Asymmetric Karplus curves for the protein side-chain (3)J couplings

Schmidt, Jürgen M. (2007) Asymmetric Karplus curves for the protein side-chain (3)J couplings. Journal of Biomolecular NMR, 37 (4). pp. 287-301. ISSN 0925-2738. (The full text of this publication is not currently available from this repository. You may be able to access a copy if URLs are provided)

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The standard Karplus equation for calculating (3)J coupling constants from any given dihedral angle requires three empirical coefficients be determined that relate to the magnitudes of three modes of the angle dependency of (3)J. Considering cosine modes only (bimodal, unimodal and baseline component), Karplus curves are generally symmetric with respect to the sign of the angle argument. Typically, their primary and secondary maxima differ in amplitude, whereas the two minima are of equal depth. However, chiral molecular topologies, such as those surrounding the main-chain and side-chain torsions in amino-acid residues, preclude, as regards substituent positioning, exact mirror-image conformations from being formed-for any given torsion-angle value. It is therefore unlikely that (3)J couplings assume identical values for the corresponding positive and negative dihedral angles. This suggests that a better empirical fit of the torsion-angle dependency of (3)J could be obtained when removing the constraint of symmetrically identical coupling constants. A sine term added to the Karplus equation allows independent modelling of both curve minima typically located near dihedral-angle values of +90 degrees and -90 degrees. Revisiting an extensive (3)J coupling dataset previously recorded to determine the side-chain torsions chi(1) in the protein flavodoxin, the asymmetric Karplus model accomplishes a more accurate fit to the experimental data. Asymmetries revealed in the angle dependencies exceed the experimental precision in determining (3)J. Accounting for these effects helps improve molecular models.

Item Type: Article
Uncontrolled keywords: data redundancy; flavodoxin; optimisation; self consistency; torsion angle; vicinal coupling constants
Subjects: Q Science > Q Science (General)
Divisions: Faculties > Science Technology and Medical Studies > School of Biosciences
Depositing User: Suzanne Duffy
Date Deposited: 18 Mar 2008 16:53
Last Modified: 06 Jun 2014 11:32
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