A. Zen, C. de Chiara, A. Pastore and C. Micheletti
Using dynamics-based comparisons to predict nucleic acid binding sites in proteins: an application to OB-fold domains
Bioinformatics 25 1876-1883 (2009) , Link to
Motivation: we have previously demonstrated that proteins may be aligned
not only by sequence or structural homology but also using their dynamical
properties. dynamics-based alignments are sensitive and powerful tools to
compare even structurally dissimilar protein families. here, we propose to
use this method to predict protein regions involved in the binding of
nucleic acids. we have used the ob fold, a motif known to promote protein-
nucleic acid interactions, to validate our approach.
Results: We have tested the method using the well characterized nucleic
acid binding family. Protein regions consensually involved in statistically-
significant dynamics-based alignments were found to correlate with nucleic
acids binding regions. The validated scheme was next used as a tool to
predict which regions of the AXH-domain representatives (a sub-family of
the OB-fold for which no DNA/RNA complex is yet available) are putatively
involved in binding nucleic acids. The method, therefore, is a promising
general approach for predicting functional regions in protein families on
the basis of comparative large-scale dynamics.
Availability: The software is available upon request from the authors, free
of charge for academic users.