Cooperative Interactions of Oligosaccharide and Peptide Moieties of a Glycopeptide Derived from IgE with Galectin-9

We previously showed that galectin-9 suppresses degranulation of mast cells through protein-glycan interaction with IgE. To elucidate the mechanism of the interaction in detail, we focused on identification and structural analysis of IgE glycans responsible for the galectin-9-induced suppression using mouse monoclonal IgE (TIB-141). TIB-141 in combination with the antigen induced degranulation of RBL-2H3 cells, which was almost completely inhibited by human and mouse galectin-9. Sequential digestion of TIB-141 with lysyl endopeptidase and trypsin resulted in the identification of a glycopeptide (H-Lys13-Try3; 48 amino acid residues) with a single N-linked oligosaccharide near the N terminus capable of neutralizing the effect of galectin-9 and another glycopeptide with two N-linked oligosaccharides (H-Lys13-Try1; 16 amino acid residues) having lower activity. Enzymatic elimination of the oligosaccharide chain from H-Lys13-Try3 and H-Lys13-Try1 completely abolished the activity. Removal of the C-terminal 38 amino acid residues of H-Lys13-Try3 with glutamyl endopeptidase, however, also resulted in loss of the activity. We determined the structures of N-linked oligosaccharides of H-Lys13-Try1. The galectin-9-binding fraction of pyridylaminated oligosaccharides contained asialo- and monosialylated bi/tri-antennary complex type oligosaccharides with a core fucose residue. The structures of the oligosaccharides were consistent with the sugar-binding specificity of galectin-9, whereas the nonbinding fraction contained monosialylated and disialylated biantennary complex type oligosaccharides with a core fucose residue. Although the oligosaccharides linked to H-Lys13-Try3 could not be fully characterized, these results indicate the possibility that cooperative binding of oligosaccharide and neighboring polypeptide structures of TIB-141 to galectin-9 affects the overall affinity and specificity of the IgE-lectin interaction.     

A 13C-NMR study on the influxes into the tricarboxylic acid cycle of a renal epithelial cell line, LLC-PK1/Cl4: the metabolism of [2-13C]glycine, L-[3-13C]alanine and L-[3-13C]aspartic acid in renal epithelial cells

Perchloric acid extracts of LLC-PK1/Cl4 cells, a renal epithelial cell line, incubated with either [2-13C]glycine L-[3-13C]alanine, or D,L-[3-13C]aspartic acid were investigated by 13C-NMR spectroscopy. All amino acids, except labelled glycine, gave rise to glycolytic products and tricarboxylic acid cycle (TCA) intermediates. For the first time we also observed activity of gamma-glutamyltransferase activity and glutathione synthetase activity in LLC-PK1 cells, as is evident from enrichment of reduced glutathione. Time courses showed that only 6% of the labelled glycine was utilized in 30 min, whereas 31% of L-alanine and 60% of L-aspartic acid was utilized during the same period. 13C-NMR was also shown to be a useful tool for the determination of amino acid uptake in LLC-PK1 cells. These uptake experiments indicated that glycine, alanine and aspartic acid are transported into Cl4 cells via a sodium-dependent process. From the relative enrichment of the glutamate carbons, we calculated the activity of pyruvate dehydrogenase to be about 61% when labelled L-alanine was the only carbon source for LLC-PK1/Cl4 cells. Experiments with labelled D,L-aspartic, however, showed that about 40% of C-3-enriched oxaloacetate (arising from a de-amination of aspartic acid) reached the pyruvate pool.     

Consequences of introducing a disulfide bond into an antibacterial and hemolytic peptide.

The effect of introducing a disulfide bridge between the N- and C-terminal ends on the structure and biological activities of the 13-residue linear peptide PKLLKTFLSKWIG(SPFK), which has both antibacterial and hemolytic activity, have been investigated. The terminal amino acids P and G in SPFK were replaced by cysteines to form a disulfide bridge. The linear peptides C(Acm)KLLKTFLSKWIC(Acm) and C(Acm) KLLKTFLSKWIC(Acm)-amide, where Acm is acetamidomethyl group, showed antibacterial activity but did not possess hemolytic activity unlike SPFK. Introduction of an S-S bridge resulted in enhanced hemolytic activity compared with SPFK. The hemolytic activity was particularly pronounced in the cyclic peptide CKLLKTFLSKWIC-amide. Circular dichroism studies indicate that the cyclic peptides tend to adopt distorted helical structures. The cyclic peptides also have a greater affinity for lipid vesicles, which could be the reason for the effective perturbation of the erythrocyte membrane.     

A three-phase liquid chromatographic method for δC analysis of amino acids from biological protein hydrolysates using liquid chromatography–isotope ratio mass spectrometry

We report a three-phase chromatographic method for the separation and analysis of δ¹³C values of underivatized amino acids from biological proteins (keratin, collagen, and casein) using liquid chromatography–isotope ratio mass spectrometry (LC–IRMS). Both precision and accuracy of δ¹³C values for standard amino acid mixtures over the range of approximately 8 to 1320 ng of carbon per amino acid on the column were assessed. The precision of δ¹³C values of amino acids was found to be better at higher concentrations, whereas accuracy improved at lower concentrations. The optimal performance for this method was achieved with between 80 and 660 ng of carbon of each amino acid on the column. At amino acid amounts lower than 20 ng of carbon on the column, precision and accuracy may become compromised. The application of this new three-phase chromatographic technique will allow the analysis of δ¹³C of amino acids to be carried out as a routine method and benefit fields of research such as biomedicine, forensics, ecology, nutrition, and palaeodiet reconstruction in archaeology.     

Selective and extensive 13C labeling of a membrane protein for solid-state NMR investigations

The selective and extensive 13C labeling of mostly hydrophobic amino acid residues in a 25 kDa membrane protein, the colicin Ia channel domain, is reported. The novel 13C labeling approach takes advantage of the amino acid biosynthetic pathways in bacteria and suppresses the synthesis of the amino acid products of the citric acid cycle. The selectivity and extensiveness of labeling significantly simplify the solid-state NMR spectra, reduce line broadening, and should permit the simultaneous measurement of multiple structural constraints. We show the assignment of most 13C resonances to specific amino acid types based on the characteristic chemical shifts, the 13C labeling pattern, and the amino acid composition of the protein. The assignment is partly confirmed by a 2D homonuclear double-quantum-filter experiment under magic-angle spinning. The high sensitivity and spectral resolution attained with this 13C-labeling protocol, which is termed TEASE for ten-amino acid selective and extensive labeling, are demonstrated.     

Stable isotope labeling of Arabidopsis thaliana cells and quantitative proteomics by mass spectrometry

Quantitative analysis of protein expression is an important tool for the examination of complex biological systems. Albeit its importance, quantitative proteomics is still a challenging task because of the high dynamic range of protein amounts in the cell and the variation in the physical properties of proteins. Stable isotope labeling by amino acids in cell culture (SILAC) has been successfully used in yeast and mammalian cells to measure relative protein abundance by mass spectrometry. Here we show for the first time that proteins from Arabidopsis thaliana cell cultures can be selectively isotope-labeled in vivo by growing cells in the presence of a single stable isotope-labeled amino acid. Among the tested amino acids ([2H3]-leucine, [13C6]arginine, and [2H4]lysine), [13C6]arginine proved to be the most suitable. Incorporation of [13C6]arginine into the proteome was homogeneous and reached efficiencies of about 80%. [13C6]Arginine-labeled A. thaliana suspension cells were used to study the regulation of glutathione S-transferase expression in response to abiotic stress caused by salicylic acid and to identify proteins that bind specifically to phosphorylated 14-3-3 binding motifs on synthesized bait peptides in affinity purification experiments. In conclusion, the combination of stable isotope labeling of plant cells and mass spectrometry is a powerful technology that can be applied to study complex biological processes that involve changes in protein expression such as cellular responses to various kinds of stress or activation of cell signaling.     

Intramolecularly hydrogen-bonded peptide conformations

Over the past few years the possible occurrence of intramolecularly hydrogen-bonded structures in linear and cyclic peptides has attracted increasing attention. In this review emphasis is given to solid-state studies, particularly by X-ray diffraction and infrared absorption techniques. Conformational energy calculations are also considered. The discussion is focused both on model peptides and biological activity polypeptide molecules. The tetrapeptide system (Formula: see text), examined allows one to discuss the extended C5 structure and the various folded conformations, namely the C7 (gamma-turn), C8, C10 (beta-turn), C11, and C13 conformations. The four latter forms may include cis peptide configurations. The oxy-analogs to the C7, C10, and C13 conformations and structures containing bifurcated hydrogen bonds are also discussed. The last sections describe intramolecularly hydrogen-bonded peptide structures involving: (1) a side-chain group, (2) the N-protecting group (in synthetic model compounds), and (3) a beta-amino acid.     

1H, 13C, and 15N NMR assignments and global folding pattern of the RNA-binding domain of the human hnRNP C proteins.

The hnRNP C1 and C2 proteins are abundant nuclear proteins that bind avidly to heterogeneous nuclear RNAs (hnRNAs) and appear to be involved with pre-mRNA processing. The RNA-binding activity of the hnRNP C proteins is contained in the amino-terminal 94 amino acid RNA-binding domain (RBD) that is identical for these two proteins. We have obtained the 1H, 13C, and 15N NMR assignments for the RBD of the human hnRNP C proteins. The assignment process was facilitated by extensive utilization of three- and four-dimensional heteronuclear-edited spectra. Sequential assignments of the backbone resonances were made using a combination of 15N-edited 3D NOESY-HMQC, 3D TOCSY-HMQC, and 3D TOCSY-NOESY-HSQC as well as 3D HNCA, HNCO, and HCACO spectra. Side-chain resonances were assigned using 3D HCCH-COSY and 3D HCH-TOCSY spectra. Four-dimensional 13C/13C-edited NOESY and 13C/15N-edited NOESY experiments were used to unambigously resolve NOEs. The overall global folding pattern was established by calculating a set of preliminary structures using constraints derived from the sequential NOEs and a small number of long-range NOEs. The beta alpha beta-beta alpha beta domain structure exhibits an antiparallel beta-sheet with the conserved RNP 1 and RNP 2 sequences [Dreyfuss et al. (1988) Trends Biochem. Sci. 13, 86-91] located adjacent to one another as the two inner strands of the beta-sheet.     

Role of lysine residues in membrane anchoring of saposin C

Molecular dynamics (MD) simulations of the N-terminal region of saposin C, containing amino acid residues 4-20 (saposin C4-20), were performed over 2.5 ns in 1,2-dioleoyl-sn-glycero-3-phosphoserine (DOPS) and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) monolayers. The simulations revealed several strong specific interactions of lysine 13 (Lys13) and lysine 17 (Lys17) in saposin C4-20 with the anionic phospholipids, which are required for membrane anchoring of the peptide. Membrane anchoring of saposin C4-20 facilitates saposin C-induced liposomal membrane fusion. Substitutions of Lys13 or Lys17 with alanine or glutamic acid led to a substantial loss of saposin C's fusogenicity. However, arginine replacement of Lys13 or Lys17 caused a partial loss of saposin C's fusogenic activity. The membrane anchoring of saposin C was altered in the presence of 0.4 M sodium chloride. Differential salt effects on Lys-mutant saposin Cs were observed using Trp fluorescence analysis. Low salt concentration had a more significant impact on Lys-mutant saposin C with a negatively charged amino acid residue replacement than those mutants with a positively charged or neutral residue replacement. These results indicate that positively charged amino acids at positions 13 and 17 are required for the fusogenic function of saposin C. In addition, the side-chain structure of lysine is crucial to the precise membrane anchoring which is necessary for the total fusion activity of saposin C. The MD simulations and vesicle size measurements of lysine-mutant saposins confirm the importance of the two lysine residues in saposin C4-20 for saposin C-induced fusion of negatively charged phospholipid membranes.     

The effect of docosahexaenoic acid moiety on the cytotoxic activity of 1,2,4-thiadiazole derivatives

Among 3-(2-aminopropyl)-1,2,4-thiadiazole derivatives containing substitutable secondary amino group and exhibiting cytotoxic activity towards rat C6 glioma cells three compounds with LD₅₀ values ranged from 6 to 48 μM have been chosen. For these compounds amides with docosahexaenoic acid were synthesized and their cytotoxic activity was studied. It was shown that, although docosahexaenoic acid itself was not toxic for C6 glioma cells, its addition to the amino derivatives of 1,2,4-thiadiazole increased or decreased their cytotoxicity. These results demonstrate that acylation of cytotoxic compounds with docosahexaenoic acid does not necessarily lead to the increase of their activity and sometimes can inactivate a parent compound. This fact should be taken into consideration because of possibility of biological attachment of docosahexaenoic acid to the amino group of anti-cancer drugs.     

Isolation and structure determination of a paralytic peptide from the hemolymph of the silkworm, Bombyx mori.

A peptide with paralytic activity in larvae of the silkworm, Bombyx mori, was isolated from its hemolymph. Purification procedures consisted of extraction with 50% acetone, Vydac C4 reversed-phase cartridge elution and 4 steps of reversed-phase HPLC. Injection of the purified peptide into 4th instar B. mori larvae caused rapid and rigid paralysis for 2 min at a dose of 3.4 ng/larva. This paralytic peptide consists of 23 amino acid residues containing 2 cysteines with an intra-disulfide bond. The complete amino acid sequence is: H-Glu-AsnPhe-Val-Gly-Gly-Cys-Ala-Thr-Gly-Phe-Lys-Arg-Thr-Ala-Asp-G ly-Arg-Cys-Lys-Pro-Thr-Phe-OH. The relationship between structure and the biologic activity of synthetic analogs indicated that the entire amino acid sequence and the intra-disulfide bond were necessary for biological activity.     

A C-NMR study on the influxes into the tricarboxylic acid cycle of a renal epithelial cell line, LLC-PK1/Cl4: the metabolism of [2-C]glycine, l-[3-C]alanine and l-[3-C]aspartic acid in renal epithelial cells

Perchloric acid extracts of LLC-PK₁/Cl₄ cells, a renal epithelial cell line, incubated with either [2-¹³C]glycine l-[3-¹³C]alanine, or d,l-[3-¹³C]aspartic acid were investigated by ¹³C-NMR spectroscopy. All amino acids, except labelled glycine, gave rise to glycolytic products and tricarboxylic acid cycle (TCA) intermediates. For the first time we also observed activity of γ-glutamyltransferase activity and glutathione synthetase activity in LLC-PK₁ cells, as is evident from enrichment of reduced glutathione. Time courseS showed that only 6% of the labelled glycine was utilized in 30 min, whereas 31% of l-alanine and 60% of l-aspartic acid was utilized during the same period. ¹³C-NMR was also shown to be a useful tool for the determination of amino acid uptake in LLC-PK₁ cells. These uptake experiments indicated that glycine alanine and aspartic acid are transported into Cl₄ cells via a sodium-dependent process. From the relative enrichment of the glutamate carbons, we calculated the activity of pyruvate dehydrogenase to be about 61% of when labelled l-alanine was the only carbon source for LLC-PK₁/Cl₄ cells. Experiments with labelled d,l-aspartic, however, showed that about 40% of C-3-enriched oxaloacetate (arising from a de-amination of aspartic acid) reached the pyruvate pool.     

Studies of structure-activity relations of complement inhibitor compstatin

Compstatin, a 13-mer cyclic peptide, is a novel and promising inhibitor of the activation of the complement system. In our search for a more active analog and better understanding of structure-functions relations, we designed a phage-displayed random peptide library based on previous knowledge of structure activity relations, in which seven amino acids deemed necessary for structure and activity were kept fixed while the remaining six were optimized. Screening of this library against C3 identified four binding clones. Synthetic peptides corresponding to these clones revealed one analog, called acetylated Ile(1)Leu/His(9)Trp/Thr(13)Gly triple replacement analog of compstatin corresponding to clone 640 (Ac-I1L/H9W/T13G), which was more active than compstatin. This newly identified peptide had 4-fold higher activity when compared with the originally isolated form of compstatin and 1.6-fold higher activity when compared with acetylated compstatin (Ac-compstatin). The structures of Ac-I1L/H9W/T13G and Ac-compstatin were studied by nuclear magnetic resonance, compared with the structure of compstatin, and found to be very similar. The binding of Ac-I1L/H9W/T13G and the equally active acetylated analog with His(9)Ala replacement (Ac-H9A) to C3 was evaluated by surface plasmon resonance, which suggested similarity in their binding mechanism but difference when compared with Ac-compstatin. Compensatory effects of flexibility outside the beta-turn and tryptophan ring stacking may be responsible for the measured activity increase in Ac-I1L/H9W/T13G and acetylated analog with His(9)Ala replacement and the variability in binding mechanism compared with Ac-compstatin. These data demonstrate that tryptophan is a key amino acid for activity. Finally, the significance of the N-terminal acetylation was examined and it was found that the hydrophobic cluster at the linked termini of compstatin is essential for binding to C3 and for activity.     

Protein kinase C activators selectively inhibit insulin-stimulated system A transport activity in skeletal muscle at a post-receptor level.

We have investigated the role of phorbol esters on different biological effects induced by insulin in muscle, such as activation of system A transport activity, glucose utilization and insulin receptor function. System A transport activity was measured by monitoring the uptake of the system A-specific analogue alpha-(methyl)aminoisobutyric acid (MeAIB), by intact rat extensor digitorum longus muscle. The addition of 12-O-tetradecanoylphorbol 13-acetate (TPA, 0.5 microM) for 60 or 180 min did not modify basal MeAIB uptake by muscle, suggesting that insulin signalling required to stimulate MeAIB transport does not involve protein kinase C activation. However, TPA added 30 min before insulin (100 nM) markedly inhibited insulin-stimulated MeAIB uptake. The addition of polymyxin B (0.1 mM) or H-7 (1 mM), protein kinase C inhibitors, alone or in combination with TPA leads to impairment of insulin-stimulated MeAIB uptake. This paradoxical pattern is incompatible with a unique action of Polymyxin B or H-7 on protein kinase C activity. Therefore these agents are not suitable tools with which to investigate whether a certain insulin effect is mediated by protein kinase C. TPA did not cause a generalized inhibition of insulin action. Thus both TPA and insulin increased 3-O-methylglucose uptake by muscle, and their effects were not additive. Furthermore, TPA did not modify insulin-stimulated lactate production by muscle. In keeping with this selective modification of insulin action, treatment of muscles with TPA did not modify insulin receptor binding or kinase activities. In conclusion, phorbol esters do not mimic insulin action on system A transport activity; however, they markedly inhibit insulin-stimulated amino acid transport, with no modification of insulin receptor function in rat skeletal muscle. It is suggested that protein kinase C activation causes a selective post-receptor modification on the biochemical pathway by which insulin activates system A amino acid transport in muscle.     

Purification of peptide hormones from chinchilla pancreas by chemical assay

Glucagon was purified from chinchilla pancreas and its biological activity determined. It was isolated using a chemical assay to identify peptides with a histidyl residue at the N-terminus. Chinchilla glucagon has the amino acid sequence HSQGTFTSDYSKHLDSRYAQEFVQWLMNT. It differs from the usual mammalian glucagon by amino acid substitutions at positions 13, 18 and 21 from the N-terminus. Despite these sequence changes, its biological activity is conserved. Chinchilla glucagon has approximately the same potency as pig glucagon in stimulating liver membrane adenyl cyclase activity. Pancreatic polypeptide was also purified from chinchilla pancreas based on its Ala1 signal and has the sequence APLEPVYPGDNATPEQMAQYAAEMRRYINMLTRPRY#.     

Patterns of intramolecular carbon isotopic heterogeneity within amino acids of autotrophs and heterotrophs

A survey of the intramolecular C isotopic composition of a variety of organisms was conducted to investigate the potential of intramolecular isotopic measurements as a tracer of biological or geochemical processes. Based on a consideration of inorganic C sources and enzymatic fractionations, contrasting predictions were made for the relative ¹³C enrichments of the -carboxyl carbons fixed by the anapleurotic ()-carboxylation pathway during amino acid synthesis by photoautotrophs and heterotrophs. To test the model predictions, the stable C isotopic compositions of the acid hydrolyzable C fraction, the total amino acid -carboxyl C fraction and the -carboxyl C of glutamate from a variety of autotrophic and heterotrophic organisms were compared. The relative ¹³C enrichments of carboxyl carbons in the bulk amino acid fraction and in glutamate conformed qualitatively to model predictions. Macroalgal taxa possessed a significantly less enriched carboxyl C fraction than did either C3 or C4 vascular plants, indicating the presence of a different -carboxylation pathway operating in these organisms. In most multicellular heterotrophs, the isotopic composition of the amino acid carboxyl carbons closely resembled that of their food sources. Amino acids are apparently assimilated into tissue proteins directly from their diets without significant metabolic modification. However, shifts in the isotopic composition of the carboxyl C fractions in some organisms were detected that were consistent with the occurrence of significant resynthesis of amino acids from non-amino acid precursors. Comparison of plant leaves and roots provided evidence of environmentally controlled assimilate partitioning. Intramolecular isotopic measurements of biological molecules provide unique insights into the origins and transformations of bio-molecules.     

N-terminal portion of motilin determines its biological activity.

This study aimed to identify the portion of the 22 amino acid sequence of motilin responsible for the biological activity of the peptide. The contraction of rabbit duodenal muscle in vitro was measured when exposed to synthetic fragments of motilin corresponding to various sequences of the C- or N-terminal portions of the molecule. Fragments 2-22 or 3-22 (where the initial amino acids of the N-terminal ending were removed) were more than 1000 times less potent than the native molecule 1-22. Fragment 1-9 (where the last 13 amino acids located at the C-terminal side of motilin were removed) was devoid of any contractile capacity, while synthetic fragments whose C-terminal structure extended beyond the 1-9 motilin sequence maintained almost complete biological activity. N-terminal amino acid sequence 1-9 is therefore an essential determinant of the contractile activity of motilin.     

In vivo biological potency of rat and human growth hormone-releasing factor and fragments of human growth hormone-releasing factor

The biological potency of the synthetic replicates of three peptides isolated from a human pancreatic tumor with growth hormone releasing activity and rat hypothalamic growth hormone-releasing factor was evaluated in conscious freely-moving rats and anesthetized rats. All 4 peptides are equipotent on a molar basis in their ability to stimulate GH secretion. Studies with synthetic fragments of the human derived material indicated that the amino-terminal amino acid is required for activity. Deletion of as many as 13 amino acids from the carboxy-terminal failed to decrease GH-releasing activity; however, deletion of 16 amino acids resulted in a significant decrease and deletion of 20 amino acids resulted in complete loss of bioactivity.     

Arginine acts as a protective and reversal agent against glycolytic inhibitors in spermatozoa.

It is known that the amino acid arginine stimulates sperm motility and glycolytic activity. We have earlier studied its efficacy as a stimulator of glycolysis in goat spermatozoa under anaerobic conditions. Here, we have assessed the influence of arginine in reversing the impairment caused by glycolytic inhibitors, iodoacetamide and iodoacetic acid. Glycolysis has been monitored by measuring the consumption of 13C labeled glucose and the amount of 13C labeled lactate produced under different experimental conditions, using 13C NMR. It is observed that both L- and D-arginine are able to prevent and reverse the inhibitory action of glycolytic inhibitors. The reversal effect of arginine gives rise to about eight times higher metabolic activity as compared to the inhibited cells while structurally related amino acids such as nitro-arginine, homo-arginine, lysine and ornithine are ineffective. The energetics of spermatozoa as measured by 31P NMR show a reduction in ATP level in cells incubated with iodoacetamide. Treatment of these cells with both L- and D-arginine restores the ATP level. The results may have significance in the treatment of male infertility.     

Synthetic analogues of antimicrobial peptides from the venom of the Central Asian spider Lachesana tarabaevi

Analogues of latarcins Ltc1 and Ltc3b, antimicrobial peptides from the venom of the Central Asian spider Lachesana tarabaevi capable of formation of amphiphilic structures in membranes without involvement of disulfide bonds, were synthesized. The amino acid sequences of the analogues correspond to immature forms of these peptides, each of them containing an additional C-terminal amino acid residue. It is concluded from the study of the biological activity of the synthesized peptides that the posttranslational C-terminal amidation of Ltc3b is a functionally important modification that ensures a high activity of the mature peptide. The lipid composition was shown to affect the interaction of synthesized peptides with artificial membranes. The analogue of Ltc3b manifested the highest activity on cholesterol-containing membranes. The mechanism of action of the studied antimicrobial peptides on membranes is discussed.