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PubMedDate not supplied

[Comparative conformational analysis of dinucleoside phosphate CpA and its analog C(3'NH)pA].

By the method of theoretical conformational analysis, on the examples of CpA and C(3'NH)pA comparison is made of conformational flexibility of dinucleoside phosphates with the natural O-P-O and abnormal N-P-O internucleotide bonds. The conformational flexibility of sugar cycles is accounted for. It is shown that substitution of the phosphodiester bond into amide ester leads to a noticeable limitation of favorable areas in conformational space of molecules and, as consequence, to the increase of the equilibrium ratio of conformers with the Pba and Mbb type of base stacking. The obtained results are used for discussion of the binding experiments of acylamino acid derivatives of CpA and C(3'NH)pA to the donor site of the peptidyl transferase center of ribosomes.

Adenosine↗
PubMed1983

[Theoretical conformation analysis of specific O-antigenic polysaccharides. Polysaccharide of Shigella dysenteriae of serotype 2].

Theoretical conformational analysis of Shigella dysenteriae serotype 2 polysaccharide containing repeating unit: -4Gal beta 1-3GalNAc alpha 1-3(GlcNAc alpha 1-4)GalNAc alpha 1-4Glc alpha 1- has been carried out. It is shown that spatial forms of the polymer are determined by conformational states of Glc alpha 1-4Gal links which form the internal bends of the chain. The structures of low energy are shown to be left three-fold helices with an axially projected repeat of approximately 12 A. N-Acetamide groups of side residues alpha-D-GlcNAc are the most accessible for intermolecular interactions and may determine immunological specificity of the polysaccharide.

Antigens, Bacterial↗
PubMed1991

[Conformational analysis of tachykinins. I. N-terminal fragments of substance P, physalemin, hylambatin, and uperolein].

Theoretical conformational analysis of N-terminal fragments of the title peptides has been carried out using the potential energy calculations. The number of conformational states for each fragment is very limited, and they are easily interconverted. Since these fragments cannot form alpha-helises, it is unlikely that upon binding of tachikinins to their receptors, their N-terminal fragments could overcome the hydrophobic barrier of the cell membrane's lipid belayer.

Amino Acid Sequence↗
PubMedDate not supplied

Depsipeptide analogues of elastin repeating sequences: conformational analysis.

In this work the effect of elimination of a specific hydrogen bond on the conformation of the repeating peptides of elastin was studied. These repeating sequences are the pentapeptide Val-Pro-Gly-Val-Gly and the hexapeptide Val-Ala-Pro-Gly-Val-Gly. These sequences have been proposed to occur in a beta-turn conformation with a hydrogen bond involving the amide NH of the internal valine residue and the carbonyl oxygen of the residue preceding proline. In the depsipeptide analogues studied in this work, this 4-1 beta-turn hydrogen bond cannot occur. We studied the depsipeptide sequences Val-Pro-Gly-Hiv-Gly and Val-Ala-Pro-Gly-Hiv-Gly (Hiv denotes S-alpha-hydroxyisovaleric acid, the hydroxy acid analogue of valine), as well as the peptide sequences Val-Pro-Gly-Val-Gly and Val-Ala-Pro-Gly-Val-Gly. Compounds studied included sequences with the Boc and benzyl ester protecting groups, derivatives with the acetyl and N-methylamide end groups and polymers of the above sequences. Our conclusions are based on a comparison of depsipeptides with analogous peptides. Conformational analysis was carried out by nmr, CD, and ir spectroscopy. We propose that in the repeating sequences of elastin an equilibrium exists between a gamma-turn structure and a beta-turn structure in the Pro-Gly segment resulting in a structure that combines flexibility with strong conformational preferences. The C7 involves the amide NH of the internal glycine and the carbonyl oxygen of the residue preceding proline. In the N-methylamide derivatives a similar equilibrium exists in the Gly-Val-Gly segment. In the depsipeptides the beta-turn cannot occur and only the gamma-turn is seen. In the polydepsipeptides the major conformational feature is a type I beta-turn involving Gly5 NH and Pro CO.

Amino Acid Sequence↗
PubMedDate not supplied

Conformational analysis and a crystal structure of bupropion, an antidepressant with dopamine reuptake blocking activity.

A conformational analysis has been performed on the antidepressant bupropion using the MM3-92 program. In addition, the structure of the compound in the crystal state was obtained. There is good agreement between the computed global minimum and the structure observed by crystallography. The three-dimensional structure of the preferred conformer of bupropion is consistent with the three-dimensional structures of other dopamine reuptake blockers such as cocaine, CFT, and methylphenidate.

Antidepressive Agents, Second-Generation↗
PubMed2001

Conformational analysis of cyclophostin and designed analogs in comparison with the potent IP3 receptor agonist adenophostin A.

A conformational analysis of 5'-6"-tethered cyclophostin was carried out in comparison with the mother compound, adenophostin A, which has a potent IP3 receptor agonistic activity. The global minimum 3'-endo/anti conformation of cyclophostin elucidated by a molecular dynamics simulation was in accord with NMR spectroscopic data. In contrast, the 2'-endo/syn conformation was dominant with respect to adenophostin A. Despite the constraint introduced by the tether, the spatial arrangement of the three phosphate groups and the adenine moiety, which are essential for the extremely high potency, was changed only moderately in comparison with adenophostin A. The observed high potency of cyclophostin (EC50 = 38 nM) also indicates that it closely resembles the bioactive conformation of adenophostin A (EC50 = 7 nM). These results led us to estimate the probable active conformation of adenophostin A by comparison with the stable conformations of cyclophostin. Finally, two other tethered analogs were designed and are expected to exhibit high potencies comparable to adenophostin A.

Adenosine↗
PubMed1995

Conformational analysis of carbohydrates inferred from NMR spectroscopy and molecular modeling. Applications to the behavior of oligo-galactomannan chains.

In both the biological functions and industrial applications of carbohydrates, their conformational behavior along with the dynamic fluctuations that their structures experience are of great significance. The elucidation of the three-dimensional characteristics of carbohydrates and carbohydrate-containing molecules is in general performed by a combination of high-resolution nuclear magnetic resonance (NMR) spectroscopy and molecular modeling. Heteronuclear couplings and nuclear Overhauser effect (NOE) data are major tools for structural determination. The angular dependence of carbon-proton coupling constants has been shown to depend also on the pathways involved. Concerning molecular modeling, the goal is to generate the ensemble of structures that are consistent with the experimental data. This approach is illustrated in the galactomannan chain. It consists of the conformational study of two model disaccharides (mannobiose and epimelibiose) of galactomannans through carbon-proton coupling constants and NOE measurements. Experimental data are then compared to results of conformational analysis that predicted the stable conformers in solution. From these results helical conformations of oligomers are generated and are discussed in terms of the influence of the position and number of galactose units on the conformation of the mannan backbone.

Carbohydrates↗
PubMed2006

Conformational analysis of methyl 5-O-methyl septanosides: effect of glycosylation on conformer populations.

Methyl 5-O-methyl-alpha-d-glycero-d-idoseptanoside (3) and methyl 5-O-methyl-beta-d-glycero-d-guloseptanoside (4) were investigated as (1-->5)-linked di-/oligoseptanoside mimetics. Here we report the synthesis of 3 and 4 and describe their preferred solution conformations through a combination of ab initio/DFT calculations and (1)H (3)J(H,H) NMR coupling constant analysis. The conformations of 3 and 4 observed in this study are discussed in comparison to those of the parent (C5 hydroxy) compounds 1 and 2. The results indicate that methyl 5-O-methyl-alpha-septanoside 3 is relatively rigid and adopts the same (3,4)TC(5,6) conformation as 1. Methyl 5-O-methyl-beta-septanoside 4 is somewhat less rigid than its parent septanoside (2). In addition to the (6,O)TC(4,5) conformation adopted by 2, beta-septanoside 4 also populates the adjacent (3,4)TC(5,6) conformation. Glycosylation at C5 on beta-septanoside 4 therefore increases its overall flexibility and allows access to alternative ring conformations.

Carbohydrate Conformation↗
PubMedDate not supplied

[Conformational analysis of peptide antagonists in the design of pseudopeptide and non-peptide antagonists].

The comparative conformational analysis of four Substance P antagonists (NK1-) having different chemical structures allowed to formulate an hypothesis for a peptidic NK1 pharmacophore. The salient features of this pharmacophore (three aromatic groups and two carbonyl functions) belong to a beta-turn conformation. Thus, this kind of conformation might be the basis for the design of newer pseudo-peptidic and non-peptidic NK1 antagonists.

Amino Acid Sequence↗
PubMed2006

Torsional anharmonicity in the conformational analysis of beta-D-galactose.

Schemes to include a treatment of torsional anharmonicity in the conformational analysis of biological molecules are introduced. The approaches combine ab initio electronic energies and harmonic frequencies with anharmonic torsional partition functions calculated using the torsional path integral Monte Carlo method on affordable potential energy surfaces. The schemes are applied to the conformational study of the monosaccharide beta-d-galactose in the gas phase. The global minimum structure is almost exclusively populated at 100 K, but a large number of conformers are present at ambient and higher temperatures. Both quantum mechanical and anharmonic effects in the torsional modes have little effect on the populations at all temperatures considered, and it is, therefore, expected that standard harmonic treatments are satisfactory for the conformational study of monosaccharides.

Galactose↗
PubMed1991

Comparative conformational analysis of [D-Pen2,D-Pen5]enkephalin (DPDPE): a molecular mechanics study.

A theoretical conformational analysis (molecular mechanics study) of the delta opioid receptor-selective enkephalin analog H-Tyr-D-Pen-Gly-Phe-D-Pen-OH (DPDPE) was performed, based on the use of the SYBYL software. The study led to the identification of several conformers that were significantly lower in energy than previously reported candidate conformers of DPDPE which, for comparative purposes, were also minimized by using the standard SYBYL force field. The results revealed a considerable degree of conformational flexibility of the DPDPE molecule, and suggested that incorporation of further conformational constraints into this enkephalin analog will be necessary in order to elucidate its receptor-bound conformation.

Amino Acid Sequence↗
PubMed1986

[Conformational analysis of the double pentasaccharide sequence of the "bisected" structure ov N-glycoproteins].

In the conformational analysis of the pentasaccharide alpha-D-Manp-(1----3)-[beta-D-GlcpNAc-(1----4)]-[alpha-D- Manp-(1----6)]-beta-D-Manp-(1----4)-D-GlcNAc, which represents the essential core structure within the bisected type of N-glycoproteins, n.m.r. experiments and GESA calculations indicated that a gg conformation is preferred for the (1----6)-glycosidic linkage. This is in contrast to the results obtained for the tetrasaccharide alpha-D-Manp-(1----3)-[alpha-D-Manp-(1----6)]-beta-D- Manp-(1----4)- D-GlcNAc, which indicated that a gt conformation with the (1----6)-linked alpha-D-mannose group folded back is preferred. The conformations of the remaining glycosidic linkages in the tetra- and penta-saccharide are similar.

Carbohydrate Conformation↗
PubMed1994

Conformational analysis and receptor modelling of m1 and m2 selective antagonists.

On the basis of an elaborate conformational analysis of m1- and m2-selective antagonists a respective pharmacophore was deduced. This then was introduced into models of the two muscarinic receptor subtypes. These models were constructed starting from bacteriorhodopsin as a template in accordance with alignment data and mutation experiments. The validity of the interaction geometries between ligands and receptor subtypes is supported by a significant correlation between calculated interaction energies and experimentally determined affinity data.

Amino Acid Sequence↗
PubMed1990

Theoretical conformational analysis of a family of alpha-helical immunocytokines.

According to the results of the theoretical conformation analysis and available experimental data, the known immunocytokines can be divided into two groups: alpha-helical (IFNs-alpha, beta, gamma, omega; IL-2, 3, 4, 5, 6, 7; G-, M-, GM-CSFs; cMGF, PDGF) and beta-pleated proteins (ILs-1 alpha, beta; TNFS-alpha, beta). IFNs-alpha, beta, gamma, omega, IL-6, G-CSF, cMGF were shown to form a family of alpha-helical globular proteins characterized by a statistically significant homology in amino acid sequences and by common features of the secondary structure formation. Comparison of the sequences of 72 IFNs-alpha, beta, omega reveals three clusters of conservative amino acid positions. Their participation in the formation of active sites of IFN-alpha, beta, omega is supposed.

Amino Acid Sequence↗
PubMedDate not supplied

[Structure-function organization of neurokinin A and neurokinin B molecules. I. Theoretical conformational analysis of neurokinin A].

The spatial structure of the neurokinin A molecule was studied by the method of theoretical conformational analysis. On the basis of fragmental analysis, stable structures of the neurokinin A molecule under polar conditions were determined. The structures can be described by four families of low-energy conformations having a relatively labile tripeptide at the C-end and a conformationally rigid heptapeptide at the N-end. It was shown that two of these conformations are virtually isoenergetic structures. One of these is an alpha-helical structure and the other forms two beta-turns at the N-terminus, which change to the turn of the alpha-helix at the C-end.

Amino Acid Sequence↗
PubMed1991

[Conformational analysis of tachykinins. III. C-terminal fragment Asx-Xaa-Phe-Yaa-Gly-Leu-Met-NH2].

Theoretical conformational analysis of C-terminal fragments of tachykinin peptides with a common amino acid sequence Asx-Xaa-Phe-Yaa-Gly-Leu-Met-NH2 suggested the conformational states to be independent of the nature of Xaa and Yaa residues. It is shown that among plausible spatial forms of the C-terminal fragments an alpha-helix with the hydrophobic coat consisted of identically oriented side chains is energetically the most stable structure. The preference of this conformation for tachykinins functioning is discussed.

Amino Acid Sequence↗
PubMed1986

Theoretical conformational analysis of brain peptides. beta-Melanocyte-stimulating hormone.

Using a semi-empirical method, an a priori conformational analysis of the octadecapeptide beta-melanocyte-stimulating hormone (beta-MSH) was carried out. The spatial structure of beta-MSH can be described by eight low-energy conformations, yielded by combinations of the most stable states of the respective free fragments. Calculations produced the values of all dihedral angles of the backbones and side chains of these forms as well as intra- and inter-residue interaction energies.

Amino Acid Sequence↗