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PubMed1991

The electrostatically driven Monte Carlo method: application to conformational analysis of decaglycine.

The Electrostatically Driven Monte Carlo (EDMC) method was applied in a study of a decamer of glycine whose conformational behavior is described by the Empirical Conformational Energy Program for Peptides (ECEPP/2) potential energy model. When free neutral end groups were used, it was found that conformations that were not alpha-helical had significantly lower potential energies than fully alpha-helical ones. However, when the N- and C-termini were blocked by acetyl and methyl amide groups, respectively, the number of unsatisfied hydrogen-bond donors and acceptors at the helix termini was diminished from 8 to 6; in this case, the possibility of forming two additional alpha-helical hydrogen bonds was an important enough factor in making the alpha-helical conformation the one with the lowest energy. The EDMC method was used as a global energy optimizer since it does not often become trapped in high-energy local minima.

Electrochemistry↗
PubMed2002

Conformational analysis of the tyrosine dipeptide analogue in the gas phase and in aqueous solution by a density functional/continuum solvent model.

The conformational behavior of a dipeptide analogue of tyrosine (TDA) has been investigated by density functional methods using the polarizable continuum model (PCM) for the description of solvent effects. Our study points out the interplay of backbone and side chain contributions in determining the relative stabilities of energy minima. In particular, stabilizing interactions between the NH bond and the aromatic ring have a significant effect. The topology of the potential energy surface is significantly modified in aqueous solution due to a general widening of low energy regions and to a stabilization of helical structures.

Algorithms↗
PubMed1996

Molecular modelling and conformational analysis of a GABAB antagonist.

Crystallographic database studies and molecular dynamics simulations in different media have enabled us to sample the conformational space of a GABAB antagonist. As a result, we have defined a pharmacophoric pattern for GABAB antagonists. This study has led us to compare the conformational preferences deduced from database studies and molecular dynamics simulations. The influence of the medium on the conformations has also been investigated.

Baclofen↗
PubMed1993

Conformational analysis of d-tubocurarine: implications for minimal dimensions of its binding site within ion channels.

All the minimum-energy conformations of d-tubocurarine were calculated by the method of molecular mechanics. The energy was minimized from 413 closed forms of the 18-member ring. The set of minimum-energy conformations includes 10 forms with energies less than 6 kcal/mol from the most stable one. Among the four lowest minimum-energy conformations, two forms correspond to those known from X-ray studies, whereas two conformations were not detected experimentally earlier. The flexibility of d-tubocurarine was estimated by calculating six paths of interconversion between the four lowest minimum-energy conformations. Using a molecular graphics technique, it was found that the most extended minimum-energy conformation of d-tubocurarine may fit in an ion channel of a rectangular profile of 8.7 x 11.2 A, while one tetrahydroisoquinoline head may fit a profile as small as 6.9 x 11.0 A. A possible model of d-tubocurarine location within the ion channel of the neuronal nicotinic acetylcholine receptor is suggested.

Binding Sites↗
PubMed1980

Conformational analysis of ribonucleosides from proton-proton coupling constants.

A graphical method is described which permits the determination in solution of conformational equilibria and parameters of ribonucleosides from proton-proton coupling constants. The method is based on the pseudorotational concept and the use of the Karplus equation. Using a large number of 1H-NMR data on ribonucleosides from the literature, on optimal set of Karplus constants, A = 10.0, B = -1.2, was obtained. It is shown that this set of Karplus constants, in connection with the pseudorotational treatment, describes satisfactorily the nucleoside conformations, especially the pucker amplitude. The solution results are compared with X-ray data and the differences are discussed. The method can be used either graphically or by direct computer treatment of the data.

Magnetic Resonance Spectroscopy↗
PubMed2005

NMR conformational analysis of p-tolyl furanopyrimidine 2'-deoxyribonucleoside and crystal structure of its 3',5'-di-O-acetyl derivative.

The conformation of a representative molecule of a new, potent class of antiviral-active modified nucleosides is determined. A bicyclic nucleoside, 3-(2'-deoxy-beta-D-ribofuranosyl)-6-(4-methylphenyl)-2,3-dihydrofuro[2,3-d]pyrimidin-2-one, shows C2'-endo and C3'-endo ribose conformations in solution (63:37, 37 degrees C; DMSO-d6), as determined by 1H NMR studies. The crystal structure of a 3',5'-di-O-acetyl-protected derivative (monoclinic, P21, a/b/c= 6.666(1)/12.225(1)/24.676(2) A, beta=90.24(1) degrees , Z=4) shows exclusively C2'-endo deoxyribose puckering. The base is found in the anti position both in solution and in crystalline form.

Crystallography, X-Ray↗
PubMed1986

Conformational analysis of the dopamine-receptor agonist 5-hydroxy-2-(dipropylamino)tetralin and its C(2)-methyl-substituted derivative.

The conformational preferences of the dopamine (DA) receptor agonist 5-hydroxy-2-(di-n-propylamino)tetralin (1) and the DA-inactive 5-hydroxy-2-methyl-2-(di-n-propylamino)tetralin (2) have been studied by use of molecular mechanics (MMP2) calculations and NMR spectroscopy. A good agreement is demonstrated between the experimentally determined (by NMR) and the calculated (by MMP2) conformational distribution of 1 and 2. In addition, there is a good agreement between bond distances and bond angles in the X-ray structure of the hydrobromide of 1 and those in the corresponding MMP2 conformation. Results obtained demonstrate that the energetically preferred conformations of 1 and 2 are different: Compound 1 preferentially adopts half-chair conformations with a pseudoequatorial nitrogen substituent whereas the low-energy conformations of compound 2 have a pseudoaxial nitrogen substituent. However, the results also indicate that the difference in conformational preferences is too small to account for the dopaminergic inactivity of 2. Therefore it is suggested that the steric bulk of the C(2)-methyl group per se prevents a proper alignment of (2S)-2 with DA receptors.

8-Hydroxy-2-(di-n-propylamino)tetralin↗
PubMed2001

Conformational analysis of nevirapine, a non-nucleoside HIV-1 reverse transcriptase inhibitor, based on quantum mechanical calculations.

The structure and the conformational behavior of the HIV-1 reverse transcriptase inhibitor, 11-cyclopropyl-5,11dihydro-4-methyl-6H-dipyrido[3,2-b2',3'-e][1,4]diazepin-6-one (nevirapine), is investigated by semiempirical (MNDO, AMI and PM3) method, ab initio at the HF/3-21G and HF/6-31G** levels and density functional theory at the B3LYP/6-31G** level. The fully optimized structure and rotational potential of the nitrogen and carbon bond in the cyclopropyl ring were examined in detail. A similar geometrical minimum is obtained from all methods which shows an almost identical structure to the geometry of the molecule in the complex structure with HIV-1 reverse transcriptase. To get some information on the structure in solution, NMR chemical shift calculations were also performed by a density functional theory at the B3LYP/6-31G** level, using GIAO approximation. The calculated 1H-NMR and 13C-NMR spectra for the energy minimum geometry agree well with the experimental results, which indicated that the geometry of nevirapine in solution is very similar to that of the molecule in the inhibition complex. Furthermore, the obtained results are compared to the conformational studies of other non-nucleoside reverse transcriptase inhibitors and reveal a common agreement of the non-nucleoside reverse transcriptase inhibitors. The specific butterfly-like shape and conformational flexibility within the side chain of the non-nucleoside reverse transcriptase inhibitors play an important role inducing conformational change of HIV-1 reverse transcriptase structure and are essential for the association at the inhibition pocket.

Anti-HIV Agents↗
PubMed1997

Conformational analysis of methyl 6-O-[(R)- and (S)-1-carboxyethyl]-alpha-D-galactopyranoside by MM and Langevin dynamics simulations.

The conformational space of methyl 6-O-[(R)- and (S)-1-carboxyethyl]-alpha-D-galactopyranoside has been investigated. A grid search employing energy minimization at each grid point over the three major degrees of freedom, namely phi, psi and omega, identified low energy regions. The R-isomer shows five low energy conformers within ca. 1 kcal mol(-1) of the global energy minimum. The S-isomer has two conformers within a few tenths of a kcal mol(-1) of the global energy minimum. Langevin dynamics simulations have been have been performed at 300 K for 30 ns of each isomer. The phi dihedral angle has as its major conformer (g-) for the R-isomer whereas it is the (g+) conformer for the S-isomer. For the psi dihedral angle the (t) conformer has the highest population for both isomers. The dihedral angle omega has the (g+) conformer most highly populated, both for the R- and S-isomer. The above five and two conformational states for the R- and S-isomers, respectively, make up 90% in each case of the populated states during the Langevin dynamics (LD) simulations. Rate constants for the omega dihedral angle have been calculated based on a number correlation function. Three bond homo- and heteronuclear, i.e. proton and carbon-13, coupling constants have been calculated from the dynamics trajectories for comparison to experimental values. The heteronuclear coupling constant H2',C6 has been measured for the S-isomer and found to be 3.3 Hz. The J value calculated from the LD simulations, namely 2.6 Hz, is in fair agreement with experiment. A comparison to the X-ray structure of the R-isomer shows that the conformation of the crystalline compound occupies the low energy region most highly populated as a single R-conformer (30%) during the LD simulations.

Carbohydrate Conformation↗
PubMed1996

Combined use of NMR, distance geometry and MD calculations for the conformational analysis of opioid peptides of the type [D(L)-Cys2, D(L)-Cys5]enkephalin.

The solution structures of a series of conformationally restricted pentapeptides with a sequence H-Tyr1-Cys2-Gly3-Phe4-Cys5-OH cyclic (2-5) disulfide, where the cysteines possess either the D or L configuration, were examined by a combined approach including NMR measurements as well as MD calculations. It turned out that at least one low energy conformer of H-Tyr1-D-Cys2-Gly3-Phe4-D-Cys5-OH cyclic (2-5) disulfide (DCDCE), as well as one conformer out of the group of calculated conformers for H-Tyr1-D-Cys2-Gly3-Phe4-Cys5-OH cyclic (2-5) disulfide (DCLCE), satisfies the NMR data obtained in this study, whereas for the derivative H-Tyr1-Cys2-Gly3-Phe4-Cys5-OH cyclic (2-5) disulfide, which contains solely L-Cys (LCLCE), there is no single structure compatible with the NMR data.

Computer Simulation↗
PubMedDate not supplied

[Local structure of cytochrome c from horse heart in solution. Conformational analysis using data of two-dimensional nuclear Overhauser effect spectroscopy].

Using the earlier suggested method the calculation of the backbone conformations of horse heart cytochrome c in oxidized (ferricytochrome c) and reduced (ferrocytochrome c) states has been performed by the two-dimensional nuclear Overhauser effect spectroscopy data. For both protein forms the secondary structure elements have been revealed and the conformations of the irregular polypeptide chain segments have been analysed. The similarity of the secondary structures of ferri- and ferrocytochrome c in solution was established from the comparison of their conformations. Small differences between the conformations of two molecule forms are shown to be localized within the polypeptide chain fragments situated in the spatial structure near the heme crevice. The comparison of the dihedral phi and psi angles in the calculated conformations of horse cytochrome C with the corresponding characteristics of X-ray structures of tuna ferri- and ferrocytochrome c made for the oxidized and reduced protein forms using the quantitative criteria testifies the similarity of their conformations in solution and crystal. In is shown that the conformational changes of the separate amino acid residues which take place as the result of the "solution-to-crystal" transition occur on the surface fragments of protein globule and do not lead to essential alterations of the secondary molecule structure.

Amino Acids↗
PubMedDate not supplied

[Conformational analysis of protein side chains using two-dimensional Overhauser nuclear effect spectroscopy].

The method has been proposed to determine the conformations of protein side-chains (dihedral angles chi 1) using two-dimensional nuclear Overhauser effect spectroscopy data. This method is grounded of the algorithm prepared on the basis of joint consideration of proton-proton distance dependences in dipeptide units of L-amino acid residues on the dihedral angles phi, psi and chi 1 with the accounting of the local sterical conditions of the polypeptide chain. The obtained results gave the possibility to bring the different regions of space (phi, psi) of amino acid residues into the line with the specific sets of nuclear Overhauser effect spectral parameters which unambiguously characterize in most cases the conformational states of their side-chains. The method efficiency was displayed on the test calculation with the utilization as the experimental data of the "model" nuclear Overhauser effect contacts derived from the X-ray atomic coordinates of the bovine pancreatic trypsin inhibitor molecule.

Animals↗
PubMed1991

Conformational analysis of peptide surrogates. Reduced and retro-amide links in blocked alanine and in secondary structures.

We have investigated the conformational effects of modifying the amide link of peptides. We studied a reverse amide bond psi [NHCO], a reduced amide bond psi [CH2NH] and a retro-reduced bond psi [NHCH2] as surrogates for the amide link [CONH] in native peptides. A complete search of the conformational space available to residues with these modified links was carried out. The local minima and the rotational barriers were described and compared to the minima of the native residue. The results are compatible with the available observed structural data. These modified links have been incorporated in secondary structure units such as beta turns, alpha helices, and parallel and anti-parallel beta sheets. It was found that a reduced amide link can lead to stabilised beta turns, while the retro modification can be incorporated in stable beta sheets. A significant reduction in the stability of alpha helices is caused by the retro links, while a reduced amide link results in only a small destabilisation.

Alanine↗
PubMed1995

Conformational analysis of the beta-amyloid peptide fragment, beta(12-28).

NMR and CD spectroscopy have been used to examine the conformation of the peptide, beta(12-28), (VHHQKLVFFAEDVGSNK) in aqueous and 60% TFE / 40% H2O solution at pH 2.4. In 60% TFE solution, the peptide is helical as confirmed by the CD spectrum and by the pattern of the NOE cross peaks detected in the NOESY spectrum of the peptide. In aqueous solution, the peptide adopts a more extended and flexible conformation. Broadening of resonances at low temperature, temperature-dependent changes in the chemical shifts of several of the CH alpha resonances and the observation of a number of NOE contacts between the hydrophobic side-chain protons of the peptide are indicative of aggregation in aqueous solution. The behavior of beta(12-28) in 60% TFE and in aqueous solution are consistent with the overall conformation and aggregation behavior reported for the larger peptide fragment, beta(1-28) and the parent beta-amyloid peptide.

Amino Acid Sequence↗
PubMed1986

Characterization and conformational analysis by Raman spectroscopy of human airway lysozyme.

Human airway lysozyme, purified from pathological bronchial secretions, is characterized by a specific activity 3-fold higher than that of hen egg-white lysozyme. The amino acid composition of human airway lysozyme is identical to that of other human lysozymes. The laser Raman spectra of human airway lysozyme and hen egg-white lysozyme in phosphate buffer solution (pH 7.2) are recorded in the range 300-1900 cm-1 at 488 nm. Drastic intensity differences are observed between the spectra analyzed in the ranges characteristic of the peptide backbone (e.g., beta-sheet; C alpha-C, C alpha-N), and of the aromatic side-chain vibrations (tyrosine, tryptophan). The deconvolution of the Raman amide I band gives secondary structures of 38% and 39% alpha-helix, 25% and 20% beta-sheet, and 37% and 41% undefined structure for the human and hen lysozymes, respectively.

Amino Acids↗
PubMed2001

NMR solution structure and conformational analysis of the calcium release agent cyclic adenosine 5'-diphosphate ribose (cADPR).

A high-resolution NMR study of the solution structure of the calcium release agent cADPR has been performed. Pseudorotationals analysis reveals that in solution both sugar rings in cADPR adopt predominantly (approximately 75%) South conformations, with the A and N rings adopting approximately 2T3 (C2'-endo(major)-C3'-exo(minor) and 4(3)T (C3'-exo-C4'-endo) conformations, respectively. The backbone torsion angles beta and gamma have also been determined. While the minor North conformers were not observed in the crystal structure of cADPR, the solution values of the major South conformers compare well to those found in crystal structure.

Adenosine Diphosphate Ribose↗
PubMedDate not supplied

Conformational analysis, molecular shape comparison, and pharmacophore identification of different allosteric modulators of muscarinic receptors.

Structurally dissimilar compounds such as alcuronium and the newly synthesized substances derived from the bisbenzyl ether TMB4 and from hexamethonium stabilize antagonist binding to M2-cholinoceptors which is indicative of an allosteric action. In order to propose a hypothesis for the common pharmacophore and the corresponding active conformations, seven flexible compounds in a data set were individually aligned onto the most active and, additionally, rigid alcuronium molecule using a torsional angle flexible fit. An S-shape conformation was found to be a plausible general active conformation. In a subsequent molecular shape analysis the overlap and the nonoverlap steric volumes, RMS alignment as well as electrostatic field potentials were employed as possible structure--activity correlation descriptors. The corresponding 3D-QSAR formulation exhibits a correlation between allosteric modulation potency and the nonoverlap steric volume as well as the proton and oxygen anion probe electrostatic field potentials. Because of large structural diversity among the small number of compounds studied, the apparent 3D-QSAR is best thought of as a convenient representation of the common spatial pharmacophore hypothesis.

Alcuronium↗