Dihedral angle

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

Zur Konformation des Bicyclo[2.2.2]octan‐Systems

Abstract: Crystals of bicyclo [2.2.2] octane-1, 4-dicarboxylic acid are monoclinic, a = 6.01 A, b = 16.73 A, c = 10.29 A, β = 115.08°, space group P21/c, with 4 molecules in the unit cell. The structure was solved with the help of direct methods and refined by full-matrix least-squares analysis of the three-dimensional intensity data. Within experimental error the bicyclo [2.2.2]-octane (BCO) skeleton has apparent D3h-symmetry, corresponding to the totally eclipsed conformation. Analysis of the thermal ellipsoids in terms of the translational and rotational motion of the BCO skeleton leads to an r.m.s. amplitude of 5.9 ± 0.2° for rotation about the threefold axis. On the assumption that the bond lengths remain effectively constant during a torsional vibration of BCO, the potential energy surface has been calculated for a range of semi-empirical potential functions. These calculations show that the energy minimum may be slightly displaced from D3h symmetry, but if so the barrier between the two such equivalent minima is only about 0.1 kcal mole−1. The energy eigenvalues and eigenfunctions for a typical variation of potential energy vs torsion angle have been calculated. From the form of the eigenfunction of the ground vibrational state we conclude that BCO has effective D3h symmetry at all temperatures as far as diffraction methods are concerned.

Conformers of saturated chains : matrix isolation, structure, ir and uv spectra of n-si4me10

Abstract: Infrared and ultraviolet spectra of the gauche and anti conformers of matrix-isolated permethyl-n-tetrasilane have been obtained separately by taking advantage of thermally induced gauche-to-anti conversion and of wavelength-selective photochemical destruction of either conformer. The resolved UV spectrum of the gauche conformer provides the first piece of experimental evidence in favor of the recently proposed reinterpretation of conformational effects on tetrasilane electronic states. According to this, it is not the energy but the intensity of the lowest singlet excitation that changes dramatically as the SiSiSiSi dihedral angle is varied, as a result of an avoided crossing between sigma sigma* and sigma pi* states. Implications for the general understanding of sigma conjugation in simple terms are discussed. Unconstrained MP2/6-31G* optimization predicts the existence of a third backbone conformer (ortho), with a dihedral angle of about 90 degrees. Its predicted (HF/3-21G*) mid-IR spectrum is indistinguishable from that of the gauche conformer, and the matrix-isolation spectra thus provide no evidence for or against its presence.

1H and 15N resonance assignments and structure of the N-terminal domain of Escherichia coli initiation factor 3.

Abstract: Initiation factor IF3 from Escherichia coli is composed of two domains connected by a hydrophilic peptide. In this study, the N-terminal domain (residues 7–83) has been overexpiessed, 15N labelled and purified. NMR assignments for this domain have been obtained by two-dimensional and three-dimensional heteronuclear and homonuclear spectroscopy. Using distance geometry and simulated annealing, a three-dimensional solution structure was calculated using 506 NOE and 56 dihedral angle restraints. The resulting structure is composed of a five-stranded antiparallel β sheet surrounded by two α helices. Since the heteronuclear 1H-15N correlation spectrum of the N-terminal domain of IF3 is an almost exact subset of that of the native protein, the assignments obtained and the structure calculated should be directly transposable to the full-length protein.

Entropy localization in proteins

Abstract: The configurational entropy of a protein is under physiological conditions a major contributor to the free energy. Its quantitative characterization is therefore an important step toward the understanding of protein function. The configurational entropy of the oncoprotein MDM2, whose determination is a challenge by experiment alone, is studied here by means of 0.4 μs molecular dynamics computer simulations in both the presence and absence of the p53-peptide ligand. By characterizing protein motions in dihedral angle space, it is found that the motional amplitudes change considerably upon ligand binding while correlations between dihedral angle motions are remarkably well conserved. This applies for backbone and side-chain dihedral angle pairs at both short- and long-range distance to the binding site. As a direct consequence, the change of the configurational entropy can be decomposed into a sum of local contributions. This significantly facilitates the understanding of the relationship between protein dynamics and thermodynamics, which is important, for example, in the context of protein-ligand and protein-protein interactions. The findings also have implications for the direct derivation of entropy changes from site-specific dynamics measurements as afforded by NMR spectroscopy.

Conversion from a virtual-bond chain to a complete polypeptide backbone chain.

Abstract: A method for generating a complete polypeptide backbone structure from a set of Cα coordinates is presented. Initial trial values of ϕ and ψ for a selected residue are chosen (essentially from an identification of the conformational region of the virtual-bond backbone, e.g., and α-helical region), and values of ϕ and ψ for the remaining residues (both towards the N- and C-terminus) are then computed, subject to the constraint that the chain have the same virtual-bond angles and virtual-bond dihedral angles as the given set of Cα coordinates. The conversion from Cα coordinates to full backbone dihedral angles (ϕ,ψ) involves the solution of a set of algebraic equations relating the virtual-bond angles and virtual-bond dihedral angles to standard peptide geometry and backbone dihedral angles. The procedure has been tested successfully on Cα coordinates taken from standard-geometry full-atom structures of bovine pancreatic trypsin inhibitor (BPTI). Some difficulty was encountered with error-sensitive residues, but on the whole the backbone generation was successful. Application of the method to Cα coordinates for BPTI derived from simplified model calculations (involving nonstandard geometry) showed that such coordinates may be inconsistent with the requirement that ϕPro be near −75°. In such a case, i.e., for residues for which the algebraic method failed, a leastsquares minimizer was then used in conjunction with the algebraic method; the mean-square deviation of the calculated Cα coordinates from the given ones was minimized by varying the backbone dihedral angles. Thus, these inconsistencies were circumvented and a full backbone structure whose Cα coordinates had an rms deviation of 0.26 A from the given set of Cα coordinates was obtained.