The next steps....

After my meeting with my supervisor yesterday, I now know what my next set of experiments will be! The answer to which is unknown, so this is classed as "proper research", which is very exciting!!

The TCV coat protein dimer (shown in the diagram below) has N-terminal tails, that are very sensitive to protease digestion when exposed. So when the virus is digested with chymotrypsin, they are cleaved off.

Chymotrypsin is a serine endopeptidase, that becomes active after cleavage with another protease trypsin; this enzyme cleaves between the arginine and isoleucine (R15 and L16), causing structural modification and formation of the substrate binding site. Chymotrypsin selectively cleaves peptide bonds formed by aromatic residues (eg. tyrosine, phenylalanine), as it prefers to cleave at large hydrophobic residues.

The question I will be answering is whether when this coat protein is attached to the RNA genome, in the rp-complex, does this cleavage still occur? It is thought that the RNA will be bound to the N-terminal tails and prevent the cleavage from occurring, but who knows?! Hopefully me in a few days once my experiments are complete!