Question

4a) From the sequence below, identify which portion could be a transmembrane helix. Please underline the portion you select in your answer. FRYVNGPVLIRKLYSWWNLIMILLQYFAIMGNLVMNTGDVNELTANTITT 4b) How did you know how long to make the helix? Explain. 4c) What lead you to pick the region you did? Explain your answer.

Answer 1

Answer:

FRYVNGPVLIRKLYSWWNLIMILLQYFAIMGNLVMNLVMNTGDVNELTANTITT

The bold region of the above sequence will be in the transmembrane region.

4.b) To predict the helix we need to know the propensity of each amino acid in the amino acid sequence to form an alpha helix of the protein. Not only the propensity of a single amino acid will dictate that but also other amino acids in its vicinity will have an effect on it. More importantly, that should follow the Ramachandran plot.

4.c) I chosen that region based on the hydropathy index of the stretch of amino acids. The region of amino acids should have hydrophobic side chain because they will interact with the hydrophobic tail of the lipids in the cell membrane. So this region has higher hydropathy index than others. This lead me to choose that region.