Axial Ligation in Blue-Copper Proteins. A W-Band Electron Spin Echo Detected Electron Paramagnetic Resonance Study of the Azurin Mutant M121H

Structural Basis for a Quadratic Relationship between Electronic Absorption and Electronic Paramagnetic Resonance Parameters of Type 1 Copper Proteins

Type 1 copper (T1Cu) proteins play important roles in electron transfer in biology, largely due to the unique structure of the T1Cu center, which is reflected by its spectroscopic properties. Previous reports have suggested a correlation between a high ratio of electronic absorbance at ∼450 nm to that at ∼600 nm (R = A₄₅₀/A₆₀₀) and a large copper(II) hyperfine coupling in the z direction (A_z) in electron paramagnetic resonance (EPR). However, this correlation does not have a clear physical meaning, nor does it hold for many proteins with a perturbed T1Cu center. To address this issue, a new parameter of R' [A₄₅₀/(A₄₅₀ + A₆₀₀)] with a better physical meaning of a fractional S_Cys pseudo-σ to Cu(II) charge transfer transition intensity is defined and a quadratic relationship between R' and A_z is found on the basis of a comprehensive analysis of ultraviolet-visible absorption, EPR, and structural parameters of T1Cu proteins. We are able to find good correlations between R' and the displacement of copper from the trigonal plane defined by the His₂Cys ligands and the angle between the N_His1-Cu-N_His2 plane and the S_Cys-Cu-axial ligand plane, providing a structural basis for the observed correlation. These findings and analyses provide a new framework for a deeper understanding of the spectroscopic and electronic properties of T1Cu proteins, which may allow better design and applications of this important class of proteins for redox and electron transfer functions.

Axial bonds at the T1 Cu site of Thermus thermophilus SG0.5JP17-16 laccase influence enzymatic properties

Laccase is a multi‐copper oxidase which oxidizes substrate at the type 1 copper site, simultaneously coupling the reduction of dioxygen to water at the trinuclear copper center. In this study, we used site‐directed mutagenesis to study the effect of axial bonds between the metal and amino acid residue side chains in lacTT. Our kinetic and spectral data showed that the replacement of the axial residue with non‐coordinating residues resulted in higher efficiency (k_cat/K_m) and a lower Cu²⁺ population at the type 1 copper site, while substitution with strongly coordinating residues resulted in lower efficiency and a higher Cu²⁺ population, as compared with the wild‐type. The redox potentials of mutants with hydrophobic axial residues (Ala and Phe) were higher than that of the wild‐type. In conclusion, these insights into the catalytic mechanism of laccase may be of use in protein engineering to fine‐tune its enzymatic properties for industrial application.

Utilizing NMR and EPR spectroscopy to probe the role of copper in prion diseases

Copper is an essential nutrient for the normal development of the brain and nervous system, although the hallmark of several neurological diseases is a change in copper concentrations in the brain and central nervous system. Prion protein (PrP) is a copper-binding, cell-surface glycoprotein that exists in two alternatively folded conformations: a normal isoform (PrP(C)) and a disease-associated isoform (PrP(Sc)). Prion diseases are a group of lethal neurodegenerative disorders that develop as a result of conformational conversion of PrP(C) into PrP(Sc). The pathogenic mechanism that triggers this conformational transformation with the subsequent development of prion diseases remains unclear. It has, however, been shown repeatedly that copper plays a significant functional role in the conformational conversion of prion proteins. In this review, we focus on current research that seeks to clarify the conformational changes associated with prion diseases and the role of copper in this mechanism, with emphasis on the latest applications of NMR and EPR spectroscopy to probe the interactions of copper with prion proteins.

Transforming a blue copper into a red copper protein: engineering cysteine and homocysteine into the axial position of azurin using site-directed mutagenesis and expressed protein ligation

Interactions of the axial ligand with its blue copper center are known to be important in tuning spectroscopic and redox properties of cupredoxins. While conversion of the blue copper center with a weak axial ligand to a green copper center containing a medium strength axial ligand has been demonstrated in cupredoxins, converting the blue copper center to a red copper center with a strong axial ligand has not been reported. Here we show that replacing Met121 in azurin from Pseudomonas aeruginosa with Cys caused an increased ratio (R(L)) of absorption at 447 nm over that at 621 nm. Whereas no axial Cu-S(Cys121) interaction in Met121Cys was detectable by extended X-ray absorption fine structure (EXAFS) spectroscopy at pH 5, similar to what was observed in native azurin with Met121 as the axial ligand, the Cu-S(Cys121) interaction at 2.74 A is clearly visible at higher pH. Despite the higher R(L) and stronger axial Cys121 interaction with Cu(II) ion, the Met121Cys variant remains largely a type 1 copper protein at low pH (with hyperfine coupling constant A( parallel) = 54 x 10(-4) cm(-1) at pH 4 and 5), or distorted type 1 or green copper protein at high pH (A(parallel) = 87 x 10(-4) cm(-1) at pH 8 and 9), attributable to the relatively long distance between the axial ligand and copper and the constraint placed by the protein scaffold. To shorten the distance between axial ligand and copper, we replaced Met121 with a nonproteinogenic amino acid homocysteine that contains an extra methylene group, resulting in a variant whose spectra (R(L)= 1.5, and A(parallel) = 180 x 10(-4) cm(-1)) and Cu-S(Cys) distance (2.22 A) are very similar to those of the red copper protein nitrosocyanin. Replacing Met121 with Cys or homocysteine resulted in lowering of the reduction potential from 222 mV in the native azurin to 95 +/- 3 mV for Met121Cys azurin and 113 +/- 6 mV for Met121Hcy azurin at pH 7. The results strongly support the "coupled distortion" model that helps explain axial ligand tuning of spectroscopic properties in cupredoxins, and demonstrate the power of using unnatural amino acids to address critical chemical biological questions.

Multiconfigurational g tensor calculations as a probe for the covalency of the copper-ligand bonds in copper(II) complexes: [CuCl4]2-, [Cu(NH3)4]2+, and plastocyanin

Calculations of the g tensor of three copper(II) complexes [Cu(NH3)4]2+, [CuCl4]2-, and plastocyanin are presented. Two different sum-over-states-based approaches are considered, making use of the multistate CASPT2 method for excitation energies and PMCAS (perturbation modified CAS) wave functions for the computation of the angular momentum and spin-orbit coupling matrix elements. Test calculations on [Cu(NH3)4]2+ and [CuCl4]2- point to the need of including in the MS-CASPT2 treatment the specific charge-transfer state with an electron excited out of the bonding counterpart of the ground-state SOMO. The computed g shifts for these two molecules present a considerable improvement with respect to the results obtained from our previous g tensor calculations based instead on CASSCF/CASPT2. This is shown to be related to an improved description of the covalency of the Cu-L bonds. For the calculations on plastocyanin, different models are used, taken from a recent (QM/MM) DFT study by Sinnecker and Neese. The effect of the surrounding protein is taken into account by surrounding the central cluster either with a dielectric continuum (epsilon = 4) or with a set of point charges. The second approach is found to be indispensable for an accurate description of environmental effects. With this approach, the calculated g values compare to within 30 ppt with the experimental data of plastocyanin.

Spectroscopic characterization of a high-potential lipo-cupredoxin found in Streptomyces coelicolor

For many streptomycetes, a distinct dependence on the "bioavailability" of copper ions for their morphological development has been reported. Analysis of the Streptomyces coelicolor genome reveals a number of gene products encoding for putative copper-binding proteins. One of these appears as an unusual copper-binding protein with a lipoprotein signal sequence and a cupredoxin-like domain harboring a putative Type-1 copper-binding motif. Cloning of this gene from S. coelicolor and subsequent heterologous expression in Escherichia coli has allowed for a thorough spectroscopic interrogation of this putative copper-binding protein. Optical and electron paramagnetic resonance spectroscopies have confirmed the presence of a "classic" Type-1 copper site with the axial ligand to the copper a methionine. Paramagnetic NMR spectroscopy on both the native Cu(II) form and Co(II)-substituted protein has yielded active-site structural information, which on comparison with that of other cupredoxin active sites reveals metal-ligand interactions most similar to the "classic" Type-1 copper site found in the amicyanin family of cupredoxins. Despite this high structural similarity, the Cu(II)/(I) midpoint potential of the S. coelicolor protein is an unprecedented +605 mV vs normal hydrogen electrode at neutral pH (amicyanin approximately +250 mV), with no active-site protonation of the N-terminal His ligand observed. Suggestions for the physiological role/function of this high-potential cupredoxin are discussed.

The strength of EPR and ENDOR techniques in revealing structure-function relationships in metalloproteins

Recent technological and methodological advances have strongly increased the potential of electron paramagnetic resonance (EPR) and electron nuclear double resonance (ENDOR) techniques to characterize the structure and dynamics of metalloproteins. These developments include the introduction of powerful pulsed EPR/ENDOR methodologies and the development of spectrometers operating at very high microwave frequencies and high magnetic fields. This overview focuses on how valuable information about metalloprotein structure-function relations can be obtained using a combination of EPR and ENDOR techniques. After an overview of the historical development and a limited theoretical description of some of the key EPR and ENDOR techniques, their potential will be highlighted using selected examples of applications to iron-, nickel-, cobalt-, and copper-containing proteins. We will end with an outlook of future developments.

A detailed resonance Raman spectrum of Nickel(II)-substituted Pseudomonas aeruginosa azurin

Nickel(II) and cobalt(II) derivatives of the blue copper protein Pseudomonas aeruginosa azurin have been studied by resonance Raman (RR) spectroscopy at liquid-nitrogen temperatures. Vibrational assignments for the observed RR bands of Ni(II)-azurin have been made through a study of (62)Ni-substituted azurin. A comparison of Ni(II)-azurin RR spectra with those of the wild type (Cu-containing) protein showed Ni(II)-S(Cys) stretching vibrations, nu(Ni-S)(Cys), at substantially lower frequencies (approximately 360 versus approximately 400 cm(-1), respectively), indicating that the Ni(II)-S(Cys) bond is much weaker than the corresponding Cu(II)-S(Cys) bond. Resonance enhanced predominantly nu(Ni-N)(His) modes indicate that the metal-N(His) bond distances in the Ni(II) derivative are the same as those in native azurin. The vibrational data also confirm a tetrahedral disposition of ligands about the metal in Ni(II)-azurin found in the protein crystallographic structures. As expected, excitation profile measurements on Ni(II)-azurin show that the nu(Ni-S)(Cys) assignable modes give maxima at the 440-nm absorption band, which confirms a S(Cys) --> Ni(II) charge-transfer origin of the 440-nm electronic transition in Ni(II)-substituted azurin.

Single-crystal EPR study at 95 GHz of the type 2 copper site of the inhibitor-bound quercetin 2,3-dioxygenase

An electron-spin-echo-detected, electron-paramagnetic-resonance study has been performed on the type 2 copper site of quercetin 2,3-dioxygenase from Aspergillus japonicus. In the protein, copper is coordinated by three histidine nitrogens and two sulfurs from the inhibitor diethyldithiocarbamate. A single crystal of the protein was studied at 95 GHz and the complete g-tensor determined. The electron-paramagnetic-resonance data are compatible with two orientations of the principal g-axes in the copper center, one of which is preferred on the basis of an analysis of the copper coordination and the d-orbitals that are involved in the unpaired-electron orbital. For this orientation, the principal z-axis of the g-tensor makes an angle of 19 degrees with the Cu-N(His112) bond and the N of His112 may be considered the axial ligand. The singly occupied molecular orbital contains a linear combination of copper dxy and dyz-orbitals, which are antibonding with atomic orbitals of histidine nitrogens and diethyldithiocarbamate sulfurs. The orientation of the g-tensor for the quercetin 2,3-dioxygenase is compared with that for type 1 copper sites.

Interpretation of the temperature-dependent color of blue copper protein mutants

The electronic absorption spectrum of the mutant of the blue copper protein amicyanin with a pseudoazurin loop (AmiPse) shows a remarkable temperature dependence. The absorption band at approximately 460 nm increases at low temperature while the transition at approximately 600 nm is not much affected by a variation of the temperature. An approximate density functional theory (DFT) study of the active site model [Cu(II)(imidazole)(2)(SCH(3))(S(CH(3))(2))](+) (protein backbone and solvation neglected) leads to two local minimum structures (axial and rhomb) which both have a geometry close to that typical for blue copper proteins. One (rhomb) has two structurally different histidine donors, and this geometry is also found in most experimental type 1 structures. The two forms axial and rhomb are distortional isomers and are energetically almost degenerate. The temperature dependence of the spectrum of AmiPse is interpreted with a temperature-dependent change of the relative population of the two local minimum structures with slightly different energy. The 460 nm transition is believed to be due to preferential population of the structure rhomb; this is in agreement with the published assignment of the high energy transition, based on thorough spectroscopic and computational studies. Consequences of a perturbation of the "gas phase" structures axial and rhomb by the protein and solvation are also discussed on the basis of published, experimentally observed structures and spectroscopic data.

Bioinformatic Comparison of Structures and Homology-Models of Matrix Metalloproteinases

The entire family of human matrix metalloproteinases (MMPs) was investigated using phylogenetic trees and homology modeling. The phylogenetic analysis indicates that individual domains of each MMP have evolved in a correlated manner. Despite their high sequence similarity, the phylogenetic tree of the catalytic domains already allows functional (e.g., linked to regulation and substrate recognition) homologies between different MMPs to be identified. The same pattern of functional homologies is confirmed by the phylogenetic analysis of the mature proteins. Structural models were built for the catalytic domains of the entire MMP family, for twelve hemopexin domains and for twelve mature proteins. The surface properties around the active site cleft of the modeled and experimental structures are quite conserved, whereas the hemopexin domains are more differentiated, possibly indicating a role in determining substrate specificity. The analysis of mature MMPs showed that the area of the interface between the catalytic and hemopexin domains is essentially conserved, with both hydrophobic and hydrophilic amino acids at the interface. The absence of specific conserved interdomain contacts suggests that the interface is tolerant to amino acid replacements, and that there may be a certain degree of plasticity with respect to the reciprocal orientation of the two domains.

Spectroscopic characterization of the Leu513His variant of fungal laccase: effect of increased axial ligand interaction on the geometric and electronic structure of the type 1 Cu site

A variety of spectroscopic techniques, combined with density functional calculations, are used to describe the electronic structure of the Leu513His variant of the type 1 Cu site in Myceliophthora thermophila laccase. This mutation changes the type 1 Cu from a blue to a green site. Electron paramagnetic resonance (EPR), optical absorption, circular dichroism, and magnetic circular dichroism (MCD) spectroscopies reveal that, relative to the trigonal planar blue type 1 Cu site in wild-type fungal laccase, the covalency and the ligand field strength at the Leu513His green type 1 Cu center decrease. Additionally, there is a significant reorientation of the d(x)()()2(-)(y)()()2( )singly occupied MO, such that the overlap with the Cys sulfur valence orbital changes from pi to sigma. A density functional study in which internal coordinates are systematically altered reveals that these changes are due to the increased strength of the axial ligand (none to His), leading to a tetragonal distortion and elongation of the equatorial Cu-ligand bonds. These calculations provide insight into the experimental differences in the EPR parameters, charge-transfer absorption spectrum, and ligand-field MCD spectrum between the axial-His variant and blue Cu centers (plastocyanin and the type 1 site in fungal laccase). There are also significant differences between the green site in the Leu513His variant and other naturally occurring, green type 1 Cu sites such as in nitrite reductase, which have short axial Cu-S(Met) bonds. The large difference in EPR parameters between these green type 1 sites derives from a change in ligand field excitation energies observed by MCD, which reflects a decrease in ligand field strength. This is associated with different steric interactions of a His vs an axial Met ligand in a tetragonally distorted type 1 site. Changes in the electronic structure of the Cu site correlate with the difference in reactivity of the green His variant relative to blue wild-type fungal laccase.

Metal-ligand interplay in blue copper proteins studied by 1H NMR spectroscopy: Cu(II)-pseudoazurin and Cu(II)-rusticyanin

The blue copper proteins (BCPs), pseudoazurin from Achromobacter cycloclastes and rusticyanin from Thiobacillus ferrooxidans, have been investigated by (1)H NMR at a magnetic field of 18.8 T. Hyperfine shifts of the protons belonging to the coordinated ligands have been identified by exchange spectroscopy, including the indirect detection for those resonances that cannot be directly observed (the beta-CH(2) of the Cys ligand, and the NH amide hydrogen bonded to the S(gamma)(Cys) atom). These data reveal that the Cu(II)-Cys interaction in pseudoazurin and rusticyanin is weakened compared to that in classic blue sites (plastocyanin and azurin). This weakening is not induced by a stronger interaction with the axial ligand, as found in stellacyanin, but might be determined by the protein folding around the metal site. The average chemical shift of the beta-CH(2) Cys ligand in all BCPs can be correlated to geometric factors of the metal site (the Cu-S(gamma)(Cys) distance and the angle between the CuN(His)N(His) plane and the Cu-S(gamma)(Cys) vector). It is concluded that the degree of tetragonal distortion is not necessarily related to the strength of the Cu(II)-S(gamma)(Cys) bond. The copper-His interaction is similar in all BCPs, even for the solvent-exposed His ligand. It is proposed that the copper xy magnetic axes in blue sites are determined by subtle geometrical differences, particularly the orientation of the His ligands. Finally, the observed chemical shifts for beta-CH(2) Cys and Ser NH protons in rusticyanin suggest that a less negative charge at the sulfur atom could contribute to the high redox potential (680 mV) of this protein.

Paramagnetic resonance of biological metal centers

The review deals with recent advances in magnetic resonance spectroscopy (hf EPR and NMR) of paramagnetic metal centers in biological macromolecules. In the first half of our chapter, we present an overview of recent technical developments in the NMR of paramagnetic bio-macromolecules. These are illustrated by a variety of examples deriving mainly from the spectroscopy of metalloproteins and their complexes. The second half focuses on recent developments in high-frequency EPR spectroscopy and the application of the technique to copper, iron, and manganese proteins. Special attention is given to the work on single crystals of copper proteins.

A new molecular mechanics force field for the oxidized form of blue copper proteins

A molecular mechanics force field for blue copper proteins has been developed, based on a rigid potential energy surface scan of the Cu(II)/His/His/Cys/Met chromophore, using DFT (B3LYP) calculations and the AMBER force field for the protein backbone. The strain-energy-minimized structures of the model chromophore alone are in excellent agreement with the DFT-optimized structure, and those of the entire set of cupredoxins (five structures are considered) are, within the experimental error limits, in good agreement with the single crystal structural data. However, the structural variation in the computed structures is much smaller than those in the experimental structures. It is shown that, due to the large error limits in the experimental data, a validation of the force field with experimental structural data is impossible because, within the error limits, all experimental structures considered are virtually identical. A validation on the basis of spectroscopic data and their correlation with experimental and computed structural data is proposed, and, as a first example, the correlation of intensity ratios of the charge transfer transitions with a specific distortion mode is presented. The quality of the correlation, using the computed structures, is higher than that with the X-ray structures, and this indicates that the computed structures are meaningful.

Pulsed EPR/ENDOR characterization of perturbations of the Cu(A) center ground state by axial methionine ligand mutations

The effect of axial ligand mutation on the Cu(A) site in the recombinant water soluble fragment of subunit II of Thermus thermophilus cytochrome c oxidase ba(3) has been investigated. The weak methionine ligand was replaced by glutamate and glutamine which are stronger ligands. Two constructs, M160T0 and M160T9, that differ in the length of the peptide were prepared. M160T0 is the original soluble fragment construct of cytochrome ba(3) that encodes 135 amino acids of subunit II, omitting the transmembrane helix that anchors the domain in the membrane. In M160T9 nine C-terminal amino acids are missing, including one histidine. The latter has been used to reduce the amount of a secondary T2 copper which is most probably coordinated to a surface histidine in M160T0. The changes in the spin density in the Cu(A) site, as manifested by the hyperfine couplings of the weakly and strongly coupled nitrogens, and of the cysteine beta-protons, were followed using a combination of advanced EPR techniques. X-band ( approximately 9 GHz) electron-spin-echo envelope modulation (ESEEM) and two-dimensional (2D) hyperfine sublevel correlation (HYSCORE) spectroscopy were employed to measure the weakly coupled (14)N nuclei, and X- and W-band (95 GHz) pulsed electron-nuclear double resonance (ENDOR) spectroscopy for probing the strongly coupled (14)N nuclei and the beta-protons. The high field measurements were extremely useful as they allowed us to resolve the T2 and Cu(A) signals in the g( perpendicular) region and gave (1)H ENDOR spectra free of overlapping (14)N signals. The effects of the M160Q and M160E mutations were: (i) increase in A( parallel)((63,65)Cu), (ii) larger hyperfine coupling of the weakly coupled backbone nitrogen of C153, (iii) reduction in the isotropic hyperfine interaction, a(iso), of some of the beta-protons making them more similar, (iv) the a(iso) value of one of the remote nitrogens of the histidine residues is decreased, thus distinguishing the two histidines, and finally, (v) the symmetry of the g-tensor remained axial. These effects were associated with an increase in the Cu-Cu distance and subtle changes in the geometry of the Cu(2)S(2) core which are consistent with the electronic structural model of Gamelin et al. (Gamelin, D. R.; Randall, D. W.; Hay, M. T.; Houser, R. P.; Mulder, T. C.; Canters, G. W.; de Vries, S.; Tolman, W. B.; Lu, Y.; Solomon, E. I. J. Am. Chem. Soc. 1998, 120, 5246-5263).

Fourier-transform EPR at high-field/high-frequency (3.4 T/95 GHz) using broadband stochastic microwave excitation

Stochastic excitation with a full-width-half-maximum bandwidth of 250 MHz was used to perform Fourier-transform (FT) high-field/high-frequency electron paramagnetic resonance (EPR) at 3.4T/95 GHz (W-band). Thereby, the required microwave peak power is reduced by a factor of tau(p)/T1 as compared to equivalent pulsed FT EPR in which the spin system with spin-lattice relaxation time T1 is excited by a single microwave pulse of length tau(p). Stochastic EPR is particularly interesting under high-field/high-frequency conditions, because the limited output power of mm microwave sources, amplifiers, and mixers makes pulse FT EPR in that frequency domain impossible, at least for the near future. On the other hand, FT spectroscopy offers several advantages compared to field-swept magnetic resonance methods, as is demonstrated by its success in NMR and X-band EPR. In this paper we describe a novel stochastic W-band microwave bridge including a bimodal induction mode transmission resonator that serves for decoupling the microwave excitation and signal detection. We report first EPR measurements and discuss experimental difficulties as well as achieved sensitivity. Moreover, we discuss future improvements and the possibility for an application of stochastic W-band FT EPR to transient signals such as those of photoexcited radical pairs in photosynthetic reaction centers.