Effect of binding in cyclic phosphorylation-dephosphorylation process and in energy transformation

Analysis and identification of potential type II helper T cell (Th2)-Related key genes and therapeutic agents for COVID-19

COVID-19 pandemic poses a severe threat to public health. However, so far, there are no effective drugs for COVID-19. Transcriptomic changes and key genes related to Th2 cells in COVID-19 have not been reported. These genes play an important role in host interactions with SARS-COV-2 and may be used as promising target. We analyzed five COVID-19-associated GEO datasets (GSE157103, GSE152641, GSE171110, GSE152418, and GSE179627) using the xCell algorithm and weighted gene co-expression network analysis (WGCNA). Results showed that 5 closely correlated modular genes to COVID-19 and Th2 cell enrichment levels, including purple, blue, pink, tan and turquoise, were intersected with differentially expressed genes (DEGs) and 648 shared genes were obtained. GO and KEGG pathway enrichment analyses revealed that they were enriched in cell proliferation, differentiation, and immune responses after virus infection. The most significantly enriched pathway involved the regulation of viral life cycle. Three key genes, namely CCNB1, BUB1, and UBE2C, may clarify the pathogenesis of COVID-19 associated with Th2 cells. 11 drug candidates were identified that could down-regulate three key genes using the cMAP database and demonstrated strong drugs binding energies aganist the three keygenes using molecular docking methods. BUB1, CCNB1 and UBE2C were identified key genes for COVID-19 and could be promising therapeutic targets.

Open cascades as simple solutions to providing ultrasensitivity and adaptation in cellular signaling

Cell signaling is achieved predominantly by reversible phosphorylation-dephosphorylation reaction cascades. Up until now, circuits conferring adaptation have all required the presence of a cascade with some type of closed topology: negative-feedback loop with a buffering node, or incoherent feed-forward loop with a proportioner node. In this paper--using Goldbeter and Koshland-type expressions--we propose a differential equation model to describe a generic, open signaling cascade that elicits an adaptation response. This is accomplished by coupling N phosphorylation-dephosphorylation cycles unidirectionally, without any explicit feedback loops. Using this model, we show that as the length of the cascade grows, the steady states of the downstream cycles reach a limiting value. In other words, our model indicates that there are a minimum number of cycles required to achieve a maximum in sensitivity and amplitude in the response of a signaling cascade. We also describe for the first time that the phenomenon of ultrasensitivity can be further subdivided into three sub-regimes, separated by sharp stimulus threshold values: OFF, OFF-ON-OFF, and ON. In the OFF-ON-OFF regime, an interesting property emerges. In the presence of a basal amount of activity, the temporal evolution of early cycles yields damped peak responses. On the other hand, the downstream cycles switch rapidly to a higher activity state for an extended period of time, prior to settling to an OFF state (OFF-ON-OFF). This response arises from the changing dynamics between a feed-forward activation module and dephosphorylation reactions. In conclusion, our model gives the new perspective that open signaling cascades embedded in complex biochemical circuits may possess the ability to show a switch-like adaptation response, without the need for any explicit feedback circuitry.