Dihedral angle

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

Can a C-H···O interaction be a determinant of conformation?

Abstract: Whether nonconventional hydrogen bonds, such as the C-H···O interaction, are a consequence or a determinant of conformation is a long-running and unresolved issue. Here we outline a solid-state and quantum mechanical study designed to investigate whether a C-H···O interaction can override the significant trans-planar conformational preferences of α-fluoroamide substituents. A profound change in dihedral angle from trans-planar((OCCF)) to cis-planar((OCCF)) observed on introducing an acceptor group for a C-H···O hydrogen bond is consistent with this interaction functioning as a determinant of conformation in certain systems. This testifies to the potential influence of the C-H···O hydrogen bond and is consistent with the assignment of this interaction as a contributor to overall conformation in both model and natural systems.

Structure-based analysis of protein dynamics: Comparison of theoretical results for hen lysozyme with X-ray diffraction and NMR relaxation data

Abstract: An analytical approach based on Gaussian network model (GNM) is proposed for predicting the rotational dynamics of proteins. The method, previously shown to successfully repro- duce X-ray crystallographic temperature factors for a series of proteins is extended here to predict bond torsional mobilities and reorientation of main chain amide groups probed by 15 N-H nuclear magnetic resonance (NMR) relaxation. The dynamics of hen egg-white lysozyme (HEWL) in the folded state is investigated using the proposed approach. Excel- lent agreement is observed between theoretical re- sults and experimental (X-ray diffraction and NMR relaxation) data. The analysis reveals the important role of coupled rotations, or cross-correlations be- tween dihedral angle librations, in defining the relax- ation mechanism on a local scale. The crystal and solution structures exhibit some differences in their local motions, but their global motions are identical. Hinge residues mediating the cooperative move- ments of the a- and b-domains are identified, which comprise residues in helix C, Glu35 and Ser36 on the loop succeeding helix B, Ile55 and Leu56 at the turn between strands II and III. The central part of the b-domain long loop and the turn between strands I and II display an enhanced mobility. Finally, kineti- cally hot residues and key interactions are identi- fied, which point at helix B and b-strand III as the structural elements underlying the stability of the tertiary structure. Proteins 1999;37:654-667.

Locating stationary points for clusters in cartesian coordinates

Abstract: Location of minima and transition states by eigenvector following using Cartesian coordinates and a projection operator is described. Comparisons with calculations employing standard internal coordinates are made for a wide variety of model clusters. The new method, suggested by Baker and Hehre, generally produces faster converagence and solves a number of problems that are inherent when using distance, bond angle, dihedral angle internal coordinates. In particiular, eigenvector-following calculations using analytic first and second energy derivatives should now be possible for much larger systems. Some example reaction paths are illustrated, including a new facetting rearrangement of 55- and 147-atom Mackay icosahedra. The basins of attraction of minima and transition states are also calculated, that is, the regions of the potential-energy surface for which stationary-point searches converge to a given structure. The superiority of the projection operator approach is again demonstrated, and the previous observation that initial geometrical contraction is helpful in transition-state searches is confirmed.