Dihedral angle

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

Molecular dynamics simulations of the conformational dynamics of tryptophan

Abstract: Molecular dynamics simulations of a single tryptophan molecule were performed using CHARMm-parametrized potential functions, where both explicit molecular and dielectric continuum models were used for the solvent. When all hydrogens were modeled explicitly, rotations about the χ 2 dihedral were more frequent than about the χ 1 dihedral. The presence or a molecular solvent damped librational motion about both dihedral angles. Conversely, when a united atom representation for hydrogen was used, rotations about the χ 2 dihedral were more frequent than about the χ 1 dihedral

Atomic resolution protein structure determination by three-dimensional transferred echo double resonance solid-state nuclear magnetic resonance spectroscopy

Abstract: We show that quantitative internuclear N15–C13 distances can be obtained in sufficient quantity to determine a complete, high-resolution structure of a moderately sized protein by magic-angle spinning solid-state NMR spectroscopy. The three-dimensional ZF-TEDOR pulse sequence is employed in combination with sparse labeling of C13 sites in the β1 domain of the immunoglobulin binding protein G (GB1), as obtained by bacterial expression with 1,3-C13 or 2-C13-glycerol as the C13 source. Quantitative dipolar trajectories are extracted from two-dimensional N15–C13 planes, in which ∼750 cross peaks are resolved. The experimental data are fit to exact theoretical trajectories for spin clusters (consisting of one C13 and several N15 each), yielding quantitative precision as good as 0.1 A for ∼350 sites, better than 0.3 A for another 150, and ∼1.0 A for 150 distances in the range of 5–8 A. Along with isotropic chemical shift-based (TALOS) dihedral angle restraints, the distance restraints are incorporated into simu...

Structural characterization of an anhydrous polymorph of paclitaxel by solid-state NMR

Abstract: The three-dimensional structure of a unique polymorph of the anticancer drug paclitaxel (Taxol®) is established using solid state NMR (SSNMR) tensor (13C & 15N) and heteronuclear correlation (1H–13C) data. The polymorph has two molecules per asymmetric unit (Z′ = 2) and is thus the first conformational characterization with Z′ > 1 established solely by SSNMR. Experimental data are correlated with structure through a series of computational models that extensively sample all conformations. For each computational model, corresponding tensor values are computed to supply comparisons with experimental information which, in turn, establishes paclitaxel’s structure. Heteronuclear correlation data at thirteen key positions provide shift assignments to the asymmetric unit for each comparison. The two distinct molecules of the asymmetric unit possess nearly identical baccatin III moieties with matching conformations of the C10 acetyl moiety and, specifically, the torsion angle formed by C30–O–C10–C9. Additionally, both are found to exhibit an extended conformation of the phenylisoserine sidechain at C13 with notable differences in the dihedral angles centered around the rotation axes of O–C13, C2′–C1′ and C3′–C2′.