Catalytic and structural role of a metal-free histidine residue in bovine Cu-Zn superoxide dismutase

Exploring the cellular antioxidant mechanism against cytotoxic silver nanoparticles: a Raman spectroscopic analysis

Silver nanoparticles (AgNPs) hold great promise for several different applications, from colorimetric sensors to antimicrobial agents. Despite their widespread incorporation in consumer products, limited understanding of the detrimental effects and cellular antioxidant responses associated with AgNPs at sublethal concentrations persists, raising concerns for human and ecological well-being. To address this gap, we synthesized AgNPs of varying sizes and evaluated their cytotoxicity against human dermal fibroblasts (HDF). Our study revealed that toxicity of AgNPs is a time- and size-dependent process, even at low exposure levels. AgNPs exhibited low short-term cytotoxicity but high long-term impact, particularly for the smallest NPs tested. Raman microspectroscopy was employed for in-time investigations of intracellular molecular variations during the first 24 h of exposure to AgNPs of 35 nm. Subtle protein and lipid degradations were detected, but no discernible damage to the DNA was observed. Signals associated with antioxidant proteins, such as superoxide dismutase (SOD), catalase (CAT) and metallothioneins (MTs), increased over time, reflecting the heightened production of these defense agents. Fluorescence microscopy further confirmed the efficacy of overexpressed antioxidant proteins in mitigating ROS formation during short-term exposure to AgNPs. This work provides valuable insights into the molecular changes and remedial strategies within the cellular environment, utilizing Raman microspectroscopy as an advanced analytical technique. These findings offer a novel perspective on the cytotoxicity mechanism of AgNPs, contributing to the development of safer materials and advice on regulatory guidelines for their biomedical applications.

Cu(Proline)2 Complex: A Model of Bio-Copper Structural Ambivalence

Complexes of Cu²⁺(d⁹) with proline may be considered a simple model to address the structural flexibility and electronic properties of copper metalloproteins. To discuss optical electronic spectra and infrared spectral responses, we use quantum chemistry applied to model systems prepared under different geometries and degree of hydration. A comparison of experimental data with calculations indicates that first explicit neighbor water clustering next to the Cu²⁺(d⁹) complex is critical for a correct description of the electronic properties of this system. We deduce that the moderately hydrated trans conformer is the main structural form of the complex in water. Further, we suggest that the antisymmetric stretching mode of the carbonyl moieties of the conformer is dominant in the spectrally broadened infrared resonance at 1605 cm⁻¹, where inhomogeneity of the transition at the blue side can be ascribed to a continuum of less optimal interactions with the solvent. Extracted structural properties and hydration features provide information on the structural flexibility/plasticity specific to Cu²⁺(d⁹) systems in correlation with the electronic behavior upon photoexcitation. We discuss the role and the nature of the axial ligand in bio-copper structural ambivalence and reactivity.

Comparison of extracellular Cys/Trp motif between Schizosaccharomyces pombe Ctr4 and Ctr5

The reduction and binding of copper ions to the Cys/Trp motif, which is characterized by two cysteines and two tryptophans, in the extracellular N-terminal domain of the copper transporter (Ctr) protein of fungi are investigated using the model peptides of Ctr4 and Ctr5 from Schizosaccharomyces pombe. The Cys/Trp motif of Ctr5 can reduce Cu(II) and ligate Cu(I), which is the same as that of Ctr4 previously reported. Titration of Cu(II) and Cu(I) ions indicates that both the Cys/Trp motifs of Ctr4 and Ctr5 reduce two Cu(II) and bind two Cu(I) per one peptide. However, the coordination structure of the Cu(I)-peptide complex differs between Ctr4 and Ctr5. Cu(I) is bound to the Cys/Trp motif of Ctr5 via cysteine thiolate-Cu(I) bonds and cation-π interaction with tryptophan, as reported for Ctr4, and a histidine residue in the Cys/Trp motif of Ctr5 is suggested to interact with Cu(I) via its Nτ atom. Ctr4 and Ctr5 exhibit a heterotrimeric form within cell membranes and the copper transport mechanism of the Ctr4/Ctr5 heterotrimer is discussed along with quantitative evaluation of the Cu(I)-binding constant of the Cys/Trp motif.

Comparative structural and conformational studies on H43R and W32F mutants of copper-zinc superoxide dismutase by molecular dynamics simulation

Recently, mutations in copper-zinc superoxide dismutase (SOD1) have been linked to familial amyotrophic lateral sclerosis (fALS), a progressive neurodegenerative disease involving motor neuron loss, paralysis and death. It is mainly due to protein misfolding and aggregation resulting from the enhanced peroxidase activity of SOD1 mutants. In this study, we have carried out a 20 ns molecular dynamics simulation for wild type (WT), H43R and W32F mutated SOD1's dimer and compared their structure and conformational properties by extracting several quantitative properties from the trajectory to understand the pathology of fALS disease. Our results show considerable differences in H43R compared to WT and W32F mutated SOD1, such as increasing distances between the critical residues results in open conformation at the active site, strong fluctuations in the important loops (Zinc and electrostatic loops) and weakening of important hydrogen bonds especially between N (His 43/Arg 43) and carbonyl oxygen (His 120) in agreement with the experimental report. The calculated buried surface area of dimer interface for WT, H43R and W32F are 682, 726 and 657 Å(2) respectively, representing the loss of dimerization in H43R. Essential dynamics reveal that overall motions of WT and W32F are mainly involved in three to four eigenvectors, but in H43R the overall motions are mainly in the first eigenvector. These data thus provide a unifying description for the structural destabilization, enhanced peroxidase activity, loss of dismutation activity and increase in aggregation propensity in the pathology of fALS diseases.

Pro-oxidant copper-binding mode of the Apo form of ALS-linked SOD1 mutant H43R denatured at physiological temperature

The mutation of Cu,Zn-superoxide dismutase (SOD1), a major antioxidant enzyme, is associated with amyotrophic lateral sclerosis (ALS). In a previous study, we showed that the metal-depleted apo form of an ALS-linked mutant, H43R, undergoes denaturation at physiological temperature (37 °C) in 90 min and acquires pro-oxidant activity in the presence of Cu(2+) and H2O2. In this study, we have examined the Cu(2+)-binding mode of denatured apo-H43R by circular dichroism (CD), fluorescent oxidation, UV Raman spectroscopy, and photooxidation. CD spectroscopy indicates that denatured apo-H43R loses native β-barrel structure and the binding of Cu(2+) to the denatured apo form induces local refolding. Fluorescent-oxidation assays in the absence and presence of Cu(2+) chelators show that denatured apo-H43R contains two Cu(2+)-binding sites with higher and lower Cu(2+) affinities and with pro-oxidant activities in the reverse order. UV Raman spectroscopy gives evidence that His residues are bound to Cu(2+) mainly through the imidazole Nτ atom at the higher-affinity site and through the Nπ atom at the lower-affinity site, sharing one His residue with each other. The Cu(2+)-binding mode of denatured apo-H43R is analogous to but different from the Cu,Zn-binding mode of the native holo form. Photooxidation experiments confirm the involvement of His residues in the pro-oxidant activity. Taken together, it is suggested that the binding of Cu(2+) induces the local refolding of denatured apo-H43R to create toxic catalytic centers that convert the enzyme from antioxidant to pro-oxidant, leading to the pathogenesis of ALS. His residues are essential for both Cu(2+)-binding and pro-oxidant activities.

UV Raman markers for structural analysis of aromatic side chains in proteins

UV Raman spectroscopy is a powerful tool for investigating the structures and interactions of the aromatic side chains of Phe, Tyr, Trp, and His in proteins. This is because Raman bands of aromatic ring vibrations are selectively enhanced with UV excitation, and intensities and wavenumbers of Raman bands sensitively reflect structures and interactions. Interpretation of protein Raman spectra is greatly assisted by using empirical correlations between spectra and structure. Many Raman bands of aromatic side chains have been proposed to be useful as markers of structures and interactions on the basis of empirical correlations. This article reviews the usefulness and limitations of the Raman markers for protonation/deprotonation, conformation, metal coordination, environmental polarity, hydrogen bonding, hydrophobic interaction, and cation-π interaction of the aromatic side chains. The utility of Raman markers is demonstrated through an application to the structural analysis of a membrane-bound proton channel protein.

INTERACTION OF THE TAUTOMERIC STATES OF HISTIDINE WITH Cu AND Zn METAL IONS – A THEORETICAL STUDY

A density functional study on the interaction of Cu 2+ and Zn 2+ metal ions at the predominant positions of N τ– H and N π– H histidine tautomers has been performed. The fully optimized energy of the isolated histidine tautomers at B3LYP/6-311++G** level of theory depicts N τ– H tautomer to be much stable compared to that of the N π– H tautomer. The interaction of metal ions forms bidentate and tridentate complexes with N τ– H tautomer, while it is absent in the case of N π– H tautomer emphasizing the role of former in structural determination of liganated proteins. The Zn 2+ ion induces a barrier-free proton transfer when interacted at the carbonyl position of N τ– H histidine tautomer necessitating the tautomer to be in the zwitterionic form for complexation. The thermodynamical analysis predicts a blue shift in the NH and CO stretching vibrational frequencies and suggests N τ– H tautomer to be best suitable for Cu 2+ and Zn 2+ ion interactions. The topological and charge transfer studies in concert with frontier molecular orbital (FMO) analysis confirm the covalent interaction, validating the findings based on the geometrical data.

Oxidation of histidine residues in copper-zinc superoxide dismutase by bicarbonate-stimulated peroxidase and thiol oxidase activities: pulse EPR and NMR studies

In this work, we investigated the oxidative modification of histidine residues induced by peroxidase and thiol oxidase activities of bovine copper-zinc superoxide dismutase (Cu-ZnSOD) using NMR and pulse EPR spectroscopy. 1D NMR and 2D-NOESY were used to determine the oxidative damage at the Zn(II) and Cu(II) active sites as well as at distant histidines. Results indicate that during treatment of SOD with hydrogen peroxide (H(2)O(2)) or cysteine in the absence of bicarbonate anion (HCO(3)(-)), both exchangeable and nonexchangeable protons were affected. Both His-44 and His-46 in the Cu(II) active site were oxidized based on the disappearance of NOESY cross-peaks between CH and NH resonances of the imidazole rings. In the Zn(II) site, only His-69, which is closer to His-44, was oxidatively modified. However, addition of HCO(3)(-) protected the active site His residues. Instead, resonances assigned to the His-41 residue, 11 Å away from the Cu(II) site, were completely abolished during both HCO(3)(-)-stimulated peroxidase activity and thiol oxidase activity in the presence of HCO(3)(-) . Additionally, ESEEM/HYSCORE and ENDOR studies of SOD treated with peroxide/Cys in the absence of HCO(3)(-) revealed that hyperfine couplings to the distal and directly coordinated nitrogens of the His-44 and His-46 ligands at the Cu(II) active site were modified. In the presence of HCO(3)(-), these modifications were absent. HCO(3)(-)-mediated, selective oxidative modification of histidines in SOD may be relevant to understanding the molecular mechanism of SOD peroxidase and thiol oxidase activities.

A fast and accurate method for predicting pKa of residues in proteins

Predicting the pH-activities of residues in proteins is an important problem in enzyme engineering and protein design. A novel predictor called 'Pred-pK(a)' was developed based on the physicochemical properties of amino acids and protein 3D structure. The Pred-pK(a) approach considers the influence of all other residues of the protein to predict the pK(a) value of an ionizable residue. An empirical equation was formulated, in which the pK(a) value was a distance-dependent function of physicochemical parameters of 20 amino acid types, describing their electrostatic and van der Waals interaction, as well as the effects of hydrogen bonds and solvation. Two sets of coefficients, {a(alpha)} and {b(l)}, were used in the predictor: {a(alpha)} is the weight factors of 20 amino acid types and {b(l)} is the weight factors of physicochemical properties of amino acids. An iterative double least square procedure was proposed to solve the two sets of weight factors alternately and iteratively in a training set. The two coefficient sets {a(alpha)} and {b(l)} thus obtained were used to predict the pK(a) values of residues in a protein. The average predictive error is +/-0.6 pH in less than a minute in common personal computer.

Identification of structurally conserved residues of proteins in absence of structural homologs using neural network ensemble

Motivation: So far various bioinformatics and machine learning techniques applied for identification of sequence and functionally conserved residues in proteins. Although few computational methods are available for the prediction of structurally conserved residues from protein structure, almost all methods require homologous structural information and structure-based alignments, which still prove to be a bottleneck in protein structure comparison studies. In this work, we developed a neural network approach for identification of structurally important residues from a single protein structure without using homologous structural information and structural alignment.

Results: A neural network ensemble (NNE) method that utilizes negative correlation learning (NCL) approach was developed for identification of structurally conserved residues (SCRs) in proteins using features that represent amino acid conservation and composition, physico-chemical properties and structural properties. The NCL-NNE method was applied to 6042 SCRs that have been extracted from 496 protein domains. This method obtained high prediction sensitivity (92.8%) and quality (Matthew's correlation coefficient is 0.852) in identification of SCRs. Further benchmarking using 60 protein domains containing 1657 SCRs that were not part of the training and testing datasets shows that the NCL-NNE can correctly predict SCRs with ∼ 90% sensitivity. These results suggest the usefulness of NCL-NNE for facilitating the identification of SCRs utilizing information derived from a single protein structure. Therefore, this method could be extremely effective in large-scale benchmarking studies where reliable structural homologs and alignments are limited.

Availability: The executable for the NCL-NNE algorithm is available at http://www3.ntu.edu.sg/home/EPNSugan/index_files/SCR.htm

Contact:epnsugan@ntu.edu.sg; chakraba@ncbi.nlm.nih.gov.

Supplementary information:Supplementary data are available at Bioinformatics online.

Spectroscopic analysis of L-histidine adsorbed on gold and silver nanoparticle surfaces investigated by surface-enhanced Raman scattering

The adsorption of l-histidine on gold (Au) and silver (Ag) nanoparticle surfaces has been comparatively analyzed by means of surface-enhanced Raman scattering (SERS). The SERS spectra of l-histidine on Ag were found to be quite different from those on Au, indicating dissimilar adsorption structures depending on metal substrates. Most peaks of l-histidine on Ag appeared to be due to coordination via the carboxylate (COO(-)) group with an imidazole ring of fairly upright geometry, whereas on Au it was assumed to adsorb with a rather flat geometry. A density functional theory (DFT) calculation was performed at the level of B3LYP/LANL2DZ to estimate the energetic stability of the binding of the imidazole ring and the carboxylate group of l-histidine with the Ag and Au atoms, respectively. Based on the DFT calculation, the carboxylate group of l-histidine was predicted to bind more favorably to Ag than to Au, and this was in line with our SERS spectral analysis.

Mechanistic basis for inflammation and tumor promotion in lungs of 2,6-di-tert-butyl-4-methylphenol-treated mice: electrophilic metabolites alkylate and inactivate antioxidant enzymes

An established model for mechanistic analysis of lung carcinogenesis involves administration of 3-methylcholanthrene to mice followed by several weekly injections of the tumor promoter 2,6-di-tert-butyl-4-methylphenol (BHT). BHT is metabolized to quinone methides (QMs) responsible for promoting tumor formation. QMs are strongly electrophilic and readily form adducts with proteins. The goal of the present study was to identify adducted proteins in the lungs of mice injected with BHT and to assess the potential impact of these modifications on tumorigenesis. Cytosolic proteins from treated mouse lungs were separated by two-dimensional electrophoresis, adducts detected by immunoblotting, and proteins identified by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Eight adducts were detected in the lungs of most, or all, of six experimental groups of BALB mice. Of these adducts, several were structural proteins, but others, namely, peroxiredoxin 6 (Prx6), Cu,Zn-superoxide dismutase (SOD1), carbonyl reductase, and selenium-binding protein 1, have direct or indirect antioxidant functions. When the 9000g supernatant fraction of mouse lung was treated with BHT-QM (2,6-di-tert-butyl-4-methylene-2,5-cyclohexadienone), substantial lipid peroxidation and increases in hydrogen peroxide and superoxide formation were observed. Studies with human Prx6 and bovine SOD1 demonstrated inhibition of enzyme activity concomitant with adduct formation. LC-MS/MS analysis of digests of adducted Prx6 demonstrated adduction of both Cys 91 and Cys 47; the latter residue is essential for peroxidatic activity. Analysis of QM-treated bovine SOD1 by matrix-assisted laser desorption/ionization time-of-flight MS demonstrated the predominance of a monoadduct at His 78. This study provides evidence that indicates Prx6, SOD1, and possibly other antioxidant enzymes in mouse lung are inhibited by BHT-derived QMs leading to enhanced levels of reactive oxygen species and inflammation and providing a mechanistic basis for the effects of BHT on lung tumorigenesis.

Steady-state and transient ultraviolet resonance Raman spectrometer for the 193-270 nm spectral region

We describe a state-of-the-art tunable ultraviolet (UV) Raman spectrometer for the 193-270 nm spectral region. This instrument allows for steady-state and transient UV Raman measurements. We utilize a 5 kHz Ti-sapphire continuously tunable laser (approximately 20 ns pulse width) between 193 nm and 240 nm for steady-state measurements. For transient Raman measurements we utilize one Coherent Infinity YAG laser to generate nanosecond infrared (IR) pump laser pulses to generate a temperature jump (T-jump) and a second Coherent Infinity YAG laser that is frequency tripled and Raman shifted into the deep UV (204 nm) for transient UV Raman excitation. Numerous other UV excitation frequencies can be utilized for selective excitation of chromophoric groups for transient Raman measurements. We constructed a subtractive dispersion double monochromator to minimize stray light. We utilize a new charge-coupled device (CCD) camera that responds efficiently to UV light, as opposed to the previous CCD and photodiode detectors, which required intensifiers for detecting UV light. For the T-jump measurements we use a second camera to simultaneously acquire the Raman spectra of the water stretching bands (2500-4000 cm(-1)) whose band-shape and frequency report the sample temperature.

Solvent-based deuterium isotope effects on the redox thermodynamics of cytochrome c

The reduction thermodynamics of cytochrome c (cytc), determined electrochemically, are found to be sensitive to solvent H/D isotope effects. Reduction of cytochrome c is enthalpically more favored in D(2)O with respect to H(2)O, but is disfavored on entropic grounds. This is consistent with a reduction-induced strengthening of the H-bonding network within the hydration sphere of the protein. No significant changes in E degrees ' occur, since the above variations are compensative. As a main result, this work shows that the oxidation-state-dependent differences in protein solvation, including electrostatics and solvent reorganization effects, play an important role in determining the individual enthalpy and entropy changes of the reduction process. It is conceivable that this is a common thermodynamic feature of all electron transport metalloproteins. The isotope effects turn out to be sensitive to buffer anions which specifically bind to cytc. Evidence is gained that the solvation thermodynamics of both redox forms of cytc are sensibly affected by strongly hydrated anions.