Dihedral angle

About: Dihedral angle is a research topic. Over the lifetime, 15718 publications have been published within this topic receiving 174904 citations.

Conformational consequences of intramolecular hydrogen bonding by OH to the directional lone-pair of sulfur in derivatives of methyl phenyl sulfide, diphenyl sulfide, and diphenyl disulfide

Abstract: Complete spectral parameters for the 1H nmr spectra of 2-hydroxyphenyl methyl sulfide, 2, 2-hydroxyphenyl phenyl sulfide, 3, bis(2-hydroxy-3-tert-butyl-5-methylphenyl) sulfide, 4, and bis(2-hydroxyphenyl) disulfide, 5, are reported for CCl4 solutions at 305 K. For 2 the parameters are consistent only with a conformation in which the C—S—C plane is roughly perpendicular to the aromatic plane. The conformational determinant is the hydrogen bond which forces the mainly 3p orbital on sulfur into the benzene plane. In 3 a similar arrangement is found about the sulfur atom, with the phenyl group lying in the C—S—C plane and therefore perpendicular to the hydroxyphenyl plane (skew conformation). In 4 two hydrogen bonds exist, yielding a gable (twist) conformation. Compound 5 exists in the axial conformation with probable C2 symmetry, the CSSC dihedral angle and the CCSS torsion angles all being near 90°. For none of the compounds is there any evidence for interactions.

Three-Dimensional Structure of the Immunophilin-like Domain of FKBP59 in Solution†,‡

Abstract: FKBP59 is a protein usually associated with heat-shock protein hsp90 and steroid receptors. The N-terminal domain of the rabbit liver protein (149 amino acids) has a sequence homology with FKBP12, binds FK506 immunosuppressor, and has a peptidyl-prolyl cis-trans isomerase activity. The three-dimensional structure of this domain (FKBP59-I) was determined using homo- and heteronuclear multidimensional NMR spectroscopy, distance geometry, and molecular dynamics methods. Structure calculations used 1290 interproton distance restraints derived from nuclear Overhauser enhancement measurements, 29 dihedral phi angle restraints, and 92 hydrogen bond restraints. For the final 22 structures, the root mean square distance from the mean atomic coordinates, calculated for well-defined secondary structure fragments, is 0.47 +/- 0.05 and 1.26 +/- 0.15 A for backbone heavy atoms (N, C alpha, C') and for all non-hydrogen atoms, respectively. The global fold contains a twisted six-stranded antiparallel beta-sheet and a short alpha-helix packed on the hydrophobic side of the sheet. The 20 N-terminal and 12 C-terminal amino acids of the domain are disordered. The main-chain structure of FKBP59-I is globally similar to the NMR-derived and X-ray structures of unbound FKBP12. An unusual hydrogen bond interaction between the indole amino proton of Trp 89 and the aromatic cycle of Phe 129 was observed. This gives a large upfield shift (-4.8 ppm) and a significant exchange protection factor. The implications of the present structure determination on the ligand binding of FKBP59 are discussed.

Analysis of conformational polymorphism in pharmaceutical solids using solid-state NMR and electronic structure calculations.

Abstract: A detailed analysis of molecular structure in three polymorphic forms of 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile is made using a combination of multidimensional solid-state NMR (SSNMR) experiments and molecular modeling via electronic structure calculations. These compounds, collectively referred to as ROY because of their red, orange, and yellow colors, share a similar molecular structure with the exception of the dihedral angle between the phenyl and thiophene rings. The ROY materials make it possible to study the influence of nearly a single degree of freedom on the associated NMR spectra. Using the 2D PASS (Antzutkin et al. J. Magn. Reson. A 1995, 115, 7) experiment, spectral editing techniques, and DFT-based calculations of the local fields, an analysis is made of the sensitivity of all carbon and nitrogen sites to changing molecular conformation. Chemical shift and dipolar coupling information obtained from these experiments vary noticeably between forms and are subsequently used to quantitatively determine aspects of molecular structure in these materials, including the coplanar angle between the phenyl and thiophene rings. The influence of motion on the methyl and nitro chemical shifts is also investigated. The accuracy of the information obtained from local field analysis and the model structure calculation demonstrates the capabilities of SSNMR as a quantitative structural method.

Three-dimensional solution structure of Ca(2+)-loaded porcine calbindin D9k determined by nuclear magnetic resonance spectroscopy.

Abstract: The three-dimensional solution structure of native, intact porcine calbindin D9k has been determined by distance geometry and restrained molecular dynamics calculations using distance and dihedral angle constraints obtained from 1H NMR spectroscopy. The protein has a well-defined global fold consisting of four helices oriented in a pairwise antiparallel manner such that two pairs of helix-loop-helix motifs (EF-hands) are joined by a linker segment. The two EF-hands are further coupled through a short beta-type interaction between the two Ca(2+)-binding loops. Overall, the structure is very similar to that of the highly homologous native, minor A form of bovine calbindin D9k determined by X-ray crystallography [Szebenyi, D. M. E., & Moffat, K. (1986) J. Biol. Chem. 261, 8761-8776]. A model structure built from the bovine calbindin D9k crystal structure shows several deviations larger than 2 A from the experimental distance constraints for the porcine protein. These structural differences are efficiently removed by subjecting the model structure to the experimental distance and dihedral angle constraints in a restrained molecular dynamics protocol, thereby generating a model that is very similar to the refined distance geometry derived structures. The N-terminal residues of the intact protein that are absent in the minor A form appear to be highly flexible and do not influence the structure of other regions of the protein. This result is important because it validates the conclusions drawn from the wide range of studies that have been carried out on minor A forms rather than the intact calbindin D9k.

Conformation dependence of the SH and CS stretch frequencies of the cysteine residue

Abstract: SYNOPSIS In order to relate the observed SH and CS stretch frequencies of the cysteine residue in proteins more closely to its conformation, we have done normal mode calculations on a model for this structure, viz., (CCONH) (CNHCO)CHCH2SH. A range of x' and x2 were studied, combined with the $,$ of the a-helix, P-sheet, glutathione, and extended-helix conformations. The force field was a combination of a scaled ab initio force field of the -CH2SH group, obtained from ethanethiol and tested on 1-propanethiol and 3-thiol-Nmethylpropionamide, and our empirical force field for the peptide group. The results provide more detailed structure-spectra correlations than are possible from experimental studies of model compounds. 0 1992 John Wiley & Sons, Inc. I NTRODU CTl ON The cysteine residue side chain, -CH2SH, is an important one in proteins, both because of its inherent properties as well as its ability to react with similar groups to form a disulfide bridge, -CH2SSCH2-, between polypeptide chains. It is therefore important to develop detailed spectroscopic correlations for characterizing its conformation. It has long been known that the SH stretch (s) mode, v(SH), is generally found in the range of 2500-2600 cm-' , being weak in the ir and strong in the Raman spectrum. Since v(SH) is sensitive to the presence of SH groups and to their environment, particularly hydrogen bonding, it has been studied in various proteins, such as hemoglobin, 122 eye lens proteins, 3-5 0-lactoglobulin, and virus protein^.^,' Conformational information with respect to the C"Cs-S-H dihedral angle ( x2) has been sought through experimental studies of model alkanethiolsg-" as well as normal mode calculations on such molecule~.'~~~~ Low-frequency torsional modes have also been studied14-16 in order to obtain information on rotational barriers. The v(CS) mode has been known to give rise to Raman bands in the 600-800-cm-' region. Confor