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At least 739 records · Page 41Linked to original sources
PubMed1998

Side-chains in native and random coil protein conformations. Analysis of NMR coupling constants and chi1 torsion angle preferences.

The behaviour of amino acid side-chains in proteins in solution has been characterised by analysing NMR 3JHalphaH beta coupling constants and crystallographic chi1 torsion angles. Side-chains both in the core of native folded proteins and in situations where there is an absence of close packing including the random coil state have been considered. An analysis of experimental 3JHalphaH beta coupling constant data for ten proteins shows that in the core of native proteins a very close similarity is observed between the chi1 conformations adopted in solution and in crystals. There is clear evidence, however, for significant motional averaging about the chi1 torsion angles in solution. Using a model of a Gaussian distribution about the average torsion angles the extent of these fluctuations has been quantified; the standard deviation for the motion is 26 degrees, the fluctuations about chi1 in the protein core being similar in size to those found for main-chain phi torsion angles in solution. From the distribution of chi1 torsion angles in a data base of protein crystal structures, torsion angle populations and coupling constants have been predicted for a random coil polypeptide. Significant variations in the chi1 distributions for different amino acids give differences in the predicted coupling constants; for 3JHalphaH beta, for example, values of 5.1 and 5.7 Hz are predicted for serine compared with 4.9 and 9.9 Hz for leucine. Experimental data for short unstructured peptides show an excellent agreement with the predictions, indicating that the overall chi1 distributions in protein crystals reflect the local preferences of the amino acids. Predictions from the protein data base therefore provide an important framework for interpreting experimental data for non-native protein conformations and for residues on the surface of folded proteins.

Crystallography↗
PubMed1994

Conformational analysis of the prototype nonclassical cannabinoid CP-47,497, using 2D NMR and computer molecular modeling.

In an effort to determine the stereochemical requirements for pharmacological activity among the series of nonclassical cannabinoids synthesized at Pfizer, we have studied the conformational properties of the parent bicyclic analog CP-47,497. For this study, we have used a combination of solution NMR and theoretical computational approaches. The energetically favored conformation has the phenolic ring almost perpendicular to the cyclohexanol ring which exists in a chair conformation. The OH bond of the phenol is preferentially coplanar with the aromatic ring and points toward the C2 ring proton, while the dimethylheptyl side chain adopts a conformation almost perpendicular to the aromatic ring. The conformational features of this nonclassical cannabinoid analog closely resemble those of its classical counterparts. The only apparent difference is the small dihedral angle (psi 1 = 62 degrees) between the planes of the two rings of CP-47,497 compared to that of the tricyclic tetrahydro- or hexahydrocannabinol analogs (psi 1 = 137 degrees). However, CP-47,497 can be perfectly superimposed over the respective tricyclic analog by rotation around the Ph-cyclohexyl bond (C6-C7 bond) and assume a conformation which is energetically higher than the preferred one by 3.0 kcal/mol. It can be argued that such a conformation may be acquired by the nonclassical analog during its interaction with the active site.

Cannabinoids↗
PubMed2006

Conformational analysis of spiro-bis-dithiepins: a peculiar case of axial chirality.

Spiro-bis-dithiepins are synthesized via dehydrative ring expansion in alpha-hydroxyalkyl spiro-bis-dithianes. Atypical of spiranes possessing axial chirality, the two most stable conformers of substituted spiro-bis-dithiepin have virtually colinear double bonds; i.e., each enantiomer exists in a form of two energy degenerate syn and anti conformations. Because of the high polarizability of the vinyl sulfide moiety, spiro-bis-dithiepins bearing electron-withdrawing substituents offer access to two-state systems possessing large dipole moments, which can be modulated by conformational events. [structure: see text]

Journal Article↗
PubMed2004

Compositional and conformational analysis of yam proteins by near infrared fourier transform Raman spectroscopy.

Fourier transform (FT)-Raman spectroscopy was employed to study the molecular structure of yam proteins isolated from three commonly consumed yam species including Dioscorea alata L., D. alata L. var. purpurea, and Dioscorea japonica. Although D. alata L. and D. alata L. var. purpurea consisted of similar amino acid residues, they still exhibited significant differences in conformational arrangement. The secondary structure of D. alata L. was mainly an alpha-helix, while D. alata L. var. purpurea was mostly in antiparallel beta-sheets. In contrast, D. japonica, which belongs to a different species, exhibited explicit differences in amino acid compositions and molecular structures of which the conformation was a mixed form of alpha-helices and antiparallel beta-sheets. FT-Raman directly proved the existence of S-S in yam proteins, implying that oligomer formation in yam proteins might be due to disulfide linking of dioscorin (32 kDa). The microenvironment of aromatic amino acids and the state of S-S in yam proteins were also discussed.

Amino Acids↗
PubMed2003

Theoretical conformational analysis for neurotransmitters in the gas phase and in aqueous solution. Norepinephrine.

The natural neurotransmitter (R)-norepinephrine takes the monocationic form in 93% abundance at the physiological tissue pH of 7.4. Ab initio and DFT/B3LYP calculations were performed for 12 protonated conformers of (R)-norepinephrine in the gas phase with geometry optimizations up to the MP2/6-311++G level, and with single-point calculations up to the QCISD(T) level at the HF/6-31G-optimized geometries. Four monohydrates were studied at the MP2/6-31G//HF/6-31G level. In the gas phase, the G1 conformer is the most stable with phenyl.NH(3)(+) gauche and HO(alc).NH(3)(+) gauche arrangements. A strained intramolecular hydrogen bond was found for conformers (G1 and T) with close NH(3)(+) and OH groups. Upon rotation of the NH(3)(+) group as a whole unit about the C(beta)-C(alpha) axis, a 3-fold potential was calculated with free energies for barriers of 3-12 kcal/mol at the HF/6-31G level. Only small deviations were found in MP2/6-311++G single-point calculations. A 2-fold potential was calculated for the phenyl rotation with free energies of 11-13 kcal/mol for the barriers at T = 310 K and p = 1 atm. A molecular mechanics docking study of (R)-norepinephrine in a model binding pocket of the beta-adrenergic receptor shows that the ligand takes a conformation close to the T(3) arrangement. The effect of aqueous solvation was considered by the free energy perturbation method implemented in Monte Carlo simulations. There are 4-5 strongly bound water molecules in hydrogen bonds to the conformers. Although hydration stabilizes mostly the G2 form with gauche phenyl.NH(3)(+) arrangement and a water-exposed NH(3)(+) group, the conformer population becomes T > G1 > G2, in agreement with the PMR spectroscopy measurements by Solmajer et al. (Z. Naturforsch. 1983, 38c, 758). Solvent effects reduce the free energies for barriers to 3-6 and 9-12 kcal/mol for rotations about the C(beta)-C(alpha) and the C(1)(ring)-C(beta) axes, respectively.

Amines↗
PubMed1987

Conformational analysis of two somatostatin analogues by 1H 500 MHz n.m.r. spectroscopy.

A series of nine closely related somatostatin analogues, containing the hexapeptide H-Cys2-Phe3-D-Trp4-Lys5-Thr6-Cys7-NH2 sequence have been synthesized by Bauer et al. The conformational properties of two of them, showing intermediate activities between those of SMS 201-995 and somatostatin, have been studied by high field n.m.r. spectroscopy in DMSO. Assignments were made using 2D-n.m.r. methods, in particular NOESY experiments and detection of long-range connectivities in aromatic residues. In all the compounds of this series, the biologically active ones as well as the inactive ones, the n.m.r. parameters are in favour of a predominant conformation with a type II' beta turn involving amino acids Phe3 to Thr6. A clearcut correlation exists between the predominant conformation at the cystine bridge side and the activity. The presence of the exocyclic amino acids Phe1 and Thr8 (ol) plays a major role in stabilization of the active conformation.

Indicators and Reagents↗
PubMed1996

Conformational analysis of blood group A trisaccharide in solution and in the binding site of Dolichos biflorus lectin using transient and transferred nuclear Overhauser enhancement (NOE) and rotating-frame NOE experiments.

The present study is concerned with the elucidation of the conformation of the blood group A trisaccharide (alpha-D-GalNAc(1-3)[alpha-L-Fuc(1-->2)] beta-D-Gal-O-R) in the combining site of Dolichos biflorus seed lectin by use of 400-MHz and 600-MHz NMR spectroscopy. D. biflorus lectin displays a unique specificity for GalNAc residues. It occurs in solution as a tetrameric assembly having a molecular mass of 110 kDa, with two carbohydrate-binding sites per molecule. First, NOE build-up curves were obtained for the free blood group A trisaccharide from one-dimensional transient NOE experiments. Simulated NOE build-up curves were constructed from an ensemble of low-energy conformers derived from previous investigations. The comparison of theoretical and experimental data indicates that an equilibrium between two families of low-energy conformers most likely reflects the solution behavior of the trisaccharide in solution. Two-dimensional transferred NOE and rotating-frame enhancements (ROE) were subsequently measured for the trisaccharide complexed with the D. biflorus seed lectin. In addition to the NOEs observed for the free trisaccharide, the transferred NOESY spectrum showed several new NOEs that were identified as spin diffusion using a rotating-frame NOESY (ROESY) experiment. Experimental interglycosidic transferred nuclear Overhauser effect (TRNOE) build-up curves were compared to theoretical curves calculated for both low-energy conformers located in the D. biflorus lectin-binding site. Calculations of theoretical TRNOE were performed using a combination of the full relaxation matrix and the protein-ligand exchange matrix. Comparison between experimental and simulated TRNOE volumes leads to the conclusion that one conformation of blood group A trisaccharide is selected upon binding by D. biflorus lectin.

ABO Blood-Group System↗