A versatile component-coupling model to account for substituent effects: application to polypeptide phi and (chi 1) torsion related (3)J data

Schmidt, Jürgen M. (2007) A versatile component-coupling model to account for substituent effects: application to polypeptide phi and (chi 1) torsion related (3)J data. Journal of Magnetic Resonance, 186 (1). pp. 34-50. ISSN 1090-7807. (Access to this publication is restricted)

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Abstract

A model is proposed for collating fundamental and incremental component couplings to account for substituent effects on 3J arising from, for example, amino-acid type variation. The unique topology patterns encountered in each of the common amino acids were modeled by assigning substituents on a 3J coupling path to four simple categories comprising only relative positions: central (inner) vs. terminal (outer) and first-sphere vs. second-sphere. Associated increment values then reflect the influences on each 3J coupling accessible for torsion-angle determination. Facility of use of this model, in comparison with previous ones, owes to its strict limitation to no more than three Karplus coefficients for each specific torsion-angle dependency derived. The model was integrated in the concept of self-consistent 3J analysis and applied to polypeptide fragments X–N–Cα–Y and X–Cα–Cβ–Y related to torsions and χ1, respectively, yielding quantitative effects of both first- and second-sphere substituents. Regarding the polypeptide backbone, the model predicts first-sphere substituent effects on -related 3J couplings to be within experimental uncertainty because main-chain topologies are identical in most amino-acid types, except for marginal effects in glycine and proline. However, effects in excess of standard errors in 3J() measurements are anticipated from second-sphere substituent variation. Regarding amino-acid side chains, first-sphere substituent effects on χ1-related 3J couplings were previously found pivotal to accurate torsion-angle interpretation. Taking additional second-sphere effects on 3J(χ1) into account is here demonstrated further to improve biomolecular structure analysis.

Item Type: Article
Uncontrolled keywords: Vicinal coupling constants; Torsion angle; Data redundance; Self-consistency; Flavodoxin
Subjects: Q Science > QR Microbiology
Divisions: Faculties > Science Technology and Medical Studies > School of Biosciences
Depositing User: Stephen Holland
Date Deposited: 19 Dec 2007 18:56
Last Modified: 06 Jun 2014 11:32
Resource URI: http://kar.kent.ac.uk/id/eprint/1421 (The current URI for this page, for reference purposes)
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