Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Conformational analysis”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,675 records · Page 93Linked to original sources
PubMed2003

Fourth 3D structure of the chitosan molecule: conformation of chitosan in its salts with medical organic acids having a phenyl group.

Chitosan salts with two medical organic acids having phenyl groups (salicylic and gentisic acids) exhibited fiber diffraction patterns of a new type of crystal which does not compare with known types I and II. The crystals, called type III salts, showed a fiber repeat of 2.550 nm and a meridional reflection at the 5th layer line. These results coupled with a conformational analysis indicate the chain conformation of chitosan with the salts to be a 5/3 helix, this helix differing from those of type I (an extended two-fold helix) and type II (a relaxed two-fold helix or a 4/1 helix). The fiber patterns of all the type III salts were similar. This observation has also been found with type II salts and is an indication that the acid ions are not arranged in regular positions in the crystals. A comparison of solid-state 13C-NMR spectra of the gentisic acid salt and the aspirin salt, which could not be crystallized, suggests that, in the latter salt, the chitosan molecules also formed a 5/3 helix.

Acids↗
PubMedDate not supplied

[Theoretic analysis of conformation of proteins. I. Minimization of potential energy of ribonuclease S].

Variation of ribonuclease S structure is analysed with the potential energy being minimized by a computer. The function of potential energy contains the potentials of bond and angle distortions, torsional and non-valent interactions. It is shown that after 100 iterations the potential energy is decreased from the value of 6500 kcal/mole to--1012 kcal/mole, 92% of complete change of energy fitting the first ten iterations. The root mean square deviation (r. ms. d.) of final structure from the initial one is 0.232 A (0.206 A for the backbone and 0.257 A for side groups). The forbidden non-valent contacts are completely removed after minimization. R. ms. d. of the equilibrium value is decreased from 0.097 to 0.006 A for bond lengths; from 7.660 to 3.65 degrees for valence an-les and from 9.44 to 6.95 degrees for rotation angles around the peptide bonds. Distribution of tensions along the protein chain after minimization is considerably changed, the tensions decreasing in average by 100 times.

Calorimetry↗
PubMed1986

[Synthesis and analysis of conformationally restricted analogs of peptide inhibitors of the angiotensin-converting enzyme].

To investigate conformations of peptide inhibitors of the angiotensin-converting enzyme in the enzyme-inhibitor complex, the synthesis, studies of inhibitory activity, and conformational calculations of analogues of bradykinin-potentiating peptides with N-methylalanine or D-alanine in place of L-proline or L-alanine residues have been carried out. All the analogues showed a sharp decrease of inhibitory activity in comparison with the natural peptides, that might be considered as an indirect confirmation of the earlier proposed "conformation of inhibition" of the above-mentioned peptides.

Amino Acid Sequence↗
PubMedDate not supplied

[Conformation of glycopeptides with L- and D-stereoisomers of Ala and Glu amino acids].

On the base of the semi-empirical method of conformational analysis low-energetic conformations have been found for the glycopeptides with the O-beta-N-acetyl-D-muramic acid or the O-beta-N-acetyl--D-glucosaminyl-(1-4)-N-acetyl-D-muramic acid in the glycan part and L-Ala--D-GluNH2, L-Ala--L-GluNH2, D-Ala--D-GluNH2 in the peptide part. It was shown that for either molecule preferentiability of any conformation is determined mainly by interactions between dipeptide and muramic acid residue.

Alanine↗
PubMed1993

Synthesis and benzodiazepine receptor affinity of N-(indol-3-ylglyoxylyl)-dipeptide derivatives. Structural requirements for inverse agonist/antagonist receptor interactions.

Several N-(indol-3-ylglyoxylyl)dipeptide derivatives 1-12 were synthesized and tested for their affinity at the benzodiazepine receptor in bovine cortical membranes. They proved to bind with low or no affinity at the receptor site. It was hypothesized that this result was not due to the steric hindrance of the dipeptide side chain, but to the establishment of intramolecular hydrogen bonds involving the indole N-H and/or the glyoxylyl C = O(2). Conformational analysis indicated that coiled conformations, with intramolecular hydrogen bonds, were energetically more favoured than the staggered, completely unfolded ones. Therefore, the low or no affinity of these compounds should be attributed to the unavailability of the N-H and/or C = O(2) groups for the binding, again confirming that both these groups are necessary for interaction with the receptor.

Animals↗
PubMedDate not supplied

Molecular similarity analysis on biologically active macrocyclic bis(bibenzyls).

Conformational analysis of marchantin A (1), a bis(diarylether) type, and riccardin A (2), a diarylether-biphenyl type macrocyclic bis(bibenzyl) was carried out by systematic unbounded multiple minimum search (SUMM). Mobility of the macrocyclic rings was analysed by variable temperature 1H-NMR study. Molecular similarity analysis was performed on the minimum energy conformers of 1 and 2 comparing their steric, electrostatic and hydrophobic properties. Correlation between complexation properties and calmodulin inhibitor activity was established. Differences in steric and electrostatic profiles may be responsible for the reduced Ca2+ affinity and activity of 2.

Bibenzyls↗
PubMed2005

Estimation of the three-dimensional pharmacophore of ligands for rat multidrug-resistance-associated protein 2 using ligand-based drug design techniques.

PURPOSE: Multidrug-resistance-associated protein 2 (Mrp2) shows a broad substrate specificity toward amphiphilic organic anions. This study identified key functional groups of ligand molecules for binding to rat Mrp2, determined their relative locations, and examined substrate specificity through receptor mapping using three-dimensional (3D) quantitative structure-activity relationship (3D-QSAR) analysis. METHODS: Ligand-binding conformations were estimated using conformational analysis (CAMDAS) and molecular superposition (SUPERPOSE) methods to clarify the substrate specificity of rat Mrp2 in relation to 3D ligand structures. RESULTS: Two types of binding conformations of ligands for rat Mrp2 were identified. 3D-QSAR comparative molecular-field analysis (CoMFA) revealed a statistically significant model for one type, in which the steric, electrostatic, and log P contributions to the binding affinity for rat Mrp2 were 63.0%, 33.4%, and 3.6%, respectively (n = 16, q2 = 0.59, n = 3, r2 = 0.99, and s = 0.08). CONCLUSIONS: The 3D pharmacophore of ligands for rat Mrp2, and the ligand-binding region of rat Mrp2, were estimated. Ligand recognition of rat Mrp2 is achieved through interactions in two hydrophobic and two electrostatically positive sites (primary binding sites). The broad substrate specificity of rat Mrp2 might result from the combination of secondary (two electrostatically positive and two electrostatically negative sites) and primary binding sites.

ATP-Binding Cassette Transporters↗
PubMed2001

The physical basis of nucleic acid base stacking in water.

It has been argued that the stacking of adenyl groups in water must be driven primarily by electrostatic interactions, based upon NMR data showing stacking for two adenyl groups joined by a 3-atom linker but not for two naphthyl groups joined by the same linker. In contrast, theoretical work has suggested that adenine stacking is driven primarily by nonelectrostatic forces, and that electrostatic interactions actually produce a net repulsion between adenines stacking in water. The present study provides evidence that the experimental data for the 3-atom-linked bis-adenyl and bis-naphthyl compounds are consistent with the theory indicating that nonelectrostatic interactions drive adenine stacking. First, a theoretical conformational analysis is found to reproduce the observed ranking of the stacking tendencies of the compounds studied experimentally. A geometric analysis identifies two possible reasons, other than stronger electrostatic interactions, why the 3-atom-linked bis-adenyl compounds should stack more than the bis-naphthyl compounds. First, stacked naphthyl groups tend to lie further apart than stacked adenyl groups, based upon both quantum calculations and crystal structures. This may prevent the bis-naphthyl compound from stacking as extensively as the bis-adenyl compound. Second, geometric analysis shows that more stacked conformations are sterically accessible to the bis-adenyl compound than to the bis-naphthyl compound because the linker is attached to the sides of the adenyl groups, but to the ends of the naphthyl groups. Finally, ab initio quantum mechanics calculations and energy decompositions for relevant conformations of adenine and naphthalene dimers support the view that stacking in these compounds is driven primarily by nonelectrostatic interactions. The present analysis illustrates the importance of considering all aspects of a molecular system when interpreting experimental data, and the value of computer models as an adjunct to chemical intuition.

Adenine↗