Conformational Features (conformational + feature)

Distribution by Scientific Domains
Distribution within Chemistry

Selected Abstracts

One-Pot Synthesis and Conformational Features of N,N,-Disubstituted Ketene Aminals.

CHEMINFORM, Issue 19 2004
Yan Shi
Abstract For Abstract see ChemInform Abstract in Full Text. [source]

Structural studies of a baboon (Papio sp.) plasma protein inhibitor of cholesteryl ester transferase

Garry W. Buchko
Abstract A 38-residue protein associated with cholesteryl ester transfer inhibition has been identified in baboons (Papio sp.). The cholesteryl ester transfer inhibitor protein (CETIP) corresponds to the N-terminus of baboon apoC-I. Relative to CETIP, baboon apoC-I is a weak inhibitor of baboon cholesteryl ester transferase (CET). To study the structural features responsible for CET inhibition, CETIP was synthesized by solid-phase methods. Using sodium dodecyl sulfate (SDS) to model the lipoprotein environment, the solution structure of CETIP was probed by optical and 1HNMR spectroscopy. Circular dichroism data show that the protein lacks a well-defined structure in water but, upon the addition of SDS, becomes helical (56%). A small blue shift of 8 nm was observed in the intrinsic tryptophan fluorescence of CETIP in the presence of saturating amounts of SDS, suggesting that tryptophan-23 is not buried deeply in the lipid environment. The helical nature of CETIP in the presence of SDS was confirmed by upfield 1H, secondary shifts and an average solution structure determined by distance geometry/simulated annealing calculations using 476 NOE-based distance restraints. The backbone (N , C, , C, = O ) root-mean-square deviation of an ensemble of 17 out of 25 calculated structures superimposed on the average structure was 1.06 0.30 using residues V4-P35 and 0.51 0.17 using residues A7-S32. Although the side-chain orientations fit the basic description of a class A amphipathic helix, both intramolecular salt bridge formation and "snorkeling" of basic side chains toward the polar face play minor, if any, roles in stabilizing the lipid-bound amphipathic structure. Conformational features of the calculated structures for CETIP are discussed relative to models of CETIP inhibition of cholesteryl ester transferase. [source]

Conformational features of crystal-surface cellulose from higher plants

Remco J. Vitor
Summary Native cellulose in higher plants forms crystalline fibrils a few nm across, with a substantial fraction of their glucan chains at the surface. The accepted crystal structures feature a flat-ribbon 21 helical chain conformation with every glucose residue locked to the next by hydrogen bonds from O-3, to O-5 and from O-2 to O-6,. Using solid-state NMR spectroscopy we show that the surface chains have a different C-6 conformation so that O-6 is not in the correct position for the hydrogen bond from O-2. We also present evidence consistent with a model in which alternate glucosyl residues are transiently or permanently twisted away from the flat-ribbon conformation of the chain, weakening the O-3, , 0-5 hydrogen bond. Previous molecular modelling and the modelling studies reported here indicate that this ,translational' chain conformation is energetically feasible and does not preclude binding of the surface chains to the interior chains, because the surface chains share the axial repeat distance of the 21 helix. Reduced intramolecular hydrogen bonding allows the surface chains to form more hydrogen bonds to external molecules in textiles, wood, paper and the living plant. [source]

Crystal structure of 4'-O-methylalpinumisoflavone at 90K

R. Kingsford-Adaboh
Abstract 4,-O-Methylalpinumisoflavone crystals which hitherto had been difficult to crystallize for X-ray diffraction analyses have been obtained from a demethylated product of O, O-dimethylalpinumisoflavone. The structural and conformational features of the crystal measured at 90 K are reported and compared with previously reported work of O,O-dimethylalpinumisoflavone and 5-O-methyl-4,-O-(3-methyl-but-2-en-1-yl) alpinumisoflavone. Each of these compounds is characterized by a six membered ring that is further fused to a benzopyrone isoflavone moiety resulting in a tricyclic ring system. This six membered ring shows a half-chair conformation in all the molecules studied, with the ring in the title compound showing the least Cremer-Pople puckering amplitude Q and shorter inter and intramolecular contacts. ( 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source]

Synthesis, NMR, and Conformational Studies of Cyclic Oligo-(1,6)-,- D -Glucosamines,

Marina L. Gening
Abstract The first synthesis of a series of homologous cyclic oligo-(1,6)-,- D -glucosamines consisting of two to seven residues and representing a new type of functionalized cyclic oligosaccharides is reported. Remarkably high yields of the studied macrocyclization reaction irrespective of the length of the acyclic precursors were observed. In the case of compounds constituted of four to seven glucosamine units ,-stereoisomers formed as side products despite the presence of a strongly participating 2- N -phthaloyl group to control ,-glycosylation. Both phenomena may be accounted for by conformational features of the linear bifunctional precursors. According to computer modeling and NMR conformational studies, the described linear (1,6)-,-linked oligoglucosamines exist in a right-handed helix-like conformation, in which the glycosyl donor and acceptor moieties are prearranged in a way that facilitates intramolecular glycosylation from the ,-side. Prepared cyclo-oligoglucosamines differ in their conformational flexibilities, as illustrated by their spectral characteristics and calculated asphericity distributions. Moreover, the obtained compounds do not possess a distinct hydrophobic cavity, which is in contrast to the well-known cyclodextrins. All these characteristics provide an excellent basis for the use of these novel cyclic oligosaccharides as scaffolds for the construction of biomolecular conjugates. [source]

Mycobacterium tuberculosis Thymidine Monophosphate Kinase Inhibitors: Biological Evaluation and Conformational Analysis of 2,- and 3,-Modified Thymidine Analogues

Philippe Van Rompaey
Abstract Mycobacterium tuberculosis thymidine monophosphate kinase (TMPKmt) has recently been introduced as a potential target for the structure-based design of anti-tuberculosis drugs. Based on the TMPKmt X-ray structure and previous S.A.R. studies, we synthesised the nucleoside analogues 3a,b, 6a,b, 7a,b, and 8a,b, modified in 2,- and 3,-position of the ribofuranose ring moiety. To our surprise, these analogues showed only moderate binding affinity (i.e. Ki between 118 and 1260 ,M). This prompted us to investigate the conformational features of these nucleosides. We concluded that compounds of this series, especially 8a,b, are strongly biased towards the "Northern" furanose ring conformation, whereas X-ray crystallography reveals a preference of TMPKmt for the opposite "Southern" conformers. This paper covers the synthesis, biological evaluation and conformational features (i.e. preferred ring puckering) of the 2,- and 3,-modified dT analogues. ( Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003) [source]

Stepwise proteolytic removal of the , subdomain in ,-lactalbumin

FEBS JOURNAL, Issue 15 2001
The protein remains folded, can form the molten globule in acid solution
Bovine ,-lactalbumin (,-LA) is an ,/, protein which adopts partly folded states when dissolved at low pH (A-state), by removal of the protein-bound calcium at neutral pH and low salt concentration (apo-state), as well as in aqueous trifluoroethanol. Previous spectroscopic studies have indicated that the A-state of ,-LA at pH 2.0, considered a prototype molten globule, has a native-like fold in which the helical core is mostly retained, while the , subdomain is less structured. Here, we investigate the conformational features of three derivatives of ,-LA characterized by a single peptide bond fission or a deletion of 12 or 19/22 amino-acid residues of the , subdomain of the native protein (approximately from residue 34 to 57). These ,-LA derivatives were obtained by limited proteolysis of the protein in its partly folded state(s). A nicked ,-LA species consisting of fragments 1-,3,40 and 41,123 (nicked-LA) was prepared by thermolytic digestion of the 123-residue chain of ,-LA in 50% (v/v) aqueous trifluoroethanol. Two truncated or gapped protein species given by fragments 1,40 and 53,123 (des,1-LA) or fragments 1,34 and 54-,57,123 (des,2-LA) were obtained by digestion of ,-LA with pepsin in acid or with proteinase K at neutral pH in its apo-state, respectively. The two protein fragments of nicked or gapped ,-LA are covalently linked by the four disulfide bridges of the native protein. CD measurements revealed that, in aqueous solution at neutral pH and in the presence of calcium, the three protein species maintain the helical secondary structure of intact ,-LA, while the tertiary structure is strongly affected by the proteolytic cleavages of the chain. Temperature effects of CD signals in the far- and near-UV region reveal a much more labile tertiary structure in the ,-LA derivatives, while the secondary structure is mostly retained even upon heating. In acid solution at pH 2.0, the three ,-LA variants adopt a conformational state essentially identical to the molten globule displayed by intact ,-LA, as demonstrated by CD measurements. Moreover, they bind strongly the fluorescent dye 8-anilinonaphthalene-1-sulfonate, which is considered a diagnostic feature of the molten globule of proteins. Therefore, the , subdomain can be removed from the ,-LA molecule without impairing the capability of the rest of the chain to adopt a molten globule state. The results of this protein dissection study provide direct experimental evidence that in the ,-LA molten globule only the , domain is structured. [source]

Investigation of penetratin peptides Part 1.

The environment dependent conformational properties of penetratin, two of its derivatives
Abstract The homeodomain, the DNA-binding domain of Antennapedia homeoprotein, is composed of three ,-helices and one ,-turn between helices II and III. Its third helix from the N -terminal (helix III) can translocate through the cell membrane into the nucleus and can be used as an intracellular vehicle for the delivery of oligopeptides and oligonucleotides. To the best of our knowledge, this helix III, called penetratin, which consists of 16 amino acids, is internalized by cells in a specific, non-receptor-mediated manner. For a better understanding of the mechanism of the transfer, the structure of penetratin was examined in both extracellular matrix-mimetic and membrane-mimetic environments; 1H-NMR and CD spectroscopic measurements were performed in mixtures of TFE/water with different ratios. The molecular conformations of two analogue peptides [(6,14-Phe)-penetratin and a 12 amino acid penetratin derivative (peptide 3)] were also studied. An atomic level comprehensive analysis of penetratin and its two analogues was performed. In a membrane-mimetic solvent system (TFEd2/water = 9 : 1), on the basis of 553 distance restraints, the 4,12 region of penetratin exhibits a bent, irregular helical structure on NMR examination. Interactions between hydrophobic amino acid residues in conjunction with H-bonds stabilize the secondary structure of the molecule. Thus, both derivatives adopt a helix-like conformation. However, while (6,14-Phe)-penetratin displays both ,-helical and 310 -helical features, the structure of peptide 3 is predominantly a 310 -helix. Of the three peptides, surprisingly (6,14-Phe)-penetratin has the largest helical content. An increase in the polarity of the molecular environment gradually disintegrates these helix-like secondary structures. In a highly aqueous molecular system (TFEd2/water = 1 : 9), the fast exchange of multiple conformers leads to too few distance restraints being extracted, therefore the NMR structures can no longer be determined. The NMR data show that only short-range order can be traced in these peptides. Under these conditions, the molecules adopt nascent helix-like structures. On the other hand, CD spectra could be recorded at any TFE/water ratio and the conformational interconversion could therefore be monitored as a function of the polarity of the molecular environment. The CD data were analysed comprehensively by the quantitative deconvolution method (CCA+). All three penetratin peptides display helical conformational features in a low dielectric medium, with significant differences as a function of their amino acid composition. However, these conformational features are gradually lost during the shift from an apolar to a polar molecular environment. Copyright 2002 European Peptide Society and John Wiley & Sons, Ltd. [source]

Fabrication of Patterned Polydiacetylene Composite Films Using a Replica-Molding (REM) Technique

Oktay Yarimaga
Abstract Functional three-dimensional (3D) micropatterns of diacetylene supramolecules embedded in a host polymer have been successfully fabricated by a replica-molding (REM) technique. Dimensional reduction as a result of liquid evaporation during the curing process does not affect the conformational features of the transferred patterns. Polymerization of the diacetylene vesicles using 254,nm UV-light irradiation from the back-side of the transparent substrate induces blue colored polydiacetylene (PDA) micro-images. Interestingly, the polymerization selectively occurs in the molded areas because of the sub-300,nm light blocking property of SU-8. 3D fluorescence patterns are readily obtained by heat treatment of the blue images on the film. [source]

Unsolvated 5,10,15,20-tetra-4-pyridylporphyrin, its sesquihydrate and its 2-chlorophenol disolvate: conformational versatility of the ligand

Sophia Lipstman
Unsolvated 5,10,15,20-tetra-4-pyridylporphyrin, C40H26N8, (I), its sesquihydrate, C40H26N81.514H2O, (II), and its 2-chlorophenol disolvate, C40H26N82C6H5ClO, (III), reveal different conformational features of the porphyrin core. In (I), the latter is severely deformed from planarity, apparently in order to optimize the intermolecular interactions and efficient crystal packing of the molecular entities. The molecular framework has a C1 symmetry. In (II), the porphyrin molecules are located on symmetry axes, preserving the marked deformation from planarity of the porphyrin core. The molecular units are interlinked into a single-framework supramolecular architecture by hydrogen bonding to one another via molecules of water, which lie on twofold rotation axes. In (III), the porphyrin molecules are located across centres of inversion and are characterized by a planar conformation of the 24-membered macrocyclic porphyrin ring. Two trans -related pyridyl substituents are hydrogen bonded to the 2-chlorophenol solvent molecules. The interporphyrin organization in (III) is similar to that observed for many other tetraarylporphyrin compounds. However, the organization observed in (I) and (II) is different and of a type rarely observed before. This study reports for the first time the crystal structure of the unsolvated tetrapyridylporphyrin. [source]

Diverse modes of 5,-[4-(aminoiminomethyl)phenyl]-[2,2,-bifuran]-5-carboximidamide (DB832) interaction with multi-stranded DNA structures

BIOPOLYMERS, Issue 1 2010
Dmitry N. Kaluzhny
Abstract The modes of binding of 5,-[4-(aminoiminomethyl)phenyl]-[2,2,-Bifuran]-5-carboximidamide (DB832) to multi-stranded DNAs: human telomere quadruplex, monomolecular R-triplex, pyr/pur/pyr triplex consisting of 12 T*(TA) triplets, and DNA double helical hairpin were studied. The optical adsorption of the ligand was used for monitoring the binding and for determination of the association constants and the numbers of binding sites. CD spectra of DB832 complexes with the oligonucleotides and the data on the energy transfer from DNA bases to the bound DB832 assisted in elucidating the binding modes. The affinity of DB832 to the studied multi-stranded DNAs was found to be greater (Kass , 107M,1) than to the duplex DNA (Kass , 2 105M,1). A considerable stabilizing effect of DB832 binding on R-triplex conformation was detected. The nature of the ligand tight binding differed for the studied multi-stranded DNA depending on their specific conformational features: recombination-type R-triplex demonstrated the highest affinity for DB832 groove binding, while pyr/pur/pyr TTA triplex favored DB832 intercalation at the end stacking contacts and the human telomere quadruplex d[AG3(T2AG3)3] accommodated the ligand in a capping mode. Additionally, the pyr/pur/pyr TTA triplex and d[AG3(T2AG3)3] quadruplex bound DB832 into their grooves, though with a markedly lesser affinity. DB832 may be useful for discrimination of the multi-sranded DNA conformations and for R-triplex stabilization. 2009 Wiley Periodicals, Inc. Biopolymers 93: 8,20, 2010. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at [source]

Quantum Mechanical Calculations of Conformationally Relevant 1H and 13C,NMR Chemical Shifts of N-, O-, and S-Substituted Calixarene Systems

Giuseppe Bifulco Prof.
Abstract QM GIAO calculations of 13C and 1H chemical shift values of the ArCH2Ar group in N-, O-, and S-substituted calixarene systems were performed with a hybrid DFT functional MPW1PW91 and 6-31G(d,p) basis set. A good reproduction of experimental data was obtained for some representative calixarenes and for a series of simplified calixarene models. This allowed the derivation of chemical shift surfaces versus , and , dihedral angles. The applicability of chemical shift surfaces in the study of calixarene conformational features is illustrated. [source]

Total Synthesis of Ouabagenin and Ouabain

Maddi, Sridhar Reddy Dr.
Abstract All done! A full account of the total synthesis of ouabagenin and ouabain has been described. The synthesis was achieved through a polyanionic cyclization strategy. Degradation studies provide an ultimate proof for a key intermediate observed in the synthesis. A full account of the total synthesis of ouabagenin and ouabain is described. A highly stereocontrolled anionic cycloaddition for the rapid construction of the basic steroid skeleton is a pivotal conversion for the whole strategy. A careful study was needed to establish the order and the sequence of functional group manipulations. Specific conformational features of the ouabain skeleton allowed us to overcome a few stereochemical problems. Degradation studies on ouabain provided an ultimate proof for a key intermediate, which is used as a relay. Late stage butenolide formation and glycosidation yielded ouabain. [source]