Modeling Protein Contact Networks
arXiv:0711.2616
Abstract
Proteins are an important class of biomolecules that serve as essential building blocks of the cells. Their three-dimensional structures are responsible for their functions. In this thesis we have investigated the protein structures using a network theoretical approach. While doing so we used a coarse-grained method, viz., complex network analysis. We model protein structures at two length scales as Protein Contact Networks (PCN) and as Long-range Interaction Networks (LINs). We found that proteins by virtue of being characterised by high amount of clustering, are small-world networks. Apart from the small-world nature, we found that proteins have another general property, viz., assortativity. This is an interesting and exceptional finding as all other complex networks (except for social networks) are known to be disassortative. Importantly, we could identify one of the major topological determinant of assortativity by building appropriate controls.
Ph.D. thesis. 118 pages including 12 tables and 37 figures. LaTeX source with included style files. Presently at National Centre for Biological Sciences, Tata Institute of Fundamantal Research, Bangalore, India
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