Homework
Weekly homework submissions:
What do you want to make? → Custom designed protein; post translational modifications/ usage of nonstandard amino acids (e.g. selenocysteine) not clear. For the purpose of this homework, may the custom protein be named Cuop. Coup is a peptidic macromolecule I plan to design, analyse and test using various computational tools. Its intended goal is to address prion activity in-vivo; work like an inhibitory drug against prion PrPSc “infectious” folding mechanism. The explanation for a protein’s ability to self-propagate a motif is intermolecular interactions between strongly bound-together amino acids (PrPSc beta sheets) and a less rigid structure (PrP alpha helices). Therefore a molecule able to prevent the interactions between the two proteins may be capable of preventing the spread of disease in high risk patients. The way I aim to achieve this is molecular docking simulations to assess if the custom protein can actually help.
Protein expression system in Asimov Kernel 1. Defining expression target What molecule are you expressing? A protein, an RNA, or an enzyme (or small set of enzymes) for a pathway. If your HW1 product is a material, food, or chemical, identify the protein(s) that produce it and design for those. Fortunately, the only molecule desribed for my final project is a single short protein (i.e. prion-binding ‘peptide’). The design logic stays simple throughout production: DNA -> mRNA -> protein of interest.
Week 3 HW: CFPS for sfGFP, PETase, Reteplase
WEEK 3 ASSIGNMENT: CFPS REACTION DESIGN FOR SFGFP, PETASE, RETEPLASE A. COMPARE CELL-FREE REACTION COMPOSITIONS (20 minutes) Why does the concentration of potassium glutamate and magnesium glutamate differ between compositions? Which is more sensitive? Referance concentration: K-glutamate (279.84 mM), Mg-glutamate (8.22 mM) are to mimic and maintain osmotic parameters of lysate in CFPS, assure ribosome, energy-replenishing enzymes, polymerase function, stabilise DNA/RNA structure etc.; both glutamic acid salts are usually found in high concentrations.