Active Sites Of Metalloproteins Research Articles

Conformation-Dependent Hydrogen-Bonding Interactions in a Switchable Artificial Metalloprotein.

Hydrogen-bonding (H-bonding) interactions in metalloprotein active sites can critically regulate enzyme function. Changes in the protein structure triggered by interplay with substrates, products, and partner proteins are often translated to the metallocofactor by way of specific changes in H-bond networks connected to the active site. However, the complexities of metalloprotein architecture and mechanism often preclude our ability to define the precise molecular interactions giving rise to these intricate regulatory pathways. To address this shortcoming, we have developed conformationally switchable artificial metalloproteins (swArMs) in which allosteric Gln-binding triggers protein conformational changes that impact the microenvironment surrounding an installed metallocofactor. Herein, we report a combined structural, spectroscopic, and computational approach to enhance the conformation-dependent changes in H-bond interactions surrounding the metallocofactor site of a swArM. Structure-informed molecular dynamics simulations were employed to predict point mutations that could enhance active site H-bond interactions preferentially in the Gln-bound holo-conformation of the swArM. Testing our predictions via the unique infrared spectral signals associated with the metallocofactor site, we have identified three key residues capable of imparting conformational control over the metallocofactor microenvironment. The resultant swArMs not only model biologically relevant structural regulation but also provide an enhanced Gln-responsive biological probe to be leveraged in future biosensing applications.

Synthesis of Transition Metal-sulfur Complexes by Si-S Bond Cleavage

Abstract: This mini-review summarizes the methods available for the synthesis of transition metalsulfur complexes, which have been used as models of metalloprotein active sites, desulfurization catalysts, and organometallic functional materials. All the methods use silicon-sulfur compounds as starting materials, exploiting the selective cleavage of Si—S bond and the subsequent incorporation of sulfur fragments into the metal complex. Mechanistic considerations are also provided. Period covered: 1968 to date.

Catalytic Reduction of Dioxygen to Water by a Bioinspired Non-Heme Iron Complex via a 2+2 Mechanism.

We report a bioinspired non-heme Fe complex with a tripodal [N3O]- ligand framework (Fe(PMG)(Cl)2) that is electrocatalytically active toward dioxygen reduction with acetic acid as a proton source in acetonitrile solution. Under electrochemical and chemical conditions, Fe(PMG)(Cl)2 selectively produces water via a 2+2 mechanism, where H2O2 is generated as a discrete intermediate species before further reduction to two equivalents of H2O. Mechanistic studies support a catalytic cycle for dioxygen reduction where an off-cycle peroxo dimer species is the resting state of the catalyst. Spectroscopic analysis of the reduced complex FeII(PMG)Cl shows the stoichiometric formation of an Fe(III)-hydroxide species following exposure to H2O2; no catalytic activity for H2O2 disproportionation is observed, although the complex is electrochemically active for H2O2 reduction to H2O. Electrochemical studies, spectrochemical experiments, and DFT calculations suggest that the carboxylate moiety of the ligand is sensitive to hydrogen-bonding interactions with the acetic acid proton donor upon reduction from Fe(III)/(II), favoring chloride loss trans to the tris-alkyl amine moiety of the ligand framework. These results offer insight into how mononuclear non-heme Fe active sites in metalloproteins distribute added charge and poise proton donors during reactions with dioxygen.

Kβ X-ray Emission Spectroscopy as a Probe of Cu(I) Sites: Application to the Cu(I) Site in Preprocessed Galactose Oxidase.

Cu(I) active sites in metalloproteins are involved in O2 activation, but their O2 reactivity is difficult to study due to the Cu(I) d10 closed shell which precludes the use of conventional spectroscopic methods. Kβ X-ray emission spectroscopy (XES) is a promising technique for investigating Cu(I) sites as it detects photons emitted by electronic transitions from occupied orbitals. Here, we demonstrate the utility of Kβ XES in probing Cu(I) sites in model complexes and a metalloprotein. Using Cu(I)Cl, emission features from double-ionization (DI) states are identified using varying incident X-ray photon energies, and a reasonable method to correct the data to remove DI contributions is presented. Kβ XES spectra of Cu(I) model complexes, having biologically relevant N/S ligands and different coordination numbers, are compared and analyzed, with the aid of density functional theory (DFT) calculations, to evaluate the sensitivity of the spectral features to the ligand environment. While the low-energy Kβ2,5 emission feature reflects the ionization energy of ligand np valence orbitals, the high-energy Kβ2,5 emission feature corresponds to transitions from molecular orbitals (MOs) having mainly Cu 3d character with the intensities determined by ligand-mediated d-p mixing. A Kβ XES spectrum of the Cu(I) site in preprocessed galactose oxidase (GOpre) supports the 1Tyr/2His structural model that was determined by our previous X-ray absorption spectroscopy and DFT study. The high-energy Kβ2,5 emission feature in the Cu(I)-GOpre data has information about the MO containing mostly Cu 3dx2-y2 character that is the frontier molecular orbital (FMO) for O2 activation, which shows the potential of Kβ XES in probing the Cu(I) FMO associated with small-molecule activation in metalloproteins.

Designing the Secondary Coordination Sphere in Small-Molecule Catalysis

AbstractThe application of secondary-sphere interactions in catalysis was inspired by the hierarchical arrangement of the microenvironment of metalloprotein active sites and has been adopted mainly in organometallic catalysis. The study of such interactions has enabled the deliberate orientation of reaction components, leading to control over reactivity and selectivity by design. Although not as common, such interaction can play a decisive role in organocatalysis. Herein, we present several examples of small-molecule organometallic- and organocatalysis, highlighting the advantages offered by carefully designing the secondary sphere.1 Introduction2 Secondary-Sphere Design in Organometallic Catalysis3 Secondary-Sphere Modification in Organocatalysis4 Using Statistical Analysis to Systematically Tune and Probe Secondary-Sphere Interactions5 Conclusion

Copper-induced spectroscopic and structural changes in short peptides derived from azurin

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.

Radical S-adenosylmethionine maquette chemistry: Cx3Cx2C peptide coordinated redox active [4Fe-4S] clusters.

The synthesis and characterization of short peptide-based maquettes of metalloprotein active sites facilitate an inquiry into their structure/function relationships and evolution. The [4Fe-4S]-maquettes of bacterial ferredoxin metalloproteins (Fd) have been used in the past to engineer redox active centers into artificial metalloenzymes. The novelty of our study is the application of maquettes to the superfamily of [4Fe-4S] cluster and S-adenosylmethionine-dependent radical metalloenzymes (radical SAM). The radical SAM superfamily enzymes contain site-differentiated, redox active [4Fe-4S] clusters coordinated to Cx3Cx2C or related motifs, which is in contrast to the Cx2Cx2C motif found in bacterial ferredoxins (Fd). Under an optimized set of experimental conditions, a high degree of reconstitution (80-100%) was achieved for both radical SAM- and Fd-maquettes. Negligible chemical speciation was observed for all sequences, with predominantly [4Fe-4S]2+ for the 'as-reconstituted' state. However, the reduction of [4Fe-4S]2+-maquettes provides low conversion (7-17%) to the paramagnetic [4Fe-4S]+ state, independent of either the spacing of the cysteine residues (Cx3Cx2C vs. Cx2Cx2C), the nature of intervening amino acids, or the length of the cluster binding motif. In the absence of the stabilizing protein environment, the reduction process is proposed to proceed via [4Fe-4S]2+ cluster disassembly and reassembly in a more reduced state. UV-Vis and EPR spectroscopic techniques are employed as analytical tools to quantitate the as-reconstituted (or oxidized) and one-electron reduced states of the [4Fe-4S] clusters, respectively. We demonstrate that short Fd and radical SAM derived 7- to 9-mer peptides containing appropriate cysteine motifs function equally well in coordinating redox active [4Fe-4S] clusters.

Redox Potentials and Electronic States of Iron Porphyrin IX Adsorbed on Single Crystal Gold Electrode Surfaces.

Metalloporphyrins are active sites in metalloproteins and synthetic catalysts. They have also been studied extensively by electrochemistry as well as being prominent targets in electrochemical scanning tunneling microscopy (STM). Previous studies of FePPIX adsorbed on graphite and alkylthiol modified Au electrodes showed a pair of reversible Fe(III/II)PPIX peaks at about -0.41 V (vs NHE) at high solution pH. We recently used iron protoporphyrin IX (FePPIX) as an intercalating probe for long-range electrochemical electron transfer through a G-quadruplex oligonucleotide (DNAzyme); this study disclosed two, rather than a single pair of voltammetric peaks with a new and dominating peak, shifted 200 mV positive relative to the ≈-0.4 V peak. Prompted by this unexpected observation, we report here a study of the voltammetry of FePPIX itself on single-crystal Au(111), (100), and (110) and polycrystalline Au electrode surfaces. In all cases the dominating pair of new Fe(III/II)PPIX redox peaks, shifted positively by more than 200 mV compared to those of previous studies appeared. This observation is supported by density functional theory (DFT) which shows that strong dispersion forces in the FePPIX/Au electronic interaction drive the midpoint potential toward positive values. The FePPIX spin states depend on interaction with the Au(111) interface, converting all the Fe(II)/(III)PPIX species into low-spin states. These results support electrochemical evidence for the nature of the electronic coupling between FePPIX and Au-surfaces, and the electronic states of adsorbate molecules, with a bearing also on recent reports of magnetic FePPIX/Au(111) interactions in ultrahigh vacuum (UHV).

High-Energy-Resolution Fluorescence-Detected X-ray Absorption of the Q Intermediate of Soluble Methane Monooxygenase.

Kα high-energy-resolution fluorescence detected X-ray absorption spectroscopy (HERFD XAS) provides a powerful tool for overcoming the limitations of conventional XAS to identify the electronic structure and coordination environment of metalloprotein active sites. Herein, Fe Kα HERFD XAS is applied to the diiron active site of soluble methane monooxygenase (sMMO) and to a series of high-valent diiron model complexes, including diamond-core [FeIV2(μ-O)2(L)2](ClO4)4] (3) and open-core [(O═FeIV-O-FeIV(OH)(L)2](ClO4)3 (4) models (where, L = tris(3,5-dimethyl-4-methoxypyridyl-2-methyl)amine) (TPA*)). Pronounced differences in the HERFD XAS pre-edge energies and intensities are observed for the open versus closed Fe2O2 cores in the model compounds. These differences are reproduced by time-dependent density functional theory (TDDFT) calculations and allow for the pre-edge energies and intensity to be directly correlated with the local active site geometric and electronic structure. A comparison of the model complex HERFD XAS data to that of MMOHQ (the key intermediate in methane oxidation) is supportive of an open-core structure. Specifically, the large pre-edge area observed for MMOHQ may be rationalized by invoking an open-core structure with a terminal FeIV═O motif, though further modulations of the core structure due to the protein environment cannot be ruled out. The present study thus motivates the need for additional experimental and theoretical studies to unambiguously assess the active site conformation of MMOHQ.

Models for Unsymmetrical Active Sites in Metalloproteins: Structural, Redox, and Magnetic Properties of Bimetallic Complexes with MII-(μ-OH)-FeIII Cores.

Bimetallic complexes are important sites in metalloproteins but are often difficult to prepare synthetically. We have previously introduced an approach to form discrete bimetallic complexes with MII-(μ-OH)-FeIII (MII = Mn, Fe) cores using the tripodal ligand N,N',N″-[2,2',2″-nitrilotris(ethane-2,1-diyl)]tris(2,4,6-trimethylbenzenesulfonamido) ([MST]3-). This series is extended to include the rest of the late 3d transition metal ions (MII = Co, Ni, Cu, Zn). All of the bimetallic complexes have similar spectroscopic and structural properties that reflect little change despite varying the MII centers. Magnetic studies performed on the complexes in solution using electron paramagnetic resonance spectroscopy showed that the observed spin states varied incrementally from S = 0 through S = 5/2; these results are consistent with antiferromagnetic coupling between the high-spin MII and FeIII centers. However, the difference in the MII ion occupancy yielded only slight changes in the magnetic exchange coupling strength, and all complexes had J values ranging from +26(4) to +35(3) cm-1.

ChemInform Abstract: A Practical Guide to High‐Resolution X‐Ray Spectroscopic Measurements and Their Applications in Bioinorganic Chemistry

AbstractReview: 91 refs.

A Practical Guide to High‐resolution X‐ray Spectroscopic Measurements and their Applications in Bioinorganic Chemistry

AbstractThe bioinorganic chemistry community has had a long history of utilizing a diverse range of spectroscopic techniques to obtain detailed geometric and electronic structural insights into metalloprotein active sites. In recent years, the development of beamlines optimized for high‐resolution X‐ray spectroscopy has provided novel tools for the elucidation of biological active site structures. These methods include both non‐resonant and resonant X‐ray emission spectroscopy. Herein, we briefly introduce both X‐ray absorption and X‐ray emission spectroscopy, and the added information that can be obtained through high‐resolution measurements. The information content of each spectroscopic approach, as well as the required instrumentation, is discussed. Applications of these methods in bioinorganic chemistry are highlighted.

ChemInform Abstract: Molecular Designs for Controlling the Local Environments Around Metal Ions

AbstractReview: 40 refs.

Molecular designs for controlling the local environments around metal ions.

The functions of metal complexes are directly linked to the local environment in which they are housed; modifications to the local environment (or secondary coordination sphere) are known to produce changes in key properties of the metal centers that can affect reactivity. Noncovalent interactions are the most common and influential forces that regulate the properties of secondary coordination spheres, which leads to complexities in structure that are often difficult to achieve in synthetic systems. Using key architectural features from the active sites of metalloproteins as inspiration, we have developed molecular systems that enforce intramolecular hydrogen bonds (H-bonds) around a metal center via incorporation of H-bond donors and acceptors into rigid ligand scaffolds. We have utilized these molecular species to probe mechanistic aspects of biological dioxygen activation and water oxidation. This Account describes the stabilization and characterization of unusual M-oxo and heterobimetallic complexes. These types of species have been implicated in a range of oxidative processes in biology but are often difficult to study because of their inherent reactivity. Our H-bonding ligand systems allowed us to prepare an Fe(III)-oxo species directly from the activation of O2 that was subsequently oxidized to form a monomeric Fe(IV)-oxo species with an S = 2 spin state, similar to those species proposed as key intermediates in non-heme monooxygenases. We also demonstrated that a single Mn(III)-oxo center that was prepared from water could be converted to a high-spin Mn(V)-oxo species via stepwise oxidation, a process that mimics the oxidative charging of the oxygen-evolving complex (OEC) of photosystem II. Current mechanisms for photosynthetic O-O bond formation invoke a Mn(IV)-oxyl species rather than the isoelectronic Mn(V)-oxo system as the key oxidant based on computational studies. However, there is no experimental information to support the existence of a Mn-oxyl radical. We therefore probed the amount of spin density on the oxido ligand of our complexes using EPR spectroscopy in conjunction with oxygen-17 labeling. Our findings showed that there is a significant amount of spin on the oxido ligand, yet the M-oxo bonds are best described as highly covalent and there is no indication that an oxyl radical is formed. These results offer the intriguing possibility that high-spin M-oxo complexes are involved in O-O bond formation in biology. Ligand redesign to incorporate H-bond accepting units (sulfonamido groups) simultaneously provided a metal ion binding pocket, adjacent H-bond acceptors, and an auxiliary binding site for a second metal ion. These properties allowed us to isolate a series of heterobimetallic complexes of Fe(III) and Mn(III) in which a group II metal ion was coordinated within the secondary coordination sphere. Examination of the influence of the second metal ion on the electron transfer properties of the primary metal center revealed unexpected similarities between Ca(II) and Sr(II) ions, a result with relevance to the OEC. In addition, the presence of a second metal ion was found to prevent intramolecular oxidation of the ligand with an O atom transfer reagent.

A Ferromagnetically Coupled (S=1) Peroxodicopper(II) Complex

AbstractCopper enzymes play important roles in the binding and activation of dioxygen in biological systems. Key copper/dioxygen intermediates have been identified and studied in synthetic analogues of the metalloprotein active sites, including the μ‐η2:η2‐peroxodicopper(II) motif relevant to type III dicopper proteins. Herein, we report the synthesis and characterization of a bioinspired dicopper system that forms a stable μ‐η1:η1‐peroxo complex whose Cu‐O‐O‐Cu torsion is constrained to around 90° by ligand design. This results in sizeable ferromagnetic coupling between the copper(II) ions, which is detected by magnetic measurements and HF‐EPR spectroscopy. The new dicopper peroxo system is the first with a triplet ground state, and it represents a snapshot of the initial stages of O2 binding at type III dicopper sites.

A Ferromagnetically Coupled (S=1) Peroxodicopper(II) Complex

Copper enzymes play important roles in the binding and activation of dioxygen in biological systems. Key copper/dioxygen intermediates have been identified and studied in synthetic analogues of the metalloprotein active sites, including the μ-η(2):η(2)-peroxodicopper(II) motif relevant to type III dicopper proteins. Herein, we report the synthesis and characterization of a bioinspired dicopper system that forms a stable μ-η(1):η(1)-peroxo complex whose Cu-O-O-Cu torsion is constrained to around 90° by ligand design. This results in sizeable ferromagnetic coupling between the copper(II) ions, which is detected by magnetic measurements and HF-EPR spectroscopy. The new dicopper peroxo system is the first with a triplet ground state, and it represents a snapshot of the initial stages of O2 binding at type III dicopper sites.

Transition metal complexes and the activation of dioxygen.

In order to address how diverse metalloprotein active sites, in particular those containing iron and copper, guide O₂binding and activation processes to perform diverse functions, studies of synthetic models of the active sites have been performed. These studies have led to deep, fundamental chemical insights into how O₂coordinates to mono- and multinuclear Fe and Cu centers and is reduced to superoxo, peroxo, hydroperoxo, and, after O-O bond scission, oxo species relevant to proposed intermediates in catalysis. Recent advances in understanding the various factors that influence the course of O₂activation by Fe and Cu complexes are surveyed, with an emphasis on evaluating the structure, bonding, and reactivity of intermediates involved. The discussion is guided by an overarching mechanistic paradigm, with differences in detail due to the involvement of disparate metal ions, nuclearities, geometries, and supporting ligands providing a rich tapestry of reaction pathways by which O₂is activated at Fe and Cu sites.

Synthesis and crystal structure of the novel metal organic framework Zn(C3H5NO2S)2

The crystal structure of the novel metal organic framework (MOF) Zn(C3H5NO2S)2 is described. This MOF can serve as a model for active sites in metalloproteins, on diverse activities such as structural or catalytic functions. Each half of the amino acid act as a bidentate ligand to one Zn and as a monodentate ligand to another Zn, while the disulphide bond presents an important structural function, stabilizing the crystal packing. The structure has been obtained ab initio from synchrotron X-ray powder diffraction data. The compound crystallizes in the orthorhombic system (space group P212121), with a = 20.0906(7), b = 9.5842(3), c = 5.018 89(13), and V = 966.40(5) Å3, with Z = 4. The structure was determined using a direct space approach, by means of the Monte Carlo technique, followed by Rietveld refinement.

Valence-to-core-detected X-ray absorption spectroscopy: targeting ligand selectivity.

X-ray absorption spectroscopy (XAS) can provide detailed insight into the electronic and geometric structures of transition-metal active sites in metalloproteins and chemical catalysts. However, standard XAS spectra inherently represent an average contribution from the entire coordination environment with limited ligand selectivity. To address this limitation, we have investigated the enhancement of XAS features using valence-to-core (VtC)-detected XAS, whereby XAS spectra are measured by monitoring fluorescence from valence-to-core X-ray emission (VtC XES) events. VtC emission corresponds to transitions from filled ligand orbitals to the metal 1s core hole, with distinct energetic shifts for ligands of differing ionization potentials. VtC-detected XAS data were obtained from multiple valence emission features for a series of well-characterized Mn model compounds; taken together, these data correspond to a VtC resonant XES (VtC RXES) plane. For comparison, standard total fluorescence yield (TFY) XAS and nonresonant XES data were obtained. Dramatic intensity variations and the appearance of new features were observed in the pre-edge region by detecting at different VtC emission energies. The TFY XAS, nonresonant XES, and VtC RXES data were all modeled within a density functional theory approach. While the TFY XAS and nonresonant XES data are readily interpreted by theory, the VtC RXES cannot be reproduced within such a simplified model. Nonetheless, dramatic changes in the experimental spectra are observed that have the potential to further the information content and selectivity of XAS. Potential applications and required theoretical developments are discussed.

‘Unconventional’ Coordination Chemistry by Metal Chelating Fragments in a Metalloprotein Active Site

The binding of three closely related chelators: 5-hydroxy-2-methyl-4H-pyran-4-thione (allothiomaltol, ATM), 3-hydroxy-2-methyl-4H-pyran-4-thione (thiomaltol, TM), and 3-hydroxy-4H-pyran-4-thione (thiopyromeconic acid, TPMA) to the active site of human carbonic anhydrase II (hCAII) has been investigated. Two of these ligands display a monodentate mode of coordination to the active site Zn2+ ion in hCAII that is not recapitulated in model complexes of the enzyme active site. This unprecedented binding mode in the hCAII-thiomaltol complex has been characterized by both X-ray crystallography and X-ray spectroscopy. In addition, the steric restrictions of the active site force the ligands into a ‘flattened’ mode of coordination compared with inorganic model complexes. This change in geometry has been shown by density functional computations to significantly decrease the strength of the metal–ligand binding. Collectively, these data demonstrate that the mode of binding by small metal-binding groups can be significantly influenced by the protein active site. Diminishing the strength of the metal–ligand bond results in unconventional modes of metal coordination not found in typical coordination compounds or even carefully engineered active site models, and understanding these effects is critical to the rational design of inhibitors that target clinically relevant metalloproteins.