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Fascination with the conformational analysis of succinic acid, as evaluated by NMR spectroscopy, and why.

A serendipitous effort to use NMR spectroscopy to determine the conformational preferences of succinate monoanion opened a Pandora's box of unexpected uncertainties as to what influences such preferences of succinic acid in its various ionization states, not only in water but also in other less polar protic solvents, as well as a range of aprotic solvents. The dianion in aprotic solvents shows substantial gauche preferences, which give the appearance of violating Coulomb's law.

Magnetic Resonance Spectroscopy↗

Conformational analysis of cholecystokinin CCK26-33 and related fragments by 1H NMR spectroscopy, fluorescence-transfer measurements, and calculations.

The conformational behavior of CCK7, Tyr-Met-Gly-Trp-Met-Asp-Phe-NH2, and CCK8, Asp-Tyr-Met-Gly-Trp-Met-Asp-Phe-NH2, in their sulfated and unsulfated forms, was studied both by 1H NMR spectroscopy in dimethyl-d6 sulfoxide and water and by fluorescence-transfer measurements at pH 7. In neutral conditions, both experimental methods show that these peptides exist preferentially in folded forms with beta and gamma turns around the sequence Gly-Trp-Met-Asp and Met-Asp-Phe-NH2, respectively. The presence of stable folded conformations is supported by through-space effects during the titration of the ionizable groups and by the weak temperature dependency of some amide protons not only in dimethyl sulfoxide but also in water. The folding of the C-terminal part, already shown in CCK5, seems to be a common conformational characteristic in CCK peptides. The N-terminal part of CCK8 presents an equilibrium between beta and gamma turns, whereas this part of the peptide is more flexible in CCK7. The low quantum yield of Tyr and the large mean distance (R = 15 A) between Tyr and Trp, determined by fluorescence-transfer measurements, support the occurrence of folded conformations pushing the aromatic rings far from each other. Interestingly, the introduction of the sulfate group enhances the folding tendency even in aqueous medium. The larger amide temperature dependency and the decrease in the R distance at acidic pH suggest that an intramolecular ionic interaction involving the N-terminal amino group and the beta-carboxyl groups of Asp32 stabilize the folded forms. Metropolis calculations performed on CCK8 support the existence of stable folded conformations closely related to those deduced from experimental data.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗

Comparative conformational analysis of peptide libraries.

Six computer-based combinatorial libraries, including tetrapeptide sequences (generated with five amino acids) and conformations (generated with five main chain and three side chain rotamers), were obtained and sequence-conformation probabilities were calculated with a molecular and statistical mechanics procedure. The structural motifs alpha-helix, beta-sheet, 3(10)-helix, reverse turn I and gamma-turn were focused in these calculations. It is shown that sequence-conformation-probability surfaces provide a broad view of structural changes accompanying changes in sequence. Numerical indices are defined to enable comparisons between frequencies of occurrence of these structural motifs in peptide libraries and in a database of low sequence identity protein structures. Fine details of sequence-conformation-probability surfaces show the effect of point mutations. Broad comparisons between different regions of these surfaces indicate how to select the occurrence of structural motifs in the combinatorial synthesis of peptide chains.

Algorithms↗

Conformational analysis of dopamine by the INDO molecular orbital method.

The results of INDO calculations on dopamine are reported. A conformational energy map and an isodistance map for the key distances N-OH1, N-OH2 in dopamine as functions of the two main torsion angles tau1 and tau2 were constructed. In addition to the three known minima of dopamine corresponding to the trans and gauche forms, two new minima were found. The key distances of the rigid analogues of dopamine, apomorphine, isoapomorphine, 2-amino-6,7-dihydroxy-1,2,3,4-tetrahydronaphthalene and isoquinoline were plotted on the isodistance map of dopamine. By taking the corresponding tau values as coordinates on the energy map, conformations of dopamine, resembling the rigid analogues, could be found. When a conformation is close to a local minimum it is assumed that this conformation is energetically favourable. The possible relation between the energy minima and the biological action of dopamine is discussed. An explanation is suggested for the lack of dopaminergic activity of isoapomorphine.

Apomorphine↗

The conformational analysis of delta 9- and delta 9,11-tetrahydrocannabinols in solution using high resolution nuclear magnetic resonance spectroscopy.

The conformation for each of two cannabinoids, delta 9-tetrahydrocannabinol (THC), the principal active constituent of marihuana, and delta 9,11-THC, a biologically inactive structural isomer of delta 9- THC, is analyzed by interpreting 1H-1H and 13C-1H coupling constants and nuclear Overhauser effects determined using one-and two-dimensional 1H and 13C NMR techniques. The interpretation of both vicinal and long range coupling constants was necessary to deduce the conformations of these tricyclic molecules with certainty, with nuclear Overhauser effect enhancements used, when appropriate, to confirm the results. These findings provide insights into the structure-activity requirements for the cannabinoids.

Dronabinol↗

Conformational analysis of a glycosylated human myelin oligodendrocyte glycoprotein peptide epitope able to detect antibody response in multiple sclerosis.

Myelin oligodendrocyte glycoprotein (MOG), a minor myelin component, is an important central nervous system specific target autoantigen for primary demyelination in autoimmune diseases such as multiple sclerosis (MS). The native structure of MOG presents a glycosylation site at position 31 (Asn(31)). It has been recently described that glycosylation of a MOG peptide epitope improved the detection of specific autoantibodies in sera of MS patients. The solution conformational behavior of two MOG derived peptides-hMOG(30-50) (1) and the glycosylated analogue [Asn(31)(N-beta-Glc)]hMOG(30-50) (2)-were investigated through NMR analysis in a water/HFA solution. Conformational studies revealed that peptides 1 and 2 adopted similar conformations in this environment. In particular, they showed strong propensity to assume a well-defined amphipatic structure encompassing residues 41-48. The N-terminal region resulted to be almost completely unstructured for both peptides. The presence in 1 of a low populated Asx-turn conformation characteristic of the Asn-Xaa-Thr glycosylation sites was the only conformational difference between peptides 1 and 2. Thus, the specific antibody recognition of peptide 2 is most likely driven by direct interactions of the antibody binding site with the Asn-linked sugar moiety.

Amino Acid Sequence↗

Conformational analysis and molecular modeling of 1-phenyl-, 4-phenyl-, and 1-benzyl-1,2,3,4-tetrahydroisoquinolines as D1 dopamine receptor ligands.

Conformational studies on a series of 1-phenyl-, 4-phenyl-, and 1-benzyl-1,2,3,4-tetrahydroisoquinolines that possess an identical substituent pattern to the prototypical D1 dopamine receptor antagonist SCH23390 [(R)-(+)-7-chloro-8-hydroxy-3-methyl-1-phenyl-2,3,4,5- tetrahydro-1H-3-benzazepine (1)] were performed with use of molecular mechanics calculations [MM2(85), with newly developed aromatic halide bending and torsional parameters that are now incorporated into MM2(87)], single-crystal X-ray analysis, and high-field NMR spectroscopy. The synthesis and biological testing of compounds 2-7 has been previously reported. The test compounds were compared both quantitatively and graphically to compound 1. Calculations on both the free-base and protonated forms of each compound were carried out. To insure that conformation space was adequately sampled, the test compounds were energy minimized from different starting geometries; ring inversion of the heterocycle was employed, as were dihedral driver calculations on the phenyl or benzyl rings. For N-methyl-6-chloro-7-hydroxy-1-phenyl-1,2,3,4-tetrahydroisoquinoline (2), it was determined that the torsion angle tau(C8a-C1-C12-C17) had energy minima at approximately 60 degrees and 240 degrees. This finding was corroborated by NMR studies that indicated a dramatic upfield chemical shift of ArH8 after ring cyclization. The nitrogen lone pair or hydrogen vector was approximately orthogonal to the plane of the substituted aromatic ring in the tetrahydroisoquinolines; this explained the upfield chemical shift of the vicinal chiral proton (H1). In all instances, the 6-membered heterocyclic ring in the energy-minimized structures preferred the half-chair conformation with the phenyl rings pseudo-equatorial. Distance comparisons of the proposed pharmacophoric atoms (Cl, N, O, centroid of the phenyl or benzyl ring) showed that the phenyl or benzyl centroid to ammonium H distance, Cl to N distance, and distance of the nitrogen above or below the plane of the isoquinoline aromatic ring are the distances most highly correlated with biological activity (r = 0.82, 0.75, 0.81, respectively). Resolution and single-crystal X-ray analysis of compound 2 showed the most active enantiomer to possess the S absolute configuration, in contrast to the benzazepine (R)-1. Least-squares fitting of the energy-minimized structures with SYBYL molecular modeling software showed (S)-(+)-2, rather than (R)-(-)-2, gave a better fit to (R)-1. Volume determinations derived from SYBYL multifit analyses aided in receptor mapping to qualitatively describe areas of "active" pharmacophore space as well as areas of "inactive" substituent space.(ABSTRACT TRUNCATED AT 400 WORDS)

Benzazepines↗

Oligofuranosides containing conformationally restricted residues: synthesis and conformational analysis.

The synthesis of a panel of arabinofuranosyl oligosaccharide analogues (5-13) in which one ring is locked into either the E(3) or OE conformation is described. The E(3)-locked scaffolds 15 and 16 required for the synthesis of 5-10 were prepared in one step from known 1,5-anhydroalditols. A number of routes were explored for the preparation of the OE-locked monosaccharide derivative 17 needed for the preparation of 11-13. The successful synthesis of 17 was achieved in 17 steps from D-arabinose. Subsequent analysis of 5-13 by 1H NMR spectroscopy demonstrated that the locked residue does not exert any detectable influence upon the conformers populated by adjacent conformationally unrestricted furanose rings.

Arabinose↗

Conformational analysis of circular dichroism spectra of insulin, proinsulin and c-peptides by non-linear regression.

A method of resolving CD spectra in alpha-helix, beta-structure and random coil conformations is described. The residue ellipticites for alpha-helix and beta-structure given by Greenfield & Fasman or by Chen,, Yang & Martinez are used together with CD spectra from at least two similar peptides to determine, by an iterative least-squares method, the number of amino acids in the three reference conformations as well as a set of residue ellipticities characteristic of the random coils of the family of peptides in question, but not necessarily of other peptides. The fits between computed and experimental spectra improve significantly and systematic deviations disappear by allowing the random coil coefficients to vary from one family of proteins to another, a liberty justified by the different types of random coils that have been encountered. The method of analysis showed that 5 M urea did not change the conformations of C-peptides of proinsulin from ox, pig and duck, all being mainly in the random coil conformation and all having 3-4 amino acids in beta-structure. Bovine insulin and proinsulin showed a transfer of amino acids from alpha-helix to beta-structure with increasing concentrations of urea, the latter at a higher concentration, indicating a stabilizing effect of the connecting peptide. The numbers of amino acids found in the alpha-helical conformation in insulin and proinsulin were equal and in agreement with the X-ray crystallographic data for insulin when the Greenfield & Fasman coefficients for alpha-helix and beta-structure were employed, whereas the Chen, Yang & Martinez coefficients yielded too few amino acids in alpha-helix in proinsulin. Both sets of coefficients estimate more beta-structure in proinsulin than in insulin.

Amino Acids↗

Differential deuterium isotope shifts and one-bond 1H-13C scalar couplings in the conformational analysis of protein glycine residues.

The one-bond deuterium isotope shift effect for glycine C alpha resonances exhibits a conformational dependence comparable to that of the corresponding 1JHC scalar coupling in both magnitude (approximately 11 Hz at 14.1 T) and dihedral angle dependence. The similarity in the conformational dependence of the 1JHC and deuterium isotope shift values suggests a common physical basis. Given the known distribution of (phi, psi) main-chain dihedral angles for glycine residues, the deuterium isotope shifts and the 1JHC scalar couplings can determine conformations in the left- and right-handed helical-to-bridge regions of the (phi, psi) plane to an accuracy of approximately 13 degrees. In the absence of stereochemical assignments, the differential deuterium isotope shifts and the 1JHC scalar couplings can be combined with limited independent structural information (e.g., the sign of phi) to determine the chirality of the deuterium substitution.

Deuterium↗

Conformational analysis of rhazinilam and three-dimensional quantitative structure-activity relationships of rhazinilam analogues.

3D QSAR of rhazinilam (1), an alkaloid isolated from Rhazya stricta (Apocynaceae) with an activity involving disassembly of microtubules and its derivatives was investigated by using the comparative molecular field analysis (CoMFA). In an effort to get a better understanding of the correlation between conformation and antitubulin activity of 1, most probable minimum energy conformation in solution of 1 was analyzed on the basis of NMR data of 1 in solution. The results indicated a correlation between the antitubulin activity of these alkaloids and the steric and electrostatic factors, which modulate their biological activity, and accounted for the potent activities of 1 with suitable relationship for the overall conformation.

Alkaloids↗

Oxygenated metabolites of anandamide and 2-arachidonoylglycerol: conformational analysis and interaction with cannabinoid receptors, membrane transporter, and fatty acid amide hydrolase.

This study was aimed at finding structural requirements for the interaction of the acyl chain of endocannabinoids with cannabinoid receptors, membrane transporter protein, and fatty acid amide hydrolase (FAAH). To this end, the flexibility of the acyl chain was restricted by introduction of an 1-hydroxy-2Z,4E-pentadiene system in anandamide (N-arachidonoylethanolamine, AEA) and 2-arachidonoylglycerol (2-AG) at various positions using different lipoxygenases. This brought about selectivity and attenuated the binding potency of AEA and 2-AG. Although the displacement constants were modest, 15(S)-hydroxy-eicosa-5Z,8Z,11Z,13E-tetraenoyl-N-(2-hydroxyethyl)amine was found to bind selectively to the CB(1) receptor, whereas its 1-arachidonoyl-sn-glycerol analogue and 13(S)-hydroxy-octadeca-9Z,11E-dienoyl-N-(2-hydroxyethyl)amine could selectively bind to the CB(2) receptor. 11(S)-Hydroxy-eicosa-5Z,8Z,12E,14Z-tetraenoyl-N-(2-hydroxyethyl)amine did not bind to either receptor, whereas 12(S)-hydroxy-eicosa-5Z,8Z,10E,14Z-tetraenoyl-N-(2-hydroxyethyl)amine did bind to both CB receptors with an affinity similar to that of AEA. All oxygenated anandamide derivatives were good inhibitors of FAAH (low micromolar K(i)) but were ineffective on the AEA transporter. 2-AG rapidly isomerizes into 1(3)-arachidonoyl-sn-glycerol. Both 1- and 3-arachidonoyl-sn-glycerol did not bind to either CB receptor and did not interfere with AEA transport. Thus, after it is isomerized, 2-AG is inactivated, thereby decreasing effective concentrations of 2-AG. Analysis of (1)H NMR spectra revealed that chloroform did not induce notably different conformations in the acyl chain of 15(S)-hydroxy-eicosa-5Z,8Z,11Z,13E-tetraenoic acid as compared with water. Molecular dynamics (MD) simulations of AEA and its analogues in the presence of explicit water molecules revealed that a tightly folded conformation of the acyl chain is not the only requirement for CB(1) binding. Structural details of the C(2)-C(15) loop, such as an sp(2) carbon at position 11, are necessary for receptor binding. The MD simulations may suggest that the average orientations of the pentyl tail of AEA and 12(S)-hydroxy-eicosa-5Z,8Z,10E,14Z-tetraenoyl-N-(2-hydroxyethyl)amine are different from that of the low-affinity, inactive ligands.

Amidohydrolases↗

Conformational analysis of 6-cis- and 6-trans-leukotriene B4-calcium complexes.

We present a computational description of the conformation of a pair of two isomeric molecules (6-cis-and 6-trans-leukotriene B4) forming a complex with one calcium ion. Our theoretical prediction of the membrane-water interface conformation and of the bulk lipid phase conformation of the two different isomeric complexes are in excellent agreement with experimental data on the leukotriene-mediated calcium ionophoresis in liposomes. The two isomers lead to vastly different conformations in the presence of Ca2+, and the most probable conformation of the permeant species shows a globular conformation able to cross a lipid membrane.

Calcium↗

[Theoretical conformational analysis of a substrate component of tetrahedral intermediates and of acyl-enzyme of carboxypeptidase A].

Semi-empirical calculation of conformational properties of covalent complexes of carboxypeptidase A with ester and peptide substrates are presented. There is a favourable form of transient tetrahedral and covalent acyl-enzyme intermediates in the active site of carboxypeptidase A. The ester and peptide substrates bind in the active site of carbopeptidase A in the same mode. The transition from one stage of the reaction to the other is followed by a small conformational change. The atom coordinates of the substrate component of these complexes are presented.

Binding Sites↗

Synthesis and conformational analysis of a non-amidine factor Xa inhibitor that incorporates 5-methyl-4,5,6,7-tetrahydrothiazolo[5,4-c]pyridine as S4 binding element.

Our exploratory study was based on the concept that a non-amidine factor Xa (fXa) inhibitor is suitable for an orally available anticoagulant. We synthesized and evaluated a series of N-(6-chloronaphthalen-2-yl)sulfonylpiperazine derivatives incorporating various fused-bicyclic rings containing an aliphatic amine expected to be S4 binding element. Among this series, 5-methyl-4,5,6,7-tetrahydrothiazolo[5,4-c]pyridine type 61 displayed orally potent anti-fXa activity and evident prolongation of prothrombin time (PT) with the moderate bioavailability in rats. The X-ray crystal analysis afforded an obvious binding mode that 5-methyl-4,5,6,7-tetrahydrothiazolo[5,4-c]pyridine and 6-chloronaphthalene respectively bound to S4 and S1 subsites. In this X-ray study, we discovered a novel intramolecular S-O close contact. Ab initio energy calculations of model compounds deduced that conformers with the most close S-O proximity were most stable. The Mulliken population analysis proposed that this energy profile was caused by both of electrostatic S-O affinity and N-O repulsion. The results of these calculations and X-ray analysis suggested a possibility that the restricted conformation effected the affinity to S4 subsite of fXa.

Animals↗

Conformational analysis of mitochondrial and microsomal cytochrome P-450 by resonance Raman spectroscopy.

Mitochondrial and microsomal cytochromes P-450SCC and P-450LM2 in the ferric substrate-free and substrate-bound states were studied by resonance Raman spectroscopy. In the spectra of cytochrome P-450SCC two conformational states (A and B) were detected, each of them constituting an equilibrium between a six-coordinated low-spin and a high-spin form. Both the conformational and the spin equilibria are pH- and temperature-dependent, which is in line with previously published results [Lange, R., Larroque, C., & Anzenbacher, P. (1992) Eur. J. Biochem. 207, 69-73)]. On the basis of well-resolved resonance Raman spectra, measured at different pH and temperatures, these equilibria were analyzed quantitatively. Both low-spin configurations of A and B exhibit different band patterns in the spin state marker band region, indicating differences in the active-site structures. While in the high-spin configuration of state A the heme iron remains weakly bound by a sixth ligand, the high-spin form of state B is five-coordinated. Binding of cholesterol to cytochrome P-450SCC causes a significant population of the high-spin forms, particularly of state A (62%). On the other hand, binding of 22R-hydroxycholesterol to the substrate-free enzyme leaves the overall spin equilibrium largely unchanged, i.e., six-coordinated low spin (76% A and 24% B). In both substrate-bound complexes, interactions between the substrate and the heme lead to small but distinct differences in the resonance Raman spectra of the low-spin form of state A. In contrast to cytochrome P-450SCC, the resonance Raman spectra of microsomal cytochrome P-450LM2 provide no indications for multiple conformers at 22 degrees C.(ABSTRACT TRUNCATED AT 250 WORDS)

Adrenal Cortex↗