+ excess. Depending on the molar Hcys : Cu2+ ratio, the interaction resulted in the formation of mixtures that appear to contain time-stable and ascorbate-reducible Cu(II) complexes (for ratios up to 2:1), and ascorbate- and oxygen-redox-inactive Cu(l) complexes (for ratios up to 4:1). Increasing the interaction ratio beyond 4:1 was associated with the sudden appearance of an O2--generating activity. The data indicate that depending on the molar ratio of interaction, Hcys and Cu2+ react to form copper complexes that can promote either antioxidant or pro-oxidant actions. We speculate that the redox activity arising from a large molar Hcys excess may partially underlie the association between hyper-homocysteinemia and a greater risk of developing oxidative-related cardiovascular diseases.
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Affiliation(s)
- Catalina Carrasco-Pozo
- Miconutrients Unit, Nutrition and Food Technology Institute (INTA), University of Chile, El Líbano 5524, Macul, PO Box 138-11, Santiago, Chile
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8
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Sóvágó I, Várnagy K, Lihi N, Grenács Á. Coordinating properties of peptides containing histidyl residues. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.04.015] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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9
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Engineering Short Preorganized Peptide Sequences for Metal Ion Coordination: Copper(II) a Case Study. Methods Enzymol 2016. [PMID: 27586340 DOI: 10.1016/bs.mie.2016.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Peptides are multidentate chiral ligands capable of coordinating different metal ions. Nowadays, they can be obtained with high yield and purity, thanks to the advances on peptide/protein chemistry as well as in equipment (peptide synthesizers). Based on the identity and length of their amino acid sequences, peptides can present different degrees of flexibility and folding. Although short peptide sequences (<20 amino acids) usually lack structure in solution, different levels of structural preorganization can be induced by introducing conformational constraints, such as β-turn/loop template sequences and backbone cyclization. For all these reasons, and the fact that one is not restricted to use proteinogenic amino acids, small peptidic scaffolds constitute a simple and versatile platform for the development of inorganic systems with tailor-made properties and functions. Here we outline a general approach to the design of short preorganized peptide sequences (10-16 amino acids) for metal ion coordination. Based on our experience, we present a general scheme for the design, synthesis, and characterization of these peptidic scaffolds and provide protocols for the study of their metal ion coordination properties.
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10
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Mann SI, Heinisch T, Weitz AC, Hendrich MP, Ward TR, Borovik AS. Modular Artificial Cupredoxins. J Am Chem Soc 2016; 138:9073-6. [PMID: 27385206 DOI: 10.1021/jacs.6b05428] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Cupredoxins are electron-transfer proteins that have active sites containing a mononuclear Cu center with an unusual trigonal monopyramidal structure (Type 1 Cu). A single Cu-Scys bond is present within the trigonal plane that is responsible for its unique physical properties. We demonstrate that a cysteine-containing variant of streptavidin (Sav) can serve as a protein host to model the structure and properties of Type 1 Cu sites. A series of artificial Cu proteins are described that rely on Sav and a series of biotinylated synthetic Cu complexes. Optical and EPR measurements highlight the presence of a Cu-Scys bond, and XRD analysis provides structural evidence. We further provide evidence that changes in the linker between the biotin and Cu complex within the synthetic constructs allows for small changes in the placement of Cu centers within Sav that have dramatic effects on the structural and physical properties of the resulting artificial metalloproteins. These findings highlight the utility of the biotin-Sav technology as an approach for simulating active sites of metalloproteins.
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Affiliation(s)
- Samuel I Mann
- Department of Chemistry, University of California-Irvine , 1102 Natural Sciences II, Irvine, California 92697, United States
| | - Tillmann Heinisch
- Department of Chemistry, University of Basel , Spitalstrasse 51, CH-4056 Basel, Switzerland
| | - Andrew C Weitz
- Department of Chemistry, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Michael P Hendrich
- Department of Chemistry, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Thomas R Ward
- Department of Chemistry, University of Basel , Spitalstrasse 51, CH-4056 Basel, Switzerland
| | - A S Borovik
- Department of Chemistry, University of California-Irvine , 1102 Natural Sciences II, Irvine, California 92697, United States
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11
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Park GY, Lee JY, Himes R, Thomas GS, Blackburn NJ, Karlin KD. Copper-peptide complex structure and reactivity when found in conserved His-X(aa)-His sequences. J Am Chem Soc 2014; 136:12532-5. [PMID: 25171435 PMCID: PMC4160276 DOI: 10.1021/ja505098v] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Indexed: 01/29/2023]
Abstract
Oxygen-activating copper proteins may possess His-X(aa)-His chelating sequences at their active sites and additionally exhibit imidiazole group δN vs εN tautomeric preferences. As shown here, such variations strongly affect copper ion's coordination geometry, redox behavior, and oxidative reactivity. Copper(I) complexes bound to either δ-HGH or ε-HGH tripeptides were synthesized and characterized. Structural investigations using X-ray absorption spectroscopy, density functional theory calculations, and solution conductivity measurements reveal that δ-HGH forms the Cu(I) dimer complex [{Cu(I)(δ-HGH)}2](2+) (1) while ε-HGH binds Cu(I) to give the monomeric complex [Cu(I)(ε-HGH)](+) (2). Only 2 exhibits any reactivity, forming a strong CO adduct, [Cu(I)(ε-HGH)(CO)](+), with properties closely matching those of the copper monooxygenase PHM. Also, 2 is reactive toward O2 or H2O2, giving a new type of O2-adduct or Cu(II)-OOH complex, respectively.
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Affiliation(s)
- Ga Young Park
- Department
of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Jung Yoon Lee
- Department
of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Richard
A. Himes
- Department
of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Gnana S. Thomas
- Institute
of Environmental Health, Oregon Health and
Sciences University, Portland, Oregon 97239, United States
| | - Ninian J. Blackburn
- Institute
of Environmental Health, Oregon Health and
Sciences University, Portland, Oregon 97239, United States
| | - Kenneth D. Karlin
- Department
of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
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12
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Zastrow ML, Pecoraro VL. Designing functional metalloproteins: from structural to catalytic metal sites. Coord Chem Rev 2013; 257:2565-2588. [PMID: 23997273 PMCID: PMC3756834 DOI: 10.1016/j.ccr.2013.02.007] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Metalloenzymes efficiently catalyze some of the most important and difficult reactions in nature. For many years, coordination chemists have effectively used small molecule models to understand these systems. More recently, protein design has been shown to be an effective approach for mimicking metal coordination environments. Since the first designed proteins were reported, much success has been seen for incorporating metal sites into proteins and attaining the desired coordination environment but until recently, this has been with a lack of significant catalytic activity. Now there are examples of designed metalloproteins that, although not yet reaching the activity of native enzymes, are considerably closer. In this review, we highlight work leading up to the design of a small metalloprotein containing two metal sites, one for structural stability (HgS3) and the other a separate catalytic zinc site to mimic carbonic anhydrase activity (ZnN3O). The first section will describe previous studies that allowed for a high affinity thiolate site that binds heavy metals in a way that stabilizes three-stranded coiled coils. The second section will examine ways of preparing histidine rich environments that lead to metal based hydrolytic catalysts. We will also discuss other recent examples of the design of structural metal sites and functional metalloenzymes. Our work demonstrates that attaining the proper first coordination geometry of a metal site can lead to a significant fraction of catalytic activity, apparently independent of the type of secondary structure of the surrounding protein environment. We are now in a position to begin to meet the challenge of building a metalloenzyme systematically from the bottom-up by engineering and analyzing interactions directly around the metal site and beyond.
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Affiliation(s)
- Melissa L. Zastrow
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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13
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Fragoso A, Lamosa P, Delgado R, Iranzo O. Harnessing the flexibility of peptidic scaffolds to control their copper(II)-coordination properties: a potentiometric and spectroscopic study. Chemistry 2013; 19:2076-88. [PMID: 23293061 DOI: 10.1002/chem.201203545] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Indexed: 02/02/2023]
Abstract
Designing small peptides that are capable of binding Cu(2+) ions mainly through the side-chain functionalities is a hard task because the amide nitrogen atoms strongly compete for Cu(2+) ion coordination. However, the design of such peptides is important for obtaining biomimetic small systems of metalloenyzmes as well as for the development of artificial systems. With this in mind, a cyclic decapeptide, C-Asp, which contained three His residues and one Asp residue, and its linear derivative, O-Asp, were synthesized. The C-Asp peptide has two Pro-Gly β-turn-inducer units and, as a result of cyclization, and as shown by CD spectroscopy, its backbone is constrained into a more defined conformation than O-Asp, which is linear and contains a single Pro-Gly unit. A detailed potentiometric, mass spectrometric, and spectroscopic study (UV/Vis, CD, and EPR spectroscopy) showed that at a 1:1 Cu(2+)/peptide ratio, both peptides formed a major [CuHL](2+) species in the pH range 5.0-7.5 (C-Asp) and 5.5-7.0 (O-Asp). The corrected stability constants of the protonated species (log K*(CuH(O-Asp))=9.28 and log K*(CuH(C-Asp))=10.79) indicate that the cyclic peptide binds Cu(2+) ions with higher affinity. In addition, the calculated value of K(eff) shows that this higher affinity for Cu(2+) ions prevails at all pH values, not only for a 1:1 ratio but even for a 2:1 ratio. The spectroscopic data of both [CuHL](2+) species are consistent with the exclusive coordination of Cu(2+) ions by the side-chain functionalities of the three His residues and the Asp residue in a square-planar or square-pyramidal geometry. Nonetheless, although these data show that, upon metal coordination, both peptides adopt a similar fold, the larger conformational constraints that are present in the cyclic scaffold results in different behaviour for both [CuHL](2+) species. CD and NMR analysis revealed the formation of a more rigid structure and a slower Cu(2+)-exchange rate for [CuH(C-Asp)](2+) compared to [CuH(O-Asp](2+). This detailed comparative study shows that cyclization has a remarkable effect on the Cu(2+)-coordination properties of the C-Asp peptide, which binds Cu(2+) ions with higher affinity at all pH values, stabilizes the [CuHL](2+) species in a wider pH range, and has a slower Cu(2+)-exchange rate compared to O-Asp.
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Affiliation(s)
- Ana Fragoso
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
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14
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Pires S, Habjanič J, Sezer M, Soares CM, Hemmingsen L, Iranzo O. Design of a Peptidic Turn with High Affinity for HgII. Inorg Chem 2012; 51:11339-48. [DOI: 10.1021/ic3008014] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Sara Pires
- Instituto de Tecnologia
Química e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-157
Oeiras, Portugal
| | - Jelena Habjanič
- Instituto de Tecnologia
Química e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-157
Oeiras, Portugal
| | - Murat Sezer
- Instituto de Tecnologia
Química e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-157
Oeiras, Portugal
| | - Cláudio M. Soares
- Instituto de Tecnologia
Química e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-157
Oeiras, Portugal
| | - Lars Hemmingsen
- Department of Chemistry, University of Copenhagen, Universitetsparken
5, 2100 København Ø, Denmark
| | - Olga Iranzo
- Instituto de Tecnologia
Química e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-157
Oeiras, Portugal
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15
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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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16
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Solution and solid state study of copper(II) ternary complexes containing amino acids of interest for brain biochemistry – 2: Homocysteine with aspartate, glutamate or methionine. Inorganica Chim Acta 2012. [DOI: 10.1016/j.ica.2012.01.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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17
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Shiga D, Nakane D, Inomata T, Funahashi Y, Masuda H, Kikuchi A, Oda M, Noda M, Uchiyama S, Fukui K, Kanaori K, Tajima K, Takano Y, Nakamura H, Tanaka T. Creation of a Type 1 Blue Copper Site within a de Novo Coiled-Coil Protein Scaffold. J Am Chem Soc 2010; 132:18191-8. [DOI: 10.1021/ja106263y] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Daigo Shiga
- Department of Material Sciences, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-chou, Nagoya 466-8555, Japan, Biometal Science Laboratory, RIKEN SPring-8 Center, 1-1-1, Kouto, Sayo, Hyogo 679-5148, Japan, Department of Biomolecular Chemistry, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan, Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita,
| | - Daisuke Nakane
- Department of Material Sciences, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-chou, Nagoya 466-8555, Japan, Biometal Science Laboratory, RIKEN SPring-8 Center, 1-1-1, Kouto, Sayo, Hyogo 679-5148, Japan, Department of Biomolecular Chemistry, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan, Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita,
| | - Tomohiko Inomata
- Department of Material Sciences, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-chou, Nagoya 466-8555, Japan, Biometal Science Laboratory, RIKEN SPring-8 Center, 1-1-1, Kouto, Sayo, Hyogo 679-5148, Japan, Department of Biomolecular Chemistry, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan, Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita,
| | - Yasuhiro Funahashi
- Department of Material Sciences, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-chou, Nagoya 466-8555, Japan, Biometal Science Laboratory, RIKEN SPring-8 Center, 1-1-1, Kouto, Sayo, Hyogo 679-5148, Japan, Department of Biomolecular Chemistry, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan, Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita,
| | - Hideki Masuda
- Department of Material Sciences, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-chou, Nagoya 466-8555, Japan, Biometal Science Laboratory, RIKEN SPring-8 Center, 1-1-1, Kouto, Sayo, Hyogo 679-5148, Japan, Department of Biomolecular Chemistry, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan, Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita,
| | - Akihiro Kikuchi
- Department of Material Sciences, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-chou, Nagoya 466-8555, Japan, Biometal Science Laboratory, RIKEN SPring-8 Center, 1-1-1, Kouto, Sayo, Hyogo 679-5148, Japan, Department of Biomolecular Chemistry, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan, Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita,
| | - Masayuki Oda
- Department of Material Sciences, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-chou, Nagoya 466-8555, Japan, Biometal Science Laboratory, RIKEN SPring-8 Center, 1-1-1, Kouto, Sayo, Hyogo 679-5148, Japan, Department of Biomolecular Chemistry, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan, Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita,
| | - Masanori Noda
- Department of Material Sciences, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-chou, Nagoya 466-8555, Japan, Biometal Science Laboratory, RIKEN SPring-8 Center, 1-1-1, Kouto, Sayo, Hyogo 679-5148, Japan, Department of Biomolecular Chemistry, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan, Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita,
| | - Susumu Uchiyama
- Department of Material Sciences, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-chou, Nagoya 466-8555, Japan, Biometal Science Laboratory, RIKEN SPring-8 Center, 1-1-1, Kouto, Sayo, Hyogo 679-5148, Japan, Department of Biomolecular Chemistry, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan, Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita,
| | - Kiichi Fukui
- Department of Material Sciences, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-chou, Nagoya 466-8555, Japan, Biometal Science Laboratory, RIKEN SPring-8 Center, 1-1-1, Kouto, Sayo, Hyogo 679-5148, Japan, Department of Biomolecular Chemistry, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan, Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita,
| | - Kenji Kanaori
- Department of Material Sciences, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-chou, Nagoya 466-8555, Japan, Biometal Science Laboratory, RIKEN SPring-8 Center, 1-1-1, Kouto, Sayo, Hyogo 679-5148, Japan, Department of Biomolecular Chemistry, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan, Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita,
| | - Kunihiko Tajima
- Department of Material Sciences, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-chou, Nagoya 466-8555, Japan, Biometal Science Laboratory, RIKEN SPring-8 Center, 1-1-1, Kouto, Sayo, Hyogo 679-5148, Japan, Department of Biomolecular Chemistry, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan, Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita,
| | - Yu Takano
- Department of Material Sciences, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-chou, Nagoya 466-8555, Japan, Biometal Science Laboratory, RIKEN SPring-8 Center, 1-1-1, Kouto, Sayo, Hyogo 679-5148, Japan, Department of Biomolecular Chemistry, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan, Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita,
| | - Haruki Nakamura
- Department of Material Sciences, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-chou, Nagoya 466-8555, Japan, Biometal Science Laboratory, RIKEN SPring-8 Center, 1-1-1, Kouto, Sayo, Hyogo 679-5148, Japan, Department of Biomolecular Chemistry, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan, Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita,
| | - Toshiki Tanaka
- Department of Material Sciences, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-chou, Nagoya 466-8555, Japan, Biometal Science Laboratory, RIKEN SPring-8 Center, 1-1-1, Kouto, Sayo, Hyogo 679-5148, Japan, Department of Biomolecular Chemistry, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan, Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita,
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18
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Chakraborty S, Touw DS, Peacock AFA, Stuckey J, Pecoraro VL. Structural comparisons of apo- and metalated three-stranded coiled coils clarify metal binding determinants in thiolate containing designed peptides. J Am Chem Soc 2010; 132:13240-50. [PMID: 20825181 PMCID: PMC3004433 DOI: 10.1021/ja101812c] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Over the past two decades, designed metallopeptides have held the promise for understanding a variety of fundamental questions in metallobiochemistry; however, these dreams have not yet been realized because of a lack of structural data to elaborate the protein scaffolds before metal complexation and the resultant metalated structures which ultimately exist. This is because there are few reports of structural characterization of such systems either in their metalated or nonmetalated forms and no examples where an apo structure and the corresponding metalated peptide assembly have both been defined by X-ray crystallography. Herein we present X-ray structures of two de novo designed parallel three-stranded coiled coils (designed using the heptad repeat (a → g)) CSL9C (CS = Coil Ser) and CSL19C in their nonmetalated forms, determined to 1.36 and 2.15 A resolutions, respectively. Leucines from either position 9 (a site) or 19 (d site) are replaced by cysteine to generate the constructs CSL9C and CSL19C, respectively, yielding thiol-rich pockets at the hydrophobic interior of these peptides, suitable to bind heavy metals such as As(III), Hg(II), Cd(II), and Pb(II). We use these structures to understand the inherent structural differences between a and d sites to clarify the basis of the observed differential spectroscopic behavior of metal binding in these types of peptides. Cys side chains of (CSL9C)(3) show alternate conformations and are partially preorganized for metal binding, whereas cysteines in (CSL19C)(3) are present as a single conformer. Zn(II) ions, which do not coordinate or influence Cys residues at the designed metal sites but are essential for forming X-ray quality crystals, are bound to His and Glu residues at the crystal packing interfaces of both structures. These "apo" structures are used to clarify the changes in metal site organization between metalated As(CSL9C)(3) and to speculate on the differential basis of Hg(II) binding in a versus d peptides. Thus, for the first time, one can establish general rules for heavy metal binding to Cys-rich sites in designed proteins which may provide insight for understanding how heavy metals bind to metallochaperones or metalloregulatory proteins.
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Affiliation(s)
- Saumen Chakraborty
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109 (USA), Fax: (+1) 734-936-7628
| | - Debra S. Touw
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109 (USA), Fax: (+1) 734-936-7628
| | - Anna F. A. Peacock
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109 (USA), Fax: (+1) 734-936-7628
| | - Jeanne Stuckey
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109 (USA)
| | - Vincent L. Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109 (USA), Fax: (+1) 734-936-7628
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19
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Pinto LD, Puppin PA, Behring VM, Flinker DH, Mercê ALR, Mangrich AS, Rey NA, Felcman J. Solution and solid state study of copper(II) ternary complexes containing amino acids of interest for brain biochemistry – 1: Aspartic or glutamic acids with methionine or cysteine. Inorganica Chim Acta 2010. [DOI: 10.1016/j.ica.2010.04.036] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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20
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Razeghifard R. Artificial photoactive proteins. PHOTOSYNTHESIS RESEARCH 2008; 98:677-685. [PMID: 18830805 DOI: 10.1007/s11120-008-9367-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2008] [Accepted: 09/09/2008] [Indexed: 05/26/2023]
Abstract
Solar power is the most abundant source of renewable energy. In this respect, the goal of making photoactive proteins is to utilize this energy to generate an electron flow. Photosystems have provided the blueprint for making such systems, since they are capable of converting the energy of light into an electron flow using a series of redox cofactors. Protein tunes the redox potential of the cofactors and arranges them such that their distance and orientation are optimal for the creation of a stable charge separation. The aim of this review is to present an overview of the literature with regard to some elegant functional structures that protein designers have created by introducing cofactors and photoactivity into synthetic proteins.
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Affiliation(s)
- Reza Razeghifard
- Division of Math, Science, and Technology, Farquhar College of Arts & Science, Nova Southeastern University, Fort Lauderdale, FL 33314, USA.
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21
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Double edge redox-implications for the interaction between endogenous thiols and copper ions: In vitro studies. Bioorg Med Chem 2008; 16:9795-803. [PMID: 18926709 DOI: 10.1016/j.bmc.2008.09.068] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2008] [Revised: 09/24/2008] [Accepted: 09/26/2008] [Indexed: 11/22/2022]
Abstract
The present study investigated the redox-consequences of the interaction between various endogenous thiols (RSH)-glutathione, cysteine, homocysteine, gamma-glutamyl-cysteine, and cysteinyl-glycine- and Cu(2+) ions, in terms of their free radical-scavenging, ascorbate-oxidizing and O2(*-)-generating properties of the resulting mixtures. Upon a brief incubation (3-30 min) with Cu(2+), the free radical-scavenging properties (towards ABTS(*)(+) and DPPH(*)) and thiol-titratable groups of the RSH added to the mixtures decreased significantly. Remarkably, both effects were only partial, even in the presence of a large molar Cu(2+)-excess, and were unaffected despite increasing the incubation time. At equimolar concentrations, the RSH/Cu(2+) mixtures led to the formation of (EPR paramagnetic) Cu(II)-complexes that were time-stable and ascorbate-reducible, but redox-inactive towards oxygen. In turn, at a slight molar thiol-excess (3:1), the mixtures resulted in the formation of time-stable Cu(I)-complexes (EPR silent) that were unreactive towards ascorbate and oxygen. The only exception was seen for the thiol, glutathione, whose mixture with Cu(2+) mixture displayed a O2(*-)-generating capacity (cytochrome c- and lucigenin-reduction). The data indicate that, depending on their molar ratio, the interaction between Cu(2+) and the tested thiols would give place to mixtures containing either: (i) time-stable and ascorbate-reducible Cu(II)-complexes which display free radical-scavenging properties, or (ii) time-stable but redox-inactive towards oxygen Cu(I)-complexes. Among the latter, the only exception was that of glutathione.
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22
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Kulon K, Valensin D, Kamysz W, Nadolny R, Gaggelli E, Valensin G, Kozłowski H. Binding of Ni2+ and Cu2+ ions to peptides with a Cys–His motif. Dalton Trans 2008:5323-30. [DOI: 10.1039/b806851h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Brines LM, Shearer J, Fender JK, Schweitzer D, Shoner SC, Barnhart D, Kaminsky W, Lovell S, Kovacs JA. Periodic trends within a series of five-coordinate thiolate-ligated [MII(SMe2N4(tren))]+ (M = Mn, Fe, Co, Ni, Cu, Zn) complexes, including a rare example of a stable CuII-thiolate. Inorg Chem 2007; 46:9267-77. [PMID: 17867686 PMCID: PMC2532082 DOI: 10.1021/ic701433p] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A series of five-coordinate thiolate-ligated complexes [M(II)(tren)N4S(Me2)]+ (M = Mn, Fe, Co, Ni, Cu, Zn; tren = tris(2-aminoethyl)amine) are reported, and their structural, electronic, and magnetic properties are compared. Isolation of dimeric [Ni(II)(SN4(tren)-RS(dang))]2 ("dang"= dangling, uncoordinated thiolate supported by H bonds), using the less bulky [(tren)N4S](1-) ligand, pointed to the need for gem-dimethyls adjacent to the sulfur to sterically prevent dimerization. All of the gem-dimethyl derivatized complexes are monomeric and, with the exception of [Ni(II)(S(Me2)N4(tren)]+, are isostructural and adopt a tetragonally distorted trigonal bipyramidal geometry favored by ligand constraints. The nickel complex uniquely adopts an approximately ideal square pyramidal geometry and resembles the active site of Ni-superoxide dismutase (Ni-SOD). Even in coordinating solvents such as MeCN, only five-coordinate structures are observed. The MII-S thiolate bonds systematically decrease in length across the series (Mn-S > Fe-S > Co-S > Ni-S approximately Cu-S < Zn-S) with exceptions occurring upon the occupation of sigma* orbitals. The copper complex, [Cu(II)(S(Me2)N4(tren)]+, represents a rare example of a stable CuII-thiolate, and models the perturbed "green" copper site of nitrite reductase. In contrast to the intensely colored, low-spin Fe(III)-thiolates, the M(II)-thiolates described herein are colorless to moderately colored and high-spin (in cases where more than one spin-state is possible), reflecting the poorer energy match between the metal d- and sulfur orbitals upon reduction of the metal ion. As the d-orbitals drop in energy proceeding across the across the series M(2+) (M= Mn, Fe, Co, Ni, Cu), the sulfur-to-metal charge-transfer transition moves into the visible region, and the redox potentials cathodically shift. The reduced M(+1) oxidation state is only accessible with copper, and the more oxidized M(+4) oxidation state is only accessible for manganese.
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Affiliation(s)
- Lisa M. Brines
- The Department of Chemistry, University of Washington: Box 351700 Seattle, WA 98195-1700
| | - Jason Shearer
- The Department of Chemistry, University of Washington: Box 351700 Seattle, WA 98195-1700
| | - Jessica K. Fender
- The Department of Chemistry, University of Washington: Box 351700 Seattle, WA 98195-1700
| | - Dirk Schweitzer
- The Department of Chemistry, University of Washington: Box 351700 Seattle, WA 98195-1700
| | - Steven C. Shoner
- The Department of Chemistry, University of Washington: Box 351700 Seattle, WA 98195-1700
| | | | | | | | - Julie A. Kovacs
- The Department of Chemistry, University of Washington: Box 351700 Seattle, WA 98195-1700
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Touw DS, Nordman CE, Stuckey JA, Pecoraro VL. Identifying important structural characteristics of arsenic resistance proteins by using designed three-stranded coiled coils. Proc Natl Acad Sci U S A 2007; 104:11969-74. [PMID: 17609383 PMCID: PMC1924535 DOI: 10.1073/pnas.0701979104] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2007] [Indexed: 11/18/2022] Open
Abstract
Arsenic, a contaminant of water supplies worldwide, is one of the most toxic inorganic ions. Despite arsenic's health impact, there is relatively little structural detail known about its interactions with proteins. Bacteria such as Escherichia coli have evolved arsenic resistance using the Ars operon that is regulated by ArsR, a repressor protein that dissociates from DNA when As(III) binds. This protein undergoes a critical conformational change upon binding As(III) with three cysteine residues. Unfortunately, structures of ArsR with or without As(III) have not been reported. Alternatively, de novo designed peptides can bind As(III) in an endo configuration within a thiolate-rich environment consistent with that proposed for both ArsR and ArsD. We report the structure of the As(III) complex of Coil Ser L9C to a 1.8-A resolution, providing x-ray characterization of As(III) in a Tris thiolate protein environment and allowing a structural basis by which to understand arsenated ArsR.
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Affiliation(s)
| | | | | | - Vincent L. Pecoraro
- *Department of Chemistry
- Biophysics Research Division, University of Michigan, Ann Arbor, MI 48109
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25
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Petros AK, Reddi AR, Kennedy ML, Hyslop AG, Gibney BR. Femtomolar Zn(II) affinity in a peptide-based ligand designed to model thiolate-rich metalloprotein active sites. Inorg Chem 2007; 45:9941-58. [PMID: 17140191 DOI: 10.1021/ic052190q] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metal-ligand interactions are critical components of metalloprotein assembly, folding, stability, electrochemistry, and catalytic function. Research over the past 3 decades on the interaction of metals with peptide and protein ligands has progressed from the characterization of amino acid-metal and polypeptide-metal complexes to the design of folded protein scaffolds containing multiple metal cofactors. De novo metalloprotein design has emerged as a valuable tool both for the modular synthesis of these complex metalloproteins and for revealing the fundamental tenets of metalloprotein structure-function relationships. Our research has focused on using the coordination chemistry of de novo designed metalloproteins to probe the interactions of metal cofactors with protein ligands relevant to biological phenomena. Herein, we present a detailed thermodynamic analysis of Fe(II), Co(II), Zn(II), and[4Fe-4S]2(+/+) binding to IGA, a 16 amino acid peptide ligand containing four cysteine residues, H2N-KLCEGG-CIGCGAC-GGW-CONH2. These studies were conducted to delineate the inherent metal-ion preferences of this unfolded tetrathiolate peptide ligand as well as to evaluate the role of the solution pH on metal-peptide complex speciation. The [4Fe-4S]2(+/+)-IGA complex is both an excellent peptide-based synthetic analogue for natural ferredoxins and is flexible enough to accommodate mononuclear metal-ion binding. Incorporation of a single ferrous ion provides the FeII-IGA complex, a spectroscopic model of a reduced rubredoxin active site that possesses limited stability in aqueous buffers. As expected based on the Irving-Williams series and hard-soft acid-base theory, the Co(II) and Zn(II) complexes of IGA are significantly more stable than the Fe(II) complex. Direct proton competition experiments, coupled with determinations of the conditional dissociation constants over a range of pH values, fully define the thermodynamic stabilities and speciation of each MII-IGA complex. The data demonstrate that FeII-IGA and CoII-IGA have formation constant values of 5.0 x 10(8) and 4.2 x 10(11) M-1, which are highly attenuated at physiological pH values. The data also evince that the formation constant for ZnII-IGA is 8.0 x 10(15) M-1, a value that exceeds the tightest natural protein Zn(II)-binding affinities. The formation constant demonstrates that the metal-ligand binding energy of a ZnII(S-Cys)4 site can stabilize a metalloprotein by -21.6 kcal/mol. Rigorous thermodynamic analyses such as those demonstrated here are critical to current research efforts in metalloprotein design, metal-induced protein folding, and metal-ion trafficking.
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Affiliation(s)
- Amy K Petros
- Department of Chemistry, Columbia University, MC 3121, New York, New York 10027, USA
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26
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Li C, Yanagisawa S, Martins BM, Messerschmidt A, Banfield MJ, Dennison C. Basic requirements for a metal-binding site in a protein: the influence of loop shortening on the cupredoxin azurin. Proc Natl Acad Sci U S A 2006; 103:7258-63. [PMID: 16651527 PMCID: PMC1464330 DOI: 10.1073/pnas.0600774103] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2006] [Indexed: 11/18/2022] Open
Abstract
The main active-site loop of the copper-binding protein azurin (a cupredoxin) has been shortened from C(112)TFPGH(117)SALM(121) to C(112)TPH(115)PFM(118) (the native loop from the cupredoxin amicyanin) and also to C(112)TPH(115)PM(117). The Cu(II) site structure is almost unaffected by shortening, as is that of the Cu(I) center at alkaline pH in the variant with the C(112)TPH(115)PM(117) loop sequence. Subtle spectroscopic differences due to alterations in the spin density distribution at the Cu(II) site can be attributed mainly to changes in the hydrogen-bonding pattern. Electron transfer is almost unaffected by the introduction of the C(112)TPH(115)PFM(118) loop, but removal of the Phe residue has a sizable effect on reactivity, probably because of diminished homodimer formation. At mildly acidic pH values, the His-115 ligand protonates and dissociates from the cuprous ion, an effect that has a dramatic influence on the reactivity of cupredoxins. These studies demonstrate that the amicyanin loop adopts a conformation identical to that found in the native protein when introduced into azurin, that a shorter than naturally occurring C-terminal active-site loop can support a functional T1 copper site, that CTPHPM is the minimal loop length required for binding this ubiquitous electron transfer center, and that the length and sequence of a metal-binding loop regulates a range of structural and functional features of the active site of a metalloprotein.
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Affiliation(s)
- Chan Li
- Institute for Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Sachiko Yanagisawa
- Institute for Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Berta M. Martins
- Elitenetzwerk Bayern Macromolecular Science, Mikrobiologie/Proteinkristallographie Laboratories, Universität Bayreuth, D-95440 Bayreuth, Germany; and
| | - Albrecht Messerschmidt
- Max-Planck-Institut für Biochemie, Abteilung Strukturforschung, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Mark J. Banfield
- Institute for Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Christopher Dennison
- Institute for Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, United Kingdom
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27
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28
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Poger D, Fuchs JF, Nedev H, Ferrand M, Crouzy S. Molecular dynamics study of the metallochaperone Hah1 in its apo and Cu(I)-loaded states: role of the conserved residue M10. FEBS Lett 2005; 579:5287-92. [PMID: 16194538 DOI: 10.1016/j.febslet.2005.08.052] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2005] [Revised: 08/05/2005] [Accepted: 08/19/2005] [Indexed: 10/25/2022]
Abstract
Molecular dynamics simulations were performed on both apo and copper forms of the human copper chaperone, Hah1. Wild-type Hah1 and a methionine (M10) to serine mutant were investigated. We have evidenced the central role of residue M10 in stabilizing the hydrophobic core of Hah1 as well as the internal structure of the metal-binding site. When copper(I) is bound, the mobility of Hah1 is reduced whereas mutation of M10 implies a drastic increase of the mobility of apoHah1, stressing the importance of this highly conserved hydrophobic residue for copper sequestration by the apoprotein.
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Affiliation(s)
- David Poger
- Laboratoire de Biophysique Moléculaire et Cellulaire, Département de Réponse et Dynamique Cellulaires, Commissariat à l'Energie Atomique, Grenoble, France
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29
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Jiang J, Nadas IA, Kim MA, Franz KJ. A Mets Motif Peptide Found in Copper Transport Proteins Selectively Binds Cu(I) with Methionine-Only Coordination. Inorg Chem 2005; 44:9787-94. [PMID: 16363848 DOI: 10.1021/ic051180m] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mets motifs, which refer to methionine-rich sequences found in the high-affinity copper transporter Ctr1, also appear in other proteins involved in copper trafficking and homeostasis, including other Ctrs as well as Pco and Cop proteins isolated from copper-resistant bacteria. To understand the coordination chemistry utilized by these proteins, we studied the copper binding properties of a peptide labeled Mets7-PcoC with the sequence Met-Thr-Gly-Met-Lys-Gly-Met-Ser. By comparing this sequence to a series of mutants containing noncoordinating norleucine in place of methionine, we confirm that all three methionine residues are involved in a thioether-only binding site that is selective for Cu(I). Two independent methods, one based on mass spectrometry and one based on rate differences for the copper-catalyzed oxidation of ascorbic acid, provide an effective K(D) of approximately 2.5 microM at pH 4.5 for the 1:1 complex of Mets7-PcoC with Cu(I). These results establish that a relatively simple peptide containing an MX(2)MX(2)M motif is sufficient to bind Cu(I) with an affinity that corresponds well with its proposed biological function of extracellular copper acquisition.
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Affiliation(s)
- Jianfeng Jiang
- Department of Chemistry, Duke University, P.O. Box 90346, Durham, North Carolina 27708, USA
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Dennison C. Ligand and loop variations at type 1 copper sites: influence on structure and reactivity. Dalton Trans 2005:3436-42. [PMID: 16234922 DOI: 10.1039/b507440c] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Type 1 (T1) copper sites promote biological electron transfer and are found in the cupredoxins and a number of copper-containing enzymes including the multi-copper oxidases. A T1 copper site usually has a distorted tetrahedral geometry with strong ligands provided by the thiolate sulfur of a Cys and the imidazole nitrogens of two His residues. The active site structure is typically completed by a weak axial Met ligand (a second weak axial interaction is found in azurin resulting in a trigonal bipyramidal geometry). The axial Met is not conserved and Gln, Phe, Leu and Val are also found in this position. Three of the four ligands at a T1 copper site are situated on a single C-terminal loop whose length and structure varies. Studies are discussed which investigate both the influence of physiologically relevant axial ligand alterations, and also of mutations to the length and structure of the ligand-containing loop, on the properties of T1 copper sites.
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Affiliation(s)
- Christopher Dennison
- Institute for Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne, UK NE2 4HH.
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Abstract
The shortest known type 1 copper binding loop (that of amicyanin, Ami) has been introduced into three different cupredoxin beta-barrel scaffolds. All of the loop-contraction variants possess copper centers with authentic type 1 properties and are redox active. The Cu(II) and Co(II) sites experience only small structural alterations upon loop contraction with the largest changes in the azurin variant (AzAmi), which can be ascribed to the removal of a hydrogen bond to the coordinating thiolate sulfur of the Cys ligand. In all cases, loop contraction leads to an increase in the pK(a) of the His ligand found on the loop in the reduced proteins, and in the pseudoazurin (Paz) and plastocyanin (Pc) variants the values are almost identical to that of Ami ( approximately 6.7). Thus, in Paz, Pc, and Ami, the length of this loop tunes the pK(a) of the His ligand. In the AzAmi variant, the pK(a) is 5.5, which is considerably higher than the estimated value for Az (<2), and other controlling factors, along with loop length, are involved. The reduction potentials of the loop-contraction variants are all lower than those of the wild-type proteins by approximately 30-60 mV, and thus this property of a type 1 copper site is fine-tuned by the C-terminal loop. The electron self-exchange rate constant of Paz is significantly diminished by the introduction of a shorter loop. However, in PcAmi only a 2-fold decrease is observed and in AzAmi there is no effect, and thus in these two cupredoxins loop contraction does not significantly influence electron-transfer reactivity. Loop contraction provides an active site environment in all of the cupredoxins which is preferable for Cu(II), whereas previous loop elongation experiments always favored the cuprous site. Thus, the ligand-containing loop plays an important role in tuning the entatic nature of a type 1 copper center.
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Affiliation(s)
- Sachiko Yanagisawa
- School of Natural Sciences, Bedson Building, University of Newcastle upon Tyne, Newcastle upon Tyne, NE1 7RU, UK
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Licini G, Prins LJ, Scrimin P. Oligopeptide Foldamers: From Structure to Function. European J Org Chem 2005. [DOI: 10.1002/ejoc.200400521] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Giulia Licini
- University of Padova, Department of Chemical Sciences, and ITM‐CNR, Padova Section, Via Marzolo, 1, 35131 Padova, Italy
| | - Leonard J. Prins
- University of Padova, Department of Chemical Sciences, and ITM‐CNR, Padova Section, Via Marzolo, 1, 35131 Padova, Italy
| | - Paolo Scrimin
- University of Padova, Department of Chemical Sciences, and ITM‐CNR, Padova Section, Via Marzolo, 1, 35131 Padova, Italy
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Frank P, Benfatto M, Szilagyi RK, D'Angelo P, Della Longa S, Hodgson KO. The Solution Structure of [Cu(aq)]2+ and Its Implications for Rack-Induced Bonding in Blue Copper Protein Active Sites. Inorg Chem 2005; 44:1922-33. [PMID: 15762718 DOI: 10.1021/ic0400639] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structure of [Cu(aq)]2+ has been investigated by using full multiple-scattering theoretical (MXAN) analysis of the copper K-edge X-ray absorption (XAS) spectrum and density functional theory (DFT) to test both ideal Td and square-planar four-coordinate, five-coordinate square-pyramidal, and six-coordinate octahedral [Cu(aq)]2+ models. The best fit was an elongated five-coordinate square pyramid with four Cu-O(eq) bonds (2 x 1.98 +/- 0.03 A and 2 x 1.95 +/- 0.03 A) and a long Cu-O(ax) bond (2.35 +/- 0.05 A). The four equatorial ligands were D2d-distorted from the mean equatorial plane by +/-(17 +/- 4) degrees, so that the overall symmetry of [Cu(H2O)5]2+ is C2v. The four-coordinate MXAN fit was nearly as good, but the water ligands (4 x 1.96 +/- 0.02 A) migrated +/-(13 +/- 4) degrees from the mean equatorial plane, making the [Cu(H2O)4]2+ model again D2d-distorted. Spectroscopically calibrated DFT calculations were carried out on the C2v elongate square-pyramidal and D2d-distorted four-coordinate MXAN copper models, providing comparative electronic structures of the experimentally observed geometries. These calculations showed 0.85e spin on Cu(II) and 0.03e electron spin on each of the four equatorial water oxygens. All covalent bonding was restricted to the equatorial plane. In the square-pyramidal model, the electrostatic Cu-O(ax) bond was worth only 96.8 kJ mol(-1), compared to 304.6 kJ mol(-1) for each Cu-O(eq) bond. Both MXAN and DFT showed the potential well of the axial bond to be broad and flat, allowing large low-energy excursions. The irregular geometry and D2d-distorted equatorial ligand set sustained by unconstrained [Cu(H2O)5]2+ warrants caution in drawing conclusions regarding structural preferences from small molecule crystal structures and raises questions about the site-structural basis of the rack-induced bonding hypothesis of blue copper proteins. Further, previously neglected protein folding thermodynamic consequences of the rack-bonding hypothesis indicate an experimental disconfirmation.
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Affiliation(s)
- Patrick Frank
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, USA.
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Affiliation(s)
- Charles J Reedy
- Department of Chemistry, Columbia University, 3000 Broadway, MC 3121, New York, New York 10027, USA
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Wu AJ, Penner-Hahn JE, Pecoraro VL. Structural, spectroscopic, and reactivity models for the manganese catalases. Chem Rev 2004; 104:903-38. [PMID: 14871145 DOI: 10.1021/cr020627v] [Citation(s) in RCA: 404] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Amy J Wu
- Willard H Dow Laboratories, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, USA
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Arnesano F, Banci L, Benvenuti M, Bertini I, Calderone V, Mangani S, Viezzoli MS. The evolutionarily conserved trimeric structure of CutA1 proteins suggests a role in signal transduction. J Biol Chem 2003; 278:45999-6006. [PMID: 12949080 DOI: 10.1074/jbc.m304398200] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
CutA1 are a protein family present in bacteria, plants, and animals, including humans. Escherichia coli CutA1 is involved in copper tolerance, whereas mammalian proteins are implicated in the anchoring of acetylcholinesterase in neuronal cell membranes. The x-ray structures of CutA1 from E. coli and rat were determined. Both proteins are trimeric in the crystals and in solution through an inter-subunit beta-sheet formation. Each subunit consists of a ferredoxin-like (beta1alpha1beta2beta3alpha2beta4) fold with an additional strand (beta5), a C-terminal helix (alpha3), and an unusual extended beta-hairpin involving strands beta2 and beta3. The bacterial CutA1 is able to bind copper(II) in vitro through His2Cys coordination in a type II water-accessible site, whereas the rat protein precipitates in the presence of copper(II). The evolutionarily conserved trimeric assembly of CutA1 is reminiscent of the architecture of PII signal transduction proteins. This similarity suggests an intriguing role of CutA1 proteins in signal transduction through allosteric communications between subunits.
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Affiliation(s)
- Fabio Arnesano
- Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy
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