Solubilisation of ferricytochrome c in methanol using a crown ether: absorption, circular dichroism and EPR spectral properties

Ferricytochrome c is normally insoluble in methanol, but its solution is facilitated by complexation with 18-crown-6. Absorption, circular dichroism and EPR spectroscopy indicate that the solubilised protein in MeOH exists in at least three conformational states, all different from the native state in neutral aqueous solution. In two states the haem iron (III) is low spin and in one state it is high spin, but it seems likely that all three forms are globular. The proportion in the high spin form increases at increasing crown ether concentration and on ageing the protein solution. The protein appears to return to its native conformation when it is restored to an aqueous environment.     

Circular dichroism studies of the complex between ferredoxin and ferredoxin-NADP reductase

Circular dichroism (CD) spectra are presented of ferredoxin, ferredoxin-NADP reductase and their complex. A change in CD occurs on complex formation which is consistent with a decrease in the Cotton effects due to the ferredoxin. This change is interpreted as due to a decrease in interaction in ferredoxin between the iron-sulphur chromophore group and the protein.     

Structure-activity relationship of amyloid fibrils

Protein aggregation is a process in which proteins self-associate into imperfectly ordered macroscopic entities. Such aggregates are generally classified as either amorphous or highly ordered, the most common form of the latter being amyloid fibrils. Amyloid fibrils composed of cross-β-sheet structure are the pathological hallmarks of several diseases including Alzheimer’s disease, but are also associated with functional states such as the fungal HET-s prion. This review aims to summarize the recent high-resolution structural studies of amyloid fibrils in light of their (potential) activities. We propose that the repetitive nature of the cross-β-sheet structure of amyloids is key for their multiple properties: the repeating motifs can translate a rather non-specific interaction into a specific one through cooperativity.     

Empirical rules for rationalising visible circular dichroism of Cu2+ and Ni2+ histidine complexes: applications to the prion protein

A natively unfolded region of the prion protein, PrP(90-126) binds Cu(2+) ions and is vital for prion propagation. Pentapeptides, acyl-GGGTH(92-96) and acyl-TNMKH(107-111), represent the minimum motif for this Cu(2+) binding region. EPR and (1)H NMR suggests that the coordination geometry for the two binding sites is very similar. However, the visible CD spectra of the two sites are very different, producing almost mirror image spectra. We have used a series of analogues of the pentapeptides containing His(96) and His(111) to rationalise these differences in the visible CD spectra. Using simple histidine-containing tri-peptides we have formulated a set of empirical rules that can predict the appearance of Cu(2+) visible CD spectra involving histidine and amide main-chain coordination.     

Revealing binding sites for myeloperoxidase on the surface of human low density lipoproteins

Low density lipoproteins (LDL) of human blood, once oxidized, provoke cholesterol accumulation in cells of arterial wall, which favors the development of atherosclerosis. Oxidative modification of LDL can result from their interaction with hypochlorous acid produced in the halogenation cycle of myeloperoxidase (MPO). On account that MPO is able to form complexes with LDL it seems important to learn the forces promoting such contacts and to spot the likely binding sites for the enzyme on the surface of LDL particles. In this study affinity chromatography on MPO-Sepharose showed that MPO-LDL complexes are uncoupled at ionic strength above 0.3 M NaCl or when pH of solution goes below 3.6. This is an evidence of ionic interaction between MPO and LDL. We used spin probes of lipid nature embedded in phospholipid monolayer so that a variety of distances between the surface of an LDL particle and the paramagnetic center of a spin probes was provided. Since MPO interaction with labeled LDL caused no alteration of EPR spectra it was concluded that lipid components of LDL are not involved in MPO binding. Analysis of Mn²⁺ distribution between LDL surface and the aqueous milieu showed that the surface negative charge of LDL is not considerably changed upon interaction with MPO. It can be suggested that interaction of LDL with MPO does not involve phospholipids that are the principal carriers of the surface charge. Among synthetic oligopeptides with amino acid sequences mimicking those of apoB-100 fragments – ¹EEEMLEN⁷, ⁵³VELEVPQ⁵⁹ and ⁴⁴⁵EQIQDDCTGDED⁴⁵⁶ – only the latter could replace MPO in the complex with LDL. It is concluded that the likely site of interaction with MPO is the amino acid stretch 445–456 of apoB-100 in LDL.     

Pathways for Electron Tunneling in Cytochrome c Oxidase

Warburg showed in 1929 that the photochemical action spectrum for CO dissociation from cytochrome c oxidase is that of a heme protein. Keilin had shown that cytochrome a does not react with oxygen, so he did not accept Warburg's view until 1939, when he discovered cytochrome a ₃. The dinuclear cytochrome a ₃-Cu_B unit was found by EPR in 1967, whereas the dinuclear nature of the Cu_A site was not universally accepted until oxidase crystal structures were published in 1995. There are negative redox interactions between cytochrome a and the other redox sites in the oxidase, so that the reduction potential of a particular site depends on the redox states of the other sites. Calculated electron-tunneling pathways for internal electron transfer in the oxidase indicate that the coupling-limited rates are 9×10⁵ (Cu _A a) and 7×10⁶ s^–1 (a a ₃); these calculations are in reasonable agreement with experimental rates, after corrections are made for driving force and reorganization energy. The best Cu_A-a pathway starts from the ligand His204 and not from the bridging sulfur of Cys196, and an efficient a-a ₃ path involves the heme ligands His378 and His376 as well as the intervening Phe377 residue. All direct paths from Cu_A to a ₃ are poor, indicating that direct Cu_A a ₃ electron transfer is much slower than the Cu_A a reaction. The pathways model suggests a means for gating the electron flow in redox-linked proton pumps.     

Detection of heme oxygenase activity in a library of four-helix bundle proteins: towards the de novo synthesis of functional heme proteins

Design and chemical synthesis of de novo heme proteins with enzymatic activity on cellulose membranes is described. 352 antiparallel four-helix bundle proteins with a single histidine for heme ligation were assembled from three different sets of short amphipathic helices on membrane-bound peptide templates. The templates were coupled by linkers to cellulose membranes of microplate format, which could be cleaved for control of intermediate and final products. The incorporation of heme and the heme oxygenase activity of the 352 proteins were monitored by measuring UV-visible spectra directly on the cellulose. The kinetics of the heme oxygenase reaction was studied by monitoring the decrease of the Soret band and the transient absorbance of verdoheme being an intermediate product in the formation of biliverdin. Four of the proteins covering a broad range of the enzymatic rate constants were selected and synthesized in solution for further characterization. Detailed studies by redox potentiometry, analytical ultracentrifugation, and electron paramagnetic resonance spectroscopy yielded information about the aggregation state of the proteins, the spin state and the putative coordination environment of the iron. The amount of five-coordinated high-spin iron and a positive reduction potential were found to promote the oxygenase activity of the proteins.     

Mononuclear and binuclear Co(III)-dioxygen adducts of bleomycin. Circular dichroism and electron paramagnetic resonance studies

Co(II) interacts with bleomycin in aqueous solution, in the presence of air, to give a short lived mononuclear superoxo-Co(III) complex (I) identified previously, by Sugiura, by electron paramagnetic resonance measurements. This complex rapidly releases O₂ to yield the dinuclear μ-peroxo-Co(III) complex (II), but is stabilized by the presence of DNA yielding a new superoxo long lived species (I′). The absorption and circular dichroism spectra of the three species (I,I′,II) have been characterized.     

Iron . bleomycin . DNA system evidence of a long-lived bleomycin . iron . oxygen intermediate

When Fe(II) is added to a bleomycin. DNA mixture in the presence of air a long-lived $\text{(}\text{t}{}_{\mathrm{<mtext>1</mtext><mtext>2</mtext>}}\text{= 45}\text{minutes}\text{)}$ EPR silent species (I′) is formed; the circular dichroism and absorption spectra of which have been characterized. This complex slowly decays yielding a ferric complex (III′) analogous to the well known low spin Fe(III). BLM species.     

Conformational study of purified epoxide hydrolase from rat liver

Hepatic epoxide hydrolase (EC 3.3.2.3) was purified from phenobarbital-treated rats by ion-exchange chromatography followed by hydrophobic chromatography. The enzyme had a specific activity of 300--400 nmol min-1 mg-1 protein with benzo[a]pyrene-4,5-oxide as the substrate. Circular dichroism (CD) spectra of the purified enzyme gave two negative bands, centered at 210 nm and 222 nm, respectively. The mean residue ellipticity at 222 nm was 12,9000 deg X cm(2) X dmol(-1), which indicated the presence of about 35% alpha-helical structures. Sodium dodecyl sulfate (SDS) greatly affected the shape of the CD spectra, which were gradually shifted to the blue. This suggested a decrease in the aggregation state of the protein. Electrostatic interactions were important in the organization of the enzyme structure since the conformation was stable between pH 7.4 and pH 10. At pH-values 5.0, 6.0 and 12.0, the CD bands underwent considerable changes in both amplitude and shape. Moreover there was a good correlation between the optimal pH range of the epoxide hydrolase activity and the organization state of the protein. After membrane reconstitution with liposomes, the conformation of the enzyme was not significantly modified by the presence of dimyristoyl L-alpha-phosphatidylcholine or other phospholipids. This constancy was obtained over a wide range of molar ratios of phospholipids to protein (0--500). However, phospholipids did increase the thermal stability of the enzyme. Fluorescence measurements of diphenylhexatriene (DPH) bound to dimyristoyl L-alpha-phosphatidylcholine indicated that addition of epoxide hydrolase modified the thermal transition of the lipid phase. On the other hand, electron paramagnetic resonance (EPR) signals of the nitroxide-labelled fatty acid, 2-(14-carboxy-tetradecyl)-2-ethyl-4,4-dimethyl-3,3,-oxazolidiny-oxyl, bound to the phospholipid, indicated that the presence of the protein decreased by about 53% the correlation time of the label, suggesting that its motion had increased. In conclusion, phospholipid-epoxide hydrolase interactions enhanced the fluidity of dimyristoyl L-alpha-phosphatidylcholine liposomes without changing the secondary structure of the enzyme. Electrostatic interactions also played an important role in the conformational stability of the protein.     

EPR study of 1Asp-3Cys ligated 4Fe-4S iron-sulfur cluster in NB-protein (BchN-BchB) of a dark-operative protochlorophyllide reductase complex

Dark-operative protochlorophyllide oxidoreductase, a nitrogenase-like enzyme, contains two [4Fe–4S] clusters, one in the L-protein ((BchL)₂) and the other in the NB-protein ((BchN–BchB)₂). The reduced NB-cluster in the NB-protein, which is ligated by 1Asp/3Cys residues, showed a broad S = 3/2 electron paramagnetic resonance signal that is rather rare in [4Fe–4S] clusters. A 4Cys-ligated NB-cluster in the mutated variant BchB–D36C protein, in which the Asp36 was replaced by a Cys, gave a rhombic normal S = 1/2 signal and lost the catalytic activity. The results suggest that Asp36 contributes to the low redox potential necessary to reduce protochlorophyllide.