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PubMed1994

Formation of amide bonds without a condensation agent and implications for origin of life.

Amide bonds are of central importance for biochemistry; in the guise of peptide bonds, they form the backbone of proteins. The formation of amide bonds without the assistance of enzymes poses a major challenge for theories of the origin of life. Enzyme-free formation of amide bonds between amino acids has been demonstrated in the presence of condensing agents such as cyanamide. Here we report the formation of amide bonds in aqueous solution in the absence of any condensing agent. We find that the formation of pyrite (FeS2) from FeS and H2S can provide the driving force for reductive acetylation of amino acids with mercaptoacetic acid (HSCH2COOH). The redox energy of pyrite formation permits the activation of the carboxylic acid group, which is converted to a species that reacts readily with amines. This process provides support for the chemo-autotrophic theory for the origin of life, in which pyrite formation supplies the energy source for the first autocatalytic reproduction cycle.

Acetylation↗
PubMed2001

A method for the amidation of recombinant peptides expressed as intein fusion proteins in Escherichia coli.

The increasing use of peptides as pharmaceutical agents, especially in the antiviral and anti-infective therapeutic areas, requires cost-effective production on a large scale. Many peptides need carboxy amidation for full activity or prolonged bioavailability. However, this modification is not possible in prokaryotes and must be done using recombinant enzymes or by expression in transgenic milk. Methods employing recombinant enzymes are appropriate for small-scale production, whereas transgenic milk expression is suitable for making complex disulfide-containing peptides required in large quantity. Here we describe a method for making amidated peptides using a modified self-cleaving vacuolar membrane ATPase (VMA) intein expression system. This system is suitable for making amidated peptides at a laboratory scale using readily available constructs and reagents. Further improvements are possible, such as reducing the size of the intein to improve the peptide yields (the VMA intein comprises 454 amino acids) and, if necessary, secreting the fusion protein to ensure correct N-terminal processing to the peptide. With such developments, this method could form the basis of a large-scale cost-effective system for the bulk production of amidated peptides without the use of recombinant enzymes or the need to cleave fusion proteins.

Amides↗
PubMed2005

Quantification of primary fatty acid amides in commercial tallow and tallow fatty acid methyl esters by HPLC-APCI-MS.

Primary fatty acid amides are a group of biologically highly active compounds which were already identified in nature. Here, these substances were determined in tallow and tallow fatty acid methyl esters for the first time. As tallow is growing in importance as an oleochemical feedstock for the soap manufacturing, the surfactant as well as the biodiesel industry, the amounts of primary fatty acid amides have to be considered. As these compounds are insoluble in tallow as well as in the corresponding product e.g. tallow fatty acid methyl esters, filter plugging can occur. For the quantification in these matrices a purification step and a LC-APCI-MS method were developed. Although quantification of these compounds can be performed by GC-MS, the presented approach omitted any derivatization and increased the sensitivity by two orders of magnitude. Internal standard calibration using heptadecanoic acid amide and validation of the method yielded a limit of detection of 18.5 fmol and recoveries for the tallow and fatty acid methyl ester matrices of 93% and 95%, respectively. A group of commercially available samples were investigated for their content of fatty acid amides resulting in an amount of up to 0.54%m/m (g per 100 g) in tallow and up to 0.16%m/m (g per 100 g) in fatty acid methyl esters.

Amides↗
PubMed2006

Amide vibrations are delocalized across the hydrophobic interface of a transmembrane helix dimer.

The tertiary interactions between amide-I vibrators on the separate helices of transmembrane helix dimers were probed by ultrafast 2D vibrational photon echo spectroscopy. The 2D IR approach proves to be a useful structural method for the study of membrane-bound structures. The 27-residue human erythrocyte protein Glycophorin A transmembrane peptide sequence: KKITLIIFG(79)VMAGVIGTILLISWG(94)IKK was labeled at G(79) and G(94) with (13)C=(16)O or (13)C=(18)O. The isotopomers and their 50:50 mixtures formed helical dimers in SDS micelles whose 2D IR spectra showed components from homodimers when both helices had either (13)C=(16)O or (13)C=(18)O substitution and a heterodimer when one had (13)C=(16)O substitution and the other had (13)C=(18)O substitution. The cross-peaks in the pure heterodimer 2D IR difference spectrum and the splitting of the homodimer peaks in the linear IR spectrum show that the amide-I mode is delocalized across a pair of helices. The excitation exchange coupling in the range 4.3-6.3 cm(-1) arises from through-space interactions between amide units on different helices. The angle between the two Gly(79) amide-I transition dipoles, estimated at 103 degrees from linear IR spectroscopy and 110 degrees from 2D IR spectroscopy, combined with the coupling led to a structural picture of the hydrophobic interface that is remarkably consistent with results from NMR on helix dimers. The helix crossing angle in SDS is estimated at 45 degrees. Two-dimensional IR spectroscopy also sets limits on the range of geometrical parameters for the helix dimers from an analysis of the coupling constant distribution.

Amides↗
PubMed1979

Do cleavages of amides by serine proteases occur through a stepwise pathway involving tetrahedral intermediates?

The mechanism of the serine protease-catalyzed cleavage of amides (acylation) was examined in terms of the basicity of the functional groups participating in the catalysis. It is proposed that the reaction does not proceed through a stepwise pathway, as opposed to the cleavage of esters and anilides, which start with general base-catalyzed formation of the tetrahedral intermediate followed by its general acid-catalyzed breakdown. Instead, the proton abstracted from the hydroxyl group of the serine by the imidazolyl group of the histidine is donated to the nitrogen atom of the leaving group of the amide before the bond between the carbonyl carbon atom of the amide and the attacking serine oxygen atom is completed. Reactions proceed by a SN2-like reaction through the cooperation of acid catalysis by the imidazolyl cation and nucleophilic attack by the serine. The mechanisms of the enzymatic hydrolyses of anilides and esters proceed through a discrete tetrahedral intermediate, but the enzymatic hydrolyses of amides probably do not.

Amides↗
PubMed1986

Exocrine secretion granules contain peptide amidation activity.

Exocrine secretion granules from the rat parotid gland contain a carboxyl-terminal peptide alpha-amidation enzyme resembling closely an enzyme from the pituitary (peptidyl-glycine alpha-amidating monooxygenase) that functions in post-translational processing of secretory polypeptides within neural and endocrine secretion granules. alpha-Amidation is a characteristic (often essential) chemical feature of a variety of biologically active regulatory peptides in animals. The parotid and pituitary activities exhibit very similar ascorbate and copper requirements, pH dependence, and kinetic properties. Further, like the pituitary enzyme(s), the parotid activity is found predominantly in secretion granule content and is discharged by exocytosis. These results establish the presence of a novel enzyme in exocrine secretion granules and suggest a potential role of the L-ascorbic acid contained in parotid granules. Two additional findings--the detection of similar levels of amidation activity in purified secretion granule fractions from other exocrine glands and the observation, in parotid granule fractions, of a B-type carboxypeptidase activity similar to that involved in post-translational processing in other systems--form a rational basis for considering whether exocrine secretion granules (like their neural and endocrine counterparts) serve as post-translational processing sites. The identity and functional role of the modified polypeptides remain to be determined.

Amides↗
PubMed2003

Evidence for distinct roles in catalysis for residues of the serine-serine-lysine catalytic triad of fatty acid amide hydrolase.

Fatty acid amide hydrolase (FAAH) is a mammalian amidase signature enzyme that inactivates neuromodulatory fatty acid amides, including the endogenous cannabinoid anandamide and the sleep-inducing substance oleamide. The recent determination of the three-dimensional structures of FAAH and two distantly related bacterial amidase signature enzymes indicates that these enzymes employ an unusual serine-serine-lysine triad for catalysis (Ser-241/Ser-217/Lys-142 in FAAH). Mutagenesis of each of the triad residues in FAAH has been shown to severely reduce amidase activity; however, how these residues contribute, both individually and in cooperation, to catalysis remains unclear. Here, through a combination of site-directed mutagenesis, enzyme kinetics, and chemical labeling experiments, we provide evidence that each FAAH triad residue plays a distinct role in catalysis. In particular, the mutation of Lys-142 to alanine indicates that this residue functions as both a base involved in the activation of the Ser-241 nucleophile and an acid that participates in the protonation of the substrate leaving group. This latter property appears to support the unusual ability of FAAH to hydrolyze amides and esters at equivalent rates. Interestingly, although structural evidence indicates that the impact of Lys-142 on catalysis probably occurs through the bridging Ser-217, the mutation of this latter residue to alanine impaired catalytic activity but left the amide/ester hydrolysis ratios of FAAH intact. Collectively, these findings suggest that FAAH possesses a specialized active site structure dedicated to a mechanism for competitive amide and ester hydrolysis where nucleophile attack and leaving group protonation occur in a coordinated manner dependent on Lys-142.

Amidohydrolases↗
PubMed1978

E.s.r. study of spin-trapped radicals formed during the photolysis of aqueous solutions of acid amides and H2O2.

Free radicals formed by the reactions of OH radicals with amides and their N-methylated derivatives in aqueous solutions have been studied. The OH radicals were produced by U.V.-photolysis of H2O2, and the short-lived amide radicals were converted to more stable nitroxide radicals by addition to a spin-trap, tert-nitrosobutane. The spin-trapped radicals were identified by e.s.r. spectroscopy. For acetamide, chloroacetamide, malonamide, succinamide and propionamide, the observed radicals were formed by H-abstraction from the carbon atoms attached to the carbonyl group. The H atom attached to the carbonyl group was abstracted in formamide. For N-methyl acetamide, N,N-dimethyl acetamide and the corresponding formamide derivatives, H-abstraction occurred only from the N-methyl group. The non-equivalency of the amide protons was observed in the spin-trapped radicals for acetamide, formamide, malonamide, succinamide and propionamide. The identification of the site of OH attack on N-methyl amides is helpful for the study of radical formation in peptides and proteins.

Acetamides↗
PubMed2003

Acidic nonsteroidal anti-inflammatory drugs inhibit rat brain fatty acid amide hydrolase in a pH-dependent manner.

Previous studies have demonstrated that fatty acid amide hydrolase, the enzyme responsible for the metabolism of anandamide, is inhibited by the acidic non-steroidal anti-inflammatory drug (NSAID) ibuprofen with a potency that increases as the assay pH is reduced. Here we show that (R)-, (S)- and (R,S)-flurbiprofen, indomethacin and niflumic acid show similar pH-dependent shifts in potency to that seen with ibuprofen. Thus, (S)-flurbiprofen inhibited 2 microM [3H]anandamide metabolism with IC50 values of 13 and 50 microM at assay pH values of 6 and 8, respectively. In contrast, the neutral compound celecoxib was a weak fatty acid amide hydrolase inhibitor and showed no pH dependency (IC50 values approximately 300 microM at both assay pH). The cyclooxygenase-2-selective inhibitors nimesulide and SC-58125 did not inhibit fatty acid amide hydrolase activity at either pH. The data are consistent with the conclusion that the non-ionised forms of the acidic NSAIDs are responsible for the inhibition of fatty acid amide hydrolase.

Amidohydrolases↗
PubMed1992

A new method for the analysis of amide-linked hydroxy fatty acids in lipid-As from gram-negative bacteria.

Lipid-A represents the ubiquitous, covalently bound hydrophobic component of bacterial lipopolysaccharides (endotoxins). Lipid-As isolated and characterized from rhizobial species have large variations in their backbone sugars, as well as in their hydroxy fatty acid substituents. The sugar backbones consist of either glucosamine and galacturonic acid or glucosamine and 2,3-diaminoglucose. The published procedures for characterizing amide-linked fatty acids do not release all these fatty acids, hence a new method was developed to characterize the amide-linked hydroxy fatty acids. This method involves a mild methanolysis procedure to release glucosamine methyl glycosides which still contain the amide-bound hydroxy fatty acids. The products were analysed by fast atom bombardment mass spectrometry (FAB-MS) and, after trimethylsilylation, by electron impact (E.I.) and chemical ionization (C.I.) gas chromatography-mass spectrometry (GC-MS). The procedure was applied to lipid-A preparations from several gram-negative bacteria. This method allows the unequivocal identification of amide-linked hydroxy fatty acids and also allows determination of the microheterogeneity of the N-acyl substituents in lipid-As from gram-negative bacteria.

Amides↗
PubMed1975

Cytotoxicity of carcinogenic aromatic amides in normal and xeroderma pigmentosum fibroblasts with different DNA repair capabilities.

The effect of exposure to UV irradiation or to the N-acetoxy-ester derivatives of four carcinogenic aromatic amides, 4-acetylaminobiphenyl (AABP), 2-acetylaminofluorene (AAF), 2-acetylaminophenanthrene, and 4-acetylaminostilbene, on cell survival was compared in strains of cultured human fibroblasts possessing normal rates of excision repair of DNA and in three strains of xeroderma pigmentosum (XP) cells, each differing in its rate of excision repair. The survival of each strain after exposure to UV reflected its capacity to repair DNA. Thus the slope of the survival curve for the XP strain with the poorest capacity for excision repair (XP12BE complementation group A) was 5.8-fold steeper than the exponential portion of the curve for the normally repairing strains; that of XP2BE (complementation group C) was 1.95-fold; and that of XP4BE (a variant capable of a normal rate of dimer excision) was only 1.3-fold steeper. The slope of the survival curves after exposure to each N-acetoxy ester derivative for these same XP strains averaged 6.4, 2.0, and 1.4 times steeper, respectively, than that of the normal strains tested. The excision repair capacity of these lines after exposure to N-acetoxy-AAF (50 muM/ml) was tested with alkaline cesium chloride density gradient centrifugation to detect incorporation of tritiated thymidine into nonreplicated DNA. The normal strains and XP4BE exhibited DNA excision repair by this method, whereas XP patients 2 and 12 did not. The cytotoxic effect of the four parent aromatic amide carcinogens, their N-hydroxy derivatives, as well as the N-acetoxy ester of each of the four N-hydroxy compounds and the N-sulfate ester of N-hydroxy-AAF and N-hydroxy-AABP in the XP2BE strain, was compared with their effect on the normal fibroblasts. The parent amides proved to be noncytotoxic at all doses tested. In contrast, the N-hydroxy derivatives of each aromatic amide were highly cytotoxic, as were the ester compounds. For each active derivative, the slope of the survival curve for XP2BE was 2-2.k times steeper than that of the normally repairing strain.

2-Acetylaminofluorene↗
PubMed1988

Synthesis and structure assignments of amide protected nucleosides and their use as phosphoramidites in deoxyoligonucleotide synthesis.

The syntheses of several amide protected deoxyguanosine- as well as thymidine nucleosides are described. These compounds were synthesized according to the Mitsunobu reaction and Michael addition. In contradiction to previous studies we have discovered that the Michael addition gives only products derived from N-alkylation. The occurrence of N- or O-alkylation was assigned by means of two dimensional 1H, 1 3 C-COLOC-NMR spectroscopy. Further, we have found that the Mitsunobu reaction used for the protection of the amide function of dG is limited to alcohols without acidic hydrogen atoms. Amide protected phosphormidites (15, 16) were used for the preparation of deoxyoligonucleotides with a large number of guanine and thymine bases using two different coupling times. We have shown that there is no experimentally detectable difference in the quality of the products if the starting monomer is amide protected or not.

Alkylation↗
PubMed2001

The enhancement of PCR amplification by low molecular weight amides.

Amplification of a DNA target by the polymerase chain reaction (PCR) often requires laborious optimization efforts. In this regard, the use of certain organic chemicals such as dimethyl sulfoxide, polyethylene glycol, betaine and formamide as cosolvents has been found to be very helpful. Unfortunately, very little is known about the precise structural features that make these additives effective and, accordingly, the number of such chemicals currently known to enhance PCR is limited. In order to address these issues, we decided to focus on formamide and undertook an extensive study of low molecular weight amides as a class to see how changing the substituents in the amide structure influences its effect on PCR. We describe here the results of this study, which involved 11 different amides, and present observations that provide a cohesive picture of structure-activity relations in this group of additives. We found several of these amides to be exceptionally effective and introduce them as novel PCR enhancers.

Acetamides↗
PubMed2004

Characterization of the sleep-wake patterns in mice lacking fatty acid amide hydrolase.

STUDY OBJECTIVES: Oleamide and anandamide are fatty acid amides implicated in the regulatory mechanisms of sleep processes. However, due to their prompt catabolism by fatty acid amide hydrolase (FAAH), their pharmacologic and behavioral effects, in vivo, disappear rapidly. To determine if, in the absence of FAAH, the hypnogenic fatty acid amides induce an increase of sleep, we characterized the sleep-wake patters in FAAH-knockout mice [FAAH (-/-)] before and after sleep deprivation. DESIGN: FAAH (-/-), FAAH (+/-), and FAAH (+/+) mice were implanted chronically for sleep, body temperature (Tb), and locomotor activity (LMA) recordings. Sleep-wake states were recorded during a 24-hour baseline session followed by 8 hours of sleep deprivation. Recovery recordings were done during the 16 hours following sleep deprivation. Total amount of wake, slow-wave sleep, and rapid eye movement sleep were calculated and compared between genotypes. The electroencephalographic spectral analysis was performed by fast Fourier transform analysis. Telemetry recordings of Tb and LMA were carried out continuously during 4 days under baseline conditions. SETTING: N/A. PATIENTS OR PARTICIPANTS: FAAH (-/-) mice and their heterozygote (+/-) and control (+/+) littermates were used. INTERVENTIONS: Sleep deprivation. MEASUREMENTS AND RESULTS: FAAH (-/-) mice possess higher values of slow-wave sleep and more intense episodes of slow-wave sleep than do control littermates under baseline conditions that are not related to differences in Tb and LMA. A rebound of slow-wave sleep and rapid eye movement sleep as well an increase in the levels of slow-wave activity were observed after sleep deprivation in all genotypes. CONCLUSION: These findings support the role of fatty acid amides as possible modulators of sleep and indicate that the homeostatic mechanisms of sleep in FAAH (-/-) mice are not disrupted.

Amidohydrolases↗
PubMed2005

Wound-inducible biosynthesis of phytoalexin hydroxycinnamic acid amides of tyramine in tryptophan and tyrosine decarboxylase transgenic tobacco lines.

The wound-activated biosynthesis of phytoalexin hydroxycinnamic acid amides of tyramine was compared in untransformed and transgenic tobacco (Nicotiana tabacum) lines that express tryptophan decarboxylase (TDC), tyrosine decarboxylase (TYDC), or both activities. Transgenic in vitro-grown tobacco lines expressing TDC activity accumulated high levels of tryptamine but not hydroxycinnamic amides of tryptamine. In contrast, transgenic tobacco lines expressing TYDC accumulated tyramine as well as p-coumaroyltyramine and feruloyltyramine. The MeOH-soluble and cell wall fractions showed higher concentrations of wound-inducible p-coumaroyltyramine and feruloyltyramine, especially at and around wound sites, in TYDC and TDC xTYDC tobacco lines compared to wild-type or TDC lines. All the enzymes involved in the biosynthesis of hydroxycinnamic acid amides of tyramine were found to be similarly wound inducible in all tobacco genotypes investigated. These results provide experimental evidence that, under some circumstances, TYDC activity can exert a rate-limiting control over the carbon flux allocated to the biosynthesis of hydroxycinnamic acid amides of tyramine.

Amides↗
PubMed2006

Automated extraction of backbone deuteration levels from amide H/2H mass spectrometry experiments.

A Fourier deconvolution method has been developed to explicitly determine the amount of backbone amide deuterium incorporated into protein regions or segments by hydrogen/deuterium (H/D) exchange with high-resolution mass spectrometry. Determination and analysis of the level and number of backbone amide exchanging in solution provide more information about the solvent accessibility of the protein than do previous centroid methods, which only calculate the average deuterons exchanged. After exchange, a protein is digested into peptides as a way of determining the exchange within a local area of the protein. The mass of a peptide upon deuteration is a sum of the natural isotope abundance, fast exchanging side-chain hydrogens (present in MALDI-TOF H/2H data) and backbone amide exchange. Removal of the components of the isotopic distribution due to the natural isotope abundances and the fast exchanging side-chains allows for a precise quantification of the levels of backbone amide exchange, as is shown by an example from protein kinase A. The deconvoluted results are affected by overlapping peptides or inconsistent mass envelopes, and evaluation procedures for these cases are discussed. Finally, a method for determining the back exchange corrected populations is presented, and its effect on the data is discussed under various circumstances.

Amides↗
PubMed1985

Destabilization of collagen structure by amides and detergents in solution.

The effects of amides and detergents on collagen to gelatin transition have been studied at neutral pH. Simple amides denature the protein. The substitution of H-atoms by the alkyl groups at the nonpolar end of amide increases the effectiveness of the compounds in destabilizing the collagen structure whereas substitution of the H-atom at the polar amide end shows marginal effects on the collagen transition. The capabilities of these reagents to denature collagen are much less pronounced than their effects on denaturing globular proteins. Anionic detergents are found to destabilize collagen at very low concentrations (below their cmc values). In this respect, the effects of the detergents on collagen are comparable to the denaturing effects of the detergents on globular proteins. The effect of detergents increases with the increase in the length of the alkyl chain. The structure of the anion in the detergent is also important as seen from the lower potency of the sulfonate containing detergent compared to the sulfate containing detergent in denaturing collagen. Cationic and nonionic detergents do not denature collagen.

Amides↗
PubMed1991

Conformational mimicry. II. An obligatory cis amide bond in a small linear peptide.

The structure of Z-Pro psi [CN4]-Ala-OBzl has been determined by X-ray crystallographic techniques. The structure crystallizes in space group P2(1) with cell constants a = 22.176(3) A, b = 6.141(1)A, c = 8.275(1) A, beta = 98.31(1), and Z = 2. The structure has been refined to a residual of 0.038 for 2538 independent data. The amide bond between the prolyl and alanyl residues is cis, a result of the presence of the tetrazole ring system, as is the urethane bond linking the benzyloxycarbonyl and the prolyl groups. A comparison of the structures in this study to other structures containing cis amide bonds shows that the tetrazole ring system, when incorporated into peptides, mimics a cis amide bond. Changes in the distance between the alpha-carbons adjacent to the tetrazole rings in the linear peptide as compared with the bicyclic diketopiperazine required a reassessment of the conformational mimicry with the cis amide bond.

Amides↗