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At least 667 records · Page 37Linked to original sources
PubMedDate not supplied

Ab initio conformational analysis of nucleic acid components: intrinsic energetic contributions to nucleic acid structure and dynamics.

In recent years, the use of high-level ab initio calculations has allowed for the intrinsic conformational properties of nucleic acid building blocks to be revisited. This has provided new insights into the intrinsic conformational energetics of these compounds and its relationship to nucleic acids structure and dynamics. In this article we review recent developments and present new results. New data include comparison of various levels of theory on conformational properties of nucleic acid building blocks, calculations on the abasic sugar, known to occur in vivo in DNA, on the TA conformation of DNA observed in the complex with the TATA box binding protein, and on inosine. Tests of the Hartree-Fock (HF), second-order Møller-Plesset (MP2), and Density Functional Theory/Becke3, Lee, Yang and Par (DFT/B3LYP) levels of theory show the overall shape of backbone torsional energy profiles (for gamma, epsilon, and chi) to be similar for the different levels, though some systematic differences are identified between the MP2 and DFT/B3LYP profiles. The east pseudorotation energy barrier in deoxyribonucleosides is also sensitive to the level of theory, with the HF and DFT/B3LYP east barriers being significantly lower (approximately 2.5 kcal/mol) than the MP2 counterpart (approximately 4.0 kcal/mol). Additional calculations at various levels of theory suggest that the east barrier in deoxyribonucleosides is between 3.0 and 4.0 kcal/mol. In the abasic sugar, the west pseudorotation energy barrier is found to be slightly lower than the east barrier and the south pucker is favored more than in standard nucleosides. Results on the TA conformation suggest that, at the nucleoside level, this conformation is significantly destabilized relative to the global energy minimum, or relative to the A- and B-DNA conformations. Deoxyribocytosine would destabilize the TA conformation more than other bases relative to the A-DNA conformation, but not relative to the B-DNA conformation.

DNA↗
PubMed1999

Interactions of macrolide antibiotics (Erythromycin A, roxithromycin, erythromycylamine [Dirithromycin], and azithromycin) with phospholipids: computer-aided conformational analysis and studies on acellular and cell culture models.

The potential of 14/15 membered macrolides to cause phospholipidosis has been prospectively assessed, and structure-effects examined, using combined experimental and conformational approaches. Biochemical studies demonstrated drug binding to phosphatidylinositol-containing liposomes and inhibition of the activity of lysosomal phospholipase A1 toward phosphatidylcholine included in the bilayer, in close correlation with the number of cationic groups carried by the drugs (erythromycin A </= roxithromycin < erythromycylamine </= azithromycin). In cultured cells (fibroblasts), phospholipidosis (affecting all major phospholipids except sphingomyelin) was observed after 3 days with the following ranking: erythromycin A </= roxithromycin < erythromycylamine < azithromycin (roxithromycin could, however, not be studied in detail due to intrinsic toxicity). The difference between erythromycylamine and azithromycin was accounted for by the lower cellular accumulation of erythromycylamine. In parallel, based on a methodology developed and validated to study drug-membrane interactions, the conformational analyses revealed that erythromycin A, roxithromycin, erythromycylamine, and azithromycin penetrate into the hydrophobic domain of a phosphatidylinositol monolayer through their desosamine and cladinose moieties, whereas their macrocycle is found close to the interface. This position allows the aminogroups carried by the macrocycle of the diaminated macrolides (erythromycylamine and azithromycin) to come into close contact with the negatively charged phosphogroup of phosphatidylinositol, whereas the amine located on the C-3 of the desosamine, common to all four drugs, is located at a greater distance from this phosphogroup. Our study suggests that all macrolides have the potential to cause phospholipidosis but that this effect is modulated by toxicodynamic and toxicokinetic parameters related to the drug structure and mainly to their cationic character.

Anti-Bacterial Agents↗
PubMed1988

Origin of the positive 225-230 nm circular dichroism band in proteins. Its application to conformational analysis.

The 225-230 nm circular dichroism band found in many disulfide-containing proteins and peptides is sensitive to environmental changes. This band is assigned to the disulfide bond, the conformation of which influences both the intensity and lambda max of the band. This property can be used to monitor subtle conformation changes observed in many polypeptides. Examples using the alpha-neurotoxins of elapid venoms and neurohypophyseal hormones are discussed.

Amino Acid Sequence↗
PubMed1983

Conformational analysis of m4(2)C-m4(2)C-m6(2)A: a chemically modified 3'-acceptor end of tRNA, studied by NMR and CD methods.

A study on the conformation of the title compound, C-C-A, and on its constituent dinucleotides is presented. 1H-NMR spectra at 360 and 500 MHz were completely assigned by decoupling experiments. Computer simulation of the spectra yielded precise proton-proton and proton-phosphorus coupling constant values. The coupling constants are analyzed in terms of torsion angles and of N- and S-type sugar pucker. 31P-NMR spectra gave some information about P-O backbone torsion angles alpha and zeta. CD spectroscopy was used to obtain insight in the base-base interaction. The C(1) and C(2) unit in C-C-A show normal preference for N-type conformation of the sugar ring, whereas the A(3) residue appears rather biased towards the S-conformation. The zeta and alpha backbone torsion angles in the C-C phosphodiester linkage in C-C-A appear to assume normal g-, g- conformation, the zeta, alpha combination in the C-A linkage is proposed to have a g+, t conformation. In the C-C fragment in C-C-A a regular stack is indicated; it is suggested that the C-A part adopts an unusual antiparallel base stack.

Base Composition↗
PubMed1996

Conformational analysis of a cyclic heptapeptide, pseudostellarin D by molecular dynamics and Monte Carlo simulations.

Restrained molecular dynamics calculation in vacuo using AMBER force field implemented in MacroModel/Batchmin showed a major solution conformation in dimethyl sulfoxide-d6 of pseudostellarin D, cyclo(Gly-Tyr-Gly-Pro-Leu-Ile-Leu-). This is a cyclic heptapeptide isolated from Pseudostellaria heterophylla possessing characteristics of a beta-bulge motif with three intramolecular hydrogen bonds, two beta-turns (one type I at Pro4 and Leu5 residues, and one type II at Leu7 and Gly1 residues) and all trans amide bonds. The solution form of pseudostellarin D, which was homologous to that observed in the solid state, was also supported by Monte Carlo simulation study.

Carbohydrate Sequence↗
PubMed1993

Conformational analysis of methyl beta-cellobioside by ROESY NMR spectroscopy and MD simulations in combination with the CROSREL method.

Methyl beta-cellobioside has been studied extensively by molecular dynamics (MD) simulations in water and by ROESY NMR spectroscopy in order to establish its solution structure. The MD simulations were started with four significantly different minimal energy conformations. The MD trajectories were analysed with respect to interproton distances and mobility, in order to find models for application in the analysis of NMR data. The ROESY spectra were analysed by using the CROSREL method, which allows quantitative analysis of ROESY spectra through correction for the offset dependence and incorporation of HOHAHA transfer estimates. These results were compared with data obtained from an initial rate analysis of the ROESY data and with the MD data. It is concluded that methyl beta-cellobioside in aqueous solution is in the same extended conformation that is also found in the solid state.

Carbohydrate Conformation↗
PubMed2005

Complete 1H and 13C NMR spectral assignment of N-aralkylsulfonamides, N-sulfonyl-1,2,3,4-tetrahydroisoquinolines and N-sulfonyl-2,3,4,5-tetrahydro-1H-2-benzazepines. Conformational analysis of N-[((3',4'-dichlorophenyl)methyl)sulfonyl]-3-methyl-2,3,4,5-tetrahydro-1H-2-benzazepin.

The complete and unambiguous assignment of the 1H NMR and 13C NMR spectra of 26 N-aralkylsulfonamides, N-sulfonyl-1,2,3,4-tetrahydroisoquinolines and N-sulfonylbenz[c]azepines was performed on the basis of APT, DEPT, homonuclear (gs-COSY) and 1H-detected heteronuclear one-bond (gs-HMQC) and long-range (gs-HMBC) correlation experiments. The methylated 2,3,4,5-tetrahydro-1H-2-benzazepine derivative 26 adopts a chair conformation as determined by 1H-1H coupling analysis and gamma-gauche effects. This is supported by a single-crystal X-ray structure analysis.

Journal Article↗
PubMed2003

Dynamic and static conformational analysis of acylated tetrahydrobenzazepines.

A detailed high-field NMR analysis of several acylated tetrahydrobenzazepines, supported by molecular mechanics calculations, indicates that the heterocyclic ring in these compounds exists in a chair conformation, with the carbonyl oriented anti to the aryl moiety in the dominant rotamer. Surprisingly, ring methylenes are typically diastereotopic at room temperature, as the barriers for the process of enantiomerization of the seven-membered ring are much higher than expected. It is shown that ring inversion is correlated (but not concerted) with rotation of the amide moiety, as the carbonyl is forced out of conjugation with the nitrogen in the transition state.

Journal Article↗
PubMed1991

[Conformational analysis of lipotropic acton of human somatotropin and peptide analogs].

Based on the results of a semi-empirical analysis, several structural types of human and sea whale somatotropins and placental lactogen lipotropic actons which correspond, apparently, to the biologically active conformation common for the given molecular family, were identified. Chemical modification of human somatotropin lipotropic acton whose conformational possibilities selectively model the most preferential structure of the natural oligopeptide are proposed.

Amino Acid Sequence↗
PubMedDate not supplied

Synthesis of 10,11-dihydroxydihydroquinidine N-oxide, a new metabolite of quinidine. Preparation and 1H-nmr spectroscopy of the metabolites of quinine and quinidine and conformational analysis via 2D COSY nmr spectroscopy.

The first synthesis of 10,11-dihydroxydihydroquinidine N-oxide [7b], a recently isolated metabolite of quinidine, was accomplished in three steps from 1b. The related congener 7a in the quinine series was also prepared, as well as two other analogues 3a and 4a. In addition, the previously reported human metabolites 2a, 5a, and 6a of quinine [1a] and those 2b, 3b, 4b, 5b, and 6b of quinidine [1b] were synthesized. The chemical shift and coupling constants for all of the metabolites of quinine and quinidine were assigned via 2D COSY 1H-nmr spectroscopy. Moreover, the conformations of these metabolites in solution were found to parallel those of the parent alkaloids, quinine [1a] and quinidine [1b], respectively.

Molecular Conformation↗
PubMedDate not supplied

[Conformational analysis of 5-substituted uracil].

The high-resolution IR-spectra of 5-nitrouracil and 5-bromouracil isolated in Ar matrices at 11 K were obtained for the first time. The conformational structure of uracil 5-substituents--thymine, 5-bromouracil, 5-nitrouracil--is calculated by the molecular mechanics and quantum--chemical MINDO/3 methods. The possibility of thymine transition to nonplanar conformations is observed.

Bromouracil↗