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PubMed1992

Use of delta-(alpha-aminoadipoyl) chromogenic amides in screening for aminoadipoyl amidohydrolases.

The synthesis of delta-(alpha-aminoadipoyl) aromatic amides and their use in screening for enzymes able to cleave delta-(alpha-aminoadipoyl) residues off the synthetic amides and cephalosporin C are described. A number of commercially available proteases and peptidases were not active with delta-(alpha-aminoadipoyl) chromogenic amides. Also, most tested microbial strains known to produce acylases did not hydrolyze these compounds. Only one microbial strain, Xanthomonas maltophila, had an appreciable activity toward the racemic form of chromogenic substrates. Activity measured in crude extracts from Xanthomonas cells indicated that this bacterium produces predominantly L-specific aminoadipoyl amidohydrolase and gamma-glutamyl hydrolase. A low level of cephalosporin C and glutaryl-cephalosporin acylase activities was also found.

Adipates↗
PubMed1991

Transport parameters in the human red cell membrane: solute-membrane interactions of amides and ureas.

We have studied the permeability of a series of hydrophilic amides and ureas through the red cell membrane by determining the three phenomenological coefficients which describe solute-membrane interaction: the hydraulic permeability (Lp), the phenomenological permeability coefficient (omega i) and the reflection coefficient (sigma i). In 55 experiments on nine solutes, we have determined that the reflection coefficient (after a small correction for solute permeation by membrane dissolution) is significantly less than 1.0 (P less than 0.003, t-test), which provides very strong evidence that solute and water fluxes are coupled as they cross the red cell membrane. It is proposed that the aqueous channel is a tripartite assembly, comprising H-bond exchange regions at both faces of the membrane, joined by a narrower sieve-specific region which crosses the lipid. The solutes bind to the H-bond exchange regions to exchange their solvation shell with the H-bonds of the channel; the existence of these regions is confirmed by the finding that the permeation of all the amides and ureas requires binding to well-characterized sites with Km values of 0.1-0.5 M. The sieve-specific regions provide the steric restraints which govern the passage of the solutes according to their size; their existence is shown by the findings that: (1) the reflection coefficient (actually the function [1-corrected sigma i]) is linearly dependent upon the solute molecular diameter; and (2) the permeability coefficient is linearly dependent upon solute molar volume. These several observations, taken together, provide strong arguments which lead to the conclusion that the amides and urea cross the red cell membrane in an aqueous pore.

Amides↗
PubMed1983

Substrate specificity of an amidating enzyme in porcine pituitary.

A series of tripeptides was synthesised and tested as substrates for an amidating enzyme present in porcine pituitary. The rates of conversion of the tripeptides to the corresponding dipeptide amides were determined by ion exchange chromatography of the radio-iodinated peptides. The experiments showed that the amidating enzyme has a mandatory requirement for glycine in position 3 of the tripeptide substrates; peptides containing lysine, glutamic acid, leucine or alanine in the C-terminal position did not undergo reaction. In studies of the substrate requirements at position 2 of the tripeptides, facile reaction took place with neutral amino acids in this position but much slower reactions occurred with basic or acidic residues. With the neutral substrates the enzyme exhibited an optimum pH value of 6.8; with histidine in position 2 the optimum reaction occurred at a higher pH, consistent with a preference shown by the enzyme for an uncharged amino acid in the penultimate position of the peptide substrate.

Amides↗
PubMed1996

Rapid estimation of relative amide proton exchange rates of 15 N-labelled proteins by a straightforward water selective NOESY-HSQC experiment.

A straightforward heteronuclear pseudo-3D NOESY-HSQC pulse sequence using radiation damping to selectively invert magnetization at the water frequency was developed to estimate the amide proton exchange rates in 15N-labelled proteins. The peak intensities in the resultant 2D spectrum allow a direct classification of amide proton exchange rates according to short (ms), intermediate (ms to s) or long (> or = s) residence times. This method was successfully used for the analysis of amide proton exchange rates in the 15N-labelled FruR DNA-binding domain and pertinent information about its dynamics was obtained.

Amides↗
PubMed1987

Cerulein mRNA and peptide alpha-amidation activity in the skin of Xenopus laevis: stimulation by norepinephrine.

The skin of Xenopus laevis, because of its high concentrations of amidated peptides, is an excellent model for the study of neuropeptide biosynthesis. In this paper we determined levels of the mRNAs which encode cerulin and characterized the enzymatic activity which likely produces the carboxyl terminal alpha-amide moiety of cerulein. This enzyme is stimulated by the addition of CuSO4 and ascorbate and requires the presence of molecular oxygen and is thus similar to the peptidyl-glycine alpha-amidating monooxygenase (PAM) described in mammals. Hybridization analysis showed that three cerulein mRNAs of different molecular sizes are present in varying proportions in the skin of individual frogs. Injection of norepinephrine into the dorsal lymph sac of Xenopus caused immediate secretion and depletion from skin of PAM activity but did not cause a comparable immediate decrease in skin levels of cerulein mRNA or total RNA. By 2 weeks after norepinephrine injection, cerulein mRNA levels increased to fourfold over control levels. By 4 weeks, skin PAM activity was almost restored to control levels.

Amides↗
PubMed1987

Stereoelectronic model to explain the resolution of enantiomeric ibuprofen amides on the Pirkle chiral stationary phase.

A chiral recognition model is proposed which incorporates the electronic and steric interactions between amide derivatives of ibuprofen and the (R)-N-(3,5-dinitrobenzoyl)phenylglycine-derived Pirkle chiral stationary phase during high-performance liquid chromatography. Based on this rationale, amide derivatives of ibuprofen were prepared using 4-chloroaniline, 4-bromoaniline, aniline, 4-methoxyaniline and 1-aminonaphthylene to improve the enantiomer separation over previously reported results with this column. The amides prepared gave separation values of 1.16, 1.16, 1.19, 1.21 and 1.23, respectively. These high separation values are consistent with the proposed model.

Amides↗
PubMed1990

Myristic acid is incorporated into the two acylatable domains of the functional glycoprotein CD9 in ester, but not in amide bonds.

CD9 is a signal-initiating glycoprotein of uncertain membrane insertion which contains more than one locus of acylation and is distinguished by being the major acylatable platelet protein. The N-terminus of CD9 is blocked to Edman degradation. We investigated whether [3H]myristic acid could be incorporated into CD9, whether that incorporation occurred via an amide linkage, and whether myristate and palmitate were differentially incorporated into the two domains. Pulse-labeling studies, performed on the human osteogenic sarcoma cell line SKOSC which expresses 22 and 24 kDa variants of CD9 demonstrated that the respective precursors of 20.5 and 23 kDa were not radiolabeled by either [3H]myristic acid or [3H]palmitic acid, but that both fatty acids could be ligated to CD9 during the later stages of protein maturation. The failure to incorporate myristic acid cotranslationally suggest that CD9 does not contain amino-terminal amide-bonded myristic acid. Incorporation of radiolabel from both fatty acids proceeded very rapidly and could be visualized after a 10 s pulse. Although myristic acid was partially metabolized into palmitic acid, incorporation of authentic [3H]myristate into CD9 could be demonstrated. The myristic acid bonds were shown to be as sensitive to hydroxylamine treatment as those linking palmitate. Both fatty acids were also incorporated into CD9 in hydroxylamine-sensitive bonds in the presence of cycloheximide, reaching 30-40% of the levels in untreated controls. The sensitivity of myristate ligands to hydroxylamine demonstrates that this fatty acid is not linked via amide, but rather via ester bonds. The sensitivity of [3H]myristate and [3H]palmitate bonds to 2-mercaptoethanol further suggests that either fatty acid is linked via thioester rather than hydroxyester bonds to each domain on CD9. Limited proteolysis analysis with Staphylococcus aureus V8 proteinase of CD9, labeled in the absence or presence of cycloheximide, showed that [3H]myristic acid and [3H]palmitic acid labeled identical peptides, and to the same extent, suggesting that myristate is an alternative substrate for the transacylase(s) involved.

Acylation↗
PubMed1994

Amide hydrogen exchange of the central B-chain helix within the T- and R-states of insulin hexamers.

Comparative analysis of the 1H-NMR spectra of human insulin shows that in the presence of the allosteric ligand, phenol, the tertiary structure of the protein is altered as evidenced by the decreased rate of amide hydrogen-deuterium exchange. In particular, exchange of amide protons in residues of the B-chain helix (B9-B20) are significantly affected suggesting either a stabilization of this helix or a reduction in the solvent accessibility of the helix in the R-state. This paper exemplifies the exchange rates of two amides (ValB18 and TyrB16) from this helix which decrease by approximately 400-fold as a result of this ligand induced conformational transition.

Allosteric Site↗
PubMed1995

Molecular mechanics and dynamics studies on two structurally related amide-modified DNA backbones for antisense technology.

The effect of the replacement of the natural phosphodiester linkage -C3'-O-PO2-O-CH2-C4'- in the DNA strand of RNA.DNA hybrid duplexes by either of the two amide linkages -C3'-CH2-CO-NH-CH2-C4'- or -C3'-CH2-NH-CO-CH2-C4' has been investigated by molecular mechanics (MM) and molecular dynamics (MD) simulations. Conformational analysis has been used to assess various low-energy conformers of the amide-modified backbones. MD simulations have been carried out to study the dynamic behavior of the modified duplexes. The modified RNA.DNA hybrid double helices kept a conservative base pairing scheme during the MD simulations. Although the general behavior has been found to be similar to that of the corresponding wild-type hybrid duplexes, some notable differences, especially regarding the sugar puckering in the amide-modified DNA strands, have been observed. The behavior of the RNA strands in the hybrid duplexes has not been affected by the modified DNA strands and is similar to that in wild-type RNA.DNA duplexes.

Amides↗
PubMed2006

Cation exchange-HPLC and mass spectrometry reveal C-terminal amidation of an IgG1 heavy chain.

A unique, late-eluting "basic peak" (relative to the "main peak") was observed by weak cation exchange-HPLC (WCX) for a recombinant monoclonal antibody (mAb) sample. Peak fractions were collected, desalted, and analyzed by high-resolution MS using a top-down characterization approach that provided accurate masses of intact mAb charge isoforms and a comprehensive profile of the structural heterogeneity. The individual light (L) and heavy (H) chain subunits from the main and basic peaks were analyzed by reversed-phase (RP) HPLC/MS after disulfide bond reduction and cysteine alkylation. Three mAb isoforms were detected, and their modifications were localized to H chain. Bottom-up characterization using RP-HPLC/MS peptide mapping and accurate mass measurements identified three distinct H chain C-terminal peptides ending in glycine, lysine, or alpha-amidated proline. The combined analyses showed that the main WCX peak mAb isoform contained two unmodified L chains and two H chains terminating in glycine. Each mAb isoform that coeluted in the basic peak consisted of two unmodified L chain subunits and a single H chain ending in glycine, but the second H chain terminated in lysine for one isoform and alpha-amidated proline for another isoform. The WCX elution positions of the isoforms were consistent with their respective net charge. To the best of our knowledge, the occurrence of C-terminal alpha-amidation in mAbs has not been reported previously.

Amides↗
PubMed2004

Bile acid amides derived from chiral amino alcohols: novel antimicrobials and antifungals.

Cholic and deoxycholic acid amides 10-17 have been synthesised from (1R,2R)-1-phenyl-2-amino-1,3-propanediol 2, (1S,2S)-1-phenyl-2-amino-1,3-propanediol 4, (1R,2R)-1-para-nitrophenyl-2-amino-1,3-propanediol 3, (1S,2S)-1-para-nitrophenyl-2-amino-1,3-propanediol 5. Amide 12 derived from N-succinimidyl ester 9 of deoxycholic acid and (1R,2R)-1-phenyl-2-amino-1,3-propanediol 2, found to be active against Cryptococcus neoformans and the amide 17 obtained from N-succinimidyl ester 9 of deoxycholic acid and (1S,2S)-1-para-nitrophenyl-2-amino-1,3-propanediol 5, is found to be potent against various gram-positive bacteria.

Amides↗
PubMed2006

Preparation and evaluation of a hydrolytically stable amide-embedded stationary phase.

We have developed a new hydrolytically stable amide-embedded stationary phase via a simple and effective synthetic method. The preparation of the new phase involves the synthesis of multifunctional silane ligands and the surface modification of porous silica particles via multiple attachments of these ligands to the silica surface. A hydrolytically stable coating was produced as a result of multiple covalent linkages formed between silane ligands and the silica surface, and cross-linking between adjacent ligands. The resulting amide-embedded stationary phase showed excellent hydrolytic stability over a wide pH range. Like other existing amide-embedded columns, this new stationary phase exhibits higher retention for polar compounds and different selectivity as compared to conventional C18 columns. The new phase is compatible with 100% aqueous mobile phases, and also provides high column efficiency and good peak shapes for both acidic and basic compounds.

Amides↗
PubMed2005

C-terminal amide to alcohol conversion changes the cardiovascular effects of endomorphins in anesthetized rats.

Endomorphin1-ol (Tyr-Pro-Trp-Phe-ol, EM1-ol) and endomorphin2-ol (Tyr-Pro-Phe-Phe-ol, EM2-ol), with C-terminal alcohol (-ol) containing, have been shown to exhibit higher affinity and lower intrinsic efficacy in vitro than endomorphins. In the present study, in order to investigate the alterations of systemic hemodynamic effects induced by C-terminal amide to alcohol conversion, responses to intravenous (i.v.) or intracerebroventricular (i.c.v.) injection of EM1-ol, EM2-ol and their parents were compared in the system arterial pressure (SAP) and heart rate (HR) of anesthetized rats. Both EM1-ol and EM2-ol induced dose-related decrease in SAP and HR when injected in doses of 3-100 nmol/kg, i.v. In terms of relative vasodepressor activity, it is interesting to note that EM2-ol was more potent than endomorphin2 [the dose of 25% decrease in SAP (DD25) = 6.01+/-3.19 and 13.99+/-1.56 nmol/kg, i.v., respectively] at a time when responses to EM1-ol were less potent than endomorphin1. Moreover, decreases in SAP in response to EM1-ol and EM2-ol were reduced by naloxone, atropine sulfate, L-NAME and bilateral vagotomy. It indicated that the vasodepressor responses were possibly mediated by a naloxone-sensitive, nitric oxide release, vagus-activated mechanism. It is noteworthy that i.c.v. injections of -ol derivatives produced dose-related decreases in SAP and HR, which were significantly less potent than endomorphins and were attenuated by naloxone and atropine sulfate. In summary, the results of the present study indicated that the C-terminal amide to alcohol conversion produced different effects on the vasodepressor activity of endomorphin1 and endomorphin2 and endowed EM2-ol distinctive hypotension characters in peripheral (i.v.) and central (i.c.v.) tissues. Moreover, these results provided indirect evidence that amidated C-terminus might play an important role in the regulation of the cardiovascular system.

Alcohols↗
PubMed1992

Amide bond cleavage monitored continuously through detection of a dansylcadaverine leaving group.

The transglutaminase-catalyzed incorporation of the fluorescent amine, dansylcadaverine, into casein derivatives, such as N,N-dimethylcasein, is accompanied by a large increase in intensity of emission (Lorand et al., Anal. Biochem. 44, 221-231, 1971). We have sought to make use of this sensitive detection device for the continuous, on-line monitoring of an amide-splitting reaction in which dansylcadaverine served as the leaving group. The transglutaminase-coupled test system comprised gamma-glutamyldansylcadaverine as the first substrate and gamma-glutamylamine cyclotransferase as the enzyme responsible for releasing dansylcadaverine from the gamma-amide. At close to saturating levels of transglutaminase, the measured rate of increase of fluorescence, i.e. the steady-state rate of dansylcadaverine incorporation into N,N-dimethylcasein, showed a near-linear relationship with the concentration of gamma-glutamylamine cyclotransferase present in the assay mixture. The general approach developed may be applicable to the assay of other amide cleaving enzymes.

Amides↗
PubMed1987

Thermal denaturation of globular proteins. Fourier transform-infrared studies of the amide III spectral region.

Fourier transform-infrared (FT-IR) spectra are reported for the amide III spectral region of the native and thermally denatured forms of chymotrypsinogen, ribonuclease, bovine serum albumin, and lysozyme. Chymotrypsinogen denatures into structures containing substantial contributions from beta-sheets, while lysozyme and bovine serum albumin show increased amounts of random-coil forms. The changes observed for ribonuclease are quite small. Bovine serum albumin shows at least six bands in the 1,260-1,320 cm-1 region which undergo large intensity changes upon thermal denaturation, and hence are assignable to alpha-helical amide III modes. The large number of observed bands suggests that slight variations in helical geometry, symmetry, or interactions result in changed amide III frequencies, so that simple correlations between narrow frequency ranges and secondary structures may not be applicable for this mode. A widened frequency range is suggested as diagnostic for helical structures.

Amides↗
PubMed1997

Comparison of the amide proton exchange behavior of the rapidly formed folding intermediate and the native state of an antibody scFv fragment.

We have investigated the stability of backbone amide protons of the intermediate and the native state of the scFv fragment of an antibody. Stopped flow experiments analyzed by MS and NMR detected the formation of an exchange protected intermediate within the deadtime of the stopped flow apparatus (17 ms). H/D exchange rates of the native protein identified a number of very stable backbone amide protons in the V(L) and the V(H) domains. In the V(L) domain, this slowly exchanging core of the scFv fragment is similar to the folding core of the intermediate, while the V(H) domain possesses a great number of very stable amide protons which are not stabilized to a significant degree in the folding intermediate of the scFv fragment.

Amides↗
PubMed1979

Characteristics of lithium iodide-containing poly(ethylene glycol) as a gas chromatographic stationary phase, and its application to analysis of amidic drugs.

The characteristics of lithium iodide-containing poly(ethylene glycol) as a gas chromatographic stationary phase have been evaluated in terms of partial free energy of transfer (delta G t0) from poly(ethylene glycol) to the lithium iodide-poly(ethylene glycol) system for a variaty of amides (n-fatty acid amides, lactams, benzamides, anilides, nicotinamides, isonicotinamides, barbiturates, pyrazolones) and several amines. The changes in relative retention and resolution of two solute peaks caused by the addition of lithium iodide to poly)ethylene glycol) are correlated with the difference in their delta Gt0 values. The application to the specific separation of some amidic drugs is demonstrated.

Amides↗
PubMed1990

Electrochemical detection of dipeptides and dipeptide amides.

A postcolumn reagent is used to create electroactive species from non-electroactive peptides. The reagent, based on the classical biuret reagent, consists of Cu(II), tartrate, bicarbonate and base. The detection is by dual electrode electrochemical detection. N-Acetylated dipeptides are oxidized at pH 12 and low potential. Dipeptides and carboxy terminal dipeptide amides give useful signals at lower pH. The dipeptide amides react with Cu(II) as do the tripeptides to yield the electronic spectrum and electrochemistry of the biuret complex. The complexes formed from the dipeptides are reversibly oxidized at potentials greater than 0.85 V vs. Ag/AgCl, 3 M NaCl. Analytically useful signals are obtained for the dipeptide amides at sensitivities equivalent to the sensitivities for longer peptides, 3-5 nA/microM, while the sensitivities for the dipeptides are about an order of magnitude lower.

Amides↗