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Conformational gel analysis and graphics systematically identifies andevaluates plausible alternatives to the side chain conformations found byconventional peptide or protein structure determination methods. The proposedanalysis determines the populations of side chain rotational isomers and theprobability distribution of these populations. The following steps are repeatedfor each side chain of a peptide or protein: first, extract the local molecularmechanics of side chain rotational isomerization from a single representativeglobal conformation; second, expand the predominant set of rotational isomersto include all probable rotational isomers down to those that constitute just asmall percentage of the population; and third, evaluate the constraints vicinalcoupling constants and NOESY cross relaxation rates place on rotational isomerpopulations. In this article we apply conformational gel analysis to the cobaltglycyl-leucine dipeptide and detail the steps necessary to generalize theanalysis to other amino acid side chains in other peptides and proteins. For aside chain buried within a protein interior, it is noteworthy that the set ofprobable rotational isomers may contain one or more rotational isomers that arenot identified by conventional NMR structure determination methods. In casessuch as this the conformational gel graphics fully accounts for the interplayof molecular mechanics and NMR data constraints on the population estimates.The analysis is particularly suited to identifying side chain rotationalisomers that constitute a small percentage of the population, but neverthelessmight be structurally and functionally very significant.

Conformational gel analysis and graphics: Measurement of side chain rotational isomer populations by NMR and molecular mechanics