title: A versatile component-coupling model to account for substituent effects: application to polypeptide phi and chi(1) torsion related (3)J data.
abstract: A model is proposed for collating fundamental and incremental component couplings to account for substituent effects on (3)J 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 (3)J 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 (3)J 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 (3)J analysis and applied to polypeptide fragments X-N-C(alpha)-Y and X-C(alpha)-C(beta)-Y related to torsions phi and chi(1), respectively, yielding quantitative effects of both first- and second-sphere substituents. Regarding the polypeptide backbone, the model predicts first-sphere substituent effects on phi-related (3)J 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 (3)J(phi) measurements are anticipated from second-sphere substituent variation. Regarding amino-acid side chains, first-sphere substituent effects on chi(1)-related (3)J couplings were previously found pivotal to accurate torsion-angle interpretation. Taking additional second-sphere effects on (3)J(chi(1)) into account is here demonstrated further to improve biomolecular structure analysis.
authors.affiliation: Biosciences Department, University of Kent, Canterbury CT2 7NJ, UK. j.m.schmidt@kent.ac.uk
authors.forename: Jürgen M
authors.initials: JM
authors.lastname: Schmidt
mesh_terms: D000465:Algorithms; D019943:Amino Acid Substitution; D000596:Amino Acids / Q000737:chemistry*; D003198:Computer Simulation; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D008956:Models, Chemical; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation
chemical_list: D000596:Amino Acids; D010455:Peptides