Detection of hydrophobic clusters in molecular dynamics protein unfolding simulations using association rules

Abstract

One way of exploring protein unfolding events associated with the development of Amyloid diseases is through the use of multiple Molecular Dynamics Protein Unfolding Simulations. The analysis of the huge amount of data generated in these simulations is not a trivial task. In the present report, we demonstrate the use of Association Rules applied to the analysis of the variation profiles of the Solvent Accessible Surface Area of the 127 amino-acid residues of the protein Transthyretin, along multiple simulations. This allowed us to identify a set of 28 hydrophobic residues forming a hydrophobic cluster that might be essential in the unfolding and folding processes of Transthyretin. © Springer-Verlag Berlin Heidelberg 2005.