Computational analysis of interactomes: Current and future perspectives for bioinformatics approaches to model the host–pathogen interaction space

Impact ofSalmonella entericaType III Secretion System Effectors on the Eukaryotic Host Cell

“…The classical yeast two-hybrid screen [69] or the quantitative proteomics technique based on stable isotope labeling of amino acids in cell culture (SILAC) are examples of efficient methods that are being used to identify interaction partners [154]. Computational methods are also useful to predict host-pathogen protein-protein interactions [155]. Structural studies of effectors, especially in complex with their cognate host partners, are also instrumental in understanding their function and their mechanisms of action [156].…”

Experimental approaches to phenotypic diversity in infection

“…Moreover, the single cell information must be integrated with tissue-, organ-, organism-and maybe even the ecosystem level to obtain a complete functional understanding. Therefore, computational modeling (for recent reviews, see [130][131][132]) at multiple scales will be essential for integrating the available information. At any rate it seems safe to predict that multi-scale approaches integrating data from quite different types of techniques is a promising avenue for deciphering the role of phenotypic heterogeneity in infectious disease.…”

Structural Bioinformatics of the Interactome

“…Structural mimicry appears to be an important component of this process (41), with pathogen proteins taking on the shape of a host protein and binding to that protein’s partners to activate or inhibit normal host pathways. Computational methods such as those described above are being used to predict host-pathogen interactomes (7, 43) with some methods incorporating protein structure (40). These approaches have been used to identify functional submodules in the native host interactomes which are affected by infection (162, 191).…”