Long Distance Charge Redistribution Upon Cu,Zn-Superoxide Dismutase Reduction

Construction of Sol-Gel Phase-Reversible Hydrogels with Tunable Properties with Native Nanofibrous Protein as Building Blocks

Reversible sol-gel transforming behaviors combined with tunable mechanical properties are vital demands for developing biomaterials. However, it remains challenging to correlate these properties with the hydrogels constructed by denatured protein as building blocks. Herein, taking advantage of naturally high-affinity coordination environments consisting of i, i + 4 His-Glu motifs offered by paramyosin, a ubiquitous nanofibrous protein, we found that Zn²⁺ rather than Ca²⁺ or Mg²⁺ has the ability to trigger the self-assembly of native abalone paramyosin (AbPM) into protein hydrogels under benign conditions, while the addition of EDTA induces the hydrogels back into protein monomers, indicative of a reversible process. By using such sol-gel reversible property, the AbPM gels can serve as a vehicle to encapsulate bioactive molecules such as curcumin, thereby protecting it from degradation from thermal and photo treatment. Notably, based on the high conserved structure of native AbPM, the mechanical property and biological activity of the fabricated AbPM hydrogels can be fined-tuned by its noncovalent interaction with small molecules. All these findings raise the possibility that native paramyosin can be explored as a new class of protein hydrogels which exhibit favorable properties that the traditional hydrogels constructed by denatured protein building blocks do not have.

Protonation of the Cysteine Axial Ligand Investigated in His/Cys c-Type Cytochrome by UV-Vis and Mid- and Far-IR Spectroscopy

His/Cys coordination was recently found in several c-type cytochromes, which could act as sensors, in electron transport or in regulation. Toward a better understanding of Cys function and reactivity in these cytochromes, we compare cytochrome c6 (c6wt) from the cyanobacterium Nostoc PCC 7120 with its Met58Cys mutant. We probe the axial ligands and heme properties by combining visible and mid- to far-FTIR difference spectroscopies. Cys58 determines the strong negative redox potential and pH dependence of M58C (E_mM58C = -375 mV, versus E_mc6wt = +339 mV). Mid-IR (notably Cys ν(SH), His ν(C₅N₁), heme δ(CmH)) and far-IR (ν(Fe(II)-His), ν(His-Fe(III)-Cys)) markers of the heme and ligands show that Cys58 remains a strong thiolate ligand of reduced Met58Cys at alkaline pH, while it is protonated at pH 7.5, is stabilized by a strong hydrogen bonding interaction, and weakly interacts with Fe(II). These data provide a benchmark for further analysis of c-type cytochromes with natural His/Cys coordination.

Nucleation and kinetics of SOD1 aggregation in human cells for ALS1

Aberrant structural formations of Cu/Zn superoxide dismutase enzyme (SOD1) are the probable mechanism by which circumscribed mutations in the SOD1 gene cause familial amyotrophic lateral sclerosis (ALS1). SOD1 forms aberrant structures which can proceed by nucleation to insoluble aggregates. Here, the SOD1 aggregation reaction was investigated predominantly by time-course studies on ALS1 variants G85R, G37R, D101G, and D101N in human embryonic kidney cells (HEK293FT), with analysis by detergent ultracentrifugation extractions and high-resolution PAGE methodologies. Nucleation was found to be pseudo-zeroth order and dependent on time and concentration at constant 37.0 °C and pH 7.4. The predominant subsets of the total SOD1 expression set which comprised the nucleation phase were both soluble and insoluble inactive monomers, trimers, and hexamers with reduced intra-disulfide bonds. Superoxide exposure via paraquat initiated the formation of SOD1 trimers in untransfected SH-SY5Y cells and increased the aggregation propensity of G85R in HEK293FT. These data show the kinetic formation of aberrant SOD1 subsets implicated in ALS1 and indicate that superoxide substrate may initiate its radical polymerization. In an instance of the utility of methodological reductionism in molecular theory: though many ALS1 variants retain their global enzymatic activity, the SOD1 subsets most implicated in causing ALS1 do not retain their specific activity.

Molecular dynamics of a far positioned SOD1 mutant V14M reveals pathogenic misfolding behavior

Human superoxide dismutase (Cu/Zn SOD1) is a homodimeric enzyme. Mutations in Cu/Zn SOD1 causes a familial form of amyotrophic lateral sclerosis (fALS), and aggregation of mutant SOD1 has been proposed to play a role in neurodegeneration. Though a majority of the mutations are point substitutions, there are a few changes that result in amino acid deletions or truncations of the polypeptide. These pathogenic mutations are scattered throughout the three-dimensional structure of the dimeric enzyme, which creates a puzzling pattern to investigate the molecular determinants of fALS. The most common hypothesis proposed that the misfolding of SOD1 mutants are primarily triggered by decreased affinity for metal ions. However, this hypothesis is challenging, as a significant number of disease-causing mutations are located far away from the metal-binding site and dimer interface. So in the present study, we have investigated the influence of such a far positioned pathogenic mutation, V14M, in altering the stability and folding of the Cu/Zn SOD1. Though the location of Val14 is far positioned, it has a vital role in the stability of SOD1 by preserving its hydrophobic cluster at one end of the β barrel domain. We have performed MD simulations of the V14M mutant for 80 ns timescale. The results reveal the fact that irrespective of its location, V14M mutation triggers a conformational change that is more similar to that of the metal-deficient holo form and could resemble an intermediate state in the folding reaction which results in protein misfolding and aggregation.

The production of nitrous oxide by the heme/nonheme diiron center of engineered myoglobins (Fe(B)Mbs) proceeds through a trans-iron-nitrosyl dimer

Denitrifying NO reductases are transmembrane protein complexes that are evolutionarily related to heme/copper terminal oxidases. They utilize a heme/nonheme diiron center to reduce two NO molecules to N₂O. Engineering a nonheme Fe_B site within the heme distal pocket of sperm whale myoglobin has offered well-defined diiron clusters for the investigation of the mechanism of NO reduction in these unique active sites. In this study, we use FTIR spectroscopy to monitor the production of N₂O in solution and to show that the presence of a distal Fe_B^II is not sufficient to produce the expected product. However, the addition of a glutamate side chain peripheral to the diiron site allows for 50% of a productive single-turnover reaction. Unproductive reactions are characterized by resonance Raman spectroscopy as dinitrosyl complexes, where one NO molecule is bound to the heme iron to form a five-coordinate low-spin {FeNO}⁷ species with ν(FeNO)_heme and ν(NO)_heme at 522 and 1660 cm^–1, and a second NO molecule is bound to the nonheme Fe_B site with a ν(NO)_FeB at 1755 cm^–1. Stopped-flow UV–vis absorption coupled with rapid-freeze-quench resonance Raman spectroscopy provide a detailed map of the reaction coordinates leading to the unproductive iron-nitrosyl dimer. Unexpectedly, NO binding to Fe_B is kinetically favored and occurs prior to the binding of a second NO to the heme iron, leading to a (six-coordinate low-spin heme-nitrosyl/Fe_B-nitrosyl) transient dinitrosyl complex with characteristic ν(FeNO)_heme at 570 ± 2 cm^–1 and ν(NO)_FeB at 1755 cm^–1. Without the addition of a peripheral glutamate, the dinitrosyl complex is converted to a dead-end product after the dissociation of the proximal histidine of the heme iron, but the added peripheral glutamate side chain in Fe_BMb2 lowers the rate of dissociation of the promixal histidine which in turn allows the (six-coordinate low-spin heme-nitrosyl/Fe_B-nitrosyl) transient dinitrosyl complex to decay with production of N₂O at a rate of 0.7 s^–1 at 4 °C. Taken together, our results support the proposed trans mechanism of NO reduction in NORs.

Identification of hepatic copper-binding proteins from tilapia by column chromatography with proteomic approaches

Although copper is an essential element, it shows cytotoxic effects when present in excessive amounts with the production of hydroxyl radicals, which can damage phospholipids and enzymes. This necessitates a tight cellular control mechanism for copper homeostasis including its uptake and removal. The high copper contents in the liver of tilapia make this fish a suitable model for the study of copper binding proteins (CBPs). The liver was dissected from tilapia injected with Cu(2+) and cytosolic fractions were separated by using Superdex 75 column chromatography followed by atomic absorption spectrometry. Fractions in two major peaks containing CBPs were analyzed by using differential proteomic approaches, and loaded on a Cu chelating ion-immobilized affinity column (Cu-IMAC). Of the 113 differentially expressed proteins in these two peaks, 28 proteins were found to have copper binding ability, including well-characterized CBPs, such as copper transporter ATP7A and metallothionein. The networks of CBPs built up by Ingenuity Pathway Analysis (IPA) would help us to understand the transportation pathway and function of CBPs, which were related to free radical scavenging, cellular development and lipid metabolism. In addition, our results suggest that Cu(2+) would compete with Fe(2+) and Ca(2+) in binding with some target proteins, such as ferritin, transferrin, and calmodulin.

CO binding and ligand discrimination in human myeloperoxidase

Despite the fact that ferrous myeloperoxidase (MPO) can bind both O(2) and NO, its ability to bind CO has been questioned. UV/visible spectroscopy was used to confirm that CO induces small spectral shifts in ferrous MPO, and Fourier transform infrared difference spectroscopy showed definitively that these arose from formation of a heme ferrous-CO compound. Recombination rates after CO photolysis were monitored at 618 and 645 nm as a function of CO concentration and pH. At pH 6.3, k(on) and k(off) were 0.14 mM(-1) x s(-1) and 0.23 s(-1), respectively, yielding an unusually high K(D) of 1.6 mM. This affinity of MPO for CO is 10 times weaker than its affinity for O(2). The observed rate constant for CO binding increased with increasing pH and was governed by a single protonatable group with a pK(a) of 7.8. Fourier transform infrared spectroscopy revealed two different conformations of bound CO with frequencies at 1927 and 1942 cm(-1). Their recombination rate constants were identical, indicative of two forms of bound CO that are in rapid thermal equilibrium rather than two distinct protein populations with different binding sites. The ratio of bound states was pH-dependent (pK(a) approximately 7.4) with the 1927 cm(-1) form favored at high pH. Structural factors that account for the ligand-binding properties of MPO are identified by comparisons with published data on a range of other ligand-binding heme proteins, and support is given to the recent suggestion that the proximal His336 in MPO is in a true imidazolate state.

Fourier transform infrared (FTIR) spectroscopy

Fourier transform infrared (FTIR) spectroscopy probes the vibrational properties of amino acids and cofactors, which are sensitive to minute structural changes. The lack of specificity of this technique, on the one hand, permits us to probe directly the vibrational properties of almost all the cofactors, amino acid side chains, and of water molecules. On the other hand, we can use reaction-induced FTIR difference spectroscopy to select vibrations corresponding to single chemical groups involved in a specific reaction. Various strategies are used to identify the IR signatures of each residue of interest in the resulting reaction-induced FTIR difference spectra. (Specific) Isotope labeling, site-directed mutagenesis, hydrogen/deuterium exchange are often used to identify the chemical groups. Studies on model compounds and the increasing use of theoretical chemistry for normal modes calculations allow us to interpret the IR frequencies in terms of specific structural characteristics of the chemical group or molecule of interest. This review presents basics of FTIR spectroscopy technique and provides specific important structural and functional information obtained from the analysis of the data from the photosystems, using this method.

Imidazolate bridged Cu(II)-Cu(II) and Cu(II)-Zn(II) complexes of a terpyridinophane azamacrocycle: a solution and solid state study

The dinuclear Cu2+ and Zn2+ as well as the mixed Cu2+-Zn2+ complexes of a 5,5''-pentaazaterpyridinophane ligand (L) are able to incorporate imidazolate (Im-) as a bridging ligand. The crystal structure of [Cu(2)L(Im)(Br)(H2O)](CF(3)SO(3))(2).3H2O (1) shows one copper coordinated by the three pyridine nitrogens of the terpyridine unit, one nitrogen of the imidazolate bridge (Im-) and one bromide anion occupying the axial position of a distorted square pyramid. The second copper atom is coordinated by the remaining imidazolate nitrogen, the three secondary nitrogens at the centre of the polyamine bridge and one water molecule that occupies the axial position. Magnetic measurements have been performed in the 2.0-300.0 K temperature range. Experimental data could be satisfactorily reproduced by using an isotropic exchange model H = -JS(1)S(2) with J = -52.3 cm(-1) and g = 2.09. Potentiometric studies have provided details of the speciation and stability constants for the mixed Cu2+-L-HIm, Zn2+-L-HIm (HIm = imidazole) and Cu2+-Zn2+-L-HIm systems. The apparent stability constant obtained at pH = 9 for the addition of imidazole to the dinuclear Cu2+ complexes is one of the highest so far reported (log K = 7.5). UV-Vis spectroscopy and paramagnetic NMR data show that imidazole coordinates to the Cu2+ ions as a bridging imidazolate ligand from pH 5 to 10. Electrochemical reduction of the Cu2+-Zn2+-L complex occurs in two successive one-electron per copper ion quasi-reversible steps. The formal potential of the Cu2+-Zn2+-L/Cu+-Zn2+-L couple is close to that of SOD. The IC50 values measured at pH 7.8 by means of the nitro blue tetrazolium method show significant SOD activity for the dinuclear Cu2+ complexes (IC50 = 2.5 microM) and moderate activity for the Cu2+-Zn2+ mixed systems (IC50 = 30 microM).

Synthesis, Structure, and Activity of Supramolecular Mimics for the Active Site and Arg141 Residue of Copper, Zinc−Superoxide Dismutase

Two supramolecular complexes, [Cu(L)(H2O)2(beta-CD)](ClO4)2.10.5H2O.CH3OH (1) and [Cu(L)(H2O)2(beta-GCD)](HClO4)(ClO4)2.10H2O (2) (L = 4-(4'-tert-butyl-benzyl)diethylenetriamine, beta-CD = beta-cyclodextrin, and beta-GCD = mono-6-deoxy-6-guanidinocycloheptaamylose cation), have been synthesized. The structure of 1 has been characterized by X-ray crystallography. The 4-tert-butyl-benzyl of [Cu(L)(H2O)2]2+ moiety in 1 as a guest inserts into the hydrophobic cavity of the beta-CD as a host along the primary hydroxyl side. On the basis of the structure data of 1, complex 2 was modeled, which showed that the distance between the Cu and C atom of the guanidinium is 5.2 A, comparable to the corresponding distance in bovine erythrocyte Cu, Zn-SOD (5.9 A) (SOD = superoxide dismutase). Apparent inclusion stability constants of the host and the guest were measured to be 0.66 (+/-0.01) x 104 and 1.15 (+/-0.03) x 104 M-1 for 1 and 2 respectively. The electronic absorption bands and electronic reflection bands of each complex are almost the same, indicating an identical structure of the complex in aqueous solution and in solid state. The two complexes showed quasi-reversible one-electron Cu(II)/Cu(I) redox waves with redox potentials of -0.345 and -0.338 V for 1 and 2, respectively. Their SOD-like activities (IC50) were measured to be 0.30 +/- 0.01 and 0.17 +/- 0.01 microM by xanthine/xanthine oxidase-NBT assay. The enhanced SOD activity of 2 by approximately 40% compared with 1 suggests that the guanidyl cation in the host of the supramolecular system of 2 can effectively mimic the side chain of Arg141 in the enzyme, which is known to be essential for high SOD activity possibly through steering of the superoxide substrate to and from the active copper ion.

The coupling between disulphide status, metallation and dimer interface strength in Cu/Zn superoxide dismutase

The gain of neurotoxic function in amyotrophic lateral sclerosis (ALS) has been linked to misfolding of the homodimeric enzyme Cu/Zn superoxide dismutase (SOD). Here, we present the crystal structure of fully cysteine-depleted human SOD (SOD(CallA)), representing a reduced, marginally stable intermediate on the folding pathway in vivo that has also been implicated as neurotoxic precursor state. A hallmark of this species is that it fails to dimerize and becomes trapped as a monomer in the absence of the active-site metals. The crystallographic data show that removal of the C57-C146 disulphide bond sets free the interface loop IV in the apo protein, whereas the same loop remains unaffected in the holo protein. Thus, the low dimerisation propensity of disulphide-reduced apoSOD seems to be of entropic origin due to increased loop flexibility in the monomeric state: in the disulphide-reduced holo protein this gain in configurational entropy upon splitting of the dimer interface is reduced by the metal coordination.

Redox infrared markers of the heme and axial ligands in microperoxidase: bases for the analysis of c-type cytochromes

Structural changes accompanying the change in the redox state of microperoxidase-8 (MP8), the heme-octapeptide obtained from cytochrome c, and its complexes with (methyl)imidazole ligands were studied by electrochemically induced Fourier transform IR (FTIR) difference spectroscopy. To correlate with confidence IR modes with a specific electronic state of the iron, we used UV-vis and electron paramagnetic resonance spectroscopy to define precisely the heme spin state in the samples at the millimolar concentration of MP8 required for FTIR difference spectroscopy. We identified four intense redox-sensitive IR heme markers, nu38 at 1,569 cm(-1) (ox)/1,554 cm(-1) (red), nu42 at 1,264 cm(-1) (ox)/1,242 cm(-1) (red), nu43 at 1,146 cm(-1) (ox), and nu44 at 1,124-1,128 cm(-1) (ox). The intensity of nu42 and nu43 was clearly enhanced for low-spin imidazole-MP8 complexes, while that of nu44 increased for high-spin MP8. These modes can thus be used as IR markers of the iron spin state in MP8 and related c-type cytochromes. Moreover, one redox-sensitive band at 1,044 cm(-1) (red) is attributed to an IR marker specific of c-type hemes, possibly the delta(CbH3)(2,4) heme mode. Other redox-sensitive IR bands were assigned to the MP8 peptide backbone and to the fifth and sixth axial heme ligands. The distinct IR frequencies for imidazole (1,075 cm(-1)) and histidine (1,105 cm(-1)) side chains in the imidazole-MP8 complex allowed us to provide the first direct determination of their pKa at pH 9 and 12, respectively.

Complexation, Structure, and Superoxide Dismutase Activity of the Imidazolate-Bridged Dinuclear Copper Moiety with β-Cyclodextrin and Its Guanidinium-Containing Derivative

An imidazolate-bridged homodinuclear complex, {[Cu(L)(H2O)]2(im)}(ClO4)3 (1), assembled with beta-cyclodextrin (betaCD) and its guanidinium-containing derivative (betaGCD), and thus a helical inclusion complex, {[Cu(L)(H2O)(betaCD)]2(im)}(ClO4)3 (2), were successfully isolated and structurally characterized. Structural analysis showed that each Cu(II) ion has a distorted square pyramidal N4Ow coordination sphere and forms a chiral chain through hydrogen-bonding and hydrophobic interactions. The UV-vis data showed that such a chain can provide the imidazolate bridge additional stability and results in the dissociation equilibrium taking place at the physiological pH. The obtained IC50 value for 2 (0.23 muM) showed a high superoxide dismutase (SOD) activity, which corresponds to a highly stable imidazolate bridge. Interestingly, the guanidinium-containing 1/betaGCD system showed higher SOD activity (IC50 = 0.16 muM), which is enhanced at least by 30% in comparison with that of guanidinium-lacking 2. This result supports that the positive guanidinium plays a role in the catalytic mechanism of Cu,Zn-SOD by ensuring that superoxide enters and peroxide leaves rapidly from the coordination sphere of the copper ion.

Electrochemically induced FTIR difference spectroscopy in the mid- to far infrared (200 μm) domain: A new setup for the analysis of metal–ligand interactions in redox proteins

We report the setup of an electrochemical cell with chemical-vapor deposition diamond windows and the use of a Bruker 66 SX FTIR spectrometer equipped with DTGS and Si-bolometer detectors and KBr and mylar beam splitters, to record on the same sample, FTIR difference spectra corresponding to the structural changes associated with the change in redox state of active sites in proteins in the whole 1800-50 cm(-1) region. With cytochrome c we show that reliable reduced-minus-oxidized FTIR difference spectra are obtained, which correspond to single molecular vibrations. Redox-sensitive IR modes of the cytochrome c are detected until 140 cm(-1) with a good signal to noise. This new setup is promising to analyze the infrared spectral region where metal-ligand vibrations are expected to contribute and to extend the analysis of vibrational properties to metal sites or redox states not accessible to (resonance) Raman spectroscopy.

FTIR Detection of Structural Changes in a Histidine Ligand during S-State Cycling of Photosynthetic Oxygen-Evolving Complex

Changes in structural coupling between the Mn cluster and a putative histidine ligand during the S-state cycling of the oxygen-evolving complex (OEC) have been detected directly by Fourier transform infrared (FTIR) spectroscopy in photosystem (PS) II core particles from the cyanobacterium Synechocystis sp. PCC6803, in which histidine residues were selectively labeled with l-[(15)N(3)]histidine. The bands sensitive to the histidine-specific isotope labeling appeared at 1120-1090 cm(-)(1) in the spectra induced upon the first-, second-, and fourth-flash illumination, for the S(2)/S(1), S(3)/S(2), and S(1)/S(0) differences, at similar frequencies with different sign and/or intensity depending on the respective S-state transitions. However, no distinctive band was observed in the third-flash induced spectrum for the S(0)/S(3) difference. The results indicate that a single histidine residue coupled with the structural changes of the OEC during the S-state cycling is responsible for the observed histidine bands, in which the histidine modes changed during the S(0)-to-S(1) transition are reversed upon the S(1)-to-S(2) and S(2)-to-S(3) transitions. The 1186(+)/1178(-) cm(-)(1) bands affected by l-[(15)N(3)]histidine labeling were observed only for the S(2)/S(1) difference, but those affected by universal (15)N labeling appeared prominently showing a clear S-state dependency. Possible origins of these bands and changes in the histidine modes during the S-state cycling are discussed.

Identification of a Cd2+- and Zn2+-Binding Site in CytochromecUsing FTIR Coupled to an ATR Microdialysis Setup and NMR Spectroscopy†

Fourier transform infrared (FTIR) difference spectroscopy allows the study of molecular changes occurring at active sites in proteins with high sensitivity. Reactions are triggered by light, potential, or temperature steps and more recently by the diffusion of buffers containing effectors above membrane proteins deposited as films on ATR crystals. We have adapted a microdialysis system to an ATR, to study metal sites in soluble proteins. In this study, we identified a Cd(2+)- or Zn(2+)-binding site in cytochrome c with dissociation constants of 17 and 42 microM, respectively, which affects the oxidation rate of ferrocytochrome c by hydrogen peroxide. Using the microdialysis ATR-FTIR setup, we determined that a histidine and the carboxylate group of a glutamate are involved in Zn(2+) binding. The implication of His 33 and Glu 104 in the binding site was deduced from the comparison of FTIR data recorded with horse heart and the variant tuna cytochrome c lacking these two amino acids. A two-dimensional NMR analysis of the Zn(2+)-binding site in horse heart cytochrome c confirmed that His 33 and residues close to the C terminus are sensitive to Zn(2+) binding. This study demonstrates that the microdialysis ATR-FTIR setup is promising for the analysis of metal sites in proteins. From H(2)O/(2)H(2)O exchange experiments, we concluded that the impact of Zn(2+) and Cd(2+) binding on the oxidation kinetics of ferrocytochrome c by H(2)O(2) is associated to the perturbation of a hydrogen-bonding network involving His 33 that is sensitive to the redox state of cytochrome c.