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PubMed1993

Common ring motifs in proteins involving asparagine or glutamine amide groups hydrogen-bonded to main-chain atoms.

We report the frequent occurrence in proteins of motifs consisting of either 9-membered or 11-membered rings that involve the side-chain amide groups of asparagine and glutamine residues. The syn CO and NH groups of these amide groups are hydrogen-bonded to the main-chain NH and CO groups of other amino acid residues. The main-chain part of both the 9-membered and 11-membered rings has the conformation of a beta-strand. One such ring motifs occurs, on average, in half of all the proteins we examined. Similar conformations are found for most examples of the 9-membered and 11-membered rings. One of the 11-membered rings is distinct, compared to the others, in that its main-chain part has a mirror-image conformation. Another of the 11-membered rings occurs at the interior of the variable domains of some antibodies and assists in linking the two beta-sheets. We observe one 9-membered ring structure in a dihydrofolate reductase complex in which the amide in the nicotinamide group of the ligand NADP is bound to the enzyme. Groups that can form hydrogen bonds in a similar way to amide groups occur in several nucleotide bases; we find one example of a 9-membered ring involving adenine and main-chain atoms in the FAD-protein complex of glutathione reductase. Both have conformations like those of the other 9-membered rings.

Amides↗
PubMed2000

NMR-Based amide hydrogen-deuterium exchange measurements for complex membrane proteins: development and critical evaluation.

A method for measuring site-specific amide hydrogen-deuterium exchange rates for membrane proteins in bilayers is reported and evaluated. This method represents an adaptation and extension of the approach of Dempsey and co-workers (Biophys. J. 70, 1777-1788 (1996)) and is based on reconstituting (15)N-labeled membrane proteins into phospholipid bilayers, followed by lyophilization and rehydration with D(2)O or H(2)O (control). Following incubation for a time t under hydrated conditions, samples are again lyophilized and then solubilized in an organic solvent system, where (1)H-(15)N HSQC spectra are recorded. Comparison of spectra from D(2)O-exposed samples to spectra from control samples yields the extent of the H-D exchange which occurred in the bilayers during time t. Measurements are site specific if specific (15)N labeling is used. The first part of this paper deals with the search for a suitable solvent system in which to solubilize complex membrane proteins in an amide "exchange-trapped" form for NMR quantitation of amide peak intensities. The second portion of the paper documents application of the overall procedure to measuring site-specific amide exchange rates in diacylglycerol kinase, a representative integral membrane protein. Both the potential usefulness and the significant limitations of the new method are documented.

Amides↗
PubMed2002

Hydrogen bonds in human ubiquitin reflected in temperature coefficients of amide protons.

Analysis of amide proton temperature coefficients (deltasigma(HN)/DeltaT) in human ubiquitin shows their usefulness in indicating hydrogen bonds. The availability of a very accurate solution structure of ubiquitin enables the precise determination of hydrogen bonds and increases the reliability of the analysis of chemical shift temperature gradients. Values of deltasigma(HN)/DeltaT more positive than -4.6 ppb/K are very good indicators of hydrogen bonds. Additionally, a weak temperature dependence of non-hydrogen-bonded amides was observed for amide protons that are significantly shifted upfield. We observed that temperature gradients of amide protons involved in short hydrogen bonds are related to donor-acceptor distances.

Amides↗
PubMed1987

Biosynthesis of the C-terminal amide in peptide hormones.

Recent developments in the study of peptide amidation are reviewed. The main areas covered are assay procedures, purification of amidating enzymes, co-factors and regulation, mechanism and specificity of the amidating reaction, and multiple forms of the amidating enzyme and glycosylation. Discussion is presented on aspects that are poorly understood and new areas open to investigation are indicated.

Amides↗
PubMed1991

Measurement of the exchange rates of rapidly exchanging amide protons: application to the study of calmodulin and its complex with a myosin light chain kinase fragment.

A technique is described for measuring the approximate exchange rates of the more labile amide protons in a protein. The technique relies on a comparison of the intensities in 1H-15N correlation spectra recorded with and without presaturation of the water resonance. To distinguish resonance attenuation caused by hydrogen exchange from attenuation caused by cross relaxation, the experiment is repeated at several different pH values and the difference in attenuation of any particular amide resonance upon presaturation is used for calculating its exchange rate. The technique is demonstrated for calmodulin and for calmodulin complexed with its binding domain of skeletal muscle myosin light chain kinase. Upon complexation, increased amide exchange rates are observed for residues Lys75 through Thr79 located in the 'central helix' of calmodulin, and for the C-terminal residues Ser147 and Lys148. In contrast, a decrease in amide exchange rate is observed at the C-terminal end of the F helix, from residues Thr110 through Glu114.

Amides↗
PubMedDate not supplied

Aspects of antibody-catalyzed primary amide hydrolysis.

Because there are many known C-terminally amidated peptides of biological importance, there is great potential in medicine and organic synthesis for antibodies that catalyze primary amide bond hydrolysis or formation. We characterized a catalytic antibody, 13D11, raised to a phosphinate hapten, that hydrolyzed the primary amide of a dansyl-alkylated derivative of (R)-phenylalaninamide (DNS-(R)F-NH2). At pH 9.0, 13D11 hydrolyzed DNS-(R)F-NH2 with a kcat of 1.65 x 10(-7) s-1 (kcat/kuncat = 132) and a Km of 432 microM, and was stereospecifically hapten-inhibited (Ki = 14.0 microM). Control experiments indicated that the catalytic activity was not the result of a contaminating protease. In accordance with the hapten being a transition-state analog of base hydrolysis, the rate of DNS-(R)F-NH2 hydrolysis increased with hydroxide concentration to an optimum pH of 9.5. Above pH 9.5, activity declined rapidly suggesting the antibody was inactivated during the long incubation period. This work demonstrates the feasibility of generating catalytic antibodies to hydrolyze unactivated amide bonds without cofactor assistance.

Amides↗
PubMedDate not supplied

Studies on the in vitro hepatic microsomal formation of amides during the metabolism of certain secondary and tertiary benzylic amines.

Part of our interest during the last few years has been to investigate the possible intermediate(s) and mechanism(s) involved in the formation of amides from N-benzylic amines. A number of benzylic amines with different aryl and alkyl moieties introduced onto the constituent nitrogen were prepared, thus creating a wide variety of secondary, tertiary and heterocyclic benzylic amines with different logP and pKa characteristics (Tables I & II). In some experiments, the possible intermediates of this reaction, i.e. nitrones (Table III), imines (Table IV) and amides themselves (Table V), were used as substrates in our metabolic studies. Their in vitro hepatic microsomal metabolism was studied in order to obtain a structure/metabolic activity relationship for the formation of amides from benzylic amines. This communication reviews these studies and reports our conclusions as to the mechanism of formation of amides from N-benzylic amines.

Amides↗
PubMed2005

The environment of amide groups in protein-ligand complexes: H-bonds and beyond.

A comprehensive structural analysis of interactions involving amide NH and C=O groups in protein-ligand complexes has been performed based on 3,275 published crystal structures (resolution < or =2.5 A). Most of the amide C=O and NH groups at the protein-ligand interface are highly buried within the binding site and involved in H-bonds with corresponding counter-groups. Small percentages of C=O and NH groups are solvated or embedded in hydrophobic environments. In particular, C=O groups show a higher propensity to be solvated or embedded in a hydrophobic environment than NH groups do. A small percentage of carbonyl groups is involved in weak hydrogen bonds with CH. Cases of dipolar interactions, involving carbonyl oxygen and electrophilic carbon atoms, such as amide, amidinium, guanidium groups, are also identified. A higher percentage of NH are in contact with aromatic carbons, interacting either through hydrogen bonds (preferably with the NH group pointing towards a ring carbon atom) or through stacking between amide plane and ring plane. Comprehensive studies such as the present one are thought to be important for future improvements in the molecular design area, in particular for the development of new scoring functions. [Figure: see text].

Amides↗
PubMed1988

A fluorometric assay for peptidyl alpha-amidation activity using high-performance liquid chromatography.

A rapid and sensitive method for the determination of peptidyl alpha-amidation activity has been developed and is based on reverse-phase high-performance liquid chromatographic separation and fluorometric detection. A dansylated tripeptide, N-dansyl-Tyr-Val-Gly-OH, is used as the substrate in the assay and the amount of alpha-amidation activity is determined by quantitating the extent of its conversion to product, N-dansyl-Tyr-Val-NH2. Both product and substrate can be detected in a single assay in quantities as low as 5 fmol by isocratic elution using C-18 reverse-phase columns. The method yields highly reproducible results and requires less than 3 min per sample for separation and quantitation. The assay procedure is applicable to the screening of a large number of samples under different pH conditions and is readily adaptable for use in a variety of studies. For example, the procedure is ideal for detecting alpha-amidation activity in various tissues, monitoring activity at the different stages during purification of a particular alpha-amidation enzyme, determining kinetic parameters of the purified enzyme, and identifying both competitive and noncompetitive inhibitors.

Amides↗
PubMed1975

Omega-1, Omega-2 and Omega-3 hydroxylation of long-chain fatty acids, amides and alcohols by a soluble enzyme system from Bacillus megaterium.

A soluble enzyme preparation from Bacillus megaterium, previously shown to hydroxylate free fatty acids to isomeric mixtures of Omega-1, Omega-2 and Omega-3 monohydroxy fatty acids in the presence of NADPH and O2, has now been shown to act also on fatty amides but not only hydrocarbons or fatty acid methyl esters. Using 14-C-labelled substrates, both the chain-length specificity and the positional specificity of hydroxylation was determined for fatty acids, alcohols and amides. The most active saturated fatty acid (pentadecanoic) was hydroxylated at a rate 10 times greater than the most active amide (myristamide) and 14 times faster than the most active alcohol (1-tetradecanol). Among the saturated fatty acids, the order of activity as hydroxylation substrates was C15 greater than C16 greater than C14 greater than C17 greater than C13 greater than C18 = C12. For amides the order was C14 greater than C12 greater than C15 greater than C16 while for alcohols it was C14 greater than C13 = C15 greater than C12 greater than C15. Four cis-monounsaturated fatty acids were also tested. Oleic, palmitoleic and cis-12-octadecenoic acids were more active than their saturated analogs but cis-5-tetradecenoate was less active than myristate. For all of the substrates mentioned above, with the possible exception of several unsaturated acids, the alkyl chains were monohydroxylated to give isomeric mixtures of the Omega-1, Omega-2 and Omega-3 derivatives. The distribution of these three isomers varied with chain-length and type of substrate but generally, the Omega-2 position was favored. The terminal methyl (Omega) group of these substrates was never hydroxylated and there did not appear to be significant hydroxylation of methylene carbons beyond the Omega-3 position. Based on the data presented here and in a previous paper, a model is proposed for the enzyme-substrate complex which involves hydrophobic binding and sequestering of the terminal methyl group of the substrate and electrostatic binding of the substrate's polar functional group.

Amides↗
PubMed1984

Amide proton exchange used to monitor the formation of a stable alpha-helix by residues 3 to 13 during folding of ribonuclease S.

We make use of the known exchange rates of individual amide proton in the S-peptide moiety of ribonuclease S (RNAase S) to determine when during folding the alpha-helix formed by residues 3 to 13 becomes stable. The method is based on pulse-labeling with [3H]H2O during the folding followed by an exchange-out step after folding that removes 3H from all amide protons of the S-peptide except from residues 7 to 14, after which S-peptide is separated rapidly from S-protein by high performance liquid chromatography. The slow-folding species of unfolded RNAase S are studied. Folding takes place in strongly native conditions (pH 6.0, 10 degrees C). The seven H-bonded amide protons of the 3-13 helix become stable to exchange at a late stage in folding at the same time as the tertiary structure of RNAase S is formed, as monitored by tyrosine absorbance. At this stage in folding, the isomerization reaction that creates the major slow-folding species has not yet been reversed. Our result for the 3-13 helix is consistent with the finding of Labhardt (1984), who has studied the kinetics of folding of RNAase S at 32 degrees C by fast circular dichroism. He finds the dichroic change expected for formation of the 3-13 helix occurring when the tertiary structure is formed. Protected amide protons are found in the S-protein moiety earlier in folding. Formation or stabilization of this folding intermediate depends upon S-peptide: the intermediate is not observed when S-protein folds alone, and folding of S-protein is twice as slow in the absence of S-peptide. Although S-peptide combines with S-protein early in folding and is needed to stabilize an S-protein folding intermediate, the S-peptide helix does not itself become stable until the tertiary structure of RNAase S is formed.

Amides↗
PubMed1989

Identification of fatty acid amides in human plasma.

A family of five long-chain fatty acid carboxamides has been identified and semi-quantified in human plasma by GC-MS. One saturated and four unsaturated amides were found. Luteal phase plasma from 16 women was studied, and all five of the amides were found in ten of the subjects, but none in the other six. The structure of these endogenous amides was established by comparing their GC and MS characteristics with those of the synthetic amides prepared by ammonolysis of corresponding long-chain fatty acid acyl chlorides.

Amides↗
PubMed1988

The use of amide local anesthetics in patients susceptible to malignant hyperthermia.

The use of amide local anesthetics in dental patients presumed to be susceptible to malignant hyperthermia (MH) is controversial. A literature review of 17 recent dental publications and their reference citations revealed that the recommendation to avoid local anesthetics of the amide type in dental treatment of MH-susceptible (MHS) patients is based on in vitro muscle investigations, unpublished communications, and a single case report suggestive of MH. Therefore, a survey of members of the Malignant Hyperthermia Association of the United States designed to determine what, if any, MH-like reactions have occurred in patients with MHS receiving dental treatment was conducted. Of a total of 307 MHS respondents, 36 (12%) reported adverse reactions to dental care. Only one respondent, however, reported symptoms suspicious of MH (fever, muscle pain) in which the administration of amide local anesthetics appeared to be closely linked. Fifty-six (18%) of the respondents have had difficulty obtaining routine dental care since being identified as MHS; this includes 27 who have been refused dental treatment or have had to undergo operative procedures without the benefit of local anesthesia. These results support the conclusions that amide local anesthetics may be administered to MHS patients without significant risk and that currently the diagnosis of MH susceptibility can adversely affect the quality of dental care.

Adolescent↗
PubMedDate not supplied

Kinetics of amide proton exchange in parvalbumin studied by 1H 2-D NMR. A comparison of the calcium and magnesium loaded forms.

The amide proton exchange rates have been measured for the pike parvalbumin loaded either with calcium (PaCa2) or with magnesium (PaMg2) by using 2-D total correlation spectroscopy experiments. The differences in the exchange rates observed between these two species were unexpected when compared with the small conformational changes induced in parvalbumin by the Ca/Mg exchange. With the calcium-loaded protein (PaCa2), a significant difference was observed for the amide proton exchange rates of residues located in the N-terminal domain AB in contrast to the slower exchange rates that were observed in the CD and EF domains. Such a difference does not exist for PaMg2, where faster exchange rates are observed over all the sequence. Since amide proton exchange rates are the signature of the solvent's accessibility in proteins, we interpreted our results in terms of difference of the equilibria between 'closed-states' and 'opened-states' for individual amide protons of the protein when calcium was replaced by magnesium. The CD and EF domains, and to a lesser extent the AB domain, would be more rigid when the protein was loaded with calcium ions. For the magnesium-loaded parvalbumin (PaMg2) the faster exchange rates we observed could be rationalized by a more flexible structure than in the case of the PaCa2.

Amides↗
PubMed1985

Amidation of, and (R)-1-amino-2-propanol attachment to, the corrin ring during vitamin B-12 biosynthesis by Clostridium tetanomorphum extracts.

Two intermediate stages in cobalamin biosynthesis, amidation of carboxylic acid groups in the corrin ring and (R)-1-amino-2-propanol attachment at propionic acid position f, have been studied using cell-free extracts from the obligate anaerobe Clostridium tetanomorphum. The preparation of an incomplete corrinoid, probably cobinic acid-a,c,d,e,g-pentaamide, as an in vitro amidation substrate was accomplished via mild acid hydrolysis of cobinamide. Weak, but reproducible activities for both amidation and (R)-1-amino-2-propanol attachment were found in crude, nucleic acid-free and DE-52 column-purified protein fractions. The amidation reaction was glutamine-dependent in crude fractions, but became ammonium ion-dependent in more purified fractions. Significant problems encountered were (a) the weak and unstable character of both enzyme activities, and (b) the irreversible changes in the visible spectra of the incomplete corrinoids employed as substrates caused by use of thiol-reducing agents in the buffers and assays.

Amides↗
PubMed2004

Protein carboxyl amidation increases the potential extent of protein polyethylene glycol conjugation.

Chemical coupling of polyethylene glycol (PEG) to therapeutic proteins reduces their immunogenicity and prolongs their circulating half-life. The limitation of this approach is the number and distribution of sites on proteins available for PEGylation (the N terminus and the -amino group of lysines). To increase the extent of PEGylation, we have developed a method to increase the number of PEGylation sites in a model protein, recombinant methionine alpha,gamma-lyase (recombinant methioninase; rMETase), an enzyme cancer therapeutic cloned from Pseudomonas putida. rMETase was first PEGylated with methoxypolyethylene glycol succinimidyl glutarate-5000 with a molar ratio of PEG:rMETase of 15:1. The carboxyl groups of the initially PEGylated protein were then conjugated with diaminobutane, resulting in carboxyl amidation. This reaction was catalyzed by 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide, a water-soluble carbodiimide. The steric hindrance provided by the PEG chains already coupled to the protein prevented cross-linking between rMETase molecules during the carboxyl amidation reaction. The carboxyl-amidated PEGylated rMETase was hyper-PEGylated at a molar ratio of PEG to PEG-rMETase of 60:1. Biochemical analysis indicated that 13 PEG chains were coupled to each subunit of rMETase after hyper-PEGylation compared with 6-8 PEG chains attached to the non-carboxyl-amidated PEG-rMETase. Approximately 15-20% of the non-PEGylated rMETase activity was retained in the hyper-PEGylated molecule. Immunogenicity of the hyper-PEG-rMETase was significantly reduced relative to PEG-rMETase and rMETase. Initial results suggest that hyper-PEGylation may become a new strategy for PEGylation of protein biologics.

Amides↗
PubMed2005

Exploration of a binding mode of indole amide analogues as potent histone deacetylase inhibitors and 3D-QSAR analyses.

Docking simulations and three-dimensional quantitative structure-activity relationship (3D-QSAR) analyses were conducted on a series of indole amide analogues as potent histone deacetylase inhibitors. The studies include comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). Selected ligands were docked into the active site of human HDAC1. Based on the docking results, a novel binding mode of indole amide analogues in the human HDAC1 catalytic core is presented, and enzyme/inhibitor interactions are discussed. The indole amide group is located in the open pocket, and anchored to the protein through a pair of hydrogen bonds with Asp99 O-atom and amide NH group on ligand. Based on the binding mode, predictive 3D-QSAR models were established, which had conventional r2 and cross-validated coefficient values (r(cv)2) up to 0.982 and 0.601 for CoMFA and 0.954 and 0.598 for CoMSIA, respectively. A comparison of the 3D-QSAR field contributions with the structural features of the binding site showed good correlation between the two analyses. The results of 3D-QSAR and docking studies validate each other and provided insight into the structural requirements for activity of this class of molecules as HDAC inhibitors. The CoMFA and CoMSIA PLS contour maps and MOLCAD-generated active site electrostatic, lipophilicity, and hydrogen-bonding potential surface maps, as well as the docking studies, provided good insights into inhibitor-HDAC interactions at the molecular level. Based on these results, novel molecules with improved activity can be designed.

Amides↗
PubMed2005

Sample preparation and gas chromatography of primary fatty acid amides.

A method for the isolation of bio-active primary fatty acid amides (PFAM's) from total lipid extract by solid-phase extraction (SPE) was developed and validated. The lowest mass of amide to be loaded and recovered by this method was detected as 0.5 microg using 500 mg of normal phase adsorbent. The isolated PFAM's were separated and quantified by GC/MS and percent recoveries were calculated. An HP-5MS column was able to provide base line separation between the saturated and unsaturated PFAM's whereas clear resolution between geometric and positional isomers having the same number of carbons was obtained using a BPX70 column. The separated amides were all 18 carbon analogs of cis-9-octadecenoamide (oleamide). Detection limits in the single ion monitoring mode were found to be on the order of 10 pg in a 1 microl injection. Solid phase extraction of amides from total lipid extract before GC/MS analysis provides clean detection and interference free analysis.

Amides↗