Analysis of Complex Networks

9.4 Comparisons and 3D Alignment of Protein Structures

Proteins are natural biopolymers made of a limited number of amino acid residues [62]. There are 20 basic amino acids plus a relatively large number of chemically modified derivatives. In proteins, amino acid residues are connected linearly by peptide links, forming chain structures often referred to as protein primary structure.

In their natural environments, protein chains usually fold into complex 3D structures [63]. Three levels of structural organization of proteins are recognized [64]. Secondary structure refers to local elements of protein fold, such as helices and strands, which normally have a size of 6 to 30 residues. The secondary structure elements (SSEs) are stabilized by hydrophobic interactions and hydrogen bonds [62,63] and are relatively well conserved in protein evolution. Tertiary structure refers to the structure of the whole polypeptide chain, as defined by the atomic coordinates [64], and may be viewed as the way the SSEs assemble. Quaternary structure refers to protein assemblies and represents the arrangement of several folded chains into a complex [64].

The function and chemical activity of proteins depend on their 3D structures [63]. Therefore the identification and measurement of structural similarities are important tasks in protein research, which are used to understand their biological role. Some practical questions that arise are, given two protein structures, how similar are they and which parts ...