A. Zen, V. Carnevale, A.M. Lesk and C. Micheletti
Correspondences between low-energy modes in enzymes: Dynamics-based
alignment of enzymatic functional families
Prot. Sci. 17 918-929 (2008)
Link to online article.
Proteins that show similarity in their equilibrium dynamics can be
aligned by identifying regions that undergo similar concerted
movements. These movements are computed from protein native structures
using coarse-grained elastic network models. We show the existence of
common large-scale movements in enzymes selected from the main
functional and structural classes. Alignment via dynamics does not
require prior detection of sequence or structural
correspondence. Indeed, a third of the statistically significant
dynamics-based alignments involve enzymes that lack substantial global
or local structural similarities. The analysis of specific
residue-residue correspondences of these structurally dissimilar
enzymes in some cases suggests a functional relationship of the
detected common dynamic features. Including dynamics-based criteria
in protein alignment thus provides a promising avenue for relating and
grouping enzymes in terms of dynamic aspects that often, though not
always, assist or accompany biological function.