Protein residue networks

Abstract

This chapter analyses the three-dimensional structure of proteins represented as residue networks. It starts by introducing the structure of proteins and how protein residue networks can be constructed. The chapter then reviews the topics of small-worldness and scale-freeness of residue networks, followed by an analysis of the centrality of amino acids in residue networks and the relationship between closeness centrality and the atomic vibrations produced by thermal fluctuations in proteins. The topological atomic displacements are used to identify regions of small and large packing in proteins; the use of closeness is presented as a tool for identifying enzyme binding sites. The global topological properties of residue networks are presented. The chapter concludes with an analysis of the universality in the topological structure classes of residue networks and the role of holes identification in detecting protein binding sites.