Analysis of the Local Sequences of Folding Sites in β Sandwich Proteins with Inter-Residue Average Distance Statistics

The Open Bioinformatics Journal 20 Apr 2011 RESEARCH ARTICLE DOI: 10.2174/1875036201105010059


The sequences of azurin and titin, β sandwich proteins, are analyzed based on inter-residue average distance statistics. A kind of predicted contact map based on inter-residue average distance statistics (Average Distance Map, ADM) is used to pinpoint regions of possible compact regions for two proteins. We compare predicted compact regions with the positions of the residues with experimental high Φ values for these proteins reported in the literature. The results reveal that the regions predicted by ADMs correspond to the positions of residues with the high Φ value. Furthermore, we perform random sampling of 3D conformations using these protein sequences with a potential derived from inter-residue average distance statistics. It is demonstrated that the residues with highest contact frequency during the simulations qualitatively correspond to the residues with the highest Φ values for these proteins. Importantly, analysis with inter-residue average distance statistics predicts the properties of folding processes of the β sandwich proteins starting from only sequence information.

Keywords: β-sandwich protein, folding, inter-residue average distance statistics, Φ values, azurin, titin.
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