Question

Please outline a brief research proposal to study the structure and function of a novel protein with known sequence but has never been investigated before.

Answer 1

The structure of the novel protein of known sequence can be studied by in-silico and wet-lab experiments.

In-silico methods

The known protein sequence can be aligned by BLAST and look for a similar sequence in the database, look for homologs of the protein in other organisms. start with protein BLAST and see if any proteins with known function match to your query protein sequentially.

you can try run secondary structure prediction (tool: JPRED) and tertiary structure prediction (eg. MODELLER, iTASSER, etc). see if any known proteins pop up in tertiary structure predictions.

WET LAB experiments

To find the structure of a novel protein, firstly the protein needs to be purified by affinity chromatography and the protein is processed and crystallized for X-ray crystallography and Nuclear magnetic resonance

To find the function of this novel protein, the sequence has been aligned by the BLAST, the protein which will be similar to this novel protein will appear on the screen after the BLAST.

BLAST will give us an idea of which type of wet lab experiments needs to be done. for eg. the novel protein sequence gets aligned to the apoptotic protein BAX, then it would suggest its function similar to BAX.

Therefore apoptotic assays and western blotting experiments could be done to find the function of novel protein in the cell (invitro experiments which include cell lines)