Effect of nickel(II) substitution on the resonance Raman and NMR spectra of Alcaligenes xylosoxidans azurin II: implications for axial-ligand bonding interactions in cupredoxin active sites

Assignment of the resonance Raman (RR) spectrum of Ni(II)-substituted azurin II from Alcaligenes xylosoxidans (NCIMB 11015) using Ni isotope substitution reveals an anomalously low Ni-S(Cys) stretching frequency of 349?cm^–1, suggesting the presence of significant axial-ligand bonding interactions. The X-ray crystal structure of Ni(II)-substituted azurin from Pseudomonas aeruginosa shows that there are two potential axial ligands to the Ni ion: a peptide carbonyl O at a distance of 2.46?Å, together with a long-range interaction from a methionine sulfur (S′) at a distance of 3.30?Å. Comparison of the RR properties of Ni(II)-substituted azurin II with stellacyanin (which contains an axial carbonyl ligand, but no methionine) suggests that the interaction from the carbonyl oxygen ligand alone is not sufficient to account for the weak Ni azurin metal-thiolate bond. Instead, it appears that a Ni-methionine bonding interaction is also required to explain the low Ni-S(Cys) stretching frequency in Ni(II)-substituted azurin II. This hypothesis is supported by NMR studies which show a large paramagnetic shift for the protons of the methionine side-chain. Thus, it appears that Ni-substituted azurin II is best described as five-coordinate, and that significant Ni(II)-methionine bonding interactions can occur at a distance of 3.3?Å.     

Vibrational mode analysis of 2-aminoadenine and its deuterated species from Raman and ultraviolet resonance Raman data

Resonance Raman spectroscopy data of 2-aminoadenine and its deuterated species (C8-deuterated, N-deuterated and C8-, N-deuterated derivatives) in aqueous solution have been collected in the spectral region between 400 and 1800 cm^–1, by using ultraviolet excitation wavelengths (_exc = 222, 257 and 281 nm) located in the three main UV absorption bands corresponding to the strongly allowed electronic transitions of the molecule of interest. Moreover, a Raman spectrum has been recorded under off-resonance conditions with a visible excitation (_exc= 488 nm). In order to assign the 2-aminoadenine in-plane vibrational bands displayed in the RRS spectra, a normal coordinate analysis has been performed by means of an empirical internal valence force field. These calculations are based on our recent normal mode analysis of adenine and guanine nucleic bases and their deuterated species, which was based on the joint use of resonance Raman spectroscopy and neutron inelastic scattering data. In the 2-aminoadenine force field proposed here, the diagonal force constants have been directly transferred from those recently obtained for adenine (and from guanine as concerns the 2-amino group), the interaction force constants (off-diagonal) then being adjusted on the basis of the actual experimental data from 2-aminoadenine and its deuterated species. The current force field is also able to assign infrared and Raman data obtained by other authors from polycrystalline samples of the pure species. Correspondence to: M. Ghomi     

The molecular force field of guanine and its deuterated species as determined from neutron inelastic scattering and resonance Raman measurements

Neutron inelastic scattering (NIS) spectra from polycrystalline samples and ultraviolet resonance Raman scattering (RRS) spectra from aqueous solutions of guanine and CS-deuterated and (N9, NI, C2-amino)-deuterated guanine are reported. These measurements allowed theoretical simulations of the vibrational wavenumbers and intensities of the NIS and RRS bands to be performed. Å valence force field enabled the normal mode wavenumbers, as well as the atomic displacements, to be calculated. The NIS intensities were simulated by considering multi-phonon interactions arising from the lattice mode couplings with the internal molecular vibrational modes. The RRS intensities were simulated within the framework of the so-called small shift approximation, by using the molecular bond-order changes induced by the electronic transition from the ground to the first electronic excited state. It is shown that NIS spectroscopy mainly provides information on the guanine out-of-plane modes of vibration, while RRS allows the in-plane stretching vibrational motions to be analyzed.     

The effect of redox state on the folding free energy of azurin

 The unfolding of oxidized and reduced azurin by guanidine hydrochloride has been monitored by circular dichroism. Dilution experiments showed the unfolding to be reversible, and the equilibrium data have been interpreted in terms of a two-state model. The protein is stabilized by the strong metal binding in the native state, so that the folding free energy is as high as –52.2 kJ mol^–1 for the oxidized protein. The reduced protein is less stable, with a folding free energy of –40.0 kJ mol^–1. A thermodynamic cycle shows, as a consequence, that unfolded azurin has a reduction potential 0.13 V above that of the folded protein. This is explained by the bipyramidal site in the native fold stabilizing Cu(II) by a rack mechanism, with the same geometry being maintained in the Cu(I) form. In the unfolded protein, on the other hand, the coordination geometries are expected to differ for the two oxidation states, Cu(I) being stabilized by the cysteine thiol group in a linear or trigonal symmetry, whereas Cu(II) prefers oxygen ligands in a tetragonal geometry. Received: 15 January 1997 / Accepted: 3 April 1997     

Resonance Raman as a direct probe for the catalytic mechanism of molybdenum oxotransferases

 Recent studies of human sulfite oxidase and Rhodobacter sphaeroides DMSO reductase have demonstrated the ability of resonance Raman to probe in detail the coordination environment of the Mo active sites in oxotransferases via Mo=O, Mo-S(dithiolene), Mo-S(Cys) or Mo-O(Ser), dithiolene chelate ring and bound substrate vibrations. Furthermore, the ability to monitor the catalytically exchangeable oxo group via isotopic labeling affords direct mechanistic information and structures for the catalytically competent Mo(IV) and Mo(VI) species. The results clearly demonstrate that sulfite oxidase cycles between cis–di-oxo-Mo(VI) and mono-oxo-Mo(IV) states during catalytic turnover, whereas DMSO reductase cycles between mono-oxo-Mo(VI) and des-oxo-Mo(IV) states. In the case of DMSO reductase, ¹⁸O-labeling experiments have provided the first direct evidence for an oxygen atom transfer mechanism involving an Mo=O species. Of particular importance is that the active-site structures and detailed mechanism of DMSO reductase in solution, as determined by resonance Raman spectroscopy, are quite different to those reported or deduced in the three X-ray crystallographic studies of DMSO reductases from Rhodobacter species. Received: 16 June 1997 / Accepted: 20 August 1997     

Vibrational analysis and molecular force field of hypoxanthine as determined from ultraviolet resonance Raman spectra of native and deuterated species

Ultraviolet resonance Raman scattering spectra from aqueous solutions of hypoxanthine and its deuterated species (C8-deuterated, N-deuterated and C8-, N-deuterated derivatives) have been collected and reported in the spectral region between 400 and 1800 cm^–1. The laser excitation wavelengths at 281 nm and 257 nm correspond to preresonance and pure resonance conditions, respectively, with the purine strongly allowed ^* electronic transition: thus the observed experimental Raman features mainly correspond to inplane vibrational modes. The latter were then assigned according to the Wilson GF method by using an empirical harmonic valence force field. Normal mode calculations are based on a non-redundant set of internal coordinates. The calculated vibrational mode wavenumbers and their isotopic shifts upon selective deuterations are in good agreement with the experimental data. The present normal mode analysis rests on the transferability of the guanine and adenine force constants proposed in recent works based on resonance Raman spectroscopy and neutron inelastic scattering data from these major purine bases. Correspondence to: M. Ghomi     

Spin-state equilibria and axial ligand bonding in FixL hydroxide: a resonance raman study

 Vibrational assignments for the Fe-OH unit of ferric alkaline forms of two deletion derivatives of Rhizobium meliloti FixL, FixL*, a functional O₂-sensing heme kinase, and FixLN, which contains only the heme domain, are made. Appearance of ²H- and ¹⁸O-sensitive Raman bands indicates that the heme group of FixL binds hydroxide as a distal ligand to form a six-coordinate complex. The alkaline FixLs are distributed between high- and low-spin states. The high- and low-spin bands corresponding to the ν (Fe-OH) modes occur at 479 and 539 cm^–1, respectively. Low temperature favors formation of the low-spin complex, indicative of a thermal spin-state equilibrium. The ν (Fe-OH) frequencies of FixLN and FixL* are 11 to 18 cm^–1 lower than those observed for the respective vibrations in alkaline myoglobin and hemoglobin. The weaker Fe-OH bond in the FixLs is attributed to a lack of hydrogen bonding on the distal side of the heme pocket. Received: 20 November 1997 / Accepted: 2 March 1998     

The resonance Raman spectrum of carotenoids as an intrinsic probe for membrane potential Oscillatory changes in the spectrum of neurosporene in the chromatophores of Rhodopseudomonas sphaeroides

The resonance Raman spectrum of the carotenoid neurosporene is shown to be a sensitive monitor of absorption shifts, and thus changes in membrane potential, in chromatophores of the GlC mutant of Rhodopseudomonas sphaeroides. For a Raman excitation wavelength at 472.7 nm, the intensities of the two most prominent resonance Raman features (v₁ and v₂) respond very differently to small shifts in the absorption maxima. Thus, the ratio intensity v₁/intensity v₂ is a sensitive probe for absorption shifts. Changes in this ratio of ～20% were observed during a valinomycin induced diffusion potential. At 5°C changes in the average intensity ratio of +6, ?4 and ?14% were brought about by oligomycin, FCCP and sodium deoxycholate, respectively. The changes in intensity ratio were temperature dependent and, in addition, effects due to the laser beam acting as an actinic light could be detected. Oscillatory changes were observed in absolute Raman and Rayleigh scattering intensities for chromatophores at 5°C and for intact cells under growing conditions.     

Non-covalent interactions in blue copper protein probed by Met16 mutation and electronic and resonance Raman spectroscopy of Achromobacter cycloclastes pseudoazurin

We have used low-temperature (77 K) resonance Raman (RR) spectroscopy as a probe of the electronic and molecular structure to investigate weak π-π interactions between the metal ion-coordinated His imidazoles and aromatic side chains in the second coordination sphere of blue copper proteins. For this purpose, the RR spectra of Met16 mutants of Achromobacter cycloclastes pseudoazurin (AcPAz) with aromatic (Met16Tyr, Met16Trp, and Met16Phe) and aliphatic (Met16Ala, Met16Val, Met16Leu, and Met16Ile) amino acid side chains have been obtained and analyzed over the 100-500 cm⁻¹ spectral region. Subtle strengthening of the Cu(II)-S(Cys) interaction on replacing Met16 with Tyr, Trp, and Phe is indicated by the upshifted (0.3-0.8 cm⁻¹) RR bands involving ν(Cu-S)_Cys stretching modes. In contrast, the RR spectra of Met16 mutants with aliphatic amino acids revealed larger (0.2-1.8 cm⁻¹) shifts of the ν(Cu-S)_Cys stretching modes to a lower frequency region, which indicate a weakening of the Cu(II)-S(Cys) bond. Comparisons of the predominantly ν(Cu-S)_Cys stretching RR peaks of the Met16X = Tyr, Trp, and Phe variants, with the molar absorptivity ratio ε₁/ε₂ of σ(∼455 nm)/π(∼595 nm) (Cys)S → Cu(II) charge-transfer bands in the optical spectrum and the axial/rhombic EPR signals, revealed a slightly more trigonal disposition of ligands about the copper(II) ion. In contrast, the RR spectra of Met16Z = Ala, Val, Leu, and Ile variants with aliphatic amino acid side chains show a more tetrahedral perturbation of the copper active site, as judged by the lower frequencies of the ν(Cu-S)_Cys stretching modes, much larger values of the ε₁/ε₂ ratio, and the increased rhombicity of the EPR spectra.     

Role of the active-site cysteine of Pseudomonas aeruginosa azurin. Crystal structure analysis of the CuII(Cys112Asp) protein

Replacement of the cysteine at position 112 of Pseudomonas aeruginosa azurin with an aspartic acid residue results in a mutant (Cys112Asp) protein that retains a strong copper-binding site. Cu^II(Cys112Asp) azurin can be reduced by excess [Ru^II(NH₃)₆]²⁺, resulting in a Cu^I protein with an electronic absorption spectrum very similar to that of wild-type Cu^I azurin. Cys112Asp azurin exhibits reversible interprotein electron-transfer reactivity with P. aeruginosa cytochrome c ₅₅₁ (μ?=?0.1?M sodium phosphate (pH?7.0);E°(Cu^II/I)?=?180 mV vs NHE); this redox activity indicates that electrons can still enter and exit the protein through the partially solvent-exposed imidazole ring of His117. The structure of Cu^II(Cys112Asp) azurin at 2.4-Å resolution shows that the active-site copper is five coordinate: the pseudo-square base of the distorted square-pyramidal structure is defined by the imidazole N^δ atoms of His46 and His117 and the oxygen atoms of an asymmetrically-bound bidentate carboxylate group of Asp112; the apical position is occupied by the oxygen atom of the backbone carbonyl group of Gly45. The Cu^II–Asp112 interaction is distinguished by an approximately 1.2-Å displacement of the metal center from the plane defined by the Asp112 carboxylate group.     

Resonance Raman characterization of the di-heme protein cytochrome c4 from Pseudomonas stutzeri

 Di-heme Pseudomonas stutzeri cytochrome c ₄ has been characterized by electronic absorption and resonance Raman spectroscopies in the ferric and ferrous forms at pH 7.5 and at room temperature. The data indicate that the two hemes are inequivalent. It is proposed that the N-terminal contains a more relaxed heme as a consequence of the relative orientation of the methionine and histidine ligands with respect to the N-Fe-N directions of the heme plane. This causes a weakening of the Fe-S bond with concomitant partial dissociation of the methionine and the formation of an Fe-aquo bond. Heme group relaxation is further accompanied by less distortion of the heme group than that associated with cytochrome c, expansion of the "core" and a negative shift of the redox potential. Received: 17 December 1996 / Accepted: 6 March 1997     

Structure of the Transmembrane Cysteine Residues in Phospholamban

Phospholamban, a 52-residue membrane protein, associates to form a pentameric complex of five long α-helices traversing the sarcoplasmic reticulum membrane of cardiac muscle cells. The transmembrane domain of the protein is largely hydrophobic, with only three cysteine residues having polar side chains, yet it functions as a Ca²⁺-selective ion channel. In this report, infrared spectroscopy is used to probe the conformation of the three cysteine side chains and to establish whether the free S-H groups form intrahelical hydrogen bonds in the pentameric complex. Vibrational spectra of a transmembrane peptide were obtained which corresponded to the transmembrane domain of wild-type phospholamban and three peptides each containing a cysteine ⇒ alanine substitution. The observed S-H frequencies argue that each of the sulfhydryl groups is hydrogen-bonded to an i-4 backbone carbonyl oxygen. Electrostatic calculations on a model of phospholamban based on molecular dynamics and mutagenesis studies, show that the sulfhydryl groups may significantly contribute to the electrostatic potential field of the protein. Received: 22 July 1996/Revised: 10 October 1996     

Electrostatic effects on the kinetics of photoinduced electron-transfer reactions of the triplet state of zinc cytochrome c with wild-type and mutant forms of Pseudomonas aeruginosa azurin

We study, by laser flash photolysis, the effects of ionic strength on the kinetics of the reaction ³Zncyt + az(II) → Zncyt⁺ + az(I), i.e., oxidative quenching of the triplet state of zinc cytochrome c by the wild-type form and the following three mutants of cupriazurin: Met44Lys, Met64Glu, and the double mutant Met44Lys/Met64Glu. Mutations in the hydrophobic patch of azurin significantly affect the reactivity of the protein with the triplet state of zinc cytochrome c. Dependence on the ionic strength of the bimolecular rate constant for the aforementioned reaction is analyzed by several electrosatic models. The two transition-state theories, Brønsted-Debye-Hückel and van Leeuwen theories, allow the best approximation to the experimental data when effective charges of the proteins are used. Protein-protein interactions are also analyzed in terms of local charges on the protein surfaces. The rate constants depend little on ionic strength, and the monopolar and dipolar electrostatic interactions between zinc cytochrome c and azurin are not well resolved. Semiquantitative analysis of electrostatic interactions indicates that azurin uses its hydrophobic patch for contact with zinc cytochrome c.     

Phenoxyl-copper(II) complexes: models for the active site of galactose oxidase

 The reaction of the macrocycles 1,4,7-tris (3,5-di-tert-butyl-2-hydroxy-benzyl)-1,4,7-triazacyclononane, L¹H₃, or 1,4,7-tris(3-tert-butyl-5-methoxy-2-hydroxy-benzyl)-1,4,7-triazacyclononane, L²H₃, with Cu(ClO₄)₂·6H₂O in methanol (in the presence of Et₃N) affords the green complexes [Cu^II(L¹H)] (1), [Cu^II(L²H)]·CH₃OH (2) and (in the presence of HClO₄) [Cu^II(L¹H₂)](ClO₄) (3) and [Cu^II(L²H₂)] (ClO₄) (4). The Cu^II ions in these complexes are five-coordinate (square-base pyramidal), and each contains a dangling, uncoordinated pendent arm (phenol). Complexes 1 and 2 contain two equatorially coordinated phenolato ligands, whereas in 3 and 4 one of these is protonated, affording a coordinated phenol. Electrochemically, these complexes can be oxidized by one electron, generating the phenoxyl-copper(II) species [Cu^II(L¹H)]^+ ·, [Cu(L²H)]^+ ·, [Cu^II(L¹H₂)]^2+ ·, and [Cu^II(L²H₂)]^2+ ·, all of which are EPR-silent. These species are excellent models for the active form of the enzyme galactose oxidase (GO). Their spectroscopic features (UV-VIS, resonance Raman) are very similar to those reported for GO and unambiguously show that the complexes are phenoxyl-copper(II) rather than phenolato-copper(III) species. Received: 10 February 1997 / Accepted: 7 April 1997     

Dynamic properties of the active site of azurin studied by the temperature dependence of the optical spectrum

Summary We report the optical absorption spectra of azurin (Pseudomonas aeruginosa) in the temperature range 290-20 K. The samples used are protein aqueous solutions containing 65% (by Vol.) glycerol as cryoprotectant. The measured spectra are deconvoluted in gaussian components and the temperature dependence of the zeroth, first and second moment of the observed bands is analyzed using the harmonic Franck-Condon approximation for the coupling between electronic transitions and nuclear vibrations. The analysis provides information on the stereodynamic properties of the active site of this protein. The possible functional relevance of these results is also suggested.     

In situ Raman spectroscopic studies of the teeth of the chiton Acanthopleura hirtosa

 In situ Raman spectroscopy, in combination with energy dispersive spectroscopy, has been used for the first time to determine the identities and locations, at the micron level, of mineral phases present in single chiton teeth that have been extensively mineralized. At the later stages of development the major lateral teeth of the chiton Acanthopleura hirtosa show characteristic spectroscopic evidence for the presence of lepidocrocite (γ-FeOOH), magnetite (Fe₃O₄), and an apatitic calcium phosphate. Goethite (α-FeOOH) and ferrihydrite (5 Fe₂O₃·9 H₂O), which have been detected previously in teeth at the early stages of mineralization, were not detected in this mature tooth. The spatial distribution of these phases was determined, providing evidence for the presence of a discrete layer of lepidocrocite between the magnetite and apatite regions, illustrating the complexity of the biomineralization process. The technique of laser Raman microscopy is shown to be ideal for the examination of small biomineralized structures in situ, such as chiton teeth. Received: 6 July 1998 / Accepted: 19 August 1998     

Sequential and coherent long-range electron transfer close to resonance with intermediate bridge groups, and new perspectives for in situ scanning tunnelling microscopy of adsorbed metalloproteins

 Three-level electron transfer follows superexchange patterns when the intermediate electronic level is off-resonance with the donor and acceptor levels. Close to resonance, new patterns emerge where the intermediate level is temporarily populated in vibrationally coherent or incoherent modes. We discuss energy and distance relations associated with such electron transfer modes. These appear to accord with fast electron transfer in several chemical and biological systems. We also discuss some recent observations on in situ scanning tunnelling microscopy of metalloproteins and large transition metal complexes which enable, in principle, a distinction between superexchange, coherent, and sequential three-level electron transfer. Received: 9 November 1997 / Accepted 16 March 1998     

The role of the medium in long-range electron transfer

 The role of the polypeptide matrix in electron transfer processes in proteins has been studied in two distinct systems: first in a protein where the induced ET is artificial, and second as part of the catalytic cycle of an enzyme. Azurins are structurally well-characterized blue single-copper proteins consisting of a rigid β-sheet polypeptide matrix. We have determined rate constants and activation parameters for intramolecular long-range electron transfer between the disulfide radical anions (generated by pulse radiolysis) and the copper(II) centre as a function of driving force and nature of the intervening medium in a large number of wild-type and single-site-mutated proteins. In ascorbate oxidase, for which the three-dimensional structure is equally well characterized, the internal ET from the type-I Cu(I) to the trinuclear Cu(II) centre has been studied. We find that the results correlate well with distance through well-defined pathways using a through-bond electron tunnelling mechanism. Received: 2 January 1997 / Accepted: 6 February 1997     

Application of Surface-Enhanced Raman Spectroscopy for Detection of Beta Amyloid Using Nanoshells

Currently, no methods exist for the definitive diagnosis of AD premortem. β-amyloid, the primary component of the senile plaques found in patients with this disease, is believed to play a role in its neurotoxicity. We are developing a nanoshell substrate, functionalized with sialic acid residues to mimic neuron cell surfaces, for the surface-enhanced Raman detection of β-amyloid. It is our hope that this sensing mechanism will be able to detect the toxic form of β-amyloid, with structural and concentration information, to aid in the diagnosis of AD and provide insight into the relationship between β-amyloid and disease progression. We have been successfully able to functionalize the nanoshells with the sialic acid residues to allow for the specific binding of β-amyloid to the substrate. We have also shown that a surface-enhanced Raman spectroscopy response using nanoshells is stable and concentration-dependent with detection into the picomolar range.