NAPS: Network Analysis of Protein Structures

Abstract

Traditionally, protein structures have been analysed by the secondary structure architecture and fold arrangement. An alternative approach that has shown promise is modelling proteins as a network of non-covalent interactions between amino acid residues. The network representation of proteins provide a systems approach to topological analysis of complex three-dimensional structures irrespective of secondary structure and fold type and provide insights into structure-function relationship. We have developed a web server for network based analysis of protein structures, NAPS, that facilitates quantitative and qualitative (visual) analysis of residue-residue interactions in: single chains, protein complex, modelled protein structures and trajectories (e.g. from molecular dynamics simulations). The user can specify atom type for network construction, distance range (in Å) and minimal amino acid separation along the sequence. NAPS provides users selection of node(s) and its neighbourhood based on centrality measures, physicochemical properties of amino acids or cluster of well-connected residues (k-cliques) for further analysis. Visual analysis of interacting domains and protein chains, and shortest path lengths between pair of residues are additional features that aid in functional analysis. NAPS support various analyses and visualization views for identifying functional residues, provide insight into mechanisms of protein folding, domain-domain and protein-protein interactions for understanding communication within and between proteins. URL:http://bioinf.iiit.ac.in/NAPS/.

Figure 1.

Network analysis of protein structure for 1CRN (chain A). (A) Network view showing the 3D network representation with nodes and backbone edges represented in blue and other edges represented by grey. (B) JSmol applet showing the 3D protein structure. On clicking a node in network view with neighbour selection option, the node in (A) and the corresponding residue in (B) are highlighted in red, and its immediate neighbouring nodes in (A) and corresponding residues in (B) are highlighted in yellow. (C) Contact map view with edges within a helix and strands highlighted in red colour. (D) Distance matrix view. (E) Shortest path analysis highlighting one of the paths between residues A27 and A46. (F) A Clique of size 5 shown.

Figure 2.

Protein complex 3FPN (chain A and B). (A) Network view showing 3D network representation with chain A and B coloured in blue and green colours respectively. The edges joining nodes of chain A and B are highlighted in magenta colour. (B) 3D protein structure in JSmol applet.