Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “dipeptides”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 487 records · Page 27Linked to original sources
PubMed1996

Enantioseparation of amino acids and dipeptides using vancomycin as chiral selector in capillary electrophoresis.

Vancomycin was applied as chiral selector for the enantiomeric separation of derivatized amino acids and dipeptides. The influence of vancomycin concentration, pH and presence of 2-propanol in the buffer were examined in order to find optimal separation conditions. Optimization was by factorial design. Further, chiral separation of derivatives prepared with three different reagents was compared. These reagents were 9-fluorenylmethyl chloroformate (FMOC), 2-(9-anthryl)ethyl chloroformate (AEOC) and dansyl chloride (dansyl). Optimum resolution was at high vancomycin concentrations, while optimum efficiency was at low vancomycin concentrations. As a consequence of the very high enantioselectivity of vancomycin, the vancomycin concentration below the amount necessary for maximal resolution can be used. Separation efficiency was relatively low, and this could be attributed to adsorption of the selector at the capillary wall. Three factors led to decreased adsorption: application of a pH above the zero mobility pH value, low vancomycin concentrations and the presence of 2-propanol. For amino acids, the resolutions of the different derivatives were: dansyl > AEOC > FMOC, while for dipeptides, the highest selectivity was with AEOC.

1-Propanol↗
PubMed2004

Selectivity of quadruplex DNA stationary phases toward amino acids in homodipeptides and alanyl dipeptides.

Series of dipeptides, including homodipeptides and alanyl dipeptides, were separated using quadruplex (G-quartet) DNA stationary phases in open-tubular capillary electrochromatography (OTCEC). The stationary phases were constructed by covalently attaching the DNA oligonucleotides to the inner capillary surface. Three different G-quartet forming oligonucleotides were investigated: the two-plane G-quartet forming thrombin-binding aptamer, the four-plane analogue of the thrombin-binding aptamer, and a two-plane oligonucleotide identical to the thrombin-binding aptamer except for the replacement of the guanine by thymine in the central bridging loop of the G-quartet structure. Results were compared with results obtained using capillary electrophoresis on a bare capillary and OTCEC using an oligonucleotide with the same base composition as the thrombin-binding aptamer but in a different sequence that does not allow G-quartet formation as the stationary phase.

Amino Acids↗
PubMed2003

Natural killer cell cytolytic activity is necessary for in vivo antitumor activity of the dipeptide L-glutamyl-L-tryptophan.

A dipeptide, L-glutamyl L-tryptophan (L-glu-L-trp), was identified in a screen for immunomodulators in the soluble fraction of the thymus. L-glu-L-trp inhibits tumor growth in mice without showing direct cellular toxicity in a variety of human tumor cell lines. L-glu-L-trp antitumor activity in vivo requires the presence of natural killer (NK) cells. Defective trafficking of cytoplasmic granules caused by the Lyst mutation also resulted in loss of antitumor activity of the dipeptide. The effect of L-glu-L-trp on tumor growth in mice with targeted gene mutations demonstrated the absolute requirement for perforin for antitumor activity. The requirement of 2 major modulators of NK cell activity, gamma interferon (IFNgamma) and interleukin (IL)-12, were also tested. L-glu-L-trp had full antitumor activity in IFNgamma knockout mice, but had significantly diminished activity in IL-12 knockout mice. These data show that L-glu-L-trp antitumor activity in mice is dependent on cytolytic cell activity of NK or NKT cells. L-glu-L-trp in vivo regulates NK cell function independent of IFNgamma but partly dependent on IL-12.

Angiogenesis Inhibitors↗
PubMed2003

Peptide models. XXXIII. Extrapolation of low-level Hartree-Fock data of peptide conformation to large basis set SCF, MP2, DFT, and CCSD(T) results. The Ramachandran surface of alanine dipeptide computed at various levels of theory.

At the dawn of the new millenium, new concepts are required for a more profound understanding of protein structures. Together with NMR and X-ray-based 3D-structure determinations in silico methods are now widely accepted. Homology-based modeling studies, molecular dynamics methods, and quantum mechanical approaches are more commonly used. Despite the steady and exponential increase in computational power, high level ab initio methods will not be in common use for studying the structure and dynamics of large peptides and proteins in the near future. We are presenting here a novel approach, in which low- and medium-level ab initio energy results are scaled, thus extrapolating to a higher level of information. This scaling is of special significance, because we observed previously on molecular properties such as energy, chemical shielding data, etc., determined at a higher theoretical level, do correlate better with experimental data, than those originating from lower theoretical treatments. The Ramachandran surface of an alanine dipeptide now determined at six different levels of theory [RHF and B3LYP 3-21G, 6-31+G(d) and 6-311++G(d,p)] serves as a suitable test. Minima, first-order critical points and partially optimized structures, determined at different levels of theory (SCF, DFT), were completed with high level energy calculations such as MP2, MP4D, and CCSD(T). For the first time three different CCSD(T) sets of energies were determined for all stable B3LYP/6-311++G(d,p) minima of an alanine dipeptide. From the simplest ab initio data (e.g., RHF/3-21G) to more complex results [CCSD(T)/6-311+G(d,p)//B3LYP/6-311++G(d,p)] all data sets were compared, analyzed in a comprehensive manner, and evaluated by means of statistics.

Alanine↗
PubMed2006

A comparative theoretical study of dipeptide solvation in water.

Molecular dynamics studies have been performed on the zwitterionic form of the dipeptide glycine-alanine in water, with focus on the solvation and electrostatic properties using a range of theoretical methods, from purely classical force fields, through mixed quantum mechanical/molecular mechanical simulations, to fully quantum mechanical Car-Parrinello calculations. The results of these studies show that the solvation pattern is similar for all methods used for most atoms in the dipeptide, but can differ substantially for some groups; namely the carboxy and aminoterminii, and the backbone amid NH group. This might have implications in other theoretical studies of peptides and proteins with charged -NH(3) (+) and -CO(2) (-) side chains solvated in water. Hybrid quantum mechanical/molecular mechanical simulations successfully reproduce the solvation patterns from the fully quantum mechanical simulations (PACS numbers: 87.14.Ee, 87.15.Aa, 87.15.He, 71.15.Pd).

Alanine↗
PubMed2006

Multiple pathways in conformational transitions of the alanine dipeptide: an application of dynamic importance sampling.

We present multiple dynamic transition pathways on the two-dimensional dihedral plane between conformational states of the alanine dipeptide. The method used in this study is dynamic importance sampling (DIMS). To perform DIMS, unbiased molecular dynamic simulations are used to generate equilibrium ensembles for the alanine dipeptide within different states. Free energy surfaces on the dihedral plane are calculated from the equilibrium simulations, and four energy minima defined from the surface are used as the starting and ending points for DIMS dynamics. The DIMS method represents an important step towards finding multiple transition pathways within complex biomolecular systems.

Alanine↗
PubMed1993

Chymotrypsin inhibitory conformation of dipeptides constructed by side chain-side chain hydrophobic interactions.

A complete series of configurational isomers (L-L, L-D, D-L and D-D) of a dipeptide Leu-Phe benzyl ester have been synthesized and assayed for chymotrypsin. In the conformational analysis by 400 MHz 1H NMR, the L-D and D-L isomers, but not the L-L and D-D isomers, showed fairly large upfield shifts (0.2-0.4 ppm) of Leu-beta CH2 and gamma CH proton signals, indicating the presence of shielding effects from the benzene ring. In addition to distinct signal splitting of Phe-beta CH2, the NOE enhancement observed between Leu-delta CH3 and Phe-phenyl groups revealed that these groups are in close proximity. These data indicated that L-D and D-L isomers form a hydrophobic core between side chains of adjacent Leu and Phe residues. When the dipeptides were examined for inhibition of chymotrypsin using Ac-Tyr-OEt as a substrate, the L-L isomer showed no inhibition, itself becoming a substrate. However, the other three isomers inhibited chymotrypsin in a competitive manner, and the D-L isomer was strongest with Ki of 2.2 x 10(-5) M. It was found that the D-L isomer was only slowly hydrolysed but the L(or D)-D isomer was not. H-D-Phe-L-Leu-OBzl with the inverse sequence of H-D-Leu-L-Phe-OBzl inhibited chymotrypsin more strongly (Ki = 6.3 x 10(-6) M).(ABSTRACT TRUNCATED AT 250 WORDS)

Chymotrypsin↗
PubMed2004

Profiling histidine-containing dipeptides in rat tissues by liquid chromatography/electrospray ionization tandem mass spectrometry.

The histidine-containing dipeptides carnosine (CAR) and structurally related anserine (ANS) and homocarnosine (HCAR), widely distributed in vertebrate organisms, have recently been proposed as endogenous quenchers for highly cytotoxic alpha,beta-unsaturated aldehydes generated by peroxidation. A sensitive, selective, specific and rapid liquid chromatographic/electrospray ionization tandem mass spectrometric assay was developed and validated for the simultaneous determination of these peptides in biological matrices in order to establish their plasma/tissue distribution. Samples (plasma or tissue homogenates from male rats) were prepared by protein precipitation with HClO(4) (1 : 1, v/v) containing H-Tyr-His-OH as internal standard. The supernatant was separated on a Phenomenex Sinergy polar-RP column with a mobile phase of water-acetonitrile-heptafluorobutyric acid (9 : 1 : 0.01, v/v/v) at a flow-rate of 0.2 ml min(-1), with a run time of 10 min. Detection was effected on an ion trap mass spectrometer equipped with an electrospray ionization interface operating in positive ionization mode. The acquisitions were in the multiple reaction monitoring mode using the following precursor --> product ion combinations: H-Tyr-His-OH (internal standard) m/z 319 --> 301; CAR m/z 227 --> 210 + 209; ANS m/z 241 --> 224 + 197 + 170; HCAR m/z 241 --> 156. The method was validated over the concentration range 15-1000 nmol g(-1) and the limit of quantification (LOQ) and limit of detection (LOD) were 12.5 and 4.2 pmol injected, respectively. The intra- and inter-day precisions were <10% (< or =17.47% at the LOQ) and the intra- and inter-assay accuracies were within +/-10% for all concentrations. The mapping profile in rat tissue gave the following results: the highest concentrations of CAR and ANS were found in skeletal muscles (soleus, gastrocnemius, tibialis), followed by the heart, cerebellum and brain (ANS below the LOQ). HCAR was found only in the brain and cerebellum. No histidine-containing dipeptides were detectable in plasma, liver, kidney and lung.

Animals↗
PubMed2004

Hydrophobic dipeptide Leu-Ile protects against neuronal death by inducing brain-derived neurotrophic factor and glial cell line-derived neurotrophic factor synthesis.

We investigated whether certain hydrophobic dipeptides, Leu-Ile, Leu-Pro, and Pro-Ile, which partially resemble the site on FK506 that binds to immunophilin, could stimulate glial cell line-derived neurotrophic factor (GDNF) and brain-derived neurotrophic factor (BDNF) synthesis in cultured neurons and found only Leu-Ile to be an active dipeptide. Leu-Ile protected against the death of mesencephalic neurons from wild-type mice but not from mice lacking the BDNF or GDNF gene. Next, we examined the effects of i.p. or i.c.v. administration of Leu-Ile on BDNF and GDNF contents. Both types of administration increased the contents of BDNF and GDNF in the striatum of mice. Also, peripheral administration of Leu-Ile inhibited dopaminergic (DA) denervation caused by unilateral injection of 6-hydroxydopamine (6-OHDA) into the striatum of mice. The number of rotations following a methamphetamine challenge was lower in the Leu-Ile-treated group than in the nontreated group. Next, we compared the calcineurin activity and immunosuppressant activity of Leu-Ile with those of FK506. Leu-Ile was not inhibitory toward calcineurin cellular activity in cultured neuronal cells. Furthermore, Leu-Ile did not suppress concanavalin A (ConA)-induced synthesis/secretion of interleukin-2 by cultured spleen cells, suggesting that the immunosuppressant activity of Leu-Ile may be negligible when used as a therapeutic tool for neurodegenerative diseases.

Animals↗
PubMed2005

High performance liquid chromatographic separation of dipeptide and tripeptide enantiomers using a chiral crown ether stationary phase.

A chiral stationary phase (CSP) based on (-)-(18-crown-6)-2,3,11,12-tetracarboxylic acid was evaluated for the direct resolution of the enantiomers of dipeptides and tripeptides. The type and concentration of the acid and the methanol content were optimized with regard to retention time and resolution using Ala-Phe as model peptide. A mobile phase consisting of 10 mM sulfuric acid in 70% aqueous methanol was applied to the separation of a set of 16 structurally diverse dipeptides and tripeptides. Generally, the configuration of the amino acid at the N-terminus determined the enantiomer elution order. With a few exceptions the LL- and LD-enantiomers interacted stronger with the CSP compared to the corresponding DD- or DL-enantiomers. The experimental conditions also allowed the simultaneous separation of all four stereoisomers of Ala-Phe. Addition of ammonium sulfate generally reduced retention times and enantiomer resolution. Addition of triethylamine as modifier led to an overall increase of the retention times while the resolution did not show a general trend, increasing in the case of Ala-Ala but decreasing in the case of Ala-Phe.

Ammonium Sulfate↗
PubMed1992

Inclusion of solvation free energy with molecular mechanics energy: alanyl dipeptide as a test case.

A combined force field of molecular mechanics and solvation free energy is tested by carrying out energy minimization and molecular dynamics on several conformations of the alanyl dipeptide. Our results are qualitatively consistent with previous experimental and computational studies, in that the addition of solvation energy stabilizes the C5 conformation of the alanyl dipeptide relative to the C7.

Calorimetry↗
PubMed2002

A critical analysis of continuum electrostatics: the screened Coulomb potential--implicit solvent model and the study of the alanine dipeptide and discrimination of misfolded structures of proteins.

An analysis of the screened Coulomb potential--implicit solvent model (SCP--ISM) is presented showing that general equations for both the electrostatic and solvation free energy can be derived in a continuum approach, using statistical averaging of the polarization field created by the solvent around the molecule. The derivation clearly shows how the concept of boundary, usually found in macroscopic approaches, is eliminated when the continuum model is obtained from a microscopic treatment using appropriate averaging techniques. The model is used to study the alanine dipeptide in aqueous solution, as well as the discrimination of native protein structures from misfolded conformations. For the alanine dipeptide the free energy surface in the phi--psi space is calculated and compared with recently reported results of a detailed molecular dynamics simulation using an explicit representation of the solvent, and with other available data. The study showed that the results obtained using the SCP--ISM are comparable to those of the explicit water calculation and compares favorably to the FDPB approach. Both transition states and energy minima show a high correlation (r > 0.98) with the results obtained in the explicit water analysis. The study of the misfolded structures of proteins comprised the analysis of three standard decoy sets, namely, the EMBL, Park and Levitt, and Baker's CASP3 sets. In all cases the SCP--ISM discriminated well the native structures of the proteins, and the best-predicted structures were always near-native (cRMSD approximately 2 A).

Alanine↗
PubMed1988

Microfolding: conformational probability map for the alanine dipeptide in water from molecular dynamics simulations.

A direct attack on the protein-folding problem has been initiated with the free energy perturbation methods of molecular dynamics. The complete conformational probability map for the alanine dipeptide is presented. This work uses the SPC model for the explicit hydration of the dipeptide. Free energy differences for the four observed minima (beta, alpha R, alpha L, C7ax) are given, and the free energy barriers between minima are outlined.

Dipeptides↗
PubMedDate not supplied

Use of a gel-forming dipeptide derivative as a carrier for antigen presentation.

A dipeptide of the formula Fmoc-Leu-Asp and some other related dipeptides were synthesized in solution by standard methods. When such peptides are dissolved in water at concentrations below 1% at 100 degrees C and cooled below 60 degrees C they form turbid solutions and eventually viscoelastic gels at lower temperatures. Such gels are thermoreversible and can also be disrupted by mechanical agitation. At a concentration of 2 mg/ml the peptide Fmoc-Leu-Asp forms an aqueous gel at 60 degrees C with a shear modulus of 80 Pa measured at a frequency of 1 rad/s. Peptide solutions undergo an abrupt increase in light scattering between 1 and 1.5 mg/ml at both 23 and 60 degrees C. By analogy with previous observations of other systems, this increase appears to be due to the formation of filamentous micelles and the aggregation of filaments into a three-dimensional network. When low molecular weight adamantanamine derivatives, which are inherently non-antigenic antiviral drugs, were incorporated into the Fmoc-Leu-Asp gel and injected into rabbits, high titre specific antibodies were efficiently produced without the need for additional adjuvant. Both the physical properties of the gel and its effect on the antigenicity of low molecular weight compounds suggest a number of practical applications.

Amino Acid Sequence↗
PubMed2005

Analogues of arginine vasopressin modified in position 2 and 3 with conformationally constrained dipeptide fragments.

This study describes the synthesis and some pharmacological properties of ten new analogues of arginine vasopressin (AVP) containing a conformationally constrained dipeptide fragment in the N-terminal part of their molecules. Amino acid residues in positions 2 and 3 of AVP and some of its agonistic analogues were replaced with -Phe-Phe and D-Phe-D-Phe, dipeptides having a -CH2-CH2- link bridging two nitrogens. All the new peptides were tested for vasopressor and antidiuretic activities. Four peptides with pA2 values ranging from 5.96 to 7.21 turned out to be weak or moderately potent V1a antagonists. The results supplied new information about the structure-activity relationship of AVP analogues. As some of these were unexpected, they point to the need for caution when extrapolating previously known effects of modifications to analogues having conformationally constrained fragments in their molecules.

Amino Acid Sequence↗
PubMed2005

The synthesis of oligomers of oxetane-based dipeptide isosteres derived from L-rhamnose or D-xylose.

Routes to oligomers (dimers, tetramers, hexamers) of five oxetane-based dipeptide isosteres have been established. Methyl 2,4-anhydro-5-azido-5-deoxy-L-rhamnonate 'monomer' led, by coupling the corresponding carboxylic acid and amine, to a 'dimer'. Reverse-aldol ring-opening occurred on attempted saponification of the dimer, so all further oligomerization was performed using TBDMS C-3 hydroxyl protection. The silyl protected L-rhamnonate monomer led in turn to the dimer (via the monomer acid and amine), the tetramer (via the dimer acid and amine) and finally the hexamer (via the tetramer acid and dimer amine). In each case the acids were obtained through saponification of the respective methyl esters and the amines were obtained by hydrogenation of the azides; coupling was TBTU-mediated. Essentially the same strategy was employed on equivalent D-lyxonate, 6-deoxy-L-altronate, 6-deoxy-D-gulonate and D-fuconate dipeptide isosteres to give the respective dimers, tetramers and hexamers.

Dipeptides↗
PubMed1993

Crystallization and preliminary X-ray analysis of the periplasmic dipeptide binding protein from Escherichia coli.

The periplasmic dipeptide-binding protein from Escherichia coli has been purified, freed of bound endogenous ligands, and crystallized. Crystals of the protein in complex with added dipeptides have been subjected to X-ray analysis. The crystals grow as hexagonal bipyramids or eye-shaped disks which have the symmetry of space group P6(1). The unit cell dimensions are a = b = 183 A, c = 212 A, and the diffraction pattern extends to 3.2 A resolution with a conventional X-ray source.

Bacterial Proteins↗
PubMed1998

Synthesis, decomposition, and vasodilator action of some new S-nitrosated dipeptides.

A number of amino acid methyl esters have been coupled to N-acetylpenicillamine to give a range of sulfur-containing dipeptides. These have been nitrosated to give a family of structurally related NO-donor drugs. The catalytic effect of copper ions upon the release of NO from these compounds is much less than that upon S-nitroso-N-acetylpenicillamine. However, all the nitrosated dipeptides respond in a similar way with little variation in the value of kCu. On the other hand, the vasodilator action of these compounds and the inhibiting effect of hemoglobin do vary quite considerably within the family. It is suggested that this indicates some tissue penetration by these drugs.

Animals↗