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At least 811 records · Page 45Linked to original sources
PubMed2006

Temporin A and its retro-analogues: synthesis, conformational analysis and antimicrobial activities.

Temporin A (TA) is a hydrophobic peptide isolated from the skin of the European red frog Rana temporaria. Strong antimicrobial activity against gram-positive cocci and Candida, as well as its small molecular weight (10-13 aa residues), makes TA an interesting antimicrobial compound. However, its synthesis is rather problematic. Here, the synthesis of two retro-analogues of TA--retro-TA and (6-1)(7-13)-TA--is reported. The synthesis of retro-TA was performed without any problems, while during the synthesis of (6-1)(7-13)-TA problems similar to those encountered during the synthesis of TA were faced. Antimicrobial assays showed minimal inhibitory concentration (MIC) values of retro-TA to be, in most cases, only one dilution higher than those of original TA, but still remained relatively low. An analysis of the circular dichroism spectra of the peptides shows that TA and (6-1)(7-13)-TA adopt an alpha-helical structure in a hydrophobic environment, while retro-TA forms mainly unordered conformation under both hydrophobic and hydrophilic conditions. One can postulate that differences in conformation of the peptide chain might be responsible for the lower antimicrobial activity of retro-TA as compared to that of the parent molecule. In any case, retro-TA can be interesting owing to its simple and nonproblematic synthesis.

Anti-Infective Agents↗
PubMed2002

Conformational analysis of the GTP-binding protein MxA using limited proteolysis.

Guanosine triphosphate (GTP)-binding proteins are known to function as molecular switches that cycle between GTP-bound and guanosine diphosphate (GDP)-bound states. Switching is achieved by the fact that G-proteins in the GTP-bound conformation can interact with a certain set of effector molecules while they interact with a different set of partners in their GDP-bound conformation. The antiviral properties of the interferon-induced MxA protein are critically dependent on the ability of MxA to bind GTP. Using limited proteolysis we analyzed the conformations of the MxA protein under nucleotide-free, GDP-bound, and GTP-bound conditions. We find that whereas the conformations of nucleotide-free MxA and GDP-bound MxA are essentially similar, GTP-binding causes a dramatic change in the conformation of MxA.

Animals↗
PubMed1996

Aldol-Promoted Reaction of R106-Sarcosine: Synthesis and Conformational Analysis of Novel R106 Analogs.

A unique semisynthetic pathway has been used as a route to novel R106 derivatives. R106-sarcosine, 2, was discovered to be a key intermediate to obtain these derivatives using classical aldol alkylation conditions. Surprisingly, the site of alkylation on 2 was found to be conformationally hindered which yielded both the D and L isomers of R106-1 (aureobasidin A), 1, and other new R106 derivatives. The scope of the alkylation was found to be highly dependent upon the reactivity potential of the electrophile. Semiempirical calculations on R106-1 and 8-(N-methylthrenonine)aureobasidin A, 7, were performed to investigate the thermodynamic stabilities of the D and L isomers. By contrast to stable conformations observed by two X-ray crystal structures of aureobasidins, the calculations indicated that the D isomers were significantly more stable. Furthermore, model semiempirical calculations to probe facial selecitivty were consistent with results obtained experimentally.

Journal Article↗
PubMed2006

A DFT conformational analysis and VCD study on methyl tetrahydrofuran-2-carboxylate.

DFT calculations were performed on (S)-methyl tetrahydrofuran-2-carboxylate to facilitate the interpretation of IR and VCD spectra. The potential energy surface could not be described unambiguously using the 6-31G* basis set in combination with different density functionals including B1LYP, B3LYP, B3P86, B3PW91, B98, BHandH, BHandHLYP, MPW1PW91 and PBE1PBE. In contrast, a uniform conformational picture could be found using the cc-pVTZ basis set. Using this large basis set and the collection of nine functionals from above, the dipole and rotational strengths were calculated, and compared to experimental values which were extracted from the experimental IR and VCD spectra for (+)-(S)-methyl tetrahydrofuran-2-carboxylate. A detailed analysis on the agreement between experiment and simulated spectra was performed by assigning the experimental bands based on the harmonic fundamentals obtained for all functionals except BHandH, which performs badly over the whole line. Assessing the dipole strengths, all tested functionals perform equally well. For the rotational strengths, differences can be observed: B3LYP, B1LYP and B98 give the highest correlation with experiment, while PBE1PBE gives the lowest correlation. Comparable conclusions are obtained using a neighborhood similarity measure.

Circular Dichroism↗
PubMed1998

Synthesis, biological activity, and conformational analysis of peptidomimetic analogues of the Saccharomyces cerevisiae alpha-factor tridecapeptide.

Biochemical and biophysical investigations on the Saccharomyces cerevisiae alpha-factor indicate that this tridecapeptide mating pheromone (WHWLQLKPGQPMY) might adopt a type II beta-turn in the center of the peptide when it binds to its G protein-coupled receptor. To test this hypothesis we synthesized analogues of alpha-factor incorporating a (R or S)-gamma-lactam conformational constraint [3-(R or S)-amino-2-oxo-1-pyrrolidineacetamido] in place of the Pro-Gly at residues 8 and 9 of the peptide and tested their biological activities and receptor binding. Analogues were purified to >99% homogeneity as evidenced by high-performance liquid chromatography and capillary electrophoresis and characterized by amino acid analysis, mass spectrometry, and nuclear magnetic resonance (NMR) spectroscopy. The restricted alpha-factor analogue WHWLQLK[(R)-gamma-lactam]QP[Nle]Y was more active than its lactam-containing diastereomeric homologue WHWLQLK[(S)-gamma-lactam]QP[Nle]Y and about equally active with the [Nle12]-alpha-factor in growth arrest and FUS1-lacZ gene induction assays. Both lactam analogues competed with tritiated [Nle12]-alpha-factor for binding to the alpha-factor receptor (Ste2p) with the (R)-gamma-lactam-containing peptide having 7-fold higher affinity than the (S)-gamma-lactam-containing homologue. Two-dimensional NMR spectroscopy and modeling analysis gave evidence that the (R)-gamma-analogue is a flexible peptide that assumes a transient gamma-turn structure around the lactam moiety. The results represent the first example of an alpha-factor analogue containing a peptidomimetic constraint that is as active as the native pheromone. The correlation between activity and structure provides further evidence that the biologically active conformation of the molecule contains a turn in the middle of the pheromone. This study provides new insights into the structural basis of alpha-factor activity and adds to the repertoire of conformationally biasing constraints that can be used to maintain and even enhance biological activity in peptide hormones.

Amides↗
PubMed2005

Conformational analysis of xylan chains.

The present study provides a theoretical description of the different levels of structural organization that characterize the xylan polysaccharide in its native and hydrophobic lauroyl esterified forms. The goal of this study was to ascertain the role played by the hydroxyl or lauroyl side groups on the conformational flexibility of the xylan chain backbone. The results reported provide a detailed description of the low-energy conformers of the dimer segments, a complete characterization of the helical structures, an insight into the disordered state of the polysaccharide chains and an estimation of the cohesion of the amorphous solids. Esterification of xylan hydroxyl groups by lauric acid has a large effect on the conformational properties of the glycosidic bonds linking two repeat units. Both the location and the relative energies of the low energy areas of the potential energy surfaces strongly differ: extended and coiled conformations are preferred for the native and hydrophobic forms, respectively. Consequently, the predicted unperturbed polymer chain extension strongly depends on the structure, predicted Lp of the native xylan of 35 A compares favourably well with the experimental ones, this characteristic dramatically decreases to 9A for the hydrophobically modified chain. Curiously, only extended 2(1) and left-handed 3(1) helical structures are calculated stable for both polymers. The estimated cohesive parameters of amorphous bulks reveal that inter-chain interactions are stronger for the xylan chain than that for modified one, the former being stabilized by hydrogen bonds whereas hydrophobic interactions play a determinant role for the latter.

Carbohydrate Conformation↗
PubMed1994

Conformational analysis, pharmacophore identification, and comparative molecular field analysis of ligands for the neuromodulatory sigma 3 receptor.

Molecular modeling studies were carried out on a series of 1-phenyl-3-amino-1,2,3,4-tetrahydronaphthalenes (phenylaminotetralins, PATs), several PAT structural analogs, and various non-PAT ligands that demonstrate a range of affinities for a novel sigma 3 receptor linked to stimulation of tyrosine hydroxylase and dopamine synthesis in rodent brain. In an effort to develop a ligand-binding model for the sigma 3 receptor, a pharmacophore mapping program (DISCO) was used to identify structural features that are common to ligands that exhibit moderate to high binding affinity for sigma 3 sites. DISCO then was utilized to propose a common pharmacophoric region that included one low-energy conformation of each compound in the training set. The resulting alignment was utilized in a comparative molecular field analysis (CoMFA) study in an attempt to correlate the steric and electrostatic fields of the molecules with the respective binding affinities at the sigma 3 receptor. A suitably predictive model was obtained from the CoMFA analysis which will be employed in the development of additional PAT analogs that could potentially display high affinity and selectivity for the sigma 3 receptor. The excluded volumes which resulted from comparing molecular volumes of active and inactive compounds were visualized to examine the limits of steric tolerance imposed by the sigma 3 receptor.

Animals↗
PubMed1985

1H- and 13C-n.m.r. assignments and conformational analysis of some monosaccharide and oligosaccharide substrate-analogues of lysozyme.

The 1H- and 13C-n.m.r. spectra of solutions of GlcNAc, beta-GlcNAc-(1----4)-GlcNAc, and beta-GlcNAc-(1----4)-beta-GlcNAc-(1----4)-GlcNAc in D2O at 50 degrees are interpreted in terms of the conformations, using a combination of 1D- and 2D-n.m.r. spectroscopy and spectra simulation techniques. Two preferred orientations of the hydroxymethyl group were found for each of these saccharides. The conformations have been compared with those found from X-ray crystallographic data and conformational energy calculations.

Animals↗
PubMed2006

Conformational analysis of XA and AX dipeptides in water by electronic circular dichroism and 1H NMR spectroscopy.

We measured the temperature-dependent electronic circular dichroism (ECD) spectra of AX, XA, and XG dipeptides in D2O. The spectra of all XA and AX peptides indicate a substantial population of the polyproline II (PPII) conformation, while the ECD spectra of LG, KG, PG, and AG were found to be quantitatively different from the alanine-based dipeptides. Additional UV absorption data indicate that the ECD spectra of the XG peptides stem from electronic coupling between the peptide and the C-terminal group, and that spectral differences reflect different orientations of the latter. We also measured the 1H NMR spectra of the investigated dipeptides to determine the 3JHalphaNH coupling constants for the C-terminal residue. The observed temperature dependence of the ECD spectra and the respective room-temperature 3JHalphaNH coupling constants were analyzed by a two-state model encompassing PPII and a beta-like conformation. The PPII propensity of alanine in the XA series is only slightly modulated by the N-terminal side chain, and is larger than 50%. As compared to AA, XA peptides containing L, P, S, K V, E, T, and I all cause a relative stabilization of the extended beta-strand conformation. The PPII fractions of XA peptides varied between 0.64 for AA and 0.58 for DA, whereas the PPII fractions of AX peptides were much lower. From the investigated AX peptides, only AL and AQ showed the expected PPII propensity. We found that AT, AI, and AV clearly prefer an extended beta-strand conformation. A quantitative comparison of AA, AAA, and AAAA revealed a hierarchy AAAA > AAA approximately AA for the PPII population, in agreement with predictions from MD calculations and results from Raman optical activity studies (McColl et al. J. Am. Chem. Soc. 2004, 126, 5076).

Alanine↗