Comprehensive host-pathogen protein-protein interaction network analysis

Abstract

Background Infectious diseases are a cruel assassin with millions of victims around the world each year. Understanding infectious mechanism of viruses is indispensable for their inhibition. One of the best ways of unveiling this mechanism is to investigate the host-pathogen protein-protein interaction network. In this paper we try to disclose many properties of this network. We focus on human as host and integrate experimentally 32,859 interaction between human proteins and virus proteins from several databases. We investigate different properties of human proteins targeted by virus proteins and find that most of them have a considerable high centrality scores in human intra protein-protein interaction network. Investigating human proteins network properties which are targeted by different virus proteins can help us to design multipurpose drugs. Results As host-pathogen protein-protein interaction network is a bipartite network and centrality measures for this type of networks are scarce, we proposed seven new centrality measures for analyzing bipartite networks. Applying them to different virus strains reveals unrandomness of attack strategies of virus proteins which could help us in drug design hence elevating the quality of life. They could also be used in detecting host essential proteins. Essential proteins are those whose functions are critical for survival of its host. One of the proposed centralities named diversity of predators, outperforms the other existing centralities in terms of detecting essential proteins and could be used as an optimal essential proteins’ marker. Conclusions Different centralities were applied to analyze human protein-protein interaction network and to detect characteristics of human proteins targeted by virus proteins. Moreover, seven new centralities were proposed to analyze host-pathogen protein-protein interaction network and to detect pathogens’ favorite host protein victims. Comparing different centralities in detecting essential proteins reveals that diversity of predator (one of the proposed centralities) is the best essential protein marker.

Lipid-related protein NECTIN2 is an important marker in the progression of carotid atherosclerosis: An intersection of clinical and basic studies

“…Regarding the function of NECTIN2 protein in CA, we focused on the ‘bridge function’ of NECTIN2 and CD226 in our protein–protein interaction network analysis (Supplementary Figure 6A). [ 35 ] We found that lipid proteins and inflammatory proteins were linked by the ligand–receptor binding of NECTIN2 and CD226. [ 36 ] As we all know, lipid metabolism plays an important role in CA progression.…”

Identifying Key Lysosome-Related Genes Associated with Drug-Resistant Breast Cancer Using Computational and Systems Biology Approach

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“…One of the ways to identify essential genes that play a vital role in diseases is to analyze the human proteinprotein interaction network (HPPIN) and centrality measures. Centrality is the most critical parameter for identifying the gravity of each gene/protein as a node in networks (16).…”

Network analysis of host-pathogen protein interactions in microbe induced cardiovascular diseases

“…Network positions of power have also been used to prioritize potential antiviral drug candidates [ 22 ]. New proposed measures of centrality coined for HPIs to aid in the design of multipurpose drugs include Connectivity of human proteins targeted by same virus protein, propagation speed, diversity of predators, decreased shortest path, component index, crown centrality and vulnerable centrality [ 23 ]. The development of novel drugs, vaccines and other therapeutics for CVDs caused by microorganisms is highly dependent on the knowledge gained from investigating HPIs [ 24 ].…”