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Knowledge of amino acid composition, alone, is verified here to be
sufficient for recognizing the structural class,
a, b, a+b,
or
a/b
of a given protein with an accuracy of 81%. This is supported by
results from exhaustive enumerations of all conformations for all
sequences of simple, compact lattice models consisting of two types
(hydrophobic and polar) of residues. Different compositions exhibit
strong affinities for certain folds. Within the limits of validity of
the lattice models, two factors appear to determine the choice of
particular folds: 1) the coordination numbers of individual sites and
2) the size and geometry of non-bonded clusters. These two properties,
collectively termed the distribution of non-bonded contacts,
are quantitatively assessed by an eigenvalue analysis of the so-called
Kirchhoff or adjacency matrices obtained by considering
the non-bonded interactions on a lattice. The analysis permits the
identification of conformations that possess the same distribution of
non-bonded contacts. Furthermore, some distributions of non-bonded
contacts are favored entropically, due to their high degeneracies.
Thus, a competition between enthalpic and entropic effects is
effective in determining the choice of a distribution for a given
composition. Based on these findings, an analysis of non-bonded
contacts in protein structures was made. The analysis shows that
proteins belonging to the four distinct folding classes exhibit
significant differences in their distributions of non-bonded contacts,
which more directly explains the success in predicting structural
class from amino acid composition. Bahar et al. Proteins 29:172-185, 1997.
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