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Predictions of protein secondary structures using factor analysis on Fourier transform infrared spectra: effect of Fourier self-deconvolution of the amide I and amide II bands.

Fourier self-deconvolution (FSD) was performed on protein amide I and II Fourier transform infrared (FTIR) spectra to test if the resultant increased band shape variation would lead to improvements in protein secondary structure prediction with our factor analysis based restricted multiple regression (RMR) methods. FTIR spectra of 23 proteins dissolved in H2O were measured and normalized to a constant amide I peak absorbance. The deconvolved spectra were renormalized by area so that the deconvolved spectra sets had the same area as before. Principal component analysis of the deconvolved spectra sets was carried out, which was followed by a selective multiple linear regression (RMR) analysis of the principal component loadings with regard to the fractional components (FC) of secondary structure. As compared to analyses based on the original spectra set, helix and sheet predictions were not noticeably improved by FSD; but, if a very large number of component spectra (16) were retained in the pool to select which loadings to be used in the RMR optimization, better predictions of turn and "other" resulted. The prediction quality varied depending on the deconvolution parameters used.

Animals↗

Identification of the TRH-like peptides pGlu-Glu-Pro amide and pGlu-Phe-Pro amide in rat thyroid: regulation by thyroid status.

Rat thyroid contains thyrotropin-releasing hormone (TRH) and TRH-like peptides which react with TRH antisera. We have identified the TRH-like peptides in the thyroid and examined whether their levels are influenced by thyroid status. The peptides were extracted from the thyroid glands of five hyperthyroid rats and purified by ion-exchange chromatography on SP-Sephadex C25 and reversed-phase high performance liquid chromatography. The principal TRH-immunoreactive component exhibited the same retention on HPLC as synthetic pGlu-Glu-Pro amide and a secondary component corresponded to synthetic pGlu-Phe-Pro amide. In agreement with these assignments the main peptide was shown to be acidic when chromatographed on DEAE-Sephadex A25 and the second peptide neutral. The levels of TRH and TRH-like peptides in the thyroid were investigated in hyper-, hypo- and euthyroid rats. Hyperthyroidism was induced by chronic subcutaneous administration of triiodothyronine (T3) and hypothyroidism was produced by addition of propylthiouracil (PTU) to the drinking water. The amounts of the peptides were determined by radioimmunoassay with a TRH-antiserum, carried out after extraction from the tissues and purification by ion exchange chromatography. The mean concentration of TRH-like peptides in the thyroids of the hyperthyroid rats was 95.5+/-25.5 pmol/g, the mean concentration in the hypothyroid rats was 11.7+/-3.4 pmol/g, and in the euthyroid rats 17.6+/-3.2 pmol/g. The concentrations of TRH were less influenced by thyroid status: the values in hyper-, hypo- and euthyroid rats were 47.5+/-9.4, 42.1+/-6.3, and 17.2+/-1.6 pmol/g respectively. The results show that the levels of the TRH-like peptides in rat thyroid are highly sensitive to thyroid status, suggesting a possible involvement in thyroid regulation.

Animals↗

Peptidylglycine alpha-amidating mono-oxygenase: neuropeptide amidation as a target for drug design.

1. Peptidylglycine alpha-amidating mono-oxygenase (PAM) is a bifunctional key enzyme in the bioactivation of neuropeptides. Its biosynthesis, distribution, functional role, and pharmacological manipulation are discussed. 2. PAM biosynthesis from a single gene precursor is characterized by alternative splicing and endoproteolytic events, which control intracellular transport, targeting, and enzyme activity. 3. The enzyme is mainly stored in secretory vesicles of many neuronal and endocrine cells with high abundance in the pituitary gland. Its functional role has been studied using enzyme inhibitors. Thus selective, peripheral PAM inhibition reduces substance P along with an anti-inflammatory action. 4. PAM-related pathologies are characterized by an increased relative abundance of alpha-amidated neuropeptides. To attenuate such hormone overproduction, novel, specific, and disease-targeted PAM inhibitors may be developed based on enzyme polymorphism.

Animals↗

Synthesis and Structure of a New Lithium Amide Ligand Precursor: A Tridentate Nitrogen-Based Donor Set of the Formula N(SiMe(2)CH(2)NMe(2))(2). Synthesis and Structure of the Group 4 Amides MCl(3)[N(SiMe(2)CH(2)NMe(2))(2)] (M = Ti, Zr, Hf).

The new lithium amide LiN(SiMe(2)CH(2)NMe(2))(2) was prepared by reaction of NH(3) with the corresponding silylamine Me(2)NSiMe(2)CH(2)NMe(2) followed by addition of butyllithium. This lithium derivative exists as a dimer in the solid state wherein the two lithium ions are bridged by the two amido units with the amine arms of each unit bonded to opposite lithium centers in an overall pseudo D(2) structure; however, in solution, a fluxional process serves to interconvert the enantiomeric forms of the dimer unit. The coordination chemistry of the lithium amide dimer has been investigated; reaction with a series of group 4 starting halides, MCl(4), leads to the corresponding complexes MCl(3)[N(SiMe(2)CH(2)NMe(2))(2)], where M = Ti, Zr, and Hf. The structures of these starting trihalides in solution and in the solid state are presented.

Journal Article↗

A study of the relationship between biological activity and prolyl amide isomer geometry in oxytocin using 5-tert-butylproline to augment the Cys(6)-Pro(7) amide cis-isomer population.

Three [5-t-BuPro(7)]oxytocin analogues were synthesized by substituting (2S,5R)-5-tert-butylproline for proline in oxytocin, [Mpa(1)]oxytocin, and [dPen(1)]oxytocin. Relative to oxytocin, [5-t-BuPro(7)]oxytocin and [Mpa(1),5-t-BuPro(7)]oxytocin exhibited strongly reduced binding affinity to the receptor; however, both peptides maintained the pharmacophore characteristics responsible for signal transfer evoking the same maximal response as oxytocin in the single-dose procedure and exhibiting partial agonistic activity in the cumulative dose-response procedure. Although [dPen(1)]oxytocin exhibited inhibitory as well as partial agonistic activity, [dPen(1),5-t-BuPro(7)]oxytocin exhibited only inhibitory potency with a similar in vitro pA(2) value of 7.50 in the absence of magnesium. In the presence of magnesium, [dPen(1), 5-t-BuPro(7)]oxytocin exhibited stronger inhibitory potency than [dPen(1)]oxytocin and no partial agonism. Assignment of the proton signals for the 5-tert-butylprolyl amide cis- and trans-isomers by two-dimensional NMR experiments in water indicated that the Cys(6)-Pro(7) peptide bond cis-isomer population was augmented relative to the prolyl peptides and measured respectively at 35%, 33%, and 20% in the 5-tert-butylproline(7) analogues of oxytocin, [Mpa(1)]oxytocin and [dPen(1)]oxytocin. Although caution must be taken when relating the increase in cis-isomer population with an influence on biological activity in [5-t-BuPro(7)]oxytocin analogues, the synthesis and evaluation of analogues 1-3 have provided additional evidence that can be used to support the hypothesis that the prolyl amide cis-isomer may favor antagonism and the trans-isomer is necessary for agonist activity.

Animals↗

Stable enols of amides ArNHC(OH)=C(CN)CO(2)R. E/Z enols, equilibria with the amides, solvent effects, and hydrogen bonding.

The structures of anilido cyano(fluoroalkoxycarbonyl)methanes ArNHCOCH(CN)CO(2)R, where R = CH(2)CF(3) or CH(CF(3))(2), Ar = p-XC(6)H(4), and X = MeO, Me, H, or Br, were investigated. In the solid state, all exist as the enols ArNHC(OH)=C(CN)CO(2)R 7 (R = CH(2)CF(3)) and 9 (R = CH(CF(3))(2)) with cis arrangement of the hydrogen-bonded ROC=O.HO moiety and a long C1=C2 bond. The product composition in solution is solvent dependent. In CDCl(3) solution, only a single enol is observed, whereas in THF-d(8) and CD(3)CN, two enols (E and Z) are the major products, and the amide is the minor product or not observed at all (K(Enol) 1.04-9 (CD(3)CN, 298 K) and 3 to >/=100 (THF, 300 K)). The percentage of the amide and the Z-enol increase upon an increase in temperature. In all solvents, the percent enol is higher for 9 than for 7. In CD(3)CN, more enol is observed when the aryl group is more electron-donating. The spectra in DMSO-d(6) and DMF-d(7) indicate the presence of mostly a single species, whose spectra do not change on addition of a base and is ascribed to the anion of the ionized carbon acid. Comparison with systems where the CN is replaced by a CO(2)R group (R = CH(2)CF(3), CH(CF(3))(2)) shows a higher percentage of enol for the CN-substituted system. Intramolecular (to CO(2)R) and intermolecular hydrogen bonds determine, to a significant extent, the stability of the enols, their Z/E ratios (e.g., Z/E (THF, 240 K) = 3.2-4.0 (7) and 0.9-1.3 (9)), and their delta(OH) in the (1)H spectra. The interconversion of Z- and E-enol by rotation around the C=C bond was studied by DNMR, and DeltaG() values of >/=15.3 and 14.1 +/- 0.4 kcal/mol for Z-7 and Z-9 were determined. Features of the NMR spectra of the enols and their anions are discussed.

Journal Article↗

Chroman amide and nicotinyl amide derivatives: inhibition of lipid peroxidation and protection against head trauma.

A series of chroman amide and nicotinyl amide derivatives was designed and synthesized for the treatment of traumatic and ischemic CNS injury. Five compounds were significantly more potent inhibitors of lipid peroxidation in vitro than the reference antioxidant, trolox (p < 0.01). Quantitative structure activity studies demonstrated that the inhibitory action was related to the ability to donate electrons, charge on hydroxy group and E(LUMO), to scavenging radicals and to the lipophilicity log P, which determines penetration of membrane lipids. ESR study indicated the ability of 12 to scavenge the hydroxyl radicals. The most promising compound, [(3,4-dihydro-6-hydroxy-2,5,7,8-tetramethyl-2H-1-benzopyran-2yl)ca rbonyl]-3'-(aminoethyl) indole (12), inhibited ex vivo lipid peroxidation in a head injury model and showed potent in vivo neuroprotective efficacy. Improvement of neurological recovery within 1 h of injury (grip test score) by as much as 200% was observed together with significant anti-anoxia activity. Compound 12 was a potent antagonist of methamphetamine-induced hypermotility resulting from dopamine release in the mouse brain. These results support the importance of cerebroprotective radical-scavenging agents for the treatment of traumatic injury and anoxia as well as provide additional evidence for the role of oxygen radicals and dopamine in brain damage.

Animals↗

Exendin(9-39)amide is an antagonist of glucagon-like peptide-1(7-36)amide in humans.

The gastrointestinal hormone, glucagon-like peptide-1(7-36)amide (GLP-1) is released after a meal. The potency of synthetic GLP-1 in stimulating insulin secretion and in inhibiting glucagon secretion indicates the putative physiological function of GLP-1. In vitro, the nonmammalian peptide, exendin(9-39)amide [ex(9-39)NH2], is a specific and competitive antagonist of GLP-1. This in vivo study examined the efficacy of ex(9-39)NH2 as an antagonist of exogenous GLP-1 and the physiological role of endogenous GLP-1. Six healthy volunteers underwent 10 experiments in random order. In each experiment, a 30-min period of euglycemia was followed by an intravenous infusion of glucose for 150 min that established a stable hyperglycemia of 8 mmol/liter. There was a concomitant intravenous infusion of one of the following: (1) saline, (2) GLP-1 (for 60 min at 0.3 pmol . kg-1 . min-1 that established physiological postprandial plasma levels, and for another 60 min at 0.9 pmol . kg-1 . min-1 to induce supraphysiological plasma levels), (3-5) ex(9-39)NH2 at 30, 60, or 300 pmol . kg-1 . min-1 + GLP-1, (6-8) ex(9-39)NH2 at 30, 60, or 300 pmol . kg-1 . min-1 + saline, (9 and 10) GIP (glucose-dependent insulinotropic peptide; for 60 min at 0.8 pmol . kg-1 . min-1, with saline or ex(9-39)NH2 at 300 pmol . kg-1 . min-1). Each volunteer received each of these concomitant infusions on separate days. ex(9-39)NH2 dose-dependently reduced the insulinotropic action of GLP-1 with the inhibitory effect declining with increasing doses of GLP-1. ex(9-39)NH2 at 300 pmol . kg-1 . min-1 blocked the insulinotropic effect of physiological doses of GLP-1 and completely antagonized the glucagonostatic effect at both doses of GLP-1. Given alone, this load of ex(9-39)NH2 increased plasma glucagon levels during euglycemia and hyperglycemia. It had no effect on plasma levels of insulin during euglycemia but decreased plasma insulin during hyperglycemia. ex(9-39)NH2 did not alter GIP-stimulated insulin secretion. These data indicate that in humans, ex(9-39)NH2 is a potent GLP-1 antagonist without any agonistic properties. The pancreatic A cell is under a tonic inhibitory control of GLP-1. At hyperglycemia, the B cell is under a tonic stimulatory control of GLP-1.

Adult↗

Parathyroid hormone (PTH)-(1-34), [Nle(8,18),Tyr34]PTH-(3-34) amide, PTH-(1-31) amide, and PTH-related peptide-(1-34) stimulate phosphatidylcholine hydrolysis in UMR-106 osteoblastic cells: comparison with effects of phorbol 12,13-dibutyrate.

Studies were performed to determine the effects of PTH and related compounds on phosphatidylcholine (PC) hydrolysis in UMR-106 cells and the pathway by which the PTH effects occurred. The responses were compared with those of phorbol 12,13-dibutyrate (PDBu). Both bovine PTH-(1-34) [bPTH-(1-34)] and PDBu stimulated PC hydrolysis within 10 min. Significant effects were elicited by concentrations of 0.3-1 nM bPTH-(1-34) and 5 nM PDBu. Dose-dependent increases were seen at higher concentrations of both compounds, however, the response to bPTH-(1-34) was reduced at 30 nM. Bovine or human PTH-(1-34) and human PTH-related peptide-(1-34) [hPTHrP-(1-34)] were equipotent in their effects, whereas bovine [Nle(8,18)Tyr34]PTH-(3-34) amide [bPTH-(3-34)] and hPTH-(1-31) amide [hPTH-(1-31)] were less potent than bPTH-(1-34). bPTH-(3-34) did not antagonize the effects of bPTH-(1-34). Down-regulation of protein kinase C isozymes by 24-h treatment with PDBu completely prevented the stimulatory effect of PDBu on PC hydrolysis, but did not significantly affect the stimulatory effect of bPTH-(1-34). Both bPTH-(1-34) and PDBu stimulated transphosphatidylation of PC, indicating a phospholipase D-stimulated mechanism. The results suggest that in the UMR-106 cell line PTH can stimulate activation of PLD by a mechanism other than through protein kinase C.

Animals↗

Glucagon-like peptide-1-(7-36)amide is transformed to glucagon-like peptide-1-(9-36)amide by dipeptidyl peptidase IV in the capillaries supplying the L cells of the porcine intestine.

The insulinotropic hormone glucagon-like peptide-1 (GLP-1) is stored in the intestinal L cell in an active form, GLP-1-(7-36)amide, but more than half of the endogenous peptide circulates in an inactive, N-terminally truncated form, GLP-1-(9-36)amide. This study examined the GLP-1 newly secreted from the porcine ileum, in vitro (isolated perfused preparation) and in vivo (anesthetized pig), to determine where this conversion occurs. Although the GLP-1 extractable from the porcine ileum is predominantly the intact peptide (94.6+/-1.7%), a large proportion of the GLP-1 that is secreted has already been degraded to the truncated form both in vitro (53.8+/-0.9% intact) and in vivo (32.9+/-10.8% intact). In the presence of a specific dipeptidyl peptidase IV (DPP IV) inhibitor (valine-pyrrolidide), the proportion of intact GLP-1 released from the perfused ileum was increased under both basal (99% intact; P < 0.05) and stimulated (86-101% intact; P < 0.05) conditions. Immunohistochemical and histochemical studies revealed specific DPP IV staining in the brush border epithelium as well as in the capillary endothelium. Double staining showed juxtapositioning of DPP IV-positive capillaries and GLP-1-containing L cells. From these results, we suggest that GLP-1 is degraded as it enters the DPP IV containing blood vessels draining the intestinal mucosa.

Animals↗

Teratogenesis of the horseshoe crab by alpha-lipoic amide (6,8-thioctic amide) in marketed vitamin tablets.

Some marketed vitamin tablets induce defects and fusion of body segments and appendages in the developing horseshoe crab. alpha-Lipoic amide may be responsible for the induction, and the other vitamins are probably not directly responsible. alpha-Lipoic acid also induces the same malformations. It is presumed that alpha-lipoic amide and alpha-lipoic acid inhibit thioldisulphide exchange and this inhibition disturbs the morphogenetic movement. As a result, the monsters may be induced by treatment with vitamin tablets.

Abnormalities, Drug-Induced↗

FMRF-amide-like immunoreactivity (FMRF-amide-LIR) in the vegetative areas and dorsal horn of the spinal cord of some rodents.

A dorsal horn fiber system is revealed along the entire length of the spinal cord of guinea pig, rat and wild hamster by means of FMRF-amide immunocytochemistry. Additionally by the same method are revealed two IR networks in the intermediate zone of the thoracic and sacral spinal cord which are identical with the described earlier by us (Galabov and Davidoff, 1976; Galabov 1980; Davidoff et al. 1985) vegetative networks. The dorsal horn fiber system on transversal sections possesses five main components identical with the components of such system described earlier by Davidoff et al. (1986) by means of SP immunocytochemistry. On horizontal sections it is composed of two FMRF-amide LIR networks: One is localized in the superficial layers of the dorsal horn (Laminae I and II) and the second in laminae IV and V, in the borders of nucleus proprius. Both networks are interconnected and in the thoracic and sacral spinal cord are connected with the vegetative networks. It is suggested that some fibers of the dorsal horn fiber system originate from dorsal-root ganglia and may represent primary sensory or visceral afferents. It is likely that this system together with the vegetative networks may represent the morphological basis for the integration of 1) the central and peripheral vegetative nervous systems and 2) the somatic and vegetative nervous system. The presence of different neuropeptides in the dorsal horn fiber system gives ground to term it as a Peptidergic Dorsal Horn Fiber System (pDHFS).

Animals↗

Rapid hydrolysis of amides under physiological conditions: influence of the microenvironment on the stability of the amide bond.

A new class of bicyclic carboxyamides 1a-9a differing with respect to substitution patterns and exo-endo geometry has been synthesized. These amides are characterized by a structure-dependent unusual rapid hydrolysis rate at physiological conditions. The corresponding bicyclic anhydrides might be used as tools for masking and modifying therapeutic agents containing amine functionalities.

Amides↗

1H NMR studies of a biosynthetic lacto-ganglio hybrid glycosphingolipid: confirmation of structure, interpretation of "anomalous" chemical shifts, and evidence for interresidue amide-amide hydrogen bonding.

Glycosphingolipids bearing GlcNAc beta 1----3 and GalNAc beta 1----4 linked to beta-Gal of lactosylceramide (lacto-ganglio hybrids), first isolated from a murine myelogenous leukemia cell line [Kannagi, R., Levery, S. B., & Hakomori, S. (1984) J. Biol. Chem. 259, 8444-8451], have since been found as normal components of mullet roe and English sole liver. In order to clarify the biosynthetic pathways responsible for its occurrence both as a product of normal tissues and as a possible mammalian cancer-associated antigen, the lacto-ganglio hybrid core structure LcGg4Cer was synthesized from Lc3Cer using a GalNAc beta 1----4 transferase preparation from English sole liver. A preliminary characterization of the enzyme, which may be identical to the GalNAc T-1 responsible for synthesis of GM2 ganglioside, is presented. The enzymatically synthesized product was analyzed by 1- and 2-D 1H NMR spectroscopy, confirmining its primary structure as GalNAc beta 1----4-(GlcNAc beta 1----3)Gal beta 1----4Glc beta 1----1Cer. In addition to assigning all nonexchangeable glycosyl proton resonances, measurements of several properties of the amide NH protons, including chemical shift, coupling constants, exchange rates, and temperature shift coefficients, were obtained and compared to those in the simpler constituent triglycosylceramides, Lc3- and Gg3Cer. An approximate three-dimensional structure for LcGg4Cer is proposed, consistent with all data obtained, which should be useful in discussing the results of 1H NMR analysis of compounds containing this core tetrasaccharide. The structure is characterized by an unusual arrangement of terminal N-acetylhexosamine residues, resulting in a pi-H hydrogen-bonding interaction between their acetamido groups.

Amides↗

Thromboxane synthetase inhibitors and antihypertensive agents. 1. N-[(1H-imidazol-1-yl)alkyl]aryl amides and N-[(1H-1,2,4-triazol-1-yl)alkyl]aryl amides.

The title compounds were prepared to investigate their potential as thromboxane synthetase inhibitors as well as antihypertensive agents. Imidazoles VIII and triazoles X were prepared to examine the effects of aromatic substitution, chain length, and heterocycle substitution upon biological activity. Imidazoles VIII and triazoles X were thromboxane synthetase inhibitors that did not inhibit prostacyclin formation. The most interesting thromboxane synthetase inhibitors prepared were 4-chloro-, 4-(trifluoromethyl)-, and 4-bromobenzamide derivatives of (1H-imidazol-1-yl)alkylamines with C5-C8 alkyl chains separating the heterocycle from the amide moiety, while the most active antihypertensive agents were 3- or 4-chloro-, -bromo, or -(trifluoromethyl)benzamides with C3 alkyl chains. The best thromboxane synthetase inhibitors in this study were up to 10 times more potent than the standard, dazoxiben (UK 37,248).

Amides↗

[Infrared spectra of erythrocyte shadows in the region of the amide I and amide II bands following microwave irradiation].

No beta-structures of protein molecules were observed by IR-spectra of intact erythrocyte shadows. Ultra high frequency irradiation in the range of 1009 mHz intensity of 45 mW/cm3 results in small conformational reconstructions of molecules in the membrane, but it does not induce a notable transition of alpha-helix or coil into beta-structure. A decrease of the intensity of lipid band by 1740 cm-1 is shown up at the spectra. Deuterium exchange for 36--38 min shows that the transition of the band amide II near 1540 cm-1 into the band 1450 cm-1 proceeds faster under UHF irradiation than in the control. The effects observed are in a direct relation-ship with the intensity of UHF-field and disappear at the intensities of 5--8 mW/cm3 and lower.

Amides↗

Fast racemisation and slow epimerisation of laterally lithiated amides: stereochemical evidence for the mechanism of inversion of amide-substituted benzyllithiums.

Tertiary 1-naphthamides racemise much more slowly than their laterally lithiated derivatives, and the relative rates of racemisation and epimerisation of these derivatives indicate that the lithium-bearing stereogenic centre inverts via a "conducted tour" mechanism, in which the lithium cation is delivered from one face to the other by coordination to the rotating amide group.

Journal Article↗

The novel kinase peptidylglycine alpha-amidating monooxygenase cytosolic interactor protein 2 interacts with the cytosolic routing determinants of the peptide processing enzyme peptidylglycine alpha-amidating monooxygenase.

The cytosolic domain of the peptide-processing integral membrane protein peptidylglycine alpha-amidating monooxygenase (PAM; EC 1.14. 17.3) contains multiple signals determining its subcellular localization. Three PAM cytosolic interactor proteins (P-CIPs) were identified using the yeast two hybrid system (Alam, M. R., Caldwel, B. D., Johnson, R. C., Darlington, D. N., Mains, R. E., and Eipper, B. A. (1996) J. Biol. Chem. 271, 28636-28640); the partial amino acid sequence of P-CIP2 suggested that it was a protein kinase. In situ hybridization and immunocytochemistry show that P-CIP2 is expressed widely throughout the brain; PAM and P-CIP2 are expressed in the same neurons. Based on subcellular fractionation, the 47-kDa P-CIP2 protein is mostly cytosolic. P-CIP2 is a highly selective kinase, phosphorylating the cytosolic domain of PAM, but not the corresponding region of furin or carboxypeptidase D. Although P-CIP2 interacts with stathmin, it does not phosphorylate stathmin. Site-directed mutagenesis, phosphoamino acid analysis, and use of synthetic peptides demonstrate that PAM-Ser(949) is the major site phosphorylated by P-CIP2. Based on both in vitro binding experiments and co-immunoprecipitation from cell extracts, P-CIP2 interacts with PAM proteins containing the wild type cytosolic domain, but not with mutant forms of PAM whose trafficking is disrupted. P-CIP2, through its highly selective phosphorylation of a key site in the cytosolic domain of PAM, appears to play a critical role in the trafficking of this protein.

Amino Acid Sequence↗