HCV genomic RNA encodes a polyprotein precursor
The polyprotein precursor encoded by HCV genomic RNA contains ~3,000 amino acid residues and is cleaved by a combination of host and viral proteases into at least 10 proteins: the core, envelope proteins (E1 and E2), p7, and non-structural 2 (NS2), NS3, NS4A, NS4B, NS5A and NS5B proteins.
HCV core protein is structurally involved in the nucleocapsid formation. The proteins, E1 and E2 are responsible for viral entry into host cells promoting viral replication and infection.
Several substrates and inhibitors targeting these envelope proteins to study the structure and functional characteristics have been designed to bind and inhibit viral particles.
A high-quality substrate to monitor the HCV protease activity
The HCV Protease FRET substrate shows very high kcat/Km values, enabling detection of activity with subnanomolar nonstructural protein 3 (NS3 protease) concentrations. It is based on fluorescence transfer between the Dabcyl and EDANS FRET partners.
Substrate cleavage is proportional to the enzyme concentration with a detection limit for NS3 between 1 nM and 250 pM. Upon cleavage of this substrate, fluorescence can be monitored at Abs/Em = 355/500 nm.