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Published online before print March 27, 2008, 10.1110/ps.073390208
Protein Science (2008), 17:918-929. Published by Cold Spring Harbor Laboratory Press. Copyright © 2008 The Protein Society
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Correspondences between low-energy modes in enzymes: Dynamics-based alignment of enzymatic functional families

Andrea Zen1, Vincenzo Carnevale1, Arthur M. Lesk2, and Cristian Micheletti1

1 International School for Advanced Studies and CNR-INFM Democritos, 34014 Trieste, Italy
2 Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA

(RECEIVED December 7, 2007; FINAL REVISION February 13, 2008; ACCEPTED February 13, 2008)

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.

Keywords: structure and function of enzymes; large-scale movements; protein alignment; dynamics-based alignment


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