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PubMed1990

Conformational analysis of xyloglucans.

Xyloglucan isolated from the elongating regions of pea stems was examined using X-ray diffraction and energy calculations. The X-ray fibre pattern suggested that the backbone (1----4)-beta-D-glucan takes an extended two-fold helix similar to common cellulose. In order to study side chains (xylosyl or fucosyl-galactosyl-xylosyl residues) of the polysaccharide, energetically preferable conformations were searched by calculation of interactions between non-bonded atom pairs. A stepwise calculation for the conformation of fucosyl-galactosyl-xylosyl residue gave 10 allowed area (phi-psi) maps which are useful to deduce xyloglucan conformations of both monocotyledons and dicotyledons in the walls of growing plant cells.

Carbohydrate Conformation↗
PubMed2003

Conformational analysis of p-tert-butylcalix[4]arene derivatives with trans-alkyl substituents on opposite methylene bridges: destabilization of the cone form by axial alkyl substituents.

The stereochemistry of calix[4]arenes substituted by a pair of identical alkyl substituents in a trans fashion at two distal bridges is analyzed. MM3 calculations suggest that increasing the bulk of the alkyl group at the bridges destabilizes those conformations possessing an axial disposition of the substituent. In contrast to the 1,3-dimethyl ether of p-tert-butylcalix[4]arene, which adopts a cone conformation, solution NMR data indicate that the 1,2-alternate conformation is preferred in the dimethyl ether derivatives 5b (alkyl = i-Pr) and 5c (alkyl = t-Bu). In the derivative substituted by the less bulky methyl substituent (5a), both the cone and 1,2-alternate forms coexist in CDCl3. Increasing the polarity of the solvent increases the relative population of the cone form of 5a and 5b. The steric destabilization ensuing from the presence of the axial substituent is so large in the cone conformation of 5c that the 1,2-alternate conformer is the major form even in polar solvents. The cone --> 1,2-alternate interconversion barrier of 5a is 18.2 kcal mol(-1), indicating that the presence of an axial methyl group both destabilizes the cone conformation and decreases its rigidity.

Journal Article↗
PubMed1993

The crystal structure and conformational analysis of substituted 2,7-dioxabicyclo[4,1,0]heptanes: 1,2-anhydro-3,4,6-tri-O-benzyl-beta-D-talopyranose.

The title compound, C28H27O5, is triclinic, space group P1 with unit cell dimensions a = 12.763(2), b = 11.130(2), c = 4.764(3) A, alpha = 73.78(3), beta = 82.89(3), gamma = 62.16(1) degrees, V = 574.8(4) A3, and Z = 1. The pyranose ring has an 4H5 conformation with some flattening at C-4. Molecular mechanisms calculations indicate that the 4H5 conformation of the pyranose ring in the title compound is the most stable conformation.

Carbohydrate Conformation↗
PubMed1983

Mode of organization of galactolipids: a conformational analysis.

Despite the fact that photosynthetic membranes show the conventional bilayer structure, their major lipid component monogalactosyldiacylglycerol does not form lamellar structure but takes up an hexagonal-II structure when dispersed alone in water and forms inverted lipids micelle structures when dispersed together with other lipid components of the photosynthetic membrane. We present here evidence that the mode of organization of these lipids can be predicted from a conformational approach allowing to describe the configuration of assembled amphiphilic molecules. The minimal conformational energy is calculated as the sum of the contributions resulting from the Van der Waals interactions, the torsional potentials, the electrostatic interaction and the transfer energy. Because of its calculated "cone shaped" structure monogalactosyldiacylglycerol forms inverted lipid structure with the hydrophilic groups pointing inward; for digalactosyldiacylglycerol, an other essential lipid constituent of photosynthetic membrane, its calculated cylindrical shape induces an organization in bilayer structures.

Galactolipids↗
PubMed1993

Molecular structures, conformational analysis, and preferential modes of binding of 3-aroyl-2-arylbenzo[b]thiophene estrogen receptor ligands: LY117018 and aryl azide photoaffinity labeling analogs.

Structural and computational modeling studies were performed on the antiestrogen LY117018 (3) and two photoaffinity labeling analogs, in which an azide replaces the basic ether side chain (methyl ether tetrafluoro azide 7 and its protio analog 8). These studies were undertaken in order to determine the conformational preferences of these compounds and to propose favorable orientational modes for their binding to the estrogen receptor. In the crystallographic studies, we found that, unlike tetrafluoro azide 7, which adopts a face-to-face stacking of the p-hydroxyphenyl and benzoyl groups in the solid state, the pendant rings in the corresponding protio analog 8 are found in a predominantly offset pi-stacked array. In LY117018, which has an ether on the benzoyl ring, stacking of the pendant rings does not occur in the crystal structure; it assumes a T-shape, with the benzoyl group oriented perpendicular to the benzo[b]thiophene nucleus. In modeling studies, analogs of LY117018, 7, and 8 were subjected to a conformational grid search by molecular mechanics, and for each compound, three low-energy conformers (and their atropisomers) were obtained. These conformers were further geometry optimized by semiempirical molecular orbital calculations. For each compound, one of the three minimum-energy conformers is quite similar to the solid-state geometry. The computational structure of the tetrafluoro azide showed the greatest stacking between the benzoyl group and the p-methoxyphenyl ring, but less stacking than was observed in the crystallographic structure. The orientational preferences of these benzo[b]thiophene ligands with the estrogen receptor were analyzed with the receptor volume mapping technique, a method based on the correspondence of the hydroxyl groups and the volume that the benzo[b]thiophene compound shares with a composite molecular volume of high-affinity estradiol-type ligands (the receptor excluded volume, RExV). If the benzo[b]thiophene nucleus is overlapped with the steroid AB rings, the best overlap with the RExV is achieved, but there is poor correspondence of the hydroxyl groups. An orientation and conformation in which the benzoyl group of the 3-benzoyl-2-aryl-benzo[b]thiophenes occupies a 7 alpha-like position relative to the steroid produces both ample volume overlap with the RExV and close approximation of the hydroxyl groups and is presented as the putative bioactive conformation.

Affinity Labels↗
PubMed2001

Synthesis and conformational analysis of fusidic acid side chain derivatives in relation to antibacterial activity.

Novel fusidic acid type antibiotics having flexible side chains are described. Saturation of the double bond between C-17 and C-20 of fusidic acid produces four stereoisomers differing in the configuration at C-17 and C-20. The structure-activity relationship of the stereoisomers was studied using computer-assisted analyses of low-energy conformations and crystallographic data. Only one of the four stereoisomers showed potent antibiotic activity comparable with that of fusidic acid, whereas the other three stereoisomers retained little or no activity. The orientation of the side chain is crucial, and there is only a limited space for bioactive side chain conformations. This investigation demonstrates the essential role of the side chain conformations in relation to antibacterial activity and contradicts earlier assumptions that the Delta17(20) bond is an essential feature in the molecule.

Anti-Bacterial Agents↗
PubMed1983

A conformational analysis of the (+) anti BPDE adduct to the guanine amino group of dCpdG.

The (+) anti isomer of benz[a]pyrene diol epoxide (BPDE), 7 beta, 8 alpha-dihydroxy-9 alpha, 10 alpha-epoxy-7,8,9,10-tetrahydrobenz [a] pyrene has been identified as the probable tumorigenic lesion in mammalian systems. It forms a predominant adduct with DNA at N2 of guanine. In order to elucidate its conformation in atomic resolution detail, minimized conformational potential energy calculations were performed for the adduct with dCpdG. A global conformation search involving about 1000 trials was made. The lowest energy conformation had stacking between the hydrocarbon and the adjacent cytidine, in agreement with CD studies on modified GpU and UpG. This conformer differed from the B form most notably in the guanine glycosidic torsion, which is high anti. The next lowest energy form had torsion angles like the B form, with guanine-cytidine stacking. These two conformers differ in energy by only 2.1 kcal./mole, suggesting that their relative stability could easily be reversed in larger polymers, or under specific environmental conditions. Other conformations, with base-hydrocarbon or base-base stacking are also found, at somewhat higher energies. The Z form is at 7.8 kcal./mole. Thus, this adduct stabilizes the B form, in contrast with the N2 linked AAF adduct, which stabilizes the Z conformation.

7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide↗
PubMed2000

Semiempirical and ab initio conformational analysis of 2-methylene-8,8-dimethyl-1,4,6,10-tetraoxaspiro[4.5] decane with application of GIAO-SCF methods to NMR spectrum interpretation.

The GIAO-SCF method for calculating isotropic nuclear magnetic shielding values has been utilized to explain certain features in the 1H-NMR spectrum of 2-methylene-8,8-dimethyl-1,4,6,10-tetraoxaspiro[4.5] decane. Population distributions of the low-energy conformers based on their ab initio energies were used to produce weighting factors for the individual calculated shielding values to calculate the weighted average of the shielding values for a complete set of conformers. The differences in 1H chemical shifts between the hydrogens of the two methyl groups and between the axial and equatorial hydrogens in 2-methylene-8,8-dimethyl-1,4,6,10-tetraoxaspiro[4.5] decane were shown to be due to energy differences between the chair and boat orientations of the six-membered ring and contribution from a twist-boat conformation. Results suggest a hypothesis that intramolecular differences in chemical shift might be calculated to a greater degree of accuracy than chemical shifts calculated relative to a standard.

Magnetic Resonance Spectroscopy↗
PubMed2003

Molecular recognition of alpha,beta-unsaturated carbonyl compounds using aluminum tris(2,6-diphenylphenoxide) (ATPH): structural and conformational analysis of ATPH complexes and application to the selective vinylogous aldol reaction.

Various alpha,beta-unsaturated carbonyl compounds were coordinated with aluminum tris(2,6-diphenylphenoxide) (ATPH) to give the corresponding Lewis acid-base complexes in a distinctive coordination fashion (selective coordination). ATPH recognizes carbonyl substrates and subsequently orients itself as it forms a stable complex through selective coordination with the carbonyl oxygen. Selective coordination also confers a conformational preference to each carbonyl compound under the steric and electronic influence of ATPH, which enables the vinylogous aldol reaction of alpha,beta-unsaturated carbonyl compounds to give the corresponding gamma-aldol products with different regio- and stereoselectivities.

Journal Article↗
PubMed2002

Photochemical synthesis, conformational analysis, and transformation of [60]fullerene-o-quinodimethane adducts bearing a hydroxy group.

The photochemical reactions of [60]fullerene with various aromatic aldehydes or ketones 1a-n carrying an alkyl group at the ortho position were examined. Some of them afforded stable o-quinodimethane adducts 2 with a hydroxy group attached to the cyclohexene ring. The adducts 2 were found to adopt one or both of two conformers A and E, which possess pseudoaxial and pseudoequatorial hydroxy groups, respectively. The conformer ratios depended remarkably on the substituents attached to the aromatic nucleus and the cyclohexene ring. The dynamic behavior of 2 was also investigated by the VT-NMR technique.

Journal Article↗
PubMed1997

Conformational analysis of three NK1 tripeptide antagonists: a proton nuclear magnetic resonance study.

Two new peptides, tailored after Ac-Thr-D-Trp(CHO)-Phe-NMeBzl (TRI), namely, Ac-Thr-D-Trp(CHO)-Phe-NMe alpha MeBzl (TRA) and Ac-Thr-D-Trp(CHO)-Oic-NMeBzl (TOI), in which Phe is replaced by (3aS, 7aS)-octahydroindole-2-carboxylic acid, proved more potent and selective NK1 antagonists. The conformational properties of all three compounds were investigated in solution by NMR spectroscopy and those of TRI analyzed in greater detail by means of systematic computer-assisted modeling. All conformers whose energy differs by less than 9 kcal/mol from the absolute minimum are different from the conformer proposed in a previous molecular modeling study by the discovers of TRI. Parallel calculations for TRA and TOI yield low-energy conformers similar to those of TRI but in a slightly different order. Comparison of the shapes of low-energy conformers of all three peptides with those of four typical rigid NK1 antagonists shows that putative bioactive conformations are indeed present in solution.

Animals↗
PubMed1990

[Synthesis, conformation analysis, and antiviral activity of benzimidazole ribofuranosides].

To study the structure-biological effect correlation in the series of nucleoside analogues containing deazapurines, a number of 2-R-benzimidazole 1-beta-D-ribofuranosides (R = H, CF3, SCF3, CH2SCF3, CH2Ph, CH2CN) have been prepared by the modified silyl method. On the basis of CD and PMR data it was shown that the compounds exist in solution mainly as syn-conformers. Calculation of the furanose ring pseudorotation parameters in terms of N-S model indicates the predominance of S-population. In contrast to acyclonucleosides, the ribofuranosides obtained are nonactive against entheroviruses and more cytotoxic.

Antiviral Agents↗
PubMed1993

Early steps in reovirus infection are associated with dramatic changes in supramolecular structure and protein conformation: analysis of virions and subviral particles by cryoelectron microscopy and image reconstruction.

Three structural forms of type 1 Lang reovirus (virions, intermediate subviral particles [ISVPs], and cores) have been examined by cryoelectron microscopy (cryoEM) and image reconstruction at 27 to 32-A resolution. Analysis of the three-dimensional maps and known biochemical composition allows determination of capsid protein location, globular shape, stoichiometry, quaternary organization, and interactions with adjacent capsid proteins. Comparisons of the virion, ISVP and core structures and examination of difference maps reveal dramatic changes in supra-molecular structure and protein conformation that are related to the early steps of reovirus infection. The intact virion (approximately 850-A diam) is designed for environmental stability in which the dsRNA genome is protected not only by tight sigma 3-mu 1, lambda 2-sigma 3, and lambda 2-mu 1 interactions in the outer capsid but also by a densely packed core shell formed primarily by lambda 1 and sigma 2. The segmented genome appears to be packed in a liquid crystalline fashion at radii < 240 A. Depending on viral growth conditions, virions undergo cleavage by enteric or endosomal/lysosomal proteases, to generate the activated ISVP (approximately 800-A diam). This transition involves the release of an outer capsid layer spanning radii from 360 to 427 A that is formed by 60 tetrameric and 60 hexameric clusters of ellipsoidal subunits of sigma 3. The vertex-associated cell attachment protein, sigma 1, also undergoes a striking change from a poorly visualized, more compact form, to an extended, flexible fiber. This conformational change may maximize interactions of sigma 1 with cell surface receptors. Transcription of viral mRNAs is mediated by the core particle (approximately 600-A diam), generated from the ISVP after penetration and uncoating. The transition from ISVP to core involves release of the 12 sigma 1 fibers and the remaining outer capsid layer formed by 200 trimers of rod-shaped mu 1 subunits that span radii from 306 to 395 A. In the virion and ISVP, flower-shaped pentamers of the lambda 2 protein are centered at the vertices. In the ISVP-to-core transition, domains of the lambda 2 subunits rotate and swing upward and outward to form a turret-like structure extending from radii 305 to 400 A, with a diameter of 184 A, and a central channel 84 A wide. This novel conformational change allows the potential diffusion of substrates for transcription and exit of newly synthesized mRNA segments.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed2000

Conformational analysis of long spacers in PROSITE patterns.

To determine if variable sequences (spacers) between conserved positions in a sequence motif or pattern share a consensus structure, three-dimensional structures containing PROSITE patterns with spacers of fixed length greater than three residues were analyzed. Structural similarities of a given pattern were evaluated by computing the backbone phi, psi and side-chain chi1 dihedral order parameters. The exact bias information in analyzing the conformational variability of the patterns was taken into account by introducing a new parameter, the bias coefficient, which describes the number and distribution of residue types found at each position of a pattern in the structures. The results of the analyses show that backbone conformational heterogeneity at a given position in a sequence motif does not necessarily correlate with the residue-type variability at that position, and the long spacer region can adopt a well-defined backbone conformation, in addition to the conserved residues. Furthermore, a PROSITE pattern may be redefined to yield two or more "refined" regular expressions, each corresponding to a distinct backbone conformation. A way in which the observed structural consensus in a pattern may be employed to improve the accuracy of function prediction from sequence is suggested.

Amino Acid Motifs↗
PubMed2004

New derivative of 1alpha,25-dihydroxy-19-norvitamin D3 with 3'-alkoxypropylidene moiety at C-2: synthesis, biological activity and conformational analysis.

In pursuit of novel biologically active Vitamin D compounds of potential therapeutic value, 1alpha,25-dihydroxy-2-[3'-(methoxymethoxy)propylidene]-19-norvitamin D(3) (7) was efficiently prepared in a convergent synthesis, starting with (-)-quinic acid and the protected 25-hydroxy Grundmann ketone 16. The key synthetic step involved Lythgoe type Wittig-Horner coupling of 16, with the phosphine oxide 15. Molecular modeling was employed to establish the A-ring conformation of the synthesized Vitamin 7. Also, preliminary modeling of its complex with the rVDR was performed and interactions between ligand and the binding domain analyzed. Analog 7 was found to be only six times less potent than 1alpha,25-(OH)(2)D(3) (1) in binding to the rat recombinant Vitamin D receptor (VDR). In comparison with hormone 1, it also showed slightly lower cellular HL-60-differentiation activity. Preliminary in vivo tests indicated unusually high calcemic activity of 7.

Animals↗
PubMed2005

Synthesis and biological activity of cyclic ADP-carbocyclic-ribose analogs: structure-activity relationship and conformational analysis of N-1-carbocyclic-ribose moiety.

Several cyclic ADP-carbocyclic-ribose analogs 3-10 modified in the N-1-carbocyclic-ribose moiety were synthesized. Their Ca2+-releasing activity was estimated in sea urchin eggs to show that the 3"-deoxy analog 6 shows 5 times more potent activity than cADPcR, but the 2",3"-didieoxy-2",3"-unsunsaturated analog 3 has very weak activity. We also calculated their stable conformation and found that 3 and 6 were significantly different in their stable conformation.

Adenosine Diphosphate↗