Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Conformational analysis”

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
PubMed2000

Conformational analysis of alkylated biuret and triuret: evidence for helicity and helical inversion in oligoisocyanates

The conformations of several oligoisocyanates have been investigated by NMR in order to study the onset and dynamics of helicity in polyisocyanates. Pentaethylbiuret and hexaethyltriuret were found to adopt turns and helices in solution. For hexaethyltriuret, symmetric and asymmetric helices are present. Not only is an interconversion of these forms observed (DeltaG(SA)(double dagger) = 9.3 +/- 0.4 kcal/mol) but also a reversal of helicity (DeltaG(PM)(double dagger) = 9.0 +/- 0.4 kcal/mol). The coalescence pattern for the latter process provides direct evidence for a concerted, conrotatory helical inversion.

Journal Article↗
PubMed2004

Conformational analysis of oleandomycin and its 8-methylene-9-oxime derivative by NMR and molecular modelling.

Conformations of the 14-membered macrolide antibiotic oleandomycin and its 8-methylene-9-oxime derivative were determined in various solvents. The experimental NMR data--coupling constants and NOE contacts--were compared with the results of molecular modelling--molecular mechanics calculations and molecular dynamics simulations. The conformational changes, on the right-hand side of the 14-membered ring, affected mostly the 3JH2,H3 values and NOE crosspeaks H3 or H4 to H11. Oleandomycin was found to be present predominantly in the C3-C5 folded-in conformations in DMSO-d6 solution, whereas in buffered D2O, acetone-d6 and CDCl3, there was a mixture of folded-in and folded-out conformational families. The predominant conformation of the 8-methylene-oleandomycin-9-oxime derivative in solution was a folded-out one although different amounts of folded-in conformation were also present depending on the solvent. Oleandrose and desosamine sugar moieties adopted the usual and expected chair conformation. The conformation around the glycosidic bonds, governing the relative orientation of sugars vs. the lactone ring, showed a certain flexibility within two conformationally close families. We believe that by combining the experimental NMR data and the molecular modelling techniques, as reported in this paper, we have made significant progress in understanding the conformational behaviour and properties of macrolides. Our belief is based on our own current studies on oleandomycins as well as on the previously reported results and best practices concerning other macrolides. A rational for macrolide conformational studies and advances in methodology has been suggested accordingly.

Carbon Isotopes↗
PubMed1990

Conformational analysis of the tachykinins in solution: substance P and physalaemin.

A determination of the solution conformational behavior of two tachykinins, substance P and physalaemin, is described. Two-dimensional homonuclear Hartmann-Hahn (HOHAHA) and rotating-frame cross relaxation spectroscopy (ROESY) are used to obtain complete proton resonance assignments. Interproton distance restraints obtained from ROESY spectroscopy are used to characterize the conformational behavior. These data show that in solution both substance P and physalaemin exist in a mixture of conformational states, rather than as a single three-dimensional structure. In water both peptides prefer to be in an extended chain structure. In methanol, their behavior is described as a mixture of beta-turn conformations in dynamic equilibrium. Solvent titration data and chemical shift temperature coefficients complement the NMR estimate of interproton distances by locating hydrogen bonds and serving to identify predominant conformational states. The C-terminal tetrapeptide segment has the same conformational behavior for both substance P and physalaemin. In physalaemin, the midsegment of the peptide may also be constrained by formation of a salt bridge. The conformational behavior of substance P and physalaemin is discussed in relation to potency and receptor binding properties.

Magnetic Resonance Spectroscopy↗
PubMed1985

Sidechain and backbone potential function for conformational analysis of proteins.

An improved potential function has been devised for the calculation of protein conformations. Each amino acid residue is represented by two points. The mainchain is traced by the sequence of C alpha atoms, and the details of sidechain structure and interactions are represented by a representative sidechain atom. This potential function has been developed from a data base of 22 high resolution protein crystal structures and includes the components of an earlier potential developed from a similar data base where each amino acid residue is represented by only its C alpha atom. In virtually all aspects of testing, the present potential betters the previous single-point potential, and is shown to be useful in the simulation of protein folding.

Amino Acid Sequence↗
PubMedDate not supplied

[Theoretical conformational analysis of noinvalent carboxypeptidase A complexes with inhibitors and substrates].

Semi-empirical calculations of conformational properties of acetyl-L-tyrosine, glycyl-L-tyrosine, acetyl-L-alanyl-L-tyrosine and acetyl-L-alanyl-L-alanyl-tyrosine and their noncovalent complexes with carboxypeptidase A (CPA) are presented. Each of these molecules binds in the active site of CPA by only one binding mode. The substrates are practically free of intramolecular tension. It is shown that the binding of an aromatic side chain of a C-terminal residue of substrate provides productive orientation of the susceptible peptide bond. The sterochemical aspects of the interactions of Tyr-248 and Glu-270 residues with the substrates are considered.

Binding Sites↗
PubMed1984

Conformational analysis of the antiulcer drug pirenzepine. X-ray investigations, molecular mechanics and quantum mechanical calculations and comparisons with structurally or pharmacologically related compounds.

The crystal structures of the antiulcer drug 5,11-dihydro-11-[(4-methyl-1-piperazinyl) acetyl]-6H-pyrido[2,3-b] [1,4]benzodiazepin-6-one dihydrochloride (pirenzepine dihydrochloride, L-S 519 CL 2, Gastrozepin) and its monoprotonated form (pirenzepine monohydrochloride, L-S 519 CL) were determined by X-ray analysis. Molecular mechanics (MMPI) and semiempirical quantum chemical (MNDO) calculations showed that the calculated minimum energy conformations of the tricycle and of the exocyclic amide group are in agreement with the crystal structures. The conformational energies of pirenzepine as a function of four important torsional angles were calculated using different semiempirical quantum chemical methods with the CNDO/2 (complete neglect of differential overlap)-, MNDO (modified neglect of diatomic overlap)- and PCILO (perturbative configuration interaction using localized orbitals)-approximations. The conformation of one local energy minimum corresponds closely to the crystal structure of pirenzepine monohydrochloride. This conformation has a spatial arrangement which is analogous to a single consistent conformation known from the literature of 24 anticholinergic agents determined from their crystal structures by a computer graphics analysis. On the other hand there are no structural relationships of any low energy conformation of pirenzepine to conformations of other classes of tricyclic compounds which could rationalize their antidepressant, neuroleptic or antihistaminic activity. This finding explains the absence of any central effect of pirenzepine following intracerebral application. The computational elucidation of the conformational requirements for the interaction with the muscarinic receptors may be helpful for the interpretation of the selectivity of pirenzepine within the muscarinic system.

Antidepressive Agents, Tricyclic↗
PubMed2002

Conformational analysis of furanose rings with PSEUROT: parametrization for rings possessing the arabino, lyxo, ribo, and xylo stereochemistry and application to arabinofuranosides.

The solution conformation of a furanose ring can be assessed through PSEUROT analysis of three-bond (1)H-(1)H coupling constants ((3)J(HH)) of the ring hydrogens. For each coupling constant, PSEUROT requires two parameters, A and B, which are used to translate the H[bond]C[bond]C[bond]H dihedral angle predicted from the (3)J(HH) into an endocyclic torsion angle from which the identity of the conformers can be determined. In this paper, we have used density functional theory methods to generate a family of envelope conformers for methyl furanosides 1-8. From these structures, A and B were calculated for each H[bond]C[bond]C[bond]H fragment. In turn, the values of these parameters for the arabinofuranose ring were used in PSEUROT calculations to determine the conformers populated by monosaccharides 1 and 2 as well as the furanose rings in oligosaccharides 9-15. The results of these analyses are consistent with the low-energy conformers identified from previous computational and X-ray crystallographic studies of 1 and 2.

Chemistry, Organic↗
PubMed1984

DNA fragment conformations. A 1H-NMR conformational analysis of the d(G-G)-chelated platinum-oligonucleotide d(A-T-G-G)cisPt.

The conformation of d(A-T-G-G) and d(A-T-G-G)cisPt has been investigated by 1H-NMR at 500 MHz and 90 MHz under various experimental conditions of temperature and concentration. Analysis of the coupling constants between the deoxyribose protons shows that all the sugar rings of d(A-T-G-G) adopt the S(C2'-endo) conformation most of the time. By contrast, in the platinated tetramer, d(A-T-G-G)cisPt, the N(C3'-endo) conformation is highly predominant for the internal dG residue while the S(C2'-endo) conformation is largely favoured for the other residues as in the case of the unplatinated compound. The relaxation time and nuclear Overhauser effect measurements indicate that the orientation of the two guanines of d(A-T-G-G)cisPt is anti in agreement with the previous results obtained for the dimers: r(G-G)cisPt, d(G-G)cisPt. On lowering the temperature from 80 degrees C to 20 degrees C, several proton resonances of d(A-T-G-G)cisPt exhibit large chemical shift and linewidth variations. The most spectacular temperature effect was observed for the internal dG(H1') and dT(H4') protons. All the delta = f(t) curves display a sigmoid form with the same mid-point temperature of 44 +/- 2 degrees C. This mid-point temperature together with the observed chemical shift and linewidth variations were found to be independent of the d(A-T-G-G)cisPt concentration. These results suggest that d(A-T-G-G)cisPt can adopt two different conformations depending on the temperature. The enthalpy for the transition between the high and low temperature conformations is about 84 kJ/mol.

Cisplatin↗
PubMed2006

Conformational analysis of a cyclopropane analogue of phenylalanine with two geminal phenyl substituents.

Quantum mechanical methods have been used to investigate the intrinsic conformational preferences of 1-amino-2,2-diphenylcyclopropanecarboxylic acid (c(3)Dip), a cyclopropane analogue of phenylalanine bearing two phenyl substituents on the same beta-carbon. Geometries, energies, and frequencies were calculated on the N-acetyl-N'-methylamide derivative at the HF and B3LYP levels using the 6-31G(d), 6-311G(d), and 6-31+G(d,p) basis sets. Four minimum energy conformations were characterized: axial C(7), equatorial C(7), right-handed helix, and polyproline II. Analysis of the whole results, which are fully consistent with available experimental data, indicates that c(3)Dip tends to promote gamma-turn conformations.

Cyclopropanes↗
PubMed1982

Conformational analysis of the adduct cis-[Pt(NH3)2 d(GpG)]+ in aqueous solution. A high field (500-300 MHz) nuclear magnetic resonance investigation.

A 500, 400 and 300 MHz proton NMR study of the reaction product of cis-Pt(NH3)2Cl2 or cis-[Pt(NH3)2 (H2O)2] (NO3)2 with the deoxydinucleotide d(GpG): cis-[Pt(NH3)2 d(GpG)] was carried out. Complete assignment of the proton resonances by decoupling experiments and computer simulation of the high field part of the spectrum yield proton-proton and proton-phosphorus coupling constants of high precision. Analysis of these coupling constants reveal a 100% N (C3'-endo) conformation for the deoxyribose ring at the 5'-terminal part of the chelated d(GpG) moiety. In contrast, the 3'-terminal -pG part of the molecule displays the normal behaviour for deoxyriboses: the sugar ring prefers to adopt an S (C2'-endo) conformation (about 70%). Extrapolating from this model compound, it is suggested that Pt chelation by a -dGpdG- sequence of DNA would require a S to N conformational change of one deoxyribose moiety as the main conformational alteration and lead to a kink in one strand of the double-helical structure of DNA.

Chemical Phenomena↗
PubMed1998

A comparative conformational analysis of thimet oligopeptidase (EC 3.4.24.15) substrates.

The specificity of thimet oligopeptidase (EC 3.4.24.15) (TOP 24.15) does not agree with theoretical models devised to explain the specificity characteristic of peptidases toward certain sequences of amino acid residues. According to previous studies peptide chains hydrolyzed by TOP 24.15 adopt similar main chain conformations, although with different and in some cases small probabilities of occurrence in aqueous solution. To determine specific structural features recognized by TOP 24.15, a conformational search including eight polypeptides with known susceptibilities for catalytic hydrolysis was executed and the distribution of each main chain conformation found in the search was tabulated. Two sets of main chain conformations were selected, those common to all peptides in the study and those common only to substrates of TOP 24.15. The former set is very small and includes mainly extended conformations. In contrast, the latter set is large and its conformations are coiled and exhibit sharp turns coincident with positions of hydrolysis by TOP 24.15. These results indicate a possible basis for the selectivity of TOP 24.15.

Kinetics↗
PubMed1990

Quantitative conformational analysis of cytochrome c bound to phospholipid vesicles studied by resonance Raman spectroscopy.

Resonance Raman spectra have been recorded from ferri-cytochrome c bound to phospholipid vesicles composed of dimyristoyl phosphatidylglycerol (DMPG), dioleoyl phosphatidylglycerol (DOPG) or dioleoyl phosphatidylglycerol-dioleoyl phosphatidylcholine (DOPG-DOPC) (70:30 mole/mole). Lipid binding induces very significant conformational changes in the protein molecule. The resonance Raman spectra differ in their content of bands originating from two different conformational species, I and II, of the protein, and from two different spin and coordination states of the heme in conformation II. Data of sufficiently high precision were obtained that the spectra of the individual species could be quantitated by a constraint interactive fitting routine using single Lorentzian profiles. In the high frequency, or marker band region (1200 to 1700 cm-1), the frequencies, half widths and relative intensities of the individual bands could be estimated from previous surface enhanced resonance Raman measurements on cytochrome c adsorbed on a silver electrode. These were then further optimized to yield both the spectral parameters and relative contents of the different species. In the low frequency, or fingerprint, region (200 to 800 cm-1), the spectral parameters of the individual species were obtained from difference spectra derived by sequential subtraction between the spectra of ferri-cytochrome c in the three different lipid systems, using the relative proportions of the species derived from the marker band region. These parameters were then subsequently refined by iterative optimization. The optimized spectral parameters in both frequency regions for the six-coordinated low spin states I and II, and for the five-coordinated high spin state II are presented.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed2004

Novel bicyclic sugar modified nucleosides: synthesis, conformational analysis and antiviral evaluation.

Methodology previously described by us was applied to the formation of novel conformationally restrained bicyclic sugar modified nucleosides, with introduction of an oxazole and a thiocarbamate ring at the 2('),3(')-positions of the ribonucleosides. Two novel alkyl derivatives of 2('),3(')-dideoxy-2('),3(')-oxazole-beta-d-uridine and a novel uridine 2('),3(')-thiocarbamate were successfully synthesised. Conformational evaluation of all the synthesised compounds was conducted using the theoretical potential energy calculation via the macromodel v.6.0 molecular modelling programme. The conformationally restrained nucleosides described were evaluated against a wide range of DNA and RNA viruses. None of the compounds showed specific antiviral effects at subtoxic concentrations.

Antiviral Agents↗
PubMed1993

Conformationally restrained analogs of sympathomimetic catecholamines. Synthesis, conformational analysis, and adrenergic activity of isochroman derivatives.

In previous papers dealing with the study of the conformations and the biopharmacological activity of conformationally restrained analogs of sympathomimetic catecholamines (NE and ISO), proposals were advanced for the three-dimensional molecular models A, B, and C; these models provided information about the steric requirements for the direct activation of alpha 1, alpha 2,beta 1, and beta 2 adrenoceptors, respectively. The 1-(aminomethyl)-6,7-dihydroxyisochromans 11 and 12 and the 1-(aminomethyl)-5,6-dihydroxyisochromans 13 and 14 (1-AMDICs) are two different types of semirigid analogs of NE and ISO. The alpha 1, alpha 2, beta 1, and beta 2 adrenergic properties of the 1-AMDICs 11-14 were evaluated in vitro, both by radioligand binding assays and by functional tests on isolated preparations, and were compared with those of their parent compounds (NE and ISO). The results of a conformational study carried out by means of both 1H NMR spectrometry and theoretical calculations indicated that, in these 1-AMDICs, the presumed active groups (aryl moiety, amine nitrogen and benzylic ethereal oxygen) are in a spatial relationship corresponding to the one found for NE and ISO in their preferred conformations, which also proved to be the pharmacophoric conformation in the models A-C. By means of a comparison of the stereostructures of the 1-AMDICs 11-14 with their biopharmacological properties, it was possible to obtain a further definition of the model B with respect to the activation of the alpha 2 adrenoceptors; the superimposition of the 1-AMDICs 11 and 12 with the molecular model C made it possible to detect an area of the beta-adrenergic receptors which might hinder the fit of adrenergic drugs that are analogs of catecholamines with these receptors.

Animals↗
PubMed1984

A potential function for conformational analysis of proteins.

We have devised a residue-residue potential function for low resolution protein conformational calculations. The interactions between residues near in sequence maintain correct secondary structure, while the long-range terms in the potential govern the larger packing features and overall globularity. The short-range terms were calculated by comparing the observed distributions of distances between C alpha atoms in 35 protein crystal structures to the expected distributions and assigning the discrepancies to a Boltzmann distribution due to an effective potential. Long-range terms were adjusted to ensure that the crystal structure of bovine pancreatic trypsin inhibitor has a lower total energy than perturbed conformations of the same molecule. Thus the empirical potential function implicity contains solvation and conformational entropy effects along with the usual Van der Waals and electrostatic energies. Extensive testing of the potential on trypsin inhibitor and other proteins establishes that it is generally applicable to small proteins, it does not attempt to compress or expand the conformations found by X-ray crystallography, standard secondary structural features are maintained under the potential, and there are so many local minima that local minimization can be trusted to return a perturbed structure to the native conformation only if they differ initially by less than 1 A.

Animals↗
PubMed1996

Structural and conformational analysis of glycan moieties in situ on isotopically 13C, 15N-enriched recombinant human chorionic gonadotropin.

The conformational properties in solution of the glycans on the alpha subunit of recombinant human chorionic gonadotropin are described, using high-resolution multinuclear NMR studies on uniformly 13C, 15N-enriched recombinant glycoprotein expressed in CHO cells. The glycan important for full biological activity of hCG, namely, that at Asn 52, appears to extend into solution both in the isolated alpha subunit and in complex with the beta subunit. The disposition of this glycan with respect to the protein backbone suggests that glycosylation maintains full biological activity of hCG either by interacting with a lectin-like region of the hCG receptor or by reducing the affinity of the hormone for the hCG receptor and preventing its down-regulation.

Carbohydrate Conformation↗