A Topological Description of Hubs in Amino Acid Interaction Networks.pdfVIP

Hindawi Publishing Corporation Advances in Bioinformatics Volume 2010, Article ID 257512, 9 pages doi:10.1155/2010/257512 Research Article A Topological Description of Hubs in Amino Acid Interaction Networks Omar Gaci Le Havre University, LITIS EA 4108, BP 540, 76058 Le Havre, France Correspondence should be addressed to Omar Gaci, omar.gaci@ Received 22 December 2009; Revised 15 February 2010; Accepted 29 March 2010 Academic Editor: Rita Casadio Copyright © 2010 Omar Gaci. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. We represent proteins by amino acid interaction networks. This is a graph whose vertices are the proteins amino acids and whose edges are the interactions between them. Once we have compared this type of graphs to the general model of scale-free networks, we analyze the existence of nodes which highly interact, the hubs. We describe these nodes taking into account their position in the primary structure to study their apparition frequency in the folded proteins. Finally, we observe that their interaction level is a consequence of the general rules which govern the folding process. 1. Introduction In this study, we treat proteins as networks of interacting amino acid pairs [4]. In particular, we consider the subgraph Proteins are biological macromolecules participating in the induced by the set of amino acids participating in the sec- large majority of processes which govern organisms. The ondary structure also called Secondary Structure Elements