Dihedral angle

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

Structure of the N-terminal cellulose-binding domain of Cellulomonas fimi CenC determined by nuclear magnetic resonance spectroscopy.

Abstract: Multidimensional heteronuclear nuclear magnetic resonance (NMR) spectroscopy was used to determine the tertiary structure of the 152 amino acid N-terminal cellulose-binding domain from Cellulomonas fimi 1,4-β-glucanase CenC (CBDN1). CBDN1 was studied in the presence of saturating concentrations of cellotetraose, but due to spectral overlap, the oligosaccharide was not included in the structure calculations. A total of 1705 interproton nuclear Overhauser effect (NOE), 56 φ, 88 ψ, 42 χ1, 9 χ2 dihedral angle, and 88 hydrogen-bond restraints were used to calculate 25 final structures. These structures have a rmsd from the average of 0.79 ± 0.11 A for all backbone atoms excluding disordered termini and 0.44 ± 0.05 A for residues with regular secondary structures. CBDN1 is composed of 10 β-strands, folded into two antiparallel β-sheets with the topology of a jelly-roll β-sandwich. The strands forming the face of the protein previously determined by chemical shift perturbations to be responsible for cellooligosa...

Docking of Protein−Protein Complexes on the Basis of Highly Ambiguous Intermolecular Distance Restraints Derived from 1HN/15N Chemical Shift Mapping and Backbone 15N−1H Residual Dipolar Couplings Using Conjoined Rigid Body/Torsion Angle Dynamics

Abstract: A simple and reliable method for docking protein−protein complexes using 1HN/15N chemical shift mapping and backbone 15N−1H residual dipolar couplings is presented and illustrated with three complexes (EIN-HPr, IIAGlc-HPr, and IIAMtl-HPr) of known structure. The 1HN/15N chemical shift mapping data are transformed into a set of highly ambiguous, intermolecular distance restraints (comprising between 400 and 3000 individual distances) with translational and some degree of orientational information content, while the dipolar couplings provide information on relative protein−protein orientation. The optimization protocol employs conjoined rigid body/torsion angle dynamics in simulated annealing calculations. The target function also comprises three nonbonded interactions terms: a van der Waals repulsion term to prevent atomic overlap, a radius of gyration term (Ergyr) to avoid expansion at the protein−protein interface, and a torsion angle database potential of mean force to bias interfacial side chain confo...

Prediction of the native conformation of a polypeptide by a statistical-mechanical procedure. I. Backbone structure of enkephalin.

Abstract: A new methodology for theoretically predicting the native, three-dimensional structure of a polypeptide is presented. Based on equilibrium statistical mechanics, an algorithm has been designed to determine the probable conformation of a polypeptide by calculating conditional free-energy maps for each residue of the macromolecule. The conditional free-energy map of each residue is computed from a set of probability integrals, obtained by summing over the interaction energies of all pairs of nonbonded atoms of the whole molecule. By locating the region(s) of lowest free energy for each map, the probable conformation for each residue can be identified. The native structure of the polypeptide is assumed to be the combination of the probable conformations of the individual residues. All multidimensional probability integrals are evaluated by an adaptive Monte Carlo algorithm (SMAPPS—Statistical-Mechanical Algorithm for Predicting Protein Structure). The Monte Carlo algorithm searches the entire conformational space, adjusting itself automatically to concentrate its sampling in regions where the magnitude of the integrand is largest (“importance sampling”). No assumptions are made about the native conformation. The only prior knowledge necessary for the prediction of the native conformation is the amino acid sequence of the polypeptide. To test the effectiveness of the algorithm, SMAPPS was applied to the prediction of the native conformation of the backbone of Met-enkephalin, a pentapeptide. In the calculations, only the backbone dihedral angles (ϕ and ψ) were allowed to vary; all side-chain (χ) and peptide-bond (ω) dihedral angles were kept fixed at the values corresponding to the alleged global minimum energy previously determined by direct energy minimization. For each conformation generated randomly by the Monte Carlo algorithm, the total conformational energy of the polypeptide was obtained from established empirical potential energy functions. Solvent effects were not included in the computations. With this initial application of SMAPPS, three distinct low-free-energy β-bend structures of Met-enkephalin were found. In particular, one of the structures has a conformation remarkably similar to the one associated with the previously alleged global minimum energy. The two additional structures of the pentapeptide have conformational energies lower than the previously computed low-energy structure. However, the Monte Carlo results are in agreement with an improved energy-minimization procedure. These initial results on the backbone structure of Met-enkephalin indicate that an equilibrium statistical-mechanical procedure, coupled with an adaptive Monte Carlo algorithm, can overcome many of the problems associated with the standard methods of direct energy minimization.

Three-Bond C−O−C−C Spin-Coupling Constants in Carbohydrates: Development of a Karplus Relationship

Abstract: A range of 13C-labeled carbohydrates containing C−O−C−C coupling pathways having different structures and dihedral angles has been prepared and used to identify structural factors affecting 3JCOCC,...