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At least 325 records · Page 18Linked to original sources
PubMed1985

Trypsin activation. Effect of the Ile-Val dipeptide concentration on Kazal inhibitor binding to bovine trypsinogen.

The effect of Ile-Val concentration (up to 2.0 M) on the thermodynamic parameters for the binding of the porcine pancreatic secretory trypsin inhibitor (Kazal inhibitor) to trypsinogen has been investigated at pH 5.5 between 7 degrees C and 42 degrees C. Thermodynamic parameters for Kazal inhibitor binding to the Ile-Val:zymogen adduct are more favorable than those observed for inhibitor association to the free proenzyme, but less so than those reported for beta-trypsin:Kazal inhibitor adduct formation (even under saturating dipeptide concentrations), suggesting that the effector dipeptide does not induce a complete rigidification of the proenzyme's activation domain. Considering the dependence of the association equilibrium constant for Kazal inhibitor binding to trypsinogen from Ile-Val concentration, thermodynamic parameters for the effector dipeptide binding to the free proenzyme and to its binary complex with Kazal inhibitor have been obtained. Differences in affinity for Ile-Val binding to the free zymogen and its binary complexes with inhibitors and substrates are indicative of the presence of different activation levels of the proenzyme, none of them exactly coincident with that of beta-trypsin. Such different discrete states should correspond to those involved in the zymogen-to-active-enzyme transition which should not be considered as an all-or-nothing process, but as a multistep event.

Animals↗
PubMed1990

ACE-like hydrolysis of gastrin analogs and CCK-8 by fundic mucosal cells of different species with release of the amidated C-terminal dipeptide.

Various gastrin analogues and CCK-8 (Asp-Tyr(SO3H)-Met-Gly-Trp-Met-Asp-Phe-NH2) are hydrolyzed in vitro by angiotensin-converting enzyme (ACE), the main and initial cleavage occurring at the Met-Asp (or Leu-Asp) bond, releasing the C-terminal dipeptide amide Asp-Phe-NH2. Tetragastrin analogues (e.g., Boc-Trp-Leu-Asp-Phe-NH2) are degraded by a vesicular membrane fraction from rat gastric mucosa, yielding the C-terminal dipeptide Asp-Phe-NH2. We report here on the degradation of gastrin analogues and CCK-8 by a gastric mucosal cell preparation containing specific gastrin receptors. We have shown that gastrin analogues were specifically degraded by gastric mucosal cells from different species (e.g., rabbit and dog) at 37 degrees C (pH 7.4), releasing the C-terminal dipeptide Asp-Phe-NH2, similarly to ACE. This cleavage was found to be temperature and pH sensitive, and was inhibited by metalloproteinase inhibitors and by captopril, strongly suggesting that this enzymatic system closely resembles ACE. We have also demonstrated that a close correlation seems to exist between the apparent affinity of the gastrin analogues for gastrin receptors on gastric mucosal cells, and their ability of being hydrolyzed by this cell preparation. Moreover, all gastrin analogues which have been demonstrated to act as gastrin antagonists remained unaffected in the incubation conditions.

Amides↗
PubMed1991

Dipeptides--analogues of N-acetylaspartylglutamate inhibit convulsive effects of excitatory amino acids in mice.

The effects of three dipeptide analogues of N-acetylaspartylglutamate on seizures elicited by intracerebroventricular (i.c.v.) injection of L-glutamate (GLU), N-methyl-D-aspartate (NMDA), kainate (KA) and intraperitoneal (i.p.) injection of pentylentetrazol (PTZ) were studied in mice. N-Ac-L-Phe-L-Glu was active against myoclonic seizures induced by GLU and NMDA under simultaneous i.c.v. injection. All dipeptides were ineffective against KA and PTZ convulsions. The anticonvulsant activity and potency of N-Ac-L-Phe-L-Glu were similar to that of gamma-D-glutamylglycine (gamma-DGG) for excitatory amino acids (EAA) induced seizures. These results indicate EAA antagonistic activity among dipeptides which have L-glutamic acid on C-terminal and acetylated N-terminal.

Animals↗
PubMed2006

A quenched fluorescent dipeptide for assaying dispase- and thermolysin-like proteases.

Metalloproteases such as dispase and thermolysin play a crucial role in the life cycle of bacteria. Commonly, they prefer hydrophobic amino acids at P1' of substrate proteins, thereby cleaving the peptide bond at the alpha amino group. Activity of such proteases has been measured by the use of tailor-made oligopeptides provided with fluorescence resonance energy transfer dyes. We can now show that the short dipeptide Dabcyl-Ser-Phe-EDANS is an appropriate substrate of dispase and thermolysin. It was cleaved by both enzymes at the single peptide bond accompanied by a steep increase in fluorescence. Substantial quenching effects of the formed products were observed only when more than 80microM substrate was hydrolyzed. High affinity of the proteases for the dipeptide resulted in low K(m) values of 91+/-9 and 104+/-18microM, which are comparable to those measured for longer peptides. Dabcyl-Ser-Phe-EDANS was also used to determine the pH and optimal temperature of dispase, which were found at pH 7.0 and 50 degrees C. Buffer substances such as acetate, citrate, and tris(hydroxymethyl)aminomethane had no significant effect on enzyme activity. Measurements up to 100 degrees C revealed that hydrolysis of the quenched fluorescent dipeptide took place only in the presence of active dispase.

Binding Sites↗
PubMed2003

WD dipeptide motifs and LXXLL motif of chicken HIRA are necessary for transcription repression and the latter motif is essential for interaction with histone deacetylase-2 in vivo.

We previously reported not only that chicken HIRA, a homolog of Saccharomyces cerevisiae transcriptional corepressors Hir1p and Hir2p, possesses seven WD dipeptide motifs and a LXXLL motif in its N-terminal half and C-terminal half, respectively, but also that the N-terminal and C-terminal halves, respectively, bind to CAF-1p48 and HDAC-1 and -2 in vitro. Seven WD dipeptide motifs in the N-terminal half of HIRA are required for the in vitro interaction with CAF-1p48. The LXXLL motif at positions 993-997 of HIRA is necessary for the in vitro interaction with HDAC-2. Here we revealed not only that the N-terminal and C-terminal halves of HIRA mediate individually transcription repressions but also that even one of the seven WD dipeptide motifs and the LXXLL motif of HIRA are essential for the mediations in vivo. Moreover, the LXXLL motif is essential for the interaction with endogenous or recombinant HDAC-2 in vivo, probably resulting in formation of the active complex, harboring the HDAC activity. Taken together, these results indicate that HIRA should participate differentially in a number of DNA-utilizing processes, including transcription repressions, through interactions of its distinct regions with CAF-1p48 and HDAC-2, respectively.

Amino Acid Motifs↗
PubMed2004

Computational analysis of responsible dipeptides for optimum pH in G/11 xylanase.

A bioinformatics method was used to search the responsible dipeptides for optimum pH in the G/11 xylanase, for dipeptides can provide position information of the related residues for rational protein design. The responsible dipeptides were found as negative YS and positive SY, GR, MR, and KR. The minimum and maximum optimum pH was calculated as 2.33 and 14.29, respectively. Compared with the known crystal structures of the G/11 xylanase, YS was found mostly in the turn area of beta-strands of S/T surface; and SY was found in the inner part of beta-strands of the S/T area near to the active site of proton donor; and the GR, MR, and KR in the coil region connecting "finger" to the alpha-helix. The result clearly explained the success of shifting of pH 0.5 U to alkaline by the introduction of arginines into S/T area of a xylanase. The result would be useful for xylanase engineering, and the adaptation mechanism to high alkaline was also discussed.

Aspergillus↗
PubMed2006

Insertion of an internal dipeptide into PNA oligomers: thermal melting studies and further functionalization.

The solid phase synthesis of PNA oligomers with the internal dipeptide Gly-Phe is presented and the interaction with complementary DNA investigated. UV absorbance melting experiments with different but complementary DNA sequences show that stable PNA x DNA duplexes are only obtained when there is no DNA base opposite the dipeptide unit. Instead, the dipeptide spacer forms a loop-like structure within the duplex. Further functionalization with N-heterocyclic ligands is described. p-Nitro-phenylalanine is introduced in place of Phe during solid phase synthesis and subsequently reduced to p-amino-phenylalanine. Reaction with activated acids provides the ligand conjugates in high yield and purity. This strategy opens a universal route to a large number of internal substitutions in PNA chemistry.

DNA↗
PubMed2004

Isomeric discrimination of arginine-containing dipeptides using electrospray ionization-ion trap mass spectrometry and the kinetic method.

The Kinetic Method (KM), applied commonly for thermochemical determinations, is used here for sterically-controlled isomeric determination of N- versus C-terminal Arg-containing dipeptide isomers (ArgX versus XArg; where X = His, Leu, Lys, Pro, Ser, Phe, and Tyr). The KM is offered as an alternate approach to direct collision-induced dissociation (CID) procedures. Through formation, isolation, and dissociation of a sterically-encumbered, metal-centered complex with electrospray ionization ion trap mass spectrometry technology, reference dipeptide molecules are screened to quantitatively differentiate a mixture of isomers based on their arrangement about the metal center. Arg-containing dipeptide molecules are chosen because of their contribution in a wide array of protein and peptide functions. Additionally, problems cited previously for evaluation of systems containing Arg residues (due to the incorporation of the guanidinium moiety) by the KM are addressed. The method is shown to be successful for highlighting favorable reference analytes (e.g., ArgPhe, ArgLeu, ProArg, PheArg, among others) for exceptional discrimination (R(iso) > 2.0) of the majority of N- and C-terminal Arg-containing peptides tested.

Arginine↗
PubMed2005

Selective adsorption and reactivity of dipeptide stereoisomers in clay mineral suspension.

Preferential adsorption of dipeptide diastereomers (dialanine, Val-Ala) on clay mineral surfaces was observed. Significantly higher adsorption of dipeptides composed from only one type of enantiomer of amino acid units in comparison to those containing both L- and D-type of amino acid units in their molecules, was experimentally proven. This selectivity was explained in terms of different hydrophobic properties of diastereomers, which are probably controlled by intramolecular interactions between nonpolar and polar parts of dipeptide molecules affected by their stereochemistry. A significantly higher reactivity of stereoisomers composed from the same type of amino acid enantiomers to form amide bonds was proven as well. Theoretical study could distinguish different properties of the diastereomers. The results of the calculations indicate possible effects of molecular stability in the stereoselectivity during the adsorption and reactions of Ala(2) diastereomers.

Adsorption↗
PubMed2006

Chemical synthesis and crystallization of the dipeptide AcPheIleNH(2) in TTAB/heptane/octanol reversed micelles.

The chemical synthesis of the dipeptide acetyl phenyl iso-leucin-amide (AcPheIleNH(2)) in tetradecyl trimethyl ammonium bromide (TTAB)/ heptane/octanol/carbonate buffer reversed micelles is described. The co-existence of the surfactant bounded minute water pools within the bulk organic solvent enables the simultaneous solubilization of the polar (IleNH(2)) and apolar (AcPheOEt) substrates, thus enabling the synthesis to take place at the micellar interface. The synthesis was favored by increasing the micellar interface via an increase in water content and surfactant concentration. The best dipeptide yield (87%) was obtained at 32 degrees C, with the largest concentrations of TTAB (200 mM) and water (1100 mM) tested. The low solubility of the dipeptide in the micellar media further led to the formation and growth of needle-like crystals during synthesis, thus enabling the removal of product from solution.

Crystallization↗
PubMed2005

Synthesis and evaluation of eight-membered cyclic pseudo-dipeptides.

In the course of the development of calpain inhibitors, we report the synthesis of eight-membered cyclic pseudo dipeptides closely related to the known inhibitor SJA6017. The ring closure was effected by metathesis of the diallyl-substituted dipeptides 6 and 7. The formation of the dipeptides under kinetic control leads to the preferential formation of the unlike diastereomer 7 over the like diastereomer 6. The relative configuration of the diastereomers was determined by NMR and modeling studies of the related cyclic compounds 8 and 9 and their derivatives. The compounds proved not to inhibit calpain.

Calpain↗
PubMed1997

Energetics of cyclic dipeptide crystal packing and solvation.

Calculations of the thermodynamics of transfer of the cyclic alanine-alanine (cAA) and glycine-glycine (cGG) dipeptides between the gas, water, and crystal phases were carried out using a combination of molecular mechanics, normal mode analysis, and continuum electrostatics. The experimental gas-to-water solvation free energy and the enthalpy of gas-to-crystal transfer of cGG are accurately reproduced by the calculations. The enthalpies of cGG and cAA crystal-to-water transfer are close to the experimental values. A combination of experimental data and normal mode analysis of cGG provides an accurate estimate of the association entropy penalty (loss of rational and translational entropy and gain in vibrational entropy) for "binding" in the crystalline phase of -14.1 cal/mol/k. This is a smaller number than most previous theoretical estimates, but it is similar to previous experimental estimates. Calculated entropies of the crystal phase underestimate the experimental entropy by about 15 cal/mol/k because of neglect of long-range lattice motions. Comparison of the intermolecular interactions in the crystals of cGG and cAA provides a possible explanation of the puzzling decrease in enthalpy, with increasing hydrophobicity seen previously for both cyclic dipeptide dissolution and protein unfolding. This decrease arises from a favorable long-range electrostatic interaction between dipeptide molecules in the crystals, which is attenuated by the more hydrophobic side chains.

Crystallization↗
PubMed2003

Potentiation of metabotropic GABAB receptors by L-amino acids and dipeptides in rat neocortex.

Selected neutral L-alpha-amino acids, and their dipeptides, were reversible, stereospecific, potentiators of GABA(B) receptor-mediated hyperpolarizing responses to baclofen (3-100 microM) in rat neocortical slices. These responses were sensitive to the GABA(B) receptor antagonist (+)-(S)-5,5-dimethylmorpholinyl-2-acetic acid (Sch50911) (30 microM). Most potent were L-Leu, L-Ile and L-Phe, as were the dipeptides L-Phe-Phe and L-Phe-Leu, and less potent were L-Met, L-Val, L-Cys, L-Cystine, L-Tyr, L-Thr, L-Arg and L-Ser. Inactive were L-Trp, L-His, L-Lys and L-Pro. These potentiators gave leftward shifts of the baclofen concentration-response curves with a Hill slope of 2, and a marked increase in the maximal hyperpolarizing responses. Selected L-amino acids and dipeptides are a class of naturally occurring GABA(B) potentiators, which may be allosteric modulators.

Allosteric Regulation↗
PubMed1997

Design of mu selective opioid dipeptide antagonists.

We have recently designed potent delta selective opioid antagonist dipeptides on the basis of a simple conformational analysis. Following a similar procedure we found a mu selective dipeptide antagonist, 2,6-dimethyl-Tyr-D-Phe-NH2. Although its selectivity is not as high as those of the quoted delta selective dipeptides it has good in vitro activity and looks very promising for further development since the 2,6-dimethyl-Tyr-D-Phe message, like the delta selective 2,6-dimethyl-Tyr-1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid counterpart, seems able to impart antagonism to longer peptides.

Animals↗
PubMed1988

Resolution of stereoisomers of dipeptides by gas chromatography on Chirasil-Val.

Several dipeptides have been separated into stereoisomers (enantiomers, diastereomers, sequential isomers) by gas chromatography on Chirasil-Val. Sufficiently volatile N-trifluoroacetyl dipeptide methyl esters were formed at ambient temperature, thus avoiding racemization (or epimerization, respectively, and cleavage of the peptide bond. This method is suitable for ascertaining the stereoisomeric composition of dipeptides in biological samples.

Chromatography, Gas↗
PubMed1977

High-pressure liquid chromatography of amino acids and dipeptides on a tripeptide bonded stationary phase.

A bonded tripeptide (L-valyl-L-phenylalanyl-L-valine) phase has been used as a stationary phase in liquid chromatography. Unique retention orders and retention variations are shown for phenylthiohydantoin (PTH) derivatives of amino acids and isomeric dipeptides using acidic and basic mobile phases. It is shown that the 25 PTH-amino acids studied here have different capacity ratios when 1% citric acid in water (ca. pH 2.5) is used as the mobile phase. The analysis time for these amino acid derivatives could be shortened without a loss in the resolution by adding 5% methanol to the above mobile phase. Of particular importance is the fact that the basic amino acids are eluted first. Isomeric dipeptides have been resolved by using deionized water (pH 5.5), and 1% sodium citrate in water (pH 7.9), as mobile phases. The data show that the nature of the mobile phases, the pH, and the ionic strength are the important factors affecting the selectivity and efficiency of the separations of amino acids and dipeptides.

Amino Acid Sequence↗
PubMed2000

Dynamics of dominance of a dipeptide insertion in reverse transcriptase of HIV-1 from patients subjected to prolonged therapy.

A small proportion (0.8%) of individuals of a cohort of HIV-1 infected patients subjected to prolonged therapy with nucleoside analogues included a recently recognised dipeptide insertion in their RT (Ser-Ser or Ser-Gly between RT codons 69 and 70). To study the dynamics of dominance of genomes with this genetic change, sequential HIV-1 isolates from two patients were analyzed with regard to consensus sequences and complexity of mutant spectra. The two patients displayed completely different, complex evolutionary patterns leading to temporary dominance of dipeptide insertions. In one patient, a virus very closely related to an ancestor virus from the same patient overtook the population at late times, displacing genomes encoding a Ser-Ser insertion. In another patient the sequential dominance of genomes with Ser-Ser insertion-->no insertion-->Ser-Gly insertion was observed. These three types of genomes coexisted in the mutant spectrum of one HIV-1 isolate. Complexity was also reflected in the shape of phylogenetic trees derived with genomes from the mutant spectrum at each time point. The results suggest that HIV-1 genomes encoding a dipeptide insertion between RT codons 69 and 70 do not show a clear selective advantage over other genomes lacking the insertion. Such an absence of a clear selective advantage will favor that such genomes encoding this RT insertion become dominant only in a transient fashion, and following disparate kinetics in different patients.

Adult↗
PubMed1999

Highly sensitive determination of N-terminal prolyl dipeptides, proline and hydroxyproline in urine by high-performance liquid chromatography using a new fluorescent labelling reagent, 4-(5,6-dimethoxy-2-phthalimidinyl)-2-methoxyphenylsulfonyl chloride.

A highly sensitive pre-column HPLC method for simultaneous determination of prolyl dipeptides, Pro and Hyp in urine was developed. The analytes were labelled with 4-(5,6-dimethoxy-2-phthalimidinyl)-2-methoxyphenylsulfonyl chloride at 70 degrees C for 20 min. The derivatives separated on tandem reversed-phase columns by a gradient elution and were monitored with fluorescence detection at 318 nm (excitation) and 392 nm (emission). The detection limits for prolyl dipeptides, Pro and Hyp were 1-5 fmol/injection (S/N = 3). Urine samples were treated with o-phthalaldehyde, followed by purification on a Bond Elut C18 column before conducting the labelling reaction. Pro-Hyp, Pro-Gly and Pro-Pro were identified as prolyl dipeptides in urine. The within-day and between-day relative standard deviations were 1.5-4.8 and 1.7-5.8%, respectively. The concentrations of Pro-Hyp, Pro-Gly, Pro-Pro, Pro and Hyp in normal human urine were 97.6 +/- 28.2, 2.74 +/- 1.48, 2.08 +/- 1.13, 6.71 +/- 3.34 and 2.30 +/- 1.59 nmol/mg creatinine, respectively.

Chromatography, High Pressure Liquid↗