Physics – Biological Physics
Scientific paper
1999-05-11
Physics
Biological Physics
21 pages, 4 figures (1 new), 4 tables (2 new), LaTeX2e and REVTeX v4, supporting material, updated author affiliations, v2 als
Scientific paper
The cobalt glycyl-leucine dipeptide is a model system for studying the effects of Karplus equation calibration, molecular mechanics accuracy, backbone conformation, and thermal motions on the measurability of side chain rotational isomer populations. We analyze measurements of 8 vicinal coupling constants about the alpha to beta-carbon and beta to gamma-carbon bonds of the leucine side chain and of 10 NOESY cross relaxation rates across these bonds. Molecular mechanics and peptide and protein crystallographic databases are an essential part of this analysis because they independently suggest that the trans gauche-plus and gauche-minus trans rotational isomers of the leucine side chain predominate. They also both suggest that puckering of the cobalt dipeptide ring system reduces the gauche-plus gauche-plus rotational isomer population to less than about 10%. At the present +/- 1 Hz calibration accuracy of Karplus equations for vicinal coupling constants, the predominant trans gauche-plus and gauche-minus trans rotational isomer populations can be measured with about 5% accuracy, but the population of the gauche-plus gauche-plus rotational isomer is probably very near or just below the limit of measurability. These estimates also depend upon qualitative assessments of the accuracy of the molecular mechanics energy wells. We introduce gel graphics that are ideally suited to presenting qualitative error and measurability estimates.
Haydock Christopher
Juranić Nenad
Likić Vladimir A.
Macura Slobodan
Prendergast Franklyn G.
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