Question

ANSWER WITH A GENERAL IDEA/MECHANISM RATIONALE

Huntingtin is a disease gene linked to Huntington's disease, a neurodegenerative disorder characterized by loss of striatal neurons. How would you design a peptide that could prohibit the loss of the neurons? Describe your rational for the design of the peptide. In detail:

1. What target sequences would you need to target the peptide to the correct location in the cell. Explain your choice.

2. What other sequences would you need for the peptide to be effective in Huntington’s disease? Explain your choices.

3. How would you express the peptide in the cells? Design your experiment.

4. How would you prove that your peptide is functioning? Design a basic experiment to test the effectiveness of your peptide.

Answer 1

Designing a peptide-inhibitor to inhibit a proteni-receptor or any other protein-protein interaction is possible based on the information of receptor binding domain of that protein or any other key interacting domain of the ligand . The crystal structure of these proteins will be available in the protein data bank. In this case, an inhibitory peptide that can block the mutated huntington protein can be designed. Designing a peptide sequence is beyong the scope of this question as it require bioinformatics tools like schrodinger or Autodoc. Using these softwares you will have to make multiple protein-ligand docking based on many criteria described in the software.

Expressing peptides in cells typically depends on the length of the peptide. A peptides less than 25 aminoacids is difficult to express in cells. In that case, peptide synthesis by chemical methods like solid phase peptide synthesis are followed. peptides with more than 30 aminoacids can be expressed in cells using expression vectors like pET. The expressed peptides then has to be purified using special columns.

How can you prove functionality of the peptides?

you have to develop an assay system for this as follows.

Express the mutated huntington protein with a fluresecent tag in a particular cell line. this flurescent protein can be treated with another flurescent tagged peptide and conduct in immunofluoresecnce (confocal) assay to prove the effective binding of the peptide.