In the study by Amano et al. the authors developed a collection of RNA sequences that showed optimal binding and specificity for Fibroblast Growth Factor 5 (FGF5). In the table below are some FGF5 binding data for the lead RNA aptamer sequences: Aptamer F5f1 F5f3 F5f1_56 F5f3_56 Kon (x 105 M-1 S-1) 3.3±0.3 1.7 +0.3 1.8 ± 0.3 1.36± 0.05 Koff (x 10-5 s-1) 20±6 10+2 2.1±0.3 12.5± 0.7 "The kinetic parameters are represented by the mean ± standard error from three independent measurements. Kd (nm) 0.7 +0.2 0.57 + 0.02 0.118 + 0.003 0.92 +0.04 Based upon this data, which aptamer would you consider to be the primary receptor for the FGF5 ligand? Explain your answer.
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Based on data, which aptamer would consider to be the primary receptor for the FGF5 ligand? Explain your answer.
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- Aberrant signaling through the Ras-BRaf-MAPK signal transduction pathway drives many cancers. This makes the pathway an attractive drug target, and many small molecules have been developed that target either Ras, BRaf or MAPK. In malignant melanoma, one mutation in particular, where valine 600 of Braf is mutated to a glutamic acid (V600E), is found in the majority of cases. This mutation makes BRaf activation independent of upstream Ras activity. Would a small molecule that targets Ras be effective in a melanoma case driven by Braf V600E? Explain your answer.Briefly describe the following properties of the Ras GTPases: a) Size, structure and cellular localization (for structure I want to know if they are lipidated and any other unique features) , b) How are they activated and inactivated (i.e. include the GEFs and GAPs), c). Give an example of downstream effector proteins, d). Are they or could they be involved in human cancer.Describe the various post-translational modifications of HIF- 1alpha and how it affects the regulation of HIF-1al pha signaling. How might HIF- alpha alter the tumor microenvironment to promote tumor growth? Propose a strategy to prevent HIF-alpha signaling in the TME. What do you think would happen in a transgenic mouse with a total knockout of HIF-alpha?
- The progressive loss of cardiac myocytes due to cell death has been associated with cardiac dysfunction and heart failure. Which of the following would lead to a significant loss of cardiac myocytes? Select all that apply Treatment of rapamycin which results in inhibition of mTOR activity Prolonged or severe ER stress with increased accumulation of unfolded proteins Activation of AMPK and phosphorylation of the TSC1 complex mTOR activation and phosphorylation of Ulk1The PYK gene codes for the expression of pyruvate kinase, which is one of the enzymestargeted for anti-cancer drug design. You have identified an RNAi that targets the mRNAof PYK gene. To study the effect of the RNAi towards pyruvate kinase, the respected RNAiis expressed in Saccharomyces cerevisiae. The level of pyruvate kinase can be detectedwith a fluorescent antibody.(a). Predict the result that you will obtain in recombinant S. cerevisiae that expresses therespected RNAi.(b). Compare the result in Q3a(i) with the wild-type S. cerevisiae.Explain why in cells that are genetically NF1–/–, basal levels of GTP-bound activated Ras are higher than normal and respond to growth factor stimulation by increasing rapidly to far higher levels.
- The Pathway presented shows you how the pathway is regulated with a Ras-GEF. Explain how adding a Ras-GAP to the cell would A) specifically affect the molecules of the signaling pathway and B) affect the response of the cell.The codon change (Gly-12 to Val-12) in human rasH that convertsit to oncogenic rasH has been associated with many types ofcancers. For this reason, researchers would like to develop drugs toinhibit oncogenic rasH. Based on your understanding of the Rasprotein, what types of drugs might you develop? In other words,what would be the structure of the drugs, and how would theyinhibit Ras protein? How would you test the efficacy of the drugs?What might be some side effects?The output of RTK pathways is often the activation of MAP Kinase. Explain how MAPK can lead to activation of a specific subset of proteins, leading to distinct effects in different cell types in response to the same growth signal.
- Cancers are often caused by overactive growth factor receptor signaling (remember growth factor receptors are enzyme-linked receptor pathways). If you were able to use gene therapy to overexpress a particular protein in a cancer cell, which of the following might be useful to overexpress in order to combatt cancer? a GAP that acts on Ras a phosphatase that acts on GPCR a protein that enhances the activity of Akt a ubiqtuin ligase that acts on the MAPK phophataseThe MARCH-1 E3-ubiquitin ligase is expressed in B cells, dendritic cells, and macrophages. The pathway regulated by MARCH-1 is targeted by some pathogens in an immune evasion strategy. In this strategy, the pathogens encode: A protein that induces degradation of MARCH-1 A protein that mimics MARCH-1 and functions similarly A protein that binds to MARCH-1 and inhibits its function A protein that is induced by IL-10 in macrophages and dendritic cells A protein that induces degradation of CD86You are given a project to characterize the effect of mutation on two newly discovered G protein coupled-receptors, GPCR-UCI and GPCR-UC2, both of which bind to the same ligand. For the cell signalling assay, you have the UMR-106 cell line that expresses both GPCR-UC1, CPCR- UC2, the corresponding G proteins, and adenyl-cyclase. A basal adenylyl cyclase activity, and thus, a baseline cAMP concentration, is detected in the cell line. (i) You found that, upon binding to the ligand, the mutation in GPCR-UC1 results in increased CAMP level but the mutation in GPCR-UC2 results in a low cAMP concentration. Based on these results, identify the subclass of G protein isoforms that the GPCRs activate. Explain your answer. (ii) If the mutation affects the G protein from GDP release, how would this affect the CAMP production after ligand binding? Explain your answer.