In the cell pathways are wired, i.e. interconnected directly or indirectly; in cancer, the pathways are rewired, the consequence of dysregulation. Rewiring can be the outcome of a number of events, including oncogenic mutations in protein coding regions, over/under expression, gene duplication/deletion - i.e. different copy number, altered splicing patterns, altered post-translational modifications, alterations in genome epigenetics or chromatin structures, and more. Enormous effort is invested by the community to elucidate the wiring and this rewiring. Despite this, figuring out the cellular network - beyond cellular diagrams illustrating pathways' connectivity - is still a significant challenge. Tracking the flow of the molecular circuitry of key cellular processes is expected to be immensely useful for selecting and evaluating signaling molecules/pathways as drug targets and for prioritizing research. However, the problem is compounded by the variability across cell types. While all pathways can be expected to take place in all cells types, which are at the basal level and which are elevated - or quenched - vary. Flagging the cellular pathway chart with this information for given cell type and state is essential. Doing this systematically will establish a major advance in cancer biology. Can we then identify pathways that can promote Ras oncogenicity and encode drug resistance? From the standpoint of the cancer cell, these pathways need to be independent - and corresponding - to the major Ras signaling pathways, MAPK and PI3K. These two properties are of cardinal importance: independence confers the ability to signal even when Ras signaling is blocked by drugs; correspondence implies that they can bestow the same functions as the MAPK or PI3K signaling do. Which cellular pathways are endowed with both properties? To identify those pathways, the first step involves determining the ultimate modes of action at the 'bottom' of the MAPK and PI3K pathways; the second step explores which other cellular pathways accomplish similar roles at the same pathway 'bottom' steps. When turned on, these pathways would act to promote cell proliferation independently and correspondingly to MAPK/PI3K. This means that in oncogenic cells these pathways - together with MAPK and PI3K - would aggravate tumor proliferation; and when Ras signaling is blocked they would substitute for the inhibited pathway. Since drug resistance often emerges, targeting these coincidentally with Ras is expected to be highly beneficial. We outlined suspect pathways - those leading to the expression (or activation) of YAP1 and c-Myc. We proposed that these pathways fulfill similar roles in cell cycle regulation from the G1 to the S phase. We also ask whether these - corresponding and independent - signaling pathways are all equally likely. This is a critical question since to minimize cell toxicity only a subset of pathways can be targeted at any given time. We suggest that the selection of the more favored pathway(s) should be cell type-dependent - here stem cell versus differentiated cell. Deciphering Independent and corresponding core pathways is crucial for complete understanding and successful pharmacology. Over the last couple of years we have been increasingly interested in the oncogenic state.
We aim to figure out the mechanisms of key proteins and their signaling networks in the cell. Among these, we have particularly focused on the Ras protein, its activation mechanism, how oncogenic mutations can shift the landscape and how it affects its signaling. Among the Ras isoforms, we focus on its most abundant isoform, KRas-4B. We seek to figure out how the membrane attachment affects its activation and signaling; the mechanism through which calmodulin acts to promote cancer through its interaction with K-Ras4B, the detailed activation mechanisms of the oncogenic mutations, and how RASSF5, which links Ras with the Hippo pathway and YAP1 acts as a tumor suppressor. Signaling pathways shape and transmit the cell's reaction to its changing environment; however, pathogens can circumvent this response by manipulating host signaling. To subvert host defense, they beat it at its own game: they hijack host pathways by mimicking the binding surfaces of host-encoded proteins. For this, it is not necessary to achieve global protein homology; imitating merely the interaction surface is sufficient. Different protein folds often interact via similar protein-protein interface architectures. This similarity in binding surfaces permits the pathogenic protein to compete with a host target protein. Thus, rather than binding a host-encoded partner, the host protein hub binds the pathogenic surrogate. The outcome can be dire: rewiring or repurposing the host pathways, shifting the cell signaling landscape and consequently the immune response. They can also cause persistent infections as well as cancer by modulating key signaling pathways, such as those involving Ras. Mapping the rewired host-pathogen 'superorganism' interaction network - along with its structural details - is critical for in-depth understanding of pathogenic mechanisms and developing efficient therapeutics. Currently, we focus on the role of molecular mimicry in pathogen host evasion as well as types of molecular mimicry mechanisms that emerged during evolution. The tumor necrosis factor receptor (TNFR) associated factor3 (TRAF3) is a key node in innate and adaptive immune signaling pathways. TRAF3 negatively regulates the activation of the canonical and non-canonical NF-kappaB pathways and is one of the key proteins in antiviral immunity. Here we provide a structural overview of TRAF3 signaling in terms of its competitive binding and consequences to the cellular network. For completion, we also include molecular mimicry of TRAF3 physiological partners by some viral proteins. By out-competing host partners, these aim to subvert TRAF3 antiviral action. Mechanistically, dynamic, competitive binding by the organism's own proteins and same-site adaptive pathogen mimicry follow the same conformational selection principles. Our premise is that irrespective of the eliciting event - physiological or acquired pathogenic trait - pathway activation (or suppression) may embrace similar conformational principles. However, even though here we largely focus on competitive binding at a shared site, similar to physiological signaling other pathogen subversion mechanisms can also be at play. Altogether, we take a comprehensive look at signaling from the structural standpoint aiming in cancer, inflammation and pathogen intervention.
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