title: Correspondences between low-energy modes in enzymes: dynamics-based alignment of enzymatic functional families.
abstract: 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.
authors: International School for Advanced Studies and CNR-INFM Democritos, 34014 Trieste, Italy.
authors: Andrea
authors: A
authors: Zen
authors: Vincenzo
authors: V
authors: Carnevale
authors: Arthur M
authors: AM
authors: Lesk
authors: Cristian
authors: C
authors: Micheletti
mesh_terms: D004798:Enzymes / Q000737:chemistry*; D019143:Evolution, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D016415:Sequence Alignment / Q000379:methods*
chemical_list: D004798:Enzymes