Dihedral angle

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

Reaction path study of helix formation in tetrapeptides: Effect of side chains

Abstract: A computational protocol to calculate steepest descent paths in flexible molecules is discussed in detail The algorithm does not use second derivatives and related matrices, and is therefore suitable for large systems The shortest reaction coordinate from the helix to the extended chain conformation is calculated for a series of different tetrapeptides The formation of a helical turn is investigated as a function of side chain properties The known reaction coordinate for isobutyryl‐ala3 ‐NH‐methyl is employed as a starting guess in path calculations for six different tetrapeptides The main results are: (i) χ1 (the side chain orientation angle) does not change significantly along the reaction coordinate Alternative static values of χ1 (60,−60) significantly affect the size of the energy barrier (≊3 kcal/mol for valine) (ii) The mechanism for the transition is similar in all the peptides examined and is based on sequential flips of backbone torsions (Ψ dihedral angles) (iii) The energy barrier which

A dihedral angle-vicinal proton coupling constant correlation for the α–β bond of amino acid residues

Abstract: A coupling constant-dihedral angle correlation for the HCαCβH system of amino acid residues in peptides has been derived from a set of model compounds covering the full range of dihedral angles. The expression obtained, J = 11.0 cos2 θ −1.4 cos θ + 1.6 sin2θ, is close to those already used in pmr studies of peptide conformation, and provides a firmer foundation for them. A factor limiting the precision of this and other “Karplus relations” is illustrated.

Studies on the conformation of amino acids. VI. Conformation of the proline ring as observed in crystal structures of amino acids and peptides.

Abstract: The paper deals with an analysis of the available crystal structure data related to proline compounds so as to obtain information about bond lengths, bond angles, and the conformation of the pyrrolidine ring. The interesting results are: 1. The atoms Cβ, Cα, N, and Cs are nearly coplanar, with the torsion angle 0 about the Cα - N bond varying from about -15° to -15°. The Cγ atom is displaced from this plane, either up or down, so that the ring exists in one of the two puckered conformations, designated A and B. Conformation A is characterized by negative and may be termed Cγ-exo when referred to the displacement of the carbonyl carbon C. Conformation B has positive x l and is Cγ-endo; Cγ-exo is slightly preferred over C-endo, although both conformations occur simultaneously in some crystal structures with partial probabilities. In the other structures, the non-occurring position for C y is found to be disallowed by intermolecular contacts. The proline conformations observed correspond to the 'envelope' type of conformation of the cyclopentane ring. In peptides, the three bonds at N are nearly coplanar, and the torsion about N- Cα bond is nearly - 60°. 2. The observed ranges of (x 1 , x 2 , x 3 , x 4 ) are (0 to –30°, 15 to 50°, –15 to - -30°, 5 to 25°) for conformation A and (20 to 35 0 , -30 to - 40 0 , 20 to 35°, 5 to -20°) for conformation B; for θ and φ the ranges are -15° to -15°, -45 to -75°. The bond lengths and bond angles are not influenced by the conformation of the ring, unlike ribose.

Collective protein dynamics and nuclear spin relaxation

Abstract: Theoretical methods are developed and applied to the protein crambin as a model system to characterize collective normal mode dynamics and their effects on correlations between torsion angle fluctuations and heteronuclear NMR relaxation parameters. Backbone N–H NMR S2 order parameters are found to be predominantly determined by local φ and ψ torsion angle fluctuations induced by collective protein modes. The ratio between Cβ–Hβ and Cα–Hα order parameters directly yields fluctuation amplitudes of the sidechain χ1 torsion angles. The results allow a more direct interpretation of motional effects monitored by nuclear spin relaxation.