  Conformational gel analysis and graphics systematically identifies and
evaluates plausible alternatives to the side chain conformations found by
conventional peptide or protein structure determination methods. The proposed
analysis determines the populations of side chain rotational isomers and the
probability distribution of these populations. The following steps are repeated
for each side chain of a peptide or protein: first, extract the local molecular
mechanics of side chain rotational isomerization from a single representative
global conformation; second, expand the predominant set of rotational isomers
to include all probable rotational isomers down to those that constitute just a
small percentage of the population; and third, evaluate the constraints vicinal
coupling constants and NOESY cross relaxation rates place on rotational isomer
populations. In this article we apply conformational gel analysis to the cobalt
glycyl-leucine dipeptide and detail the steps necessary to generalize the
analysis to other amino acid side chains in other peptides and proteins. For a
side chain buried within a protein interior, it is noteworthy that the set of
probable rotational isomers may contain one or more rotational isomers that are
not identified by conventional NMR structure determination methods. In cases
such as this the conformational gel graphics fully accounts for the interplay
of molecular mechanics and NMR data constraints on the population estimates.
The analysis is particularly suited to identifying side chain rotational
isomers that constitute a small percentage of the population, but nevertheless
might be structurally and functionally very significant.
