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PubMed2004

Conformational analysis of complex oligosaccharides: the CICADA approach to the uromodulin O-glycans.

Uromodulin is the pregnancy-associated Tamm-Horsfall glycoprotein, with the enhanced ability to inhibit T-cell proliferation. Pregnancy-associated structural changes mainly occur in the O-glycosylation of this glycoprotein. These include up to 12 glycan structures, made up of an unusual core type 2 sequence terminated with one, two, or three sialyl Lewis(x) sequences; this type of O-glycans could serve as E- and P-selectin ligands. The present work focuses on the most complex one; a tetradecamer made up of a type 2 core carrying three sialyl Lewis(x) branches. Five different monosaccharides are assembled by 14 glycosidic linkages. The conformational behavior of the constituting disaccharide segments was evaluated using the flexible residue procedure of the MM3 molecular mechanics procedure. For each disaccharide, the adiabatic energy surface, along with the local energy minima were established. All these results were used for the generation, prior to complete optimization of the tetradecamer. This was followed by a complete exploration of conformational hyperspace throughout the use of the single coordinate method as implemented in the CICADA program. Despite the potential flexibility of the tetradecasaccharide, only four conformational families occur, accounting for more than 95% of the total low energy conformations. For each family, the molecular properties (electrostatic, lipophilicity, and hydrogen potential) were studied. The shape of the tetradecasaccharide is best described as a flat ribbon, flanked by three branches having terminal sialyl residues. Two of the branches interact through nonbonded interactions, bringing further energy stabilization, and limiting the conformational flexibility of the sialyl residues. Only one branch maintains the original conformational features of sialyl Lewis(x). This O-glycan can be seen as a fascinating example of 'dendrimeric' structure, where the spatial arrangement of three S-Le(x) epitopes may favor its complementary 'presentations' for the interactions with E- and P-selectins.

Carbohydrate Conformation↗
PubMed1990

Backbone modifications in cyclic peptides. Conformational analysis of a cyclic pseudopentapeptide containing a thiomethylene ether amide bond replacement.

NMR and X-ray crystallographic studies have shown that cyclic pentapeptides of the general structure cyclo(D-Xxx-Pro-Gly-Pro-Gly) possess beta- and gamma-turn intramolecular hydrogen bonds. As part of our continuing series surveying the compatibility of various amide bond replacements on peptide structure, we have synthesized cyclo(D-Phe-Pro psi[CH2S]Gly-Pro-Gly). The pseudopeptide was prepared by solid phase methods and cleaved from the resin by a new procedure involving phase transfer catalysis using K2CO3 and tetrabutylammonium hydrogen sulfate. Cyclization was carried out with the use of DPPA, HOBt, and DMAP to afford the product in 69% yield. The conformational behavior of the pseudopeptide was analyzed by 1H and 13C (1D and 2D) NMR techniques. The backbone modification replaced the amide bond that is involved in a gamma-turn intramolecular hydrogen bond in the all-amide structure. In CDCl3, the pseudopeptide adopted the same all-trans conformation as its parent, although the remaining beta-turn hydrogen bond was weaker according to delta delta/delta TNH measurements. In DMSO-d6, the all-trans conformer and a second conformer were observed in a ratio of 55:45. These conformers, which slowly interconverted on the NMR time scale, could be separately assigned; peaks due to chemical exchange were readily distinguishable by the ROESY technique as reported earlier by others. 13C and ROESY experiments suggested the minor conformer contained one cis amide bond at the Gly1-Pro2 position. Thus, both the location and type of amide surrogate are important determinants affecting the compatibility of the replacement with a particular conformational feature.

Amino Acid Sequence↗
PubMed1994

Conformational analysis of hemopexin by Fourier-transform infrared and circular dichroism spectroscopy.

Hemopexin is a serum glycoprotein that binds heme with the highest known affinity of any characterized heme-binding protein and plays an important role in receptor-mediated cellular heme uptake. Complete understanding of the function of hemopexin will require the elucidation of its molecular structure. Previous analysis of the secondary structure of hemopexin by far-UV circular dichroism (CD) failed due to the unusual positive ellipticity of this protein at 233 nm. In this paper, we present an examination of the structure of hemopexin by both Fourier-transform infrared (FTIR) and circular dichroism spectroscopy. Our studies show that hemopexin contains about 55% beta-structure, 15% alpha-helix, and 20% turns. The two isolated structural domains of hemopexin each have secondary structures similar to hemopexin. Although there are significant tertiary conformational changes indicated by the CD spectra, the overall secondary structure of hemopexin is not affected by binding heme. However, moderate changes in secondary structure do occur when the heme-binding domain of hemopexin associates with heme. In spite of the exceptionally tight binding at neutral pH, heme is released from the bis-histidyl heme-hemopexin complex at pH 5.0. Under this acidic condition, hemopexin maintains the same overall secondary structure as the native protein and is able to resume the heme-binding function and the native structure of the heme-protein (as indicated by the CD spectra) when returned to neutral pH. We propose that the state of hemopexin identified in vitro at pH 5.0 resembles that of this protein in the acidic environment of the endosomes in vivo when hemopexin releases heme during receptor-mediated endocytosis.

Circular Dichroism↗
PubMed2002

Glycoside-clustering round calixarenes toward the development of multivalent ligands. Synthesis and conformational analysis of Calix[4]arene O- and C-glycoconjugates.

Bis- and tetra-O- and C-glycosyl calixarenes (calixsugars) have been prepared by tethering carbohydrate moieties to a tetrapropoxycalix[4]arene scaffold through alkyl chains. Two methodologies have been employed. One consisted of the stereoselective multiple glycosylation of upper rim calix[4]arene polyols leading to calix-O-glycosides; the other involved a multiple Wittig olefination of upper rim calix[4]arene-derived polyaldehydes by the use of sugar phosphoranes and reduction of the alkene double bonds affording calix-C-glycosides. The NMR spectra and NOE experiments of bis-glycosylated products indicate that compounds bearing sugar-protected residues exist preferentially in solution in a flattened cone arrangement (far conformation) whereas deprotected derivatives adopt a close conformation. Calculations by molecular mechanics of the latter compounds point to a close conformation as well in gas phase.

Calixarenes↗
PubMed1984

Carbon-13 NMR in conformational analysis of nucleic acid fragments. 3. The magnitude of torsional angle epsilon in d(TpA) from CCOP and HCOP NMR coupling constants.

Carbon-13 NMR spectra of the deoxyribonucleotide d(TpA), 3',5'-cyclic AMP and 3',5'-cyclic dAMP were measured. It is shown that the different substitution of C2' in deoxyribonucleotides versus ribonucleotides does not affect the vicinal C2'-C3'-O3'-P coupling to a measurable extent. Therefore, the same set of Karplus parameters may be used for the C2'-C3-O3'-P couplings in ribonucleotides and in deoxyribonucleotides. Vicinal carbon-phosphorus and proton-phosphorus coupling constants are used to calculate the magnitude of the torsion angle epsilon (C4'-C3'-O3'-P), which amounts to 195(0) in the trans conformer and to 261(0) in the gauche(-) conformer.

Cyclic AMP↗
PubMed1995

Porcine class pi glutathione S-transferase: anionic ligand binding and conformational analysis.

The equilibrium binding of the non-substrate ligands 8-anilino-1-naphthalene sulfonate and bromosulfophthalein to porcine class pi glutathione S-transferase (pGSTP1-1) was studied using a variety of techniques (size-exclusion HPLC, steady-state fluorescence, second-derivative spectroscopy, and chemical modification of cysteines). Both ligands share the same binding site which has a highly hydrophobic surface. Occupation of the site inhibits catalytic function with glutathione and 1-chloro-2,4-dinitrobenzene in a non-competitive manner. Data obtained from different structural probes either located at strategic regions of pGSTP1-1 (Trp-28, Trp-38 and Cys-45) or distributed throughout the protein molecule (tyrosine residues) suggest that binding induces a microstructural change that impacts on the functional conformation of the active site.

Anilino Naphthalenesulfonates↗
PubMed2005

Conformational analysis of the C-terminal Gly-Leu-Met-NH2 tripeptide of substance P bound to the NK-1 receptor.

We examined the effect of simultaneously incorporating proline or proline-amino acid chimeras in positions 9, 10, and/or 11 of substance P, on the affinity for the two NK-1 binding sites and on second-messenger activation. Because these 3-substituted prolines constrain not only the (phi,psi) values of the peptide backbone, but also the chi space of the amino acid side chain, we were able to gather data on the structural requirements for high-affinity binding to the NK-1 receptor. We were able to confirm that this C-terminal component is crucial and that it should adopt an extended conformation close to a polyproline II structure when bound to the receptor. The partial additivity of these constraints, more specifically, for the NK-1M site, suggests that the peptide backbone flexibility around the hinge-point residue Gly9 is essential to subtly position crucial side chains.

Animals↗
PubMed1997

X-ray and conformational analysis of arabinan.

Fibers prepared from the enzymically debranched plant polysaccharide arabinan, containing (1-->5)-linked alpha-L-arabinofuranose residues, produce X-ray diffraction patterns containing concentric rings indicative of a high degree of structural organization. The measured unit cell dimensions and fiber density are consistent with a 2-fold helix passing through each unit cell. According to model-building techniques and energy calculations, a total of seven molecular structures (three with C2'-endo and four with C3'-endo sugars), all of pitch 8.74 A, and hence seven different crystal-packing arrangements are the most probable. While intrachain hydrogen bonds are only present in three cases, interhelix association is facilitated by hydrogen bonds in all allomorphs. Small energy differences between them suggest that easy conformational transitions may be made from one form to another. This polymorphism and the tendency to form microcrystals in the solid state might confer upon arabinan the observed fat mimetic properties.

Carbohydrate Conformation↗
PubMed2002

Synthesis, conformational analysis and antiviral and antitumoral activity of new 1,2-disubstituted carbocyclic nucleosides.

New 1',2'-cis-disubstituted 8-azapurine-based carbocyclic analogues of nucleosides with or without a methylene between the carbocycle and the base were synthesised, starting from appropriate amino alcohols, via 6-chloro-8-azapurines; their antiviral and antitumoral activities were evaluated; and their structures were compared with that of 2',3'-dideoxyadenosine (ddA) on the basis of AM1 calculations. No new compound had antiviral activity. The one with the best overall antitumoral activity against L1210, Molt4/C8 and CEM/0 cells, compound 10, was that in which the position of the hydroxymethyl group on the carbocycle relative to the heterocyclic base was closest to that found in the best-fitting low-energy conformer of ddA.

Antineoplastic Agents↗
PubMed1983

cis-Platinum induced distortions in DNA. Conformational analysis of d(GpCpG) and cis-pt(NH3)2[d(GpCpG)], studied by 500-MHz NMR.

Proton NMR studies at 500 MHz in aqueous solution were carried out on the G-G chelated deoxytrinucleosidediphosphate platinum complex cis-Pt(NH3)2[d(GpCpG], on the uncoordinated trinucleotide d(GpCpG) and on the constituent monomers cis-Pt(NH3)2[d(Gp)]2, cis-Pt(NH3)2[d(pG)]2, d(Gp), d(pCp) and d(pG). Complete NMR spectral assignments are given and chemical shifts and coupling constants are analysed to obtain an impression of the detailed structure of d(GpCpG) and the distortion of the structure due to chelation with [cis-Pt(NH3)2]2+. Platination of the guanosine monophosphates affects the sugar conformational equilibrium to favour the N conformation of the deoxyribose ring. This feature is also apparent in ribose mononucleotides and is possibly caused by an increased anomeric effect. In cis-Pt(NH3)2[d(pG)]2 the phase angle of pseudorotation of the S-type sugar ring is 20 degrees higher than in 'free' d(pG) which might be an indication for an ionic interaction between the positive platinum and the negatively charged phosphate. It appears that d(GpCpG) reverts from a predominantly random coil to a normal right-handed B-DNA-like single-helical structure at lower temperatures, whereas the conformational features of cis-Pt(NH3)2[d(GpCpG)] are largely temperature-independent. In the latter compound much conformational freedom along the backbone angles is seen. The cytosine protons and deoxyribose protons exhibit almost no shielding effect as should normally be exerted by the guanine bases in stacking positions. This is interpreted in terms of a 'turning away' of the cytosine residue from both chelating guanines. Conformational features of cis-Pt(NH3)2[d(GpCpG)[ are compared with the 'bulge-out' of the ribose-trinucleotide m6(2)ApUpm6(2)A.

Binding Sites↗
PubMed1991

Conformational analysis of 1-kestose by molecular mechanics and by n.m.r. spectroscopy.

Models of the trisaccharide, 1-kestose [beta-D-fructofuranosyl-(2----1)-beta-D-fructofuranosyl-(2 in equilibrium with 1)-alpha-D -glucopyranoside], were analyzed with the molecular mechanics computer program MM2(87) to ascertain their inter-ring torsion angles, primary alcohol side-group orientations, and ring puckering. The most striking result was that the modeling predicted and n.m.r. spectroscopy corroborated that the central fructofuranose ring takes a different form from that previously observed in the crystal. No other studies of fructofuranoses have observed that crystallographic form, thus suggesting that the 18 hydrogen bonds created upon crystallization of 1-kestose support the ring deformation. Because this trisaccharide is too complex for a complete study of conformation space, only structures having inter-ring conformations that were at energetic valleys in previous studies of the constituent disaccharides were analyzed. The model of the model disaccharides, although they were generally close to the linkage conformations observed in the crystal structure, differing by an average of 19 degrees.

Carbohydrate Conformation↗
PubMed2004

Synthesis, antimicrobial activity and conformational analysis of novel substituted pyridines: BF(3)-promoted reaction of hydrazine with 2-alkoxy pyridines.

Some new 2-alkoxy-3-cyano-4,6-diarylpyridines 3,4 were synthesized by condensation of different alpha,beta-unsaturated ketones 1 with malononitrile 2, followed by cyclization in sodium alkoxide/alcohol system. Lewis acid-catalyzed reaction of 4 with hydrazine afforded the corresponding 1H-pyrazolo[3,4-b]pyridines 5. The potency of the results as antimicrobial agents has been evaluated. The structure of the newly prepared compounds was assessed by microanalysis, IR and NMR spectra. Molecular mechanics (MM2) and semiemperical (AM1) molecular orbital calculations have been performed for the most biologically active compounds 5b and c to get insight into their molecular structures and to learn more about their stable molecular conformations.

Anti-Infective Agents↗
PubMed1990

Structural and conformational analysis of metal-containing peptides by one- and two-dimensional NMR spectroscopy. The case of thymulin.

Thymulin (formerly called FTS) is a well-defined nonapeptide hormone produced by thymic epithelial cells. Its biological activity and antigenicity depend on the presence of the metal zinc in the molecule. The interaction between this metal ion and thymulin has been investigated by means of one- and two-dimensional NMR experiments. These experiments were performed in dimethyl-d6 sulfoxide solution and in aqueous medium with different metal:peptide ratios. The results are compared with those obtained for complexes of thymulin with other metal ions (Cu2+ and Al3+) and for the [Ala4]- and [Ala8]-analogs in terms of biological activity. These comparative studies suggest that the 1:1 complex is the only conformation recognized by the antibodies. From the NOESY data, a spatial conformation has been proposed for this complex. This conformation should be the physiological one and could lead to a better insight into the conformation requirements at receptor sites.

Amino Acid Sequence↗
PubMed1990

An n.m.r. and conformational analysis of the terminal trisaccharide from the serologically active glycolipid of Mycobacterium leprae in different solvents.

The 1H- and 13C-n.m.r. spectra of allyl 2-O-[4-O-(3,6-di-O-methyl-beta-D-glucopyranosyl)-2,3-di-O-methyl-alpha-L -rhamnopyranosyl]-3-O-methyl-alpha-L-rhamnopyranoside (3), a glycoside of the terminal trisaccharide found in the phenolic glycolipid I from Mycobacterium leprae, and those of the two component disaccharides, allyl 4-O-(3,6-di-O-methyl-beta-D-glucopyranosyl)-2,3-di-O- methyl-alpha-L-rhamnopyranoside (1) and allyl 2-O-(2,3-di-O-methyl-alpha-L-rhamnopyranosyl)-3-O-methyl-alpha-L- rhamnopyranoside (2) have been assigned completely by 1D and 2D techniques. The preferred conformations, determined by chemical shift and n.O.e. studies, were different in D2O, CD3OD, and CDCl3. The preferred conformation of 3 accorded with the results of hard-sphere exo-anomeric (HSEA) calculations.

Carbohydrate Conformation↗
PubMed1986

Conformational analysis of the B and Z forms of the d(m5C-G)3 and d(br5C-G)3 hexamers in solution. A 300-MHz and 500-MHz NMR study.

The B and the Z forms of the DNA hexamers d(m5C-G)3 and d(br5C-G)3 were investigated by means of NMR spectroscopy. It is demonstrated that the low-salt form of d(m5C-G)3 is a B DNA structure. The form, which becomes increasingly predominant when increasing amounts of MgCl2 and/or methanol are added to the solution, has Z DNA characteristics. It is shown that the major geometrical features of the Z form of d(m5C-G)3 in the crystal structure are maintained in solution, with the dC residues S sugar conformation, gamma + and the base in the anti orientation and the dG residues N (except the 3'-terminal residue), gamma t and syn. Neither the Z form of the methylated nor that of the brominated compound resembles the Z' form, in which the deoxy guanosine sugar rings adopt a C1'-exo conformation. Substitution of m5C by br5C causes no perceptible conformational changes in either the B or in the Z forms.

Bromine↗
PubMedDate not supplied

[Theoretical conformational analysis of noncovalent complexes of purine nucleotides with ribonuclease].

Semiempirical potential energy calculations have been carried out to locate possible binding sites for purine nucleoside phosphates at the RNase S active center. The nucleobase of adenosine or 8-oxoadenosine was shown to be accommodated at the pyrimidine binding site of the enzyme provided the nucleoside must be "syn". The mutual orientation of 8-oxoadenosine carbonyl group and NH-group of Thr-45 suggests a formation of a corresponding hydrogen bond in the enzyme--nucleotide complex. The formation of the hydrogen bond was postulated earlier to be essential for specific recognition of the substrate by RNase. The results obtained are in good agreement with the postulate. The "leaving group" binding site at the RNase S active center was found to be nonspecific toward conformation (syn-anti) of purine nucleotides studied. In addition, optimal conformation of dinucleosidemonophosphate bound to the enzyme active site was estimated for Pyr-P-Pur substrates.

Adenosine↗
PubMed2003

Conformational analysis of melittin in solution phase: vibrational circular dichroism study.

The vibrational absorption and vibrational circular dichroism (VCD) spectra of melittin in D(2)O solutions at different pH values, different salt concentrations, or different 2,2,2-trifluoroethanol (TFE) concentrations are recorded in the amide I' (1850-1600 cm(-1)) region. Two models are used to simulate this peptide in different conditions, and a coupled oscillator program is used to obtain the calculated absorption and VCD spectra. This study indicates that melittin adopts a mixed structure in D(2)O solution at low pH, low salt concentration, or low TFE concentration. With an increase in pH, salt concentration, or TFE concentration, the structure changes to alpha-helix and further increases lead to aggregation. These results demonstrate the versatility of VCD in probing the conformations of peptides under different environmental perturbations.

Circular Dichroism↗