Dihedral angle

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

Three-dimensional structure in solution of the polypeptide cardiac stimulant anthopleurin-A.

Abstract: The three-dimensional structure in aqueous solution of the 49-residue polypeptide anthopleurin-A (AP-A), from the sea anemone Anthopleura xanthogrammica, has been determined from 1H NMR data. A restraint set consisting of 411 interproton distance restraints inferred from NOEs and 19 backbone and 13 side chain dihedral angle restraints from spin-spin coupling constants, as well as 15 lower bound restraints based on the absence of NOEs in the spectra, was used as input for distance geometry calculations in DIANA and simulated annealing and restrained energy minimization in X-PLOR. Stereospecific assignments for 12 beta-methylene pairs were also included. The final set of 20 structures had mean pairwise rms differences over the whole molecule of 2.04 A for the backbone heavy atoms (N, C alpha, and C) and 2.59 A for all heavy atoms. For the well-defined region encompassing residues 2-7 and 17-49, the corresponding values were 0.82 and 1.27 A, respectively. AP-A adopts a compact structure consisting of four short strands of antiparallel beta-sheet (residues 2-4, 20-23, 34-37, and 45-48) connected by three loops. The first loop commences with a type I beta-turn which includes two important Asp residues; this loop is the least well-defined region of the protein, although a beta-turn involving residues 13-16 is observed in nearly half the structures. The loop linking the second and third strands is constrained by the 29-47 disulfide bond and contains two well-defined beta-turns, while the third loop contains the Gly40-Pro41 sequence, which has been identified previously as the site of cis-trans isomerism. The carboxylate group of Asp7 is close to the epsilon-ammonium group of Lys37, suggesting that they may form a salt bridge. A pH titration monitored by 2D NMR supports this by showing that Asp7 has a low pKa. It is proposed that this region of the molecule and the nearby residues Asp9 and His39 form part of the molecular surface which interacts with the mammalian cardiac sodium channel.

Solution structures of proteins from NMR data and modeling: Alternative folds for neutrophil peptide 5

Abstract: The structure of neutrophil peptide 5 in solution has recently been reported (Pardi et al., 1988). The structure determination was accomplished by using a distance geometry algorithm and 107 interproton distance constraints obtained from 2D NMR data. In each of the eight independent solutions to the distance geometry equations, the overall fold of the polypeptide backbone was identical and the root mean square (rms) deviation between backbone atoms of the superimposed structures was small (approximately 2.4 A). In this paper we report additional NP-5 structures obtained by using a new structure generation algorithm: a Monte Carlo search in torsion angle space. These structures have a large rms backbone deviation from the distance geometry structures (approximately 5.0 A). The backbone topologies differ in significant respects from the distance geometry structures and from each other. Structures are found that are pseudo mirror images of part or all of the fold corresponding to that first obtained with the distance geometry procedure. For small proteins, the problem of distinguishing the correct structure among pseudo mirror images is likely to be greater than previously recognized. When a set of test distance constraints constructed from a novel Monte Carlo structure is used as input in the distance geometry algorithm, the fold of the resulting structure does not correspond to that of the target. The results also demonstrate that the previously accepted criteria (the magnitude of the rms deviation between multiple solutions of the distance geometry equations) for defining the accuracy and precision of a peptide structure generated from NMR data are inadequate. An energetic analysis of structures corresponding to the different folding topologies has been carried out. The molecular mechanics energies obtained by minimization and molecular dynamics refinement provide sufficient information to eliminate certain alternative structures. On the basis of a careful comparison of the different trial structures with the experimental data, it is concluded that the NP-5 peptide fold which was originally reported is most consistent with the data. An alternative fold corresponding to structures with low energies and small total distance violations is ruled out because for this fold predicted NOEs are not observed experimentally.

Density functional study on the structures and vibrational spectra of the radical anion and cation of biphenyl

Abstract: Density functional theory using the 6–31G ∗ basis set and two non-local exchange-correlation functionals (B-YLP and B3-LYP) has been applied to the calculations of the structures and vibrational spectra of the radical anion and cation, of biphenyl. The B3-LYP dihedral angles between the two phenyl rings are 5.8 ° and 19.5 ° for the radical anion and cation respectively. Upon ionization, structural changes occur in the direction from benzenoid to quinoid. The unsealed vibrational frequencies calculated at the B-YLP/6–31G ∗ level are mostly in agreement with the frequencies in the Raman spectra of the radical anion and cation of the normal and perdeuterated species reported in the literature. The calculations predict that both the radical anion and cation give rise to a very strong infrared band, and that this band arises from a mode in which the benzenoid-to-quinoid deformation occurs out of phase in the two phenyl rings.

Improvements to the ABSINTH Force Field for Proteins Based on Experimentally Derived Amino Acid Specific Backbone Conformational Statistics.

Abstract: We present an improved version of the ABSINTH implicit solvation model and force field paradigm (termed ABSINTH-C) by incorporating a grid-based term that bootstraps against experimentally derived and computationally optimized conformational statistics for blocked amino acids. These statistics provide high-resolution descriptions of the intrinsic backbone dihedral angle preferences for all 20 amino acids. The original ABSINTH model generates Ramachandran plots that are too shallow in terms of the basin structures and too permissive in terms of dihedral angle preferences. We bootstrap against the reference optimized landscapes and incorporate CMAP-like residue-specific terms that help us reproduce the intrinsic dihedral angle preferences of individual amino acids. These corrections that lead to ABSINTH-C are achieved by balancing the incorporation of the new residue-specific terms with the accuracies inherent to the original ABSINTH model. We demonstrate the robustness of ABSINTH-C through a series of exam...