Home About us Contact
|
Home About us Contact | ||
|
|
||
Conformational Study (conformational + study)
Selected AbstractsConformational Study of Short Peptoid Models for Future Applications as Potent Antimicrobial CompoundsMACROMOLECULAR THEORY AND SIMULATIONS, Issue 3 2007Fateh Singh Nandel Abstract Development of peptides as clinically useful drugs is limited by their poor metabolic stability and low bioavailability. Recent progresses in chemical synthesis and design have led to several strategies for producing potent mimetics. This study aims to analyze sequence/structure requirements and composition for antimicrobial peptoid designs, as use of peptoids is one of the most representative approaches to meet the goal of biomimicry. Analysis of the designs showed that for maximum activity and minimum hemolysis, the plane of the aromatic residues should be at an angle between 0 and 90,° with respect to membranes, cationic residues need not be at the terminal position, and central positions should be uniform in NIle, NLys, and NPhe residues. [source] Metal Binding Properties of Fluorescent Analogues of Trichogin GA,IV: A Conformational Study by Time-Resolved Spectroscopy and Molecular Mechanics InvestigationsCHEMBIOCHEM, Issue 1 2009Mariano Venanzi Prof. Abstract The metal ion binding properties of two fluorescent analogues of trichogin GA,IV, which is a natural undecapeptide showing significant antimicrobial activity, were studied by circular dichroism, time-resolved optical spectroscopy, and molecular mechanics calculations. Binding of CaII and GdIII to the peptides investigated was shown to promote a structural transition from highly helical conformations to folded structures characterized by formation of a loop that embedded the metal ion. Time-resolved spectroscopy revealed that peptide dynamics is also remarkably affected by ion binding: peptide-backbone motions slowed down to the microsecond time scale. Finally, molecular mechanics calculations emphasized the role of the central Gly5-Gly6 motif, which allowed for the twisting of the peptide segment that gave rise to the formation of the binding cavity. [source] Synthesis of 3-Aminolactams as X-Gly Constrained Pseudodipeptides and Conformational Study of a Trp-Gly Surrogate.CHEMINFORM, Issue 16 2004Marta Ecija No abstract is available for this article. [source] ChemInform Abstract: Cyclophane-Type Bis-calix[4]arenes: Efficient Synthesis via Quadruple Cycloadditive Macrocyclization and Conformational Study.CHEMINFORM, Issue 11 2001Gil Tae Hwang Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a "Full Text" option. The original article is trackable via the "References" option. [source] Conformational study on glycosylated asparagine-oligopeptides by NMR spectroscopy and molecular dynamics calculationsJOURNAL OF PEPTIDE SCIENCE, Issue 8 2005Stefania Mazzini Abstract The conformational properties of the homo oligomers of increasing chain length Boc-(Asn)n -NHMe (n = 2, 4, 5), (GlcNAc-,-Asn)n -NHMe (n = 2, 4, 5, 8) and Boc-[GlcNAc(Ac)3 -,-Asn]n -NHMe (n = 2, 4, 5) were studied by using NOE experiments and molecular dynamic calculations (MD). Sequential NOEs and medium range NOEs, including (i,i+2) interactions, were detected by ROESY experiments and quantified. The calculated inter-proton distances are longer than those characteristic of ,-turn secondary structures. Owing to the large conformational motions expected for linear peptides, MD simulations were performed without NMR constraints, with explicit water and by applying different treatments of the electrostatic interactions. In agreement with the NOE results, the simulations showed, for all peptides, the presence of both folded and unfolded structures. The existence of significant populations of ,-turn structures can be excluded for all the examined compounds, but two families of structures were more often recognized. The first one with sinusoidal or S-shaped forms, and another family of large turns together with some more extended conformations. Only the glycosylated pentapeptide shows in vacuo a large amount of structures with helical shaped form. The results achieved in water and in DMSO are compared and discussed, together with the effect of the glycosylation. Copyright © 2005 European Peptide Society and John Wiley & Sons, Ltd. [source] Conformational study of AZT in aqueous solution and adsorbed on a silver surface by means of Raman spectroscopyJOURNAL OF RAMAN SPECTROSCOPY, Issue 1 2002Laura Rivas The adsorption and conformation of the anti-HIV drug AZT, and also thymine and 2,-deoxythymidine, were studied on Ag colloids by surface-enhanced Raman spectroscopy, showing that the conformational change induced by the adsorption on an Ag surface is similar to that induced by an alkaline pH, both related to deprotonation of the N-3 atom leading to the C-3,- endo conformer. Copyright © 2002 John Wiley & Sons, Ltd. [source] Formation of the B Ring in Steroids and Hopanoids from SqualeneEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 10 2004B. Andes Hess Jr. Abstract A theoretical conformational study based on density functional calculations provides evidence that the sterol and nonsterol cyclizations of squalene to triterpenes are controlled by conformational effects as has been previously suggested. It was found that different conformers of a model system of squalene give rise to the chair,boat conformation found in the steroids and the chair,chair conformation of the pentacyclic 3-deoxytriterpenes for their A and B rings. It is suggested that the enzymes play a key role in holding the substrate in the proper orientation for these cyclizations to occur. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004) [source] Synthesis and conformational study of P -heterocyclic androst-5-ene derivativesHETEROATOM CHEMISTRY, Issue 1 2008Éva Frank The reactions of (20R)-3,-acetoxy-21-hydroxymethylpregn-5-en-20-ol (2) and (20R)-3,-acetoxypregn-5-ene-20,21-diol (11) with phenylphosphonic dichloride 3 and aryl dichlorophosphates 4,6 afforded novel types of P -heterocyclic androst-5-ene derivatives 7,10 and 12 as epimeric pairs. The diastereomers were separated by column chromatography and were characterized by NMR spectroscopy. Estimation of the stereostructures of the corresponding epimers by B3LYP/631G(d) DFT ab initio calculations suggested that the six-membered hetero ring in compounds 7b and 8a,10a adopts predominantly a chair conformation, with the P -substituents in their preferred orientation. The cyclic phosphonate moiety in 7a or 8b,10b, however, seems to exist as an equilibrium mixture of chair,distorted- boat or chair,chair forms. The theoretical calculations indicate that the conformational equilibrium is shifted toward the distorted- boat conformer for 7a, with a pseudoequatorial P -phenyl substituent, whereas for 8b,10b the chair conformer with an equatorial P -phenoxy group predominates. © 2008 Wiley Periodicals, Inc. Heteroatom Chem 19:7,14, 2008; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/hc.20372 [source] Ab initio conformational study of the P6 potential surface: Evidence for a low-lying one-electron-bonded isomerHETEROATOM CHEMISTRY, Issue 2 2007Philippe C. Hiberty The low-lying isomers of the P6 species are investigated at various levels of calculations, ranging from MP2/6-31G(d) to CCSD(T) in triple-zeta basis set involving polarization functions up to f. In addition to the five possible normal-valent isomers, which obey the octet rules, several other conformations are found to be stationary points on the potential energy surface. Among the five normal-valent isomers, the benzvalene structure is found to be the most stable one, in agreement with former studies. The benzene-like D6h planar hexagon is the least stable one, lying 32.3 kcal/mol over benzvalene, and spontaneously distorts to a less symmetrical, nonplanar six-membered ring. Above the benzvalene structure, and lying, respectively, 5.8 and 15.8 kcal/mol higher, the two lowest lying isomers are the prismane and the chair-like forms. This latter conformation, which does not obey the octet rule, exhibits two one-electron PP hemibonds and can be considered as a generic model for a new category of heterobenzene analogs, among which is the recently discovered dimer of diphosphirenyl radical. © 2007 Wiley Periodicals, Inc. Heteroatom Chem 18:129,134, 2007; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/hc.20324 [source] A computational study of the carboxylic acid of phloroglucinol in vacuo and in water solutionINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 3 2010Liliana Mammino Abstract 2,4,6-Trihydroxybenzoic acid (FA) is the carboxylic acid of phloroglucinol and, in turn, the parent compound of many biologically active compounds. The biological activities of FA are "extreme" among trihydroxybenzoic acids (e.g., lowest antioxidant activity, highest toxicity toward crustaceans). A complete MP2/6-31++G(d,p) conformational study in vacuo shows that the lowest energy conformers contain two intramolecular hydrogen bonds between the COOH function and the two ortho phenolic OH, with the Z form of COOH preferred over the E form. Comparisons with conformers in which the H-bonds are removed enable fairly reliable evaluations of their energy, because of an off-plane shift of COOH on H-bond removal, decreasing the effects of lone pair repulsion. Comparisons with the other hydroxybenzoic acids (extensively calculated in vacuo at the same level of theory) suggest that FA has the strongest intramolecular H-bonds. PCM calculations of FA in water solution show the same sequence of relative stabilities as in vacuo, with narrower differences because of the greater solvent stabilization of higher energy conformers. Calculations of adducts with water molecules H-bonded to different donor,acceptor centers of FA show the preferred arrangements of water molecules around the different regions of FA and confirm that the stronger intramolecular H-bonds are not broken on competition with the possibility of formation of intermolecular H-bonds. HF/6-31++G(d,p) calculations of adducts, in which the FA molecule is completely surrounded by water molecules, show that 14,16 water molecules (depending on the FA conformer geometry) realize arrangements corresponding to a presumable first solvation layer, with all the water molecules directly H-bonded to donor,acceptor centers of FA or bridging water molecules directly H-bonded to them. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source] Probing structural requirements of fMLP receptor: On the size of the hydrophobic pocket corresponding to residue 2 of the tripeptideJOURNAL OF PEPTIDE SCIENCE, Issue 2 2002Susanna Spisani Abstract The conformationally constrained f- L -Met-Acnc- L -Phe-OMe (n = 4,9,12) tripeptides, analogues of the chemoattractant f- L -Met- L -Leu- L -Phe-OH, were synthesized in solution by classical methods and fully characterized. These compounds and the published f- L -Met-Xxx- L -Phe-OMe (Xxx = Aib and Acnc where n = 3, 5,8) analogues were compared to determine the combined effect of backbone preferred conformation and side-chain bulkiness at position 2 on the relation of 3D-structure to biological activity. A conformational study of all the analogues was performed in solution by FT-IR absorption and 1H-NMR techniques. In parallel, each peptide was tested for its ability to induce chemotaxis, superoxide anion production and lysozyme secretion from human neutrophils. The biological and conformational data are discussed in relation to the proposed model of the chemotactic receptor on neutrophils, in particular of the hydrophobic pocket accommodating residue 2 of the tripeptide. Copyright © 2002 European Peptide Society and John Wiley & Sons, Ltd. [source] 1H and 13C NMR conformational study of 2-(benzotriazol-1-yl)-substituted tetrahydrofuransJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 3 2003Alan R. Katritzky Abstract Assignments of the proton and carbon NMR signals for 2-(benzotriazol-1-yl)tetrahydrofurans 1,6 are based on 1H,1H COSY, NOESY, 1H,13C heteronuclear HETCOR, 1H,13C heteronuclear long-range HETCOR-LR and nuclear Overhauser enhancement experiments, and supported by selective spin decoupling experiments. The electronic and steric effects of the 2-benzotriazolyl substituent on the 1H and 13C NMR chemical shifts are evaluated and discussed. Conformational isomers cis and trans are distinguished by the magnitude of the J(H,2,H,3) coupling constant, by one-bond 1J(C,2, H,2) coupling constants and by 13C chemical shifts of the C-2 anomeric carbon. The benzotriazol-1-yl group prefers the pseudo-axial orientation in each of 1,6. The stereochemistry and conformation of 6 are rigorously demonstrated by an x-ray structure. Copyright © 2003 John Wiley & Sons, Ltd. [source] Structure and conformational analysis of a bidentate pro-ligand, C21H34N2S2, from powder synchrotron diffraction data and solid-state DFTB calculationsACTA CRYSTALLOGRAPHICA SECTION B, Issue 5 2009Edward E. Ávila The molecular and crystalline structure of ethyl 1,,2,,3,,4,,4a,,5,,6,,7,-octahydrodispiro[cyclohexane-1,2,-quinazoline-4,,1,,-cyclohexane]-8,-carbodithioate (I) was solved and refined from powder synchrotron X-ray diffraction data. The initial model for the structural solution in direct space using the simulated annealing algorithm implemented in DASH [David et al. (2006). J. Appl. Cryst.39, 910,915] was obtained performing a conformational study on the fused six-membered rings of the octahydroquinazoline system and the two spiran cyclohexane rings of (I). The best model was chosen using experimental evidence from 1H and 13C NMR [Contreras et al. (2001). J. Heterocycl. Chem.38, 1223,1225] in combination with semi-empirical AM1 calculations. In the refined structure the two spiran rings have the chair conformation, while both of the fused rings in the octahydroquinazoline system have half-chair conformations compared with in-vacuum density-functional theory (DFT) B3LYP/6-311G*, DFTB (density-functional tight-binding) theoretical calculations in the solid state and other related structures from X-ray diffraction data. Compound (I) presents weak intramolecular hydrogen bonds of the type N,H...S and C,H...S, which produce delocalization of the electron density in the generated rings described by graph symbols S(6) and S(5). Packing of the molecules is dominated by van der Waals interactions. [source] Structural studies of wheat flour glutenin polymers by CD spectroscopyBIOPOLYMERS, Issue 4 2004S. Fisichella Abstract A dissolution procedure of unreduced glutenin polymers of three wheat flour varieties (WRU 6981, Alisei 1, and Alisei 2) by sonication in the presence of SDS (sodium dodecyl sulphate), after the elimination of albumins, globulins, and gliadins, was achieved, and the molecular weight distribution of glutenin polymers obtained by this method was measured by matrix assisted laser desorption ionization,time of flight (MALDI-TOF) mass spectrometry. A structural study by CD spectroscopy at different temperatures of WRU 6981 glutenin polymer and of 1Ax1 high- Mr (relative molecular mass) glutenin subunit, which is the only high- Mr subunit contained in WRU 6981 flour, was undertaken to understand if the information obtained from the single subunit were applicable to the total polymer. CD spectroscopy also has been employed to study the glutenin polymers obtained by Alisei 1 and Alisei 2 wheat flours; Alisei 1 biotype contained 1Bx7 and 1Dx2+1Dy12 high-Mr subunits, whereas the Alisei 2 biotype contained only 1Bx7 and 1Dy12 subunits. A conformational study was undertaken by CD spectroscopy at different temperatures and in the presence of some chemical denaturant agents, such as urea and sodium dodecyl sulphate, in order to obtain information about their intrinsic stability and to verify if the 1Dx2 subunit presence determined a different structural behavior between Alisei 1 and Alisei 2 polymers. MALDI-TOF mass spectrometric experiments showed that the glutenin polymers molecular weights were in the mass range of 500,000,5,000,000. CD spectra indicated that a single conformational state did not predominate in the temperature range studied but equilibrium between two distinct conformational states existed; moreover, all the changes induced by urea and by SDS followed a multistep transition process. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004 [source] | ||||||||||