Alkyl free radicals from the beta-scission of fatty acid alkoxyl radicals as detected by spin trapping in a lipoxygenase system

2-Methyl-2-nitrosopropane (tNB)-radical adducts from incubation mixtures of fatty acids and soybean lipoxygenase in borate buffer (pH 9.0) were measured by electron paramagnetic resonance (EPR). In addition to the previously reported six-line signal of secondary carbon-centered radicals (RCHR'), a weak signal submerged in the baseline was detected after the peroxidation phase was finished. We propose that this radical is a decomposition product formed via beta-scission of fatty acid alkoxyl radicals. EPR spectra of tNB-radical adducts formed in mixtures of either linoleic acid, arachidonic acid, or 15-hydroperoxyeicosatetraenoic acid with lipoxygenase exhibited hyperfine structure characteristic of tNB/.CH2CH2-R with hyperfine coupling constants: aN = 17.1 G; aH beta = 11.2 G (2H); and aH gamma = 0.6 G (2H). In the case of linolenic acid, this radical tNB/.CH=CH-R' with hyperfine coupling constants: aN = 17.1 G; aH beta = 10.9 G (2H); aH gamma = 1.1 G; and aH delta = 0.5 G. In accord with the decomposition scheme of hydroperoxides derived from unsaturated fatty acids, the radical adducts tNB/.CH2CH2-R and tNB/.CH2-CH=CH-R' were assigned as the pentyl and 2-pentenyl radicals, respectively.     

Aromatic side-chain contributions to the far ultraviolet circular dichroism of peptides and proteins

The rotational strength of the L_a transition in phenylalanine and tyrosine side chains has been calculated for dipeptides with various backbone and side-chain conformations. Similar calculations have also been performed for tripeptides in the β-turn conformation with aromatic residues at the corners of the turn. The interaction of the aromatic ring with neighboring peptides generates rotational strengths in the L_a transition of the order of 0.1 Debye-Bohr magneton. When the preferred backbone and side-chain conformations are considered, it is found that the most probable conformations have positive L_a bonds. This result accounts for the observation that the N-acyl amino acid amides of L -Tyr and L Phe have positive L_a bands. It also suggests that, although other interactions may affect the numerical value and even the sign, there will be a significant positive contribution to the rotational strength of aromatic residues in globular proteins from nearest-neighbor interactions. Calculations on proteins of known conformation at the nearest-neighbor level confirm the tendency toward positive L_a contributions for Phe and Tyr residues. This contribution can be of the order of 10% of the observed CD even in proteins with rather strong amide contributions. In some proteins, such as the gene 5 protein from bacteriophage fd and many snake-venom toxins, side-chain contributions from Tyr and Trp residues manifest themselves as positive CD bands in the 225–250-nm region. The magnitude of the nearest-neighbor contributions and the trend toward positive contributions are consistent with the observation of such CD bands in globular proteins. No special stacking interaction among aromatic side chains needs to be invoked.     

Interaction of the pyridoindole stobadine with alkoxyl and stable free radicals

Stobadine, a pyridoindole derivative which has been synthesized in search of new antiarrhytmic drugs, was able to interact with alpha-diphenyl-beta-picrylhydrazyl (DPPH^.) a stable free radical. Its scavenging potential was in the same order of magnitude as that of well known strong antioxidants. The scavenging effect of antioxidants tested increased in the order: stobadine, ascorbic acid, trolox, cysteine. Stobadine exerted a scavenging effect also towards alkoxyl radicals in a nonpolar solvent in the canthaxantin bleaching test. In this test stobadine was more effective than trolox.     

Fluorinated aldehydes and ketones acting as quasi-substrate inhibitors of acetylcholinesterase.

1. The inhibition of acetylcholinesterase (acetylcholine hydrolase, EC 3.1.1.7) by compounds containing trifluoromethyl-carbonyl groups was investigated and related to the effects observed with structurally similar, non-fluorinated chemicals. 2. Compounds that in aqueous solution readily form hydrates inhibit acetylcholinesterase in a time-dependent process. On the other hand non-hydrated, carbonyl-containing compounds showed rapid and reversible, time-independent enzyme inactivation when assayed under steady state conditions. 3. m-N,N,N-Trimethylammonium-acetophenone acts as a rapid and reversible, time-independent, linear competitive inhibitor of acetylcholinesterase (Ki = 5.0 . 10(-7) M). 4. The most potent enzyme inhibitor tested in this series was N,N,N,-trimethylammonium-m-trifluoroacetophenone. It gives time-dependent inhibition and the concentration which inactivates eel acetylcholinesterase to 50% of the original activity after 30 min exposure is 1.3 . 10(-8) M. The bimolecular rate constant for this reaction is 1.8 . 10(6) 1 . mol-1 . min-1. The enzyme-inhibitor complex is very stable as the inhibited enzyme after 8 days of dialysis is reactivated to 20% only. This compound represents a quasi-substrate inhibitor of acetylcholinesterase.     

Influence of DNA binding on the formation and reactions of tryptophan and tyrosine radicals in peptides and proteins

The rate constant of the one-electron oxidation of the tryptophan (Trp) or tyrosine (Tyr) residues by Br- X 2 radical anions is strongly decreased when the peptides are bound to DNA. Oxidation by N X 3 is much less affected by binding. These results can be explained by electrostatic repulsion between the charged polyphosphate backbone and the Br- X 2 radicals. Once oxidized, the interacting aromatic residues react with the DNA in a first order process with a rate constant of the order 10(3) s-1. These results have been extended to the single strand binding protein: the product of gene 32 of phage T4 (gp 32). The pulse radiolysis study suggests that one Trp residue of the protein oxidized by the Br- X 2 radicals reacts with the DNA in the complex while one Tyr residue is buried upon association. It is also shown that the exposure of Trp and Tyr residues to radical attack depends on whether the T4 SSB protein is bound to native or heat-denatured DNA.     

Bioreduction of aldehydes and ketones using Manihot species

Biocatalysis constitutes an important tool in organic synthesis, especially for the preparation of chiral molecules of biological interest. A series of aliphatic and aromatic aldehydes and two ketones were reduced using plant cell preparations from Manihot esculenta and Manihot dulcis roots. The reduced products were typically obtained in excellent yields (80-96%), and with excellent enantiomeric excess (94-98%), except for vanillin. Esters, a nitrile, and an amide were also examined, but were not reduced. Preliminary conversion rate studies are reported. This is the first attempt to perform the biotransformation of carbonyl compounds using Manihot species.     

The synthesis and study of side-chain lactam-bridged peptides

Side-chain lactam bridges linking amino acid residues that are spaced several residues apart in the linear sequence offer a convenient and flexible method for introducing conformational constraints into a peptide structure. The availability of a variety of selectively cleavable protecting groups for amines and carboxylic acids allows for several approaches to the synthesis of monocyclic, dicyclic, and bicyclic lactam-bridged peptides by solid-phase methods. Multicyclic structures are also accessible, but segment-condensation syntheses with solution-phase cyclizations are most likely to provide the best synthetic approach to these more complex constrained peptides. Lactam bridges linking (i, i + 3)-, (i, i + 4), and (i, i + 7)-spaced residue pairs have all proven useful for stabilization of alpha helices, and (i, i + 3)-linked residues have also been demonstrated to stabilize beta-turns. These structures are finding an increasing number of applications in protein biology, including studies of protein folding, protein aggregation, peptide ligand-receptor recognition, and the development of more potent peptide therapeutics. Defining the functional roles of the amphiphilic alpha-helices in medium-sized peptide hormones, and studying helix propagation from rigid, alpha-helix initiating bicyclic peptides are among the most exciting developments currently underway in this field.     

The reducing capacities of cyanobacteria for aldehydes and ketones

Summary Several strains of filamentous and unicellular cyanobacteria are capable of converting aldehydes and ketones into their corresponding alcohols during the active growth phase. Efficient conversions have been observed with aliphatic aldehydes, methyl and ethyl ketones. Cyanobacteria proved to be potent reducters of nor-carotenoids, acyclic monoterpene aldehydes and ketopantolactone. Neither bicyclic monoterpene ketones nor aromatic aldehydes have been reduced by any cyanobacterial strain so far tested.     

The generation of hydroxyl and alkoxyl radicals from the interaction of ferrous bipyridyl with peroxides.

Reaction conditions by which the iron-chelate ferrous bipyridyl can be used as a Fenton reagent to generate specifically alkoxyl radical (.OR) from its corresponding alkyl hydroperoxide (ROOH) without producing hydroxyl radical (.OH) as a result of autoxidation are described. In this manner, the relative ability of common .OH-scavenging agents to react with .OH and various .OR species could be assessed. When .OH was generated from H2O2, 4-methylmercapto-2-oxobutyrate, ethanol and benzoate all were oxidized. When .OR (cumoxyl radical, t-butoxyl radical or ethoxyl radical) was generated specifically, each was found to oxidize 4-methylmercapto-2-oxobutyrate and ethanol. In contrast with .OH, however, none of the .OR radicals mediated the decarboxylation of benzoate. Cross-competition studies with the scavengers showed that, in contrast with the .OH-dependent reaction, the .OR-dependent oxidation of 4-methylmercapto-2-oxobutyrate and ethanol was not inhibited by benzoate. Rate constants for ferrous bipyridyl oxidation by ROOH and by H2O2 were found to be essentially the same, and therefore the differential oxidation of the various scavengers was not a reflection of iron-peroxide interaction, but rather an interaction between generated oxy radicals and the scavengers. In contrast with the H2O2 system, catalase did not inhibit the oxidation of 4-methylmercapto-2-oxobutyrate or ethanol by either the cumene hydroperoxide or the t-butyl hydroperoxide system, suggesting that the oxidizing species was not derived from H2O2. These results suggest that benzoate decarboxylation might serve as a more specific probe to detect the presence of .OH than either 4-methylmercapto-2-oxobutyrate or ethanol, which react readily with .OR.     

Stimulation of tarsal receptors of the blowfly by aliphatic aldehydes and ketones

Rejection of eight aldehydes, eight ketones, five secondary alcohols, and 3-pentanol has been studied in the blowfly Phormia regina Meigen. The data agree with results previously reported for normal alcohols and several series of glycols in showing a logarithmic increase in stimulating effect with increasing chain length. The order of increasing effectiveness among the different species of compounds thus far investigated is the following: polyglycols, diols, secondary alcohols, iso-alcohols, normal alcohols, ketones, iso-aldehydes, normal aldehydes. Curves relating the logarithms of threshold concentration to the logarithms of chain length for diols, alcohols, aldehydes, and ketones show inflections in the 3 to 6 carbon range. Above and below the region of inflection the curves are nearly rectilinear. The slopes for the upper limbs (smaller molecules) are of the order of -2; for the lower limbs, about -10. Comparisons of the threshold data with numerical values for molecular weights, molecular areas and volumes, oil-water distribution coefficients, activity coefficients, standard free energies, vapor pressures, boiling points, melting points, dipole moments, dielectric constants, and degree of association are discussed briefly, and it is concluded that none of the comparisons serves to bring the data from the several series and from the two portions of each series into a single homogeneous system. A qualitative comparison with water solubilities shows fewer discrepancies. It is suggested that the existence of a combination of aqueous and lipoid phases at the receptor surface would fit best with what is presently known about the relationship between chemical structure and stimulating effect in contact chemoreception. In this hypothesis the smaller and more highly water-soluble compounds are envisaged as gaining access to the receptors partly through the aqueous phase, the larger molecules predominantly through the lipoid phase.     

Analysis of side-chain rotamers in transmembrane proteins

We measured the frequency of side-chain rotamers in 14 alpha-helical and 16 beta-barrel membrane protein structures and found that the membrane environment considerably perturbs the rotamer frequencies compared to soluble proteins. Although there are limited experimental data, we found statistically significant changes in rotamer preferences depending on the residue environment. Rotamer distributions were influenced by whether the residues were lipid or protein facing, and whether the residues were found near the N- or C-terminus. Hydrogen-bonding interactions with the helical backbone perturbs the rotamer populations of Ser and His. Trp and Tyr favor side-chain conformations that allow their side chains to extend their polar atoms out of the membrane core, thereby aligning the side-chain polarity gradient with the polarity gradient of the membrane. Our results demonstrate how the membrane environment influences protein structures, providing information that will be useful in the structure prediction and design of transmembrane proteins.     

Boltzmann-type distribution of side-chain conformation in proteins

We analyze packing imperfections in globular proteins as reflected in deviations of torsion angles from the equilibrium values for the isolated side chains. The distribution of conformations of methionine and lysine residues in a database of high-resolution structures is compared with energies of model compounds calculated with high-level quantum-mechanics. The distribution of the C-C and C-S torsion angles (chi(3)) correlates well with the Boltzmann factor of the torsion energy, exp(-betaE) of the model compounds C(2)H(5)-C(2)H(5) and C(2)H(5)-S-CH(3). An exponential relation was again found between the relative occurrence of g+, g- and t conformations for C(alpha)-C(beta) bonds in long side chains and the energy differences of rotamers of alpha-amino n-butyric acid, when dependence on backbone conformation was taken into account. The distribution of all 27 rotamers of methionine was correlated with the energy differences between the model's rotamers, corrected for clashes with nearby residues, the correlation being good for a set with backbone in the beta-conformation, but less clear for backbone alpha-conformation. In all correlations, the value of the coefficient beta corresponds to a temperature of circa 300 K. These results can be interpreted with a model that considers the structure of a folded protein as resulting from packing imperfectly complementary parts, with a requirement of an overall low energy. Compromises are required to optimize the fit of nonbonded contacts with surrounding groups, and side chains assume conformations away from the energy minimum. An exponential distribution is a most probable distribution, and this can be established easily under conditions other than thermal equilibrium.     

Analysis of side-chain orientations in homologous proteins

The side-chain conformations of topologically equivalent residues in seven pairs of proteins ranging in sequence homology from 16% to 60% are compared. Both identical and mutated residues are included. For proteins with greater than 40% homology, it is found that at least 80% of the side-chain orientations of identical residues and 75% or more of the mutated residues in each pair of proteins have matching gamma atom dihedral angles (+/- 40 degrees); the comparison is not based strictly on chi 1 angles. Further, if a match is obtained at the gamma position, there is a high probability of matching for the delta atom(s) of the side-chain. For proteins with less than 25% homology the percentages are somewhat lower. Trends observed for conservative substitutions are essentially the same as those noted for mutated residues in general. Side-chain accessibility does not affect the probability of matches of identical residues; however, less accessible pairs of mutated residues have 10 to 20% higher matching probabilities than do exposed residues. Mismatches can frequently be related to large B-factors, certain types of amino acid substitutions, or the appearance of multiple minima on the side-chain potential energy surfaces and are most likely to occur for certain small residues (Ser, Thr, Val). Analysis of all the results makes possible the formulation of a set of rules for side-chain positioning in the modeling of homologous proteins.     

Variability in the pKa of histidine side-chains correlates with burial within proteins

Acidic pKas of histidines buried within the protein interior are frequently rationalized on the contradictory basis of either polar interactions within the protein or the effects of a hydrophobic environment. To examine these relationships, we surveyed the buried surface area, depth of burial, polar interactions, and crystallographic temperature factors of histidines of known pKa. It has been found that buried environments of histidines do not always result in acidic pKas. Instead, the variability of histidine pKas increases for residues where the majority of the side-chain is buried. Because buried histidines are always found in mixed polar/apolar environments, multiple environmental contributions to pKa values must be considered. However, the quantitative relationships between heterogeneous environments and pKa values are not immediately apparent from the available data.     

Spin trapping of lipid radicals with DEPMPO-derived spin traps: detection of superoxide, alkyl and alkoxyl radicals in aqueous and lipid phase

The spin trap 5-(diethoxyphosphoryl)-5-methyl-1-pyrroline N-oxide (DEPMPO) forms a superoxide adduct with a half-life of almost 15 min. DEPMPO is very hydrophilic and its use for the detection of radicals in the lipid phase (lipid-derived radicals and superoxide generated in the lipid phase) is therefore limited due to its very low concentration in the lipid phase. For the detection of lipid-derived radicals, three derivatives of DEPMPO with increasing degree of lipid solubility have been investigated: 5-(di-n-propoxyphosphoryl)-5-methyl-1-pyrroline N-oxide (DPPMPO), 5-(di-n-butoxyphosphoryl)-5-methyl-1-pyrroline N-oxide (DBPMPO), and 5-(bis-(2-ethylhexyloxy)phosphoryl)-5-methyl-1-pyrroline N-oxide (DEHPMPO). As compared with the spin trap DMPO, the half-lives of the respective superoxide adducts were clearly higher in aqueous solutions of the spin traps, which facilitates qualitative ESR measurements. The stability of the superoxide spin adducts formed with the various lipophilic spin traps in aqueous buffer were similar to those observed with DEPMPO (half-life: 7-11 min.). In model experiments using Fe(3+)-catalyzed nucleophilic addition of methanol or tert-butanol to the respective spin trap the respective alkoxyl radical adducts were formed in aqueous solution as transient species in the presence of high concentrations of the alcohol. Upon dilution with water the alkoxyl group was substituted by water, giving the respective hydroxyl adduct of the spin trap. Care must therefore be taken when Fenton-type reactions are used for the generation of radicals such as the use of Fe(2+) complexes with phosphate or DTPA or inactivation of iron by addition of "Desferal" (Novarti's Pharma GmbH, Vienna, Austria) after a short incubation time. Addition of Fe(2+) under anaerobic conditions to an aqueous suspension of linoleic acid hydroperoxide and the spin trap resulted in the detection of three different species: a carbon-centered radical adduct, an acyl radical adduct, and the hydroxyl adduct. In the presence of oxygen a different species was observed with DEPMPO, DPPMPO, and DBPMPO, which was only slightly suppressed upon the addition of SOD, possibly the respective spin adduct of either the alkylperoxyl radical or, in analogy to DMPO, a secondary alkoxyl radical.     

The interrelationships of side-chain and main-chain conformations in proteins

The accurate determination of a large number of protein structures by X-ray crystallography makes it possible to conduct a reliable statistical analysis of the distribution of the main-chain and side-chain conformational angles, how these are dependent on residue type, adjacent residue in the sequence, secondary structure, residue-residue interactions and location at the polypeptide chain termini. The interrelationship between the main-chain (phi, psi) and side-chain (chi 1) torsion angles leads to a classification of amino acid residues that simplify the folding alphabet considerably and can be a guide to the design of new proteins or mutational studies. Analyses of residues occurring with disallowed main-chain conformation or with multiple conformations shed some light on why some residues are less favoured in thermophiles.     

Dissociation action of cationic peptides with hydrophobic radicals on functional coupling between serpentine type receptors and GTP-binding proteins

The coupling of hormone-activated receptor and heterotrimeric G protein is an important step of the signal transduction through adenylyl cyclase signal system (ACS). The numerous literature data and own results show that G protein-interacting regions, that are localized in cytoplasmic loops of receptors, have considerable positive charge, can form amphiphilic alpha-helices and are tightly associated with the membrane. We studied the influence of model cationic peptides on both basal and stimulated by hormones and nonhormonal agents adenylyl cyclase (AC) activity and on GTP binding activity of heterotrimeric G proteins in skeletal muscles of rats and smooth muscles of mollusc Anodonta cygnea. Peptides with hydrophobic radicals of caprinoyl acid (C10): Lys(C10)-His-Glu-Lys-Lys-(C10)-His-Glu-Lys-Lys(C10)-His-Glu-Lys-Lys(C10)- His-Glu-Lys-Ala-amide (peptide I), Cys-Lys(C10)-X-Tyr-Lys-Ala-Lys7-Trp-Lys-amide (II), Cys-X-Trp-Lys-Lys(C10)-Lys2-Lys(C10)-Lys3-Lys(C10)-Tyr-Lys-Lys(C10)-Lys-Lys- amide (III), where X--epsilon-aminocaproyl acid residue, were synthesized by solid-phase methodology. IC50 values for inhibiting the influence of peptides on serotonin-(molluscs) and isoproterenol-stimulated (rats) AC activity were: for peptide I--56 and 70 mkM, for peptide II--32 and 47 mkM, for peptide III--22 and 28 mkM, respectively. At the same time the peptides weakly decreased AC activity stimulated by nonhormonal agents (NaF, Gpp[NH]p, forskolin). Peptides I--III stimulated basal activity of the enzyme in both investigated tissues. The maximum stimulating effects (28--52%) of the peptides were observed at their concentration 10 mkM. Peptides (10--100 mkM) increased Gpp[NH]p binding in plasma membranes of mollusc and rat muscles and strongly decreased the influence of the hormones on the binding. Based on the obtained data we supposed that cationic peptides with hydrophobic radicals mimic G protein-binding regions of the receptors and can be involved in the regulation of functional coupling between the receptors and G proteins.     

Separation, detection, and quantification of hydroperoxides formed at side-chain and backbone sites on amino acids, peptides, and proteins

Hydroperoxides are major reaction products of radicals and singlet oxygen with amino acids, peptides, and proteins. However, there are few data on the distribution of hydroperoxides in biological samples and their sites of formation on peptides and proteins. In this study we show that normal-or reversed-phase gradient HPLC can be employed to separate hydroperoxides present in complex systems, with detection by postcolumn oxidation of ferrous xylenol orange to the ferric species and optical detection at 560 nm. The limit of detection (10-25 pmol) is comparable to chemiluminescence detection. This method has been used to separate and detect hydroperoxides, generated by hydroxyl radicals and singlet oxygen, on amino acids, peptides, proteins, plasma, and intact and lysed cells. In conjunction with EPR spin trapping and LC/MS/MS, we have obtained data on the sites of hydroperoxide formation. A unique fingerprint of hydroperoxides formed at alpha-carbon (backbone) positions has been identified; such backbone hydroperoxides are formed in significant yields only when the amino acid is part of a peptide or protein. Only side-chain hydroperoxides are detected with free amino acids. These data indicate that free amino acids are poor models of protein damage induced by radicals or other oxidants.