Dihedral angle

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

Insights into the mobility of methyl-bearing side chains in proteins from 3JCC and 3JCN couplings

Abstract: Side-chain dynamics in proteins can be characterized by the NMR measurement of 13C and 2H relaxation rates. Evaluation of the corresponding spectral densities limits the slowest motions that can be studied quantitatively to the time scale on which the overall molecular tumbling takes place. A different measure for the degree of side-chain order about the Cα−Cβ bond (χ1 angle) can be derived from 3JC‘-Cγ and 3JN-Cγ couplings. These couplings can be measured at high accuracy, in particular for Thr, Ile, and Val residues. In conjunction with the known backbone structures of ubiquitin and the third IgG-binding domain of protein G, and an extensive set of 13C−1H side-chain dipolar coupling measurements in oriented media, these 3J couplings were used to parametrize empirical Karplus relationships for 3JC‘-Cγ and 3JN-Cγ. These Karplus curves agree well with results from DFT calculations, including an unusual phase shift, which causes the maximum 3JCC and 3JCN couplings to occur for dihedral angles slightly small...

Determination of the three-dimensional solution structure of the antihypertensive and antiviral protein BDS-I from the sea anemone Anemonia sulcata: a study using nuclear magnetic resonance and hybrid distance geometry-dynamical simulated annealing.

Abstract: The three-dimensional solution structure of the antihypertensive and antiviral protein BDS-I from the sea anemone Anemonia sulcata has been determined on the basis of 489 interproton and 24 hydrogen-bonding distance restraints supplemented by 23 {phi} backbone and 21 {sub {chi}1} side-chain torsion angle restraints derived from nuclear magnetic resonance (NMR) measurements. A total of 42 structures is calculated by a hybrid metric matrix distance geometry-dynamical simulated annealing approach. Both the backbone and side-chain atom positions are well defined. The average atomic rms difference between the 42 individual SA structures and the mean structure obtained by averaging their coordinates is 0.67 {plus minus} 0.12 {angstrom} for the backbone atoms and 0.90 {plus minus} 0.17 {angstrom} for all atoms. The core of the protein is formed by a triple-stranded antiparallel {beta}-sheet composed of residues 14-16 (strand 1), 30-34 (strand 2), and 37-41 (strand 3) with an additional mini-antiparallel {beta}-sheet at the N-terminus (residues 6-9). The first and second strands of the triple-stranded antiparallel {beta}-sheet are connected by a long exposed loop. A number of side-chain interactions are discussed in light of the structure.

The Molecular Structure of Cyclobutane

Abstract: The cyclobutane molecule has been found by electron diffraction to have the following bond distances and bond angles: C–C, 1.568±0.02A; C–H, 1.098±0.04A; ∠HCH, 114±8°. On the average the ring is nonplanar, with dihedral angle 20° (+10°, −20°), but the equilibrium symmetry may be either D_(2d) (puckered ring) or D_(4h) (planar ring with low rigidity leading to large amplitude of out‐of‐plane bending). This point is discussed in connection with earlier spectroscopic work. The long bond distances found in four‐membered rings are contrasted against the short distances in three‐membered rings, and the strain energies, bond distances, and HCH angles of cycloalkanes are discussed in terms of modern valence concepts. It is suggested that the potential energy arising from a repulsion of the nonbonded carbon atoms may contribute significantly to the apparently anomalously high strain energy of cyclobutane. The repulsive force associated with such a potential is shown to account satisfactorily for the long C–C distances.

Dihedral angles of trialanine in D2O determined by combining FTIR and polarized visible Raman spectroscopy.

Abstract: We have measured the polarized visible Raman and FTIR spectra of trialanine and triglycine in D(2)O at acid, neutral, and alkaline pD. From the Raman spectra we obtained the isotropic and the anisotropic scattering. A self-consistent spectral analysis of the region between 1550 and 1800 cm(-1) was carried out to obtain the intensities, frequencies, and halfwidths of the respective amide I bands. A model was developed by means of which the intensity ratios of the amide I bands in all spectra and the respective frequency differences were utilized to determine the orientational angle theta between the peptide groups and the strength of excitonic coupling between the corresponding amide I modes. By exploiting results from a recent ab initio study on triglycine (Torii, H; Tasumi, M. J. Raman Spectrosc. 1998, 29, 81), we used these parameters to determine the dihedral angles phi and psi between the peptide groups. Our results show that trialanine adopts a 3(1)-helical structure in D(2)O for all of its three protonation states. The structure is insensitive to the carboxylate protonation and changes only slightly with N-terminal protonation. Triglycine is structurally more heterogeneous in the zwitterionic and the cationic state. Our spectral analysis suggests that 3(1)-helices coexist with right-handed alpha-helical and/or with beta-turn conformations. The N-terminal protonation stabilizes the 3(1)-structure. Our study provides compelling evidence that tripeptides adopt stable conformations in aqueous solution and that they are suitable model systems to investigate the initiation of secondary structure formation.

The far infrared spectrum of H2O2. First observation of the staggering of the levels and determination of the cis barrier

Abstract: High resolution spectra of H2O2, recorded by means of Fourier transform spectroscopy between 30 and 460 cm−1, have been analyzed leading to the determination of the rotational levels of the torsional states (n,τ) for n=0,1,2,3. In order to reproduce these energy levels, Watson type Hamiltonians have been used and it has been possible to observe a staggering of the levels with n=2 and 3 caused by the cis barrier. The torsional band centers have then been fitted using a torsional Hamiltonian of the form {Bγγ,J2γ} +V(γ) with the potential function V(γ) written as V(γ)=V1 cos 2γ+V2 cos 4γ+V3 cos 6γ+V4 cos 8γ where the torsional coordinate 2γ is the dihedral angle defining the relative position of the two O–H bonds. The potential constants in cm−1 are V1=1036.97±23.1 cm−1, V2=657.53±5.2 cm−1, V3=50.89±3.3 cm−1, V4=2.524±0.83 cm−1 which correspond to barrier heights Vtrans =387.07±0.20 cm−1, Vcis =2562.8±60 cm−1, and to a potential minimum located at 2γ=111.9°±0.4° from the cis configuration. It is also shown t...