In selecting a method to produce a recombinant protein, a researcher is faced with a bewildering array of choices as to where to start. To facilitate decision-making, we describe a consensus 'what to try first' strategy based on our collective analysis of the expression and purification of over 10,000 different proteins. This review presents methods that could be applied at the outset of any project, a prioritized list of alternate strategies and a list of pitfalls that trip many new investigators.
Oncoproteins from DNA tumor viruses associate with critical cellular proteins to regulate cell proliferation, survival, and differentiation. Human papillomavirus (HPV) E6 oncoproteins have been previously shown to associate with a cellular HECT domain ubiquitin ligase termed E6AP (UBE3A). Here we show that the E6-E6AP complex associates with and targets the degradation of the protein tyrosine phosphatase PTPN3 (PTPH1) in vitro and in living cells. PTPN3 is a membrane-associated tyrosine phosphatase with FERM, PDZ, and PTP domains previously implicated in regulating tyrosine phosphorylation of growth factor receptors and p97 VCP (valosin-containing protein, termed Cdc48 in Saccharomyces cerevisiae) and is mutated in a subset of colon cancers. Degradation of PTPN3 by E6 requires E6AP, the proteasome, and an interaction between the carboxy terminus of E6 and the PDZ domain of PTPN3. In transduced keratinocytes, E6 confers reduced growth factor requirements, a function that requires the PDZ ligand of E6 and that can in part be replicated by inhibiting the expression of PTPN3. This report demonstrates the potential of E6 to regulate phosphotyrosine metabolism through the targeted degradation of a tyrosine phosphatase.Papillomaviruses are causative agents of benign epithelial tumors in vertebrates. A subset of these benign epithelial tumors may develop into epithelial malignancies, and the progression to malignancy is associated with particular papillomavirus types. The subset of human papillomavirus (HPV) types associated with cancer is termed "high risk." Most human genital cancers contain integrated high-risk HPV genomes that express the viral E6 and E7 oncoproteins (reviewed in reference 28); continued expression of E6 and E7 is required for cancer cell proliferation, and in certain HPV-expressing cancer cell lines, negative regulation of E6 and E7 expression results in the cessation of proliferation and entry of the cells into a terminal differentiation pathway (11,14).Papillomavirus E6 oncoproteins are small zinc-binding proteins with conserved overall structure but diverse activities, and considerable effort has been directed toward establishing their cellular targets (reviewed in reference 25). The cancer-associated E6 oncoprotein from HPV type 16 (HPV-16) (16E6) and bovine papillomavirus E6 (BE6) directly interact with cellular proteins by interaction with LXXLL peptide sequences on the target protein, and this interaction is required for cellular transformation (3, 41). 16E6 interacts with an LXXLL peptide sequence found on the cellular E3 ubiquitin ligase E6AP and together with E6AP binds to the p53 tumor suppressor protein (17), resulting in its ubiquitin-mediated degradation by the proteasome. The efficient in vivo degradation of p53 requires both E6AP and the E3 ubiquitin ligase activity of E6AP (7). E6 proteins have also been reported to target the degradation of other cellular proteins, initially identified through yeast two-hybrid interaction searches or candidate approaches. A group of cellular prote...
Background: LongChaiJiangXue formula (LCJX) has the effect of not only clearing up excessive erythrocytes but also relieving clinical symptoms of Polycythemia vera (PV). Material/Methods: The chemical constitution of LCJX was identified from Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform(TCMSP). Seven hundred and fifty-nine targets were identified and a total of 248 targets were screened out after discarding duplication and genes without any ID in databases. GeneCards database, OMIM database, and GEO database were searched for differential expression genes. The network was built by Cytoscape (3.7.2) software and the protein-protein interaction (PPI) networks of PV and LCJX were merged by https://string-db.org . Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment was processed by the R platform. The molecular docking technology was used to further analyze the intense of the assosiation of the compounds and targets. Results: 73 compounds of LCJX were chosen as the candidate active compounds. The compound-targets network contained 105 nods and 216 edges that presented the interaction of agents and targets. The PPI network of LCJX targets involved 59 nodes and 168 edges. The network showed that the key nodes were concentrated in signal transducer and activator of transcription-3(STAT-3), interleukin-6(IL-6), Janus kinase 2(JAK2), and vascular endothelial growth factor-A(VEGFA). The most enriched terms in the GO analysis in the GO biological processes(BP) were reactive oxygen species metabolic process, response to lipopolysaccharide, and response to oxidative stress. According to GO molecular functions(MF), the central nodes were generally enriched in cytokine receptor binding, cytokine activity, and heme binding. Regarding the GO cell components(CC), the terms included vesicle lumen, cytoplasmic vesicle lumen, and secretory granule lumen. In light of the KEGG enrichment analysis, the Hepatitis B, AGE-RAGE signaling pathway in diabetic complications, Kaposi sarcoma-associated herpesvirus infection, measles, Human cytomegalovirus infection, and JAK-STAT signaling pathway were significantly enriched. The molecular docking technology found that puerarin and saikosaponin A had relative stronger affinity with VEGFA, HIF-1A, JAK2 and STAT3 than other compounds in terms of the binding free energy. Conclusions: The effect of LCJX on PV is achieved through a series of complex mechanisms. Network pharmacology and molecular docking are powerful tools to reveal the effect of compound Chinese medicine on the disease.
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