RESEARCH ARTICLE
Analysis of the Local Sequences of Folding Sites in β Sandwich Proteins with Inter-Residue Average Distance Statistics
Yuko Ishizuka1, Takeshi Kikuchi*, 2
Article Information
Identifiers and Pagination:
Year: 2011Volume: 5
First Page: 59
Last Page: 68
Publisher ID: TOBIOIJ-5-59
DOI: 10.2174/1875036201105010059
Article History:
Received Date: 28/12/2010Revision Received Date: 21/02/2011
Acceptance Date: 08/03/2011
Electronic publication date: 20/04/2011
Collection year: 2011
open-access license: This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International Public License (CC-BY 4.0), a copy of which is available at: https://creativecommons.org/licenses/by/4.0/legalcode. This license permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Abstract
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.
