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Studies on a wide-spectrum intestinal dipeptide uptake system in the monkey and in the human.

1. The intestinal transport of glycine and leucine residues of glycyl-L-leucine was studied in the monkey and in the human in vitro. Uptake of both [14C]glycyl-L-leuine and glycyl-L-[14C]leucine show similar Kt values, but there is a marked difference in the Vmax. values. Preliminary studies suggest that this anomalous difference in the Vmax. values may be due to the greater efflux rate of glycine from the tissue. 2. Arrhenius plots of both [14C]glycyl-L-leucine uptake and glycyl-L-[14C]leucine uptake in the monkey intestine show a discontinuity at about 20 degrees C. The activation energies above and below the discontinuity are similar for both [14C]glycyl-L-leucine uptake and glycyl-L-[14C]leucine uptake. These similarities in uptake characteristics suggest that the dipeptide glycyl-L-leucine is transported as one unit. 3. In the monkey intestine, glycyl-L-leucine uptake is inhibited by a wide variety of dipeptides, including those containing acidic and basic amino acids. The inhibition was shown to be competitive by using four representative dipeptides namely: L-alanyl-L-alanine, L-alanyl-L-leucine, L-glutamyl-L-glutamic acid and L-lysyl-L-lysine. The results strongly suggest that in the monkey intestine there may be a dipeptide-uptake system with an extremely broad specificity. These results were also confirmed in the human in a limited way.

Alanine↗

A molecular dynamics study of the dielectric properties of aqueous solutions of alanine and alanine dipeptide.

Molecular dynamics simulations were used to compute the frequency-dependent dielectric susceptibility of aqueous solutions of alanine and alanine dipeptide. We studied four alanine solutions, ranging in concentration from 0.13-0.55 mol/liter, and two solutions of alanine dipeptide (0.13 and 0.27 mol/liter). In accord with experiment we find a strong dielectric increment for both solutes, whose molecular origin is shown to be the zwitterionic nature of the solutes. The dynamic properties were analyzed based on a dielectric component analysis into solute, a first hydration shell, and all remaining (bulk) waters. The results of this three component decomposition were interpreted directly, as well as by uniting the solute and hydration shell component to a "suprasolute" component. In both approaches three contributions to the frequency-dependent dielectric properties can be discerned. The quantitatively largest and fastest component arises from bulk water [i.e., water not influenced by the solute(s)]. The interaction between waters surrounding the solute(s) (the hydration shell) and bulk water molecules leads to a relaxation process occurring on an intermediate time scale. The slowest relaxation process originates from the solute(s) and the interaction of the solute(s) with the first hydration shell and bulk water. The primary importance of the hydration shell is the exchange of shell and bulk waters; the self-contribution from bound water molecules is comparatively small. While in the alanine solutions the solute-water cross-terms are more important than the solute self-term, the solute contribution is larger in the dipeptide solutions. In the latter systems a much clearer separation of time scales between water and alanine dipeptide related properties is observed. The similarities and differences of the dielectric properties of the amino acid/peptide solutions studied in this work and of solutions of mono- and disaccharides and of the protein ubiquitin are discussed.

Alanine↗

Two initiation sites detected in the small s1 species of reovirus mRNA by dipeptide synthesis in vitro.

Reovirus mRNAs directed the synthesis of fMet dipeptides in a translation initiation system reconstituted from rabbit reticulocyte initiation and elongation factors, Artemia salina 80S ribosomes, yeast fMet-tRNAiMet and Escherichia coli3H-labeled aminoacyl tRNAs. As predicted from the GC(U,G) codon that follows the 5'-proximal AUG in half of the viral mRNA species, fMet-Ala was the predominant dipeptide product obtained in response to a mixture of mRNAs or to the separated size classes of medium (m) and small (s) mRNA. The four individual small mRNA species each directed the synthesis of an fMet dipeptide that was consistent with the utilization of the 5'-proximal AUG for initiation. In addition to fMet-Asp, the s1 mRNA also directed fMet-Glu synthesis indicative of initiation in a second reading frame at the 5'-penultimate AUG. The tripeptide fMet-Glu-Tyr was also synthesized from s1 mRNA, which further verified this second initiation site. mRNAs containing 5'-terminal GpppG were 10-15% as active as the corresponding m7G-capped templates. The dipeptide assay provides a rapid method for determining initiation sites in individual mRNAs or in mixtures of mRNAs.

Amino Acid Sequence↗

An active mechanism for completion of the final stage of protein degradation in the liver, lysosomal transport of dipeptides.

Accumulation of products of proteolysis (e.g. dipeptides) in lysosomes may have pathological consequences. In the present experiment we have investigated the existence of a dipeptide transporter in a membrane preparation of liver lysosomes using Gly-3H-Gln as the probe. The results showed that (a) there was transport of Gly-Gln into an osmotically reactive space inside the lysosomal membrane vesicles; (b) transport was stimulated by acidification (pH 5.0) of the external medium; (c) there was a coupling between transport of protons and Gly-Gln with a stoichiometry of 1:1; (d) the presence of both acidic pH and membrane potential was necessary for uphill transport of Gly-Gln; (e) a single transporter with a Km of 4.67 mM mediated the uptake of Gly-Gln; and (f) Gly-Gln uptake was inhibited by dipeptides and tripeptides but not by amino acids. The results suggest the presence of a low affinity proton-coupled oligopeptide transporter in the liver lysosomal membrane which mediates transfer of dipeptides from a region of low dipeptidase activity (intralysosome) to a region of high dipeptidase activity (cytosol). In this manner, the transporter provides an active mechanism for completion of the final stage of protein degradation.

Amino Acids↗

A dipeptide metalloendoprotease substrate completely blocks the response of cells in culture to cholera toxin.

Prior exposure (15 min at 37 degrees C) of several cell types (Vero, SH-SY5Y neuroblastoma, human intestinal epithelial T84) to 3 mm N-benzoyloxycarbonyl-Gly-Phe-amide (Cbz-Gly-Phe-NH(2)), a competitive substrate for metalloendoproteases, completely suppressed cholera toxin (CT)-induced intracellular cAMP accumulation. The specificity of the inhibitory effect was demonstrated by the complete lack of effect of the dipeptide Cbz-Gly-Gly-NH(2), an inactive analogue of Cbz-Gly-Phe-NH(2). The effect was reversible and dose- (IC(50) as low as 0.2 mm depending on the cell type) and time-dependent. Adding Cbz-Gly-Phe-NH(2) during the lag phase caused a diminution of its inhibitory effect similar to that observed with brefeldin A (BFA). Whereas the dipeptide completely suppressed the CT-induced adenylate cyclase (AC) activity, a direct effect on AC is unlikely since the elevation of intracellular cAMP by forskolin was only slightly reduced. The A(1) peptide of CT and NAD(+) activated the AC to the same extent in membranes from control and Cbz-Gly-Phe-NH(2)-treated cells or when Cbz-Gly-Phe-NH(2) was added directly to the assay. The inhibitory effects of suboptimal amounts of Cbz-Gly-Phe-NH(2) and BFA were not additive pointing to a similar mode of action of the two substances. However, Madin-Darby canine kidney cells of which the Golgi structure is BFA-resistant were not resistant to the inhibitory action of Cbz-Gly-Phe-NH(2) on CT cytotoxicity. Several lines of evidence indicate that a perturbation of intracellular Ca(2+) homeostasis by Cbz-Gly-Phe-NH(2) is not responsible for the inhibitory effect of the dipeptide. The dipeptide had also no effect on the binding of (125)I-CT to cells and even increased its intracellular internalization. In contrast with BFA, Cbz-Gly-Phe-NH(2) did not completely suppress the formation of the catalytically active A(1) fragment from bound CT. The data are compatible with a role of metalloendoprotease activity in the intracellular trafficking and processing of CT, although other mechanisms of action of Cbz-Gly-Phe-NH(2) cannot be excluded.

Adenylyl Cyclases↗

Classification of nuclear receptors based on amino acid composition and dipeptide composition.

Nuclear receptors are key transcription factors that regulate crucial gene networks responsible for cell growth, differentiation, and homeostasis. Nuclear receptors form a superfamily of phylogenetically related proteins and control functions associated with major diseases (e.g. diabetes, osteoporosis, and cancer). In this study, a novel method has been developed for classifying the subfamilies of nuclear receptors. The classification was achieved on the basis of amino acid and dipeptide composition from a sequence of receptors using support vector machines. The training and testing was done on a non-redundant data set of 282 proteins obtained from the NucleaRDB data base (1). The performance of all classifiers was evaluated using a 5-fold cross validation test. In the 5-fold cross-validation, the data set was randomly partitioned into five equal sets and evaluated five times on each distinct set while keeping the remaining four sets for training. It was found that different subfamilies of nuclear receptors were quite closely correlated in terms of amino acid composition as well as dipeptide composition. The overall accuracy of amino acid composition-based and dipeptide composition-based classifiers were 82.6 and 97.5%, respectively. Therefore, our results prove that different subfamilies of nuclear receptors are predictable with considerable accuracy using amino acid or dipeptide composition. Furthermore, based on above approach, an online web service, NRpred, was developed, which is available at www.imtech.res.in/raghava/nrpred.

Amino Acid Sequence↗

Synthesis and evaluation of dipeptide amides containing N omega-nitroarginine and D-2,4-diaminobutyric acids as inhibitors of neuronal nitric oxide synthase.

Selective inhibition of the isoforms of nitric oxide synthase (NOS) could be beneficial in the treatment of certain disease states arising from the overproduction of nitric oxide by NOS. Recently, we reported dipeptide amides containing a basic amine side chain as potent and selective inhibitors of neuronal NOS (Huang H. et al. (1999) J. Med. Chem., 42, 3147). The most potent nNOS inhibitor among these compounds is L-ArgNO2-L-Dbu-NH2 (1) (Ki = 130 nM), which also exhibits the highest selectivity over eNOS (> 1500-fold). The D,D-dipeptide, D-Lys-D-ArgNO2-NH2 (3) also shows high potency and selectivity. Here the dipeptide amides containing ArgNO2 and D-Dbu (9-12) were synthesized and evaluated. They are all modest inhibitors of nNOS, but poor inhibitors of eNOS and iNOS. D-Dbu-D-ArgNO2-NH2 (12) exhibits decreased inhibitory potency as compared with 3. A hypothesis regarding the binding at the active site of nNOS is proposed to explain the potency differences between the L- and D-form dipeptide amides.

Amides↗

Hydrolysis of proline dipeptides completely fulfills the proline requirement in a proline-auxotrophic Chinese hamster ovary cell line.

Proline- and hydroxyproline-containing oligopeptides may be important in protein nutrition because intestinal hydrolases are incapable of recognizing their imido bonds. Peripheral tissues have a cytosolic enzyme prolidase that cleaves dipeptides containing C-terminal proline (X-Pro) or hydroxyproline. The role of dipeptides in intracellular metabolism is uncertain. This study examined the ability of X-Pro to provide proline to the proline-auxotrophic cell line, CHO-K1. The action of prolidase on exogenously supplied Gly-Pro, the most abundant dipeptide product of digestion, provided adequate proline to support normal cell growth of CHO-K1 cells in a dose-dependent manner. The growth curve generated by addition of Gly-Pro to CHO-K1 cells was similar to that due to proline. Two other structurally unrelated X-Pro also supported growth indistinguishably from Gly-Pro. Gly-Hyp was completely ineffective for growth. The ability of X-Pro to sustain cultures of a proline-auxotrophic cell line may be important in elucidating intracellular nutritional and physiological functions for those dipeptides.

Animals↗

ESLpred: SVM-based method for subcellular localization of eukaryotic proteins using dipeptide composition and PSI-BLAST.

Automated prediction of subcellular localization of proteins is an important step in the functional annotation of genomes. The existing subcellular localization prediction methods are based on either amino acid composition or N-terminal characteristics of the proteins. In this paper, support vector machine (SVM) has been used to predict the subcellular location of eukaryotic proteins from their different features such as amino acid composition, dipeptide composition and physico-chemical properties. The SVM module based on dipeptide composition performed better than the SVM modules based on amino acid composition or physico-chemical properties. In addition, PSI-BLAST was also used to search the query sequence against the dataset of proteins (experimentally annotated proteins) to predict its subcellular location. In order to improve the prediction accuracy, we developed a hybrid module using all features of a protein, which consisted of an input vector of 458 dimensions (400 dipeptide compositions, 33 properties, 20 amino acid compositions of the protein and 5 from PSI-BLAST output). Using this hybrid approach, the prediction accuracies of nuclear, cytoplasmic, mitochondrial and extracellular proteins reached 95.3, 85.2, 68.2 and 88.9%, respectively. The overall prediction accuracy of SVM modules based on amino acid composition, physico-chemical properties, dipeptide composition and the hybrid approach was 78.1, 77.8, 82.9 and 88.0%, respectively. The accuracy of all the modules was evaluated using a 5-fold cross-validation technique. Assigning a reliability index (reliability index > or =3), 73.5% of prediction can be made with an accuracy of 96.4%. Based on the above approach, an online web server ESLpred was developed, which is available at http://www.imtech.res.in/raghava/eslpred/.

Artificial Intelligence↗

Substrate specificity of the periplasmic dipeptide-binding protein from Escherichia coli: experimental basis for the design of peptide prodrugs.

Pure dipeptide-binding protein (DppA) from Escherichia coli was studied in a filter binding assay to determine its binding specificity. A substrate:DppA stoichiometry of 1:1 was found with both [14C]AlaAla and Ala[14C]Phe. Surprisingly, substrate binding did not vary over the pH range pH 3-9.5. Different dipeptides yielded liganded protein with various pI values, implying that DppA can undergo subtly different conformational changes to accommodate different substrates. Using [125I]Tyr-peptides as substrates in competition assays, the relative binding affinities for a range of dipeptides were found to parallel their overall transport rates into E. coli through the dipeptide permease (Dpp), showing that DppA alone controls the specificity of Dpp. With a series of substituted glycyl peptides, binding affinity was progressively enhanced by alkylation (with methyl to butyl) of the N-terminal alpha-amino group. Thus, results from this approach provide an essential experimental basis, which complements the information from the crystal structure of DppA, for the design of peptidomimetic antibacterials targeted for transport through Dpp.

Amino Acids, Branched-Chain↗

Conformation and structure of acidic dipeptides. Crystal structure of glycyl-L-aspartic acid dihydrate.

The crystal structure of the acidic dipeptide glycyl-L-aspartic acid dihydrate, Gly-L-Asp X 2H2O, C6H10N2O5 X 2H2O, has been determined by means of three-dimensional counter X-ray data. The dipeptide crystallizes in space group P212121 of the orthorhombic system with four formula units in a cell of dimensions of a = 9.611(4), b = 9.775(6), and c = 10.845(4)A. The structure was solved by direct methods and refined by least-squares methods to a final value of the weighted R-factor of 0.035 using all 1191 observed intensity data. The dipeptide occurs in the crystal as a zwitterion, with the glycyl N-terminus protonated and the aspartyl main chain carboxyl group deprotonated. The conformation about the peptide bond is fully trans extended, with an omega angle of -175.9 degrees. While there is extensive intermolecular hydrogen bonding in the crystals, there is no intramolecular hydrogen bonding either here or in the solid state structures of related dipeptides.

Dipeptides↗

Specific inhibition of endopeptidase 24.16 by dipeptides.

The inhibitory effect of various dipeptides on the neurotensin-degrading metallopeptidase, endopeptidase 24.16, was examined. These dipeptides mimick the Pro10-Tyr11 bond of neurotensin that is hydrolyzed by endopeptidase 24.16. Among a series of Pro-Xaa dipeptides, the most potent inhibitory effect was elicited by Pro-Ile (Ki approximately 90 microM) with Pro-Ile greater than Pro-Met greater than Pro-Phe. All the Xaa-Tyr dipeptides were unable to inhibit endopeptidase 24.16. The effect of Pro-Ile on several purified peptidases was assessed by means of fluorigenic assays and HPLC analysis. A 5 mM concentration of Pro-Ile does not inhibit endopeptidase 24.11, endopeptidase 24.15, angiotensin-converting enzyme, proline endopeptidase, trypsin, leucine aminopeptidase, pyroglutamyl aminopeptidase I and carboxypeptidase B. The only enzyme that was affected by Pro-Ile was carboxypeptidase A, although it was with a 50-fold lower potency (Ki approximately 5 mM) than for endopeptidase 24.16. By means of fluorimetric substrates with a series of hydrolysing activities, we demonstrate that Pro-Ile can be used as a specific inhibitor of endopeptidase 24.16, even in a complex mixture of peptidase activities such as found in whole rat brain homogenate.

Amino Acid Sequence↗

Scavenging of singlet molecular oxygen by imidazole compounds: high and sustained activities of carboxy terminal histidine dipeptides and exceptional activity of imidazole-4-acetic acid.

Singlet molecular oxygen was generated by illumination of phenosafranin in phosphate buffer at pH 7.5. Relative efficiencies of various imidazole compounds to form endoperoxides were assayed by following at 25 degrees C the rate of light- and imidazole-dependent bleaching of N,N-dimethyl-4-nitrosoaniline. Of over 30 imidazole compounds tested, imidazole-4-acetic acid, a major catabolite of histamine in mammals, exhibited the highest activity. L-Carnosine (beta-alanyl-L-histidine), a natural dipeptide prevalent in striated muscle of mammals, possessed several properties important for a physiologically significant scavenger of singlet oxygen. On a molar basis, this readily water-soluble C-terminal histidine dipeptide reacted with singlet oxygen two- to four-fold faster than free L-histidine and approximately two-fold faster than the N-terminal L-histidine dipeptides tested. Furthermore scavenging ability of L-carnosine did not appreciably increase or decrease with time of reaction, in contrast to behaviors exhibited by a number of other imidazole compounds that included some other C-terminal L-histidine dipeptides. The fungal metabolite, ergothioneine, blocked singlet oxygen generation by illuminated phenosafranin.

Carnosine↗

Site of intestinal dipeptide hydrolysis.

1. Sacs of everted small intestine of the hamster have been used to study the site of final hydrolysis of twelve dipeptides. 2. The results suggest that L-alanyl-glycine, glycyl-glycine, L-valyl-L-valine, L-alanyl-L-valine, L-valyl-L-alanine and L-prolyl-glycine are hydrolysed beyond the locus of the active transport mechanism for D-glucose, perhaps even within the cell. These may be designated class 1 (deep) dipeptides. 3. In contrast, superficial (perhaps even surface) hydrolysis seems to occur with L-alanyl-L-alanine, L-leucly-L-leucine, glycyl-L-alanine, L-alanyl-L-leucine, L-leucyl-L-alanine and glycyl-L-proline. These may be designated class 2 (superficial) dipeptides. 4. All the dipeptides were able to partially inhibit D-glucose active transport, the findings supporting the view that more than one mechanism may exist for the active absorption of the sugar.

Animals↗

Mechanism of action of anticandidal dipeptides containing inhibitors of glucosamine-6-phosphate synthase.

The mechanism of anticandidal action of novel synthetic dipeptides containing N3-(4-methoxyfumaroyl)-L-2,3-diaminopropanoic acid (FMDP) residues was shown to be consistent with the "warhead delivery" concept. FMDP dipeptides were shown to be transported into Candida albicans cells by the di-tripeptide permease and subsequently hydrolyzed by intracellular peptidases, especially aminopeptidase. The anticandidal activity of the particular FMDP dipeptide was influenced by the rate of its transport and, to a lower extent, by the intracellular cleavage rate. A high transport rate accompanied by a high cleavage rate resulted in the high anticandidal activity of L-norvalyl-FMDP. The strong growth-inhibitory effect of this compound was the consequence of inhibition of the enzyme glucosamine-6-phosphate synthase by the released FMDP. The action of L-norvalyl-FMDP on exponentially growing C. albicans cells resulted in a sharp decrease of incorporation of 14C label from [14C]glucose into chitin, mannoprotein, and glucan. This effect, as well as the growth-inhibitory effect, was fully reversed by exogenous N-acetyl-D-glucosamine. Glucosamine-6-phosphate synthase was proved to be the only essential target for FMDP dipeptides. Scanning electron microscopy of C. albicans cells treated with L-norvalyl-FMDP revealed highly distorted, wrinkled, and collapsed forms. Cells formed long, bulbous chains, and partial lysis occurred.

Biological Transport↗

Regulation of dipeptide transport in Saccharomyces cerevisiae by micromolar amino acid concentrations.

Prototrophic Saccharomyces cerevisiae X2180, when grown on unsupplemented minimal medium, displayed little sensitivity to ethionine- and m-fluorophenylalanine-containing toxic dipeptides. We examined the influence of the 20 naturally occurring amino acids on sensitivity to toxic dipeptides. A number of these amino acids, at concentrations as low as 1 microM (leucine and tryptophan), produced large increases in sensitivity to leucyl-ethionine, alanyl-ethionine, and leucyl-m-fluorophenylalanine. Sensitivity to ethionine and m-fluorophenylalanine remained high under either set of conditions. The addition of 0.15 mM tryptophan to a growing culture resulted in the induction of dipeptide transport, as indicated by a 25-fold increase in the initial rate of L-leucyl-L-[3H]leucine accumulation. This increase, which was prevented by the addition of cycloheximide, began within 30 min and peaked approximately 240 min after a shift to medium containing tryptophan. Comparable increases in peptidase activity were not apparent in crude cell extracts from tryptophan-induced cultures. We concluded that S. cerevisiae possesses a specific mechanism for the induction of dipeptide transport that can respond to very low concentrations of amino acids.

Amino Acids↗

Relationships between mucosal hydrolysis and transport of two phenylalanine dipeptides.

In order to investigate the source of free amino acids found in the gut lumen during absorption of dipeptides, as well as evaluating the role of brush border peptidases in the mucosal hydrolysis of dipeptides during absorption, rates of dipeptide disappearance and appearance of hydrolytic products were measured during perfusion of rat jejunum and ileum in vivo with buffered and unbuffered 10 mM solutions of glycl-L-phenylalanine (Gly-Phe) and L-phenylalanyl-glycine (Phe-Gly). Mucosal brush border peptidase activity was then measured in the perfused segments in vitro at luminal pH and at two substrate concentrations. In addition cytosol peptidase activity in the perfused segments was measured at pH 7-4 and at 10 mM substrate concentrations. In the jejunum, there was a relationship between rates of free phenylalanine appearance in vivo (Phe-Gly greater than Gly-Phe) and rates of brush border (Phe-Gly greater than Gly-Phe) rather than cytosol (Gly-Phe greater than Phe-Gly) peptidase activities. No constant relationship between free phenylalanine appearance and hydrolysis of the dipeptides by either brush border or cytosol peptidases was observed in the ileal studies. These findings suggest that, in the jejunum, hydrolytic products originate from the surface of the cell whereas, in the ileum, hydrolytic products originate from both the intracellular compartment as well as from the surface of the mucosal cell. In the jejunum, in vitro rates of brush border hydrolysis of Gly-Phe were always less than in vivo disappearance rates, whereas rates of Phe-Gly brush border hydrolysis always exceeded luminal disappearance rates. These data imply that Gly-Phe is predominantly transported intact and hydrolysed by cytosol peptidases, In contrast, brush border peptidases play an importnat role in the mucosal hydrolysis of Phe-Gly.

Animals↗

Metabolism of dipeptides and their constituent amino acids by liver, gut, kidney, and muscle.

Oligopeptides may enter the bloodstream from endogenous and exogenous sources. Using an organ-balance technique in conscious dogs, we investigated the role of individual organs in removal of two model oligopeptides (glycylleucine and glycylglycine) from plasma under steady-state conditions. Despite an identical infusion rate, arterial concentration of glycylglycine was twofold greater than that of glycylleucine. This appeared to be a result of greater fractional extraction of glycylleucine than glycylglycine by organs. Although all of the organs examined participated in removal of dipeptides from plasma, their roles varied. Liver, kidney, muscle, and gut accounted for the disappearance of 25, 24, 12, and 10% of the infused amount of glycylleucine, respectively. With glycylglycine as the substrate, disappearance across kidney accounted for 37% of the infused amount, whereas muscle, liver, and gut accounted for 18, 15, and 11%, respectively. Finally, we investigated glycine and leucine balances across organs with infusion of these amino acids in free and dipeptide forms. Glycine and leucine balances were uniquely more positive across muscle during the infusion of glycylleucine than the corresponding amino acid mixture. The possible mechanisms included release of products of glycylleucine hydrolysis by all organs except muscle. We conclude that molecular structure influences the organ extraction of dipeptides; if extraction, particularly by the liver, is not sufficiently rapid, kidney assumes a greater role than other organs in dipeptide removal from plasma.

Amino Acids↗