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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- RNAi is currently being tested as a therapeutic tool for genetic diseases and other conditions. Consider the following: cystic fibrosis caused by loss of function of the CFTR gene, HIV infection, and cancer caused by hyperactivity of a growth factor receptor. Which of these may be treatable by RNAi, and which not? Explain your reasoning.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.Tumor cells from a person with leukemia have been analyzed to determine which oncogene is involved in the transformation. After partial sequencing of the gene, the predicted gene product is identified as a tyrosine kinase. Which of the following proteins would most likely be encoded by an oncogene and exhibit tyrosine kinase activity? A. Nuclear transcriptional activator B. Epidermal growth factor C. Membrane-associated G protein D. Platelet-derived growth factor E. Growth factor receptor
- which of hthe following would result in a persisting proliferation response to growth factor receptor activation after the ligand is no longer binding to its rceptor kinase? 1. Both a mutation that blocks the GTPas activity of Ras and a mutation that blocks the exchange of GDP with GTP would cause the response to persist. 2. a mutation that blocks the GTPas activity of Ras 3. neither a mutation that blocks the GTPas activity of Ras nor a mutation that blocks the exchange of GDP with GTP would cause the response to persist 4. a mutatiaon that blocks the exchange of GDP with GTPOne important role of Fas and Fas ligand is to mediate the elimination of tumor cells by killer lymphocytes. In a study of 35 primary lung and colon tumors, half the tumors were found to have amplified and overexpressed a gene for a secreted protein that binds to Fas ligand. How do you suppose that overexpression of this protein might contribute to the survival of these tumor cells? Explain your reasoning.Mutation in the fibroblast growth factor receptor (FGFR) gene results in achondroplasia (dwarfism), which is a dominant condition caused by a single base substitution (GGG>AGG) that changes the amino acid glycine at position 480 to arginine (G480R) in the FGFR protein. FGFR is normally active when FGF binds to it, but the mutant FGFR is always on to stimulate signaling that inhibits excessive bone growth. How can gene therapy be used to treat achondroplasia? Select all that apply. RNAi that knocks down the mutant FGFR expression Adeno-associated viral (AAV) vector that carries the wild-type FGFR Retroviral vector that carries the wild-type FGFR CRISPR with the wild-type FGFR donor DNA
- While investigating the function of a specific growth factor receptor gene from humans, researchers found that two types of proteins are synthesized from this gene. A larger protein containing a membrane spanning domain recognizes growth factors at the cell surface, stimulating a specific downstream signaling pathway. In contrast, a related, smaller protein is secreted from the cell and binds available growth factor circulating in the blood, thus inhibiting the downstream signaling pathway. Speculate on how the cell synthesizes these disparate proteins.Some of the most common mutations associated with cancer are found in the small G protein Ras. Oncogenic mutants of Ras lead to constitutive signaling. Suggest several possible mechanisms for why these forms of Ras show constitutive signaling. Conversely, mutations of Ras have been isolated that have dominant-negative activity (that is, they block signaling by the normal, endogenous G protein). Suggest possible mechanisms for how these mutants block signaling.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?
- Vascular endothelial growth factor receptor 2 (VEGFR-2) is an endothelial cell-specific receptor that has inherent tyrosine kinase activity. The binding of the Vascular endothelial growth factor (VEGF) ligand to its receptor plays an important role in angiogenesis, a process by which new capillaries are formed. Enhanced angiogenesis is associated with a number of diseases including cancer. Your goal is to develop a homogeneous in vitro TR-FRET kinase assay for VEGFR-2 (purified protein) in an attempt to identify small molecules that inhibit kinase activity and in turn modulate angiogenesis. Based on this background, please answer the following questions If you wanted to measure the kinase activity of VEGFR-2, what are some of the conventional methods/assays you would use?Vascular endothelial growth factor receptor 2 (VEGFR-2) is an endothelial cell-specific receptor that has inherent tyrosine kinase activity. The binding of the Vascular endothelial growth factor (VEGF) ligand to its receptor plays an important role in angiogenesis, a process by which new capillaries are formed. Enhanced angiogenesis is associated with a number of diseases including cancer. Your goal is to develop a homogeneous in vitro TR-FRET kinase assay for VEGFR-2 (purified protein) in an attempt to identify small molecules that inhibit kinase activity and in turn modulate angiogenesis. Based on this background, please answer the following questions How would you determine robustness of the assay and validate the assay?Vascular endothelial growth factor receptor 2 (VEGFR-2) is an endothelial cell-specific receptor that has inherent tyrosine kinase activity. The binding of the Vascular endothelial growth factor (VEGF) ligand to its receptor plays an important role in angiogenesis, a process by which new capillaries are formed. Enhanced angiogenesis is associated with a number of diseases including cancer. Your goal is to develop a homogeneous in vitro TR-FRET kinase assay for VEGFR-2 (purified protein) in an attempt to identify small molecules that inhibit kinase activity and in turn modulate angiogenesis. Based on this background, please answer the following questions How would you apply a TR-FRET assay to measure the in vitro kinase activity of VEGFR-2? Describe in steps the assay design and potential readout outcome.