ALBERT

Description: Background: The three-dimensional structure of a protein can be described as a graph where nodes represent residues andthe strength of non-covalent interactions between them are edges. These protein contact networks can beseparated into long and short-range interactions networks depending on the positions of amino acids inprimary structure. Long-range interactions play a distinct role in determining the tertiary structure of aprotein while short-range interactions could largely contribute to the secondary structure formations. Inaddition, physico chemical properties and the linear arrangement of amino acids of the primary structure ofa protein determines its three dimensional structure. Here, we present an extensive analysis of proteincontact subnetworks based on the London van der Waals interactions of amino acids at different lengthscales. We further subdivided those networks in hydrophobic, hydrophilic and charged residues networksand have tried to correlate their influence in the overall topology and organization of a protein. Results: The largest connected component (LCC) of long (LRN)-, short (SRN)- and all-range (ARN) networks withinproteins exhibit a transition behaviour when plotted against different interaction strengths of edges amongamino acid nodes. While short-range networks having chain like structures exhibit highly cooperativetransition; long- and all-range networks, which are more similar to each other, have non-chain like structuresand show less cooperativity. Further, the hydrophobic residues subnetworks in long- and all-range networkshave similar transition behaviours with all residues all-range networks, but the hydrophilic and chargedresidues networks don't. While the nature of transitions of LCC's sizes is same in SRNs for thermophilesand mesophiles, there exists a clear difference in LRNs. The presence of larger size of interconnectedlong-range interactions in thermophiles than mesophiles, even at higher interaction strength between aminoacids, give extra stability to the tertiary structure of the thermophiles. All the subnetworks at different lengthscales (ARNs, LRNs and SRNs) show assortativity mixing property of their participating amino acids.While there exists a significant higher percentage of hydrophobic subclusters over others in ARNs andLRNs; we do not find the assortative mixing behaviour of any the subclusters in SRNs. The clusteringcoefficient of hydrophobic subclusters in long-range network is the highest among types of subnetworks.There exist highly cliquish hydrophobic nodes followed by charged nodes in LRNs and ARNs; on the otherhand, we observe the highest dominance of charged residues cliques in short-range networks. Studies on theperimeter of the cliques also show higher occurrences of hydrophobic and charged residues' cliques. Conclusions: The simple framework of protein contact networks and their subnetworks based on London van der Waalsforce is able to capture several known properties of protein structure as well as can unravel several newfeatures. The thermophiles do not only have the higher number of long-range interactions; they also havelarger cluster of connected residues at higher interaction strengths among amino acids, than their mesophiliccounterparts. It can reestablish the significant role of long-range hydrophobic clusters in protein folding andstabilization; at the same time, it shed light on the higher communication ability of hydrophobicsubnetworks over the others. The results give an indication of the controlling role of hydrophobicsubclusters in determining protein's folding rate. The occurrences of higher perimeters of hydrophobic andcharged cliques imply the role of charged residues as well as hydrophobic residues in stabilizing the distantpart of primary structure of a protein through London van der Waals interaction.