My protein cleaves very poorly with factor Xa. Is there anything I can do to improve cleavage?
We presume that, in these cases, the fusion protein folds so that the factor Xa site is inaccessible. In theory anything that perturbs the structure might uncover the site. We’ve tried increasing the temperature, changing buffers and salt conditions, and adding detergents. The only thing that worked was low concentrations of SDS (0.01 to 0.05%; see Ellinger et al., 1991, Virol. 180, 811- 3). Another researcher found that calcium worked – his protein of interest was a calcium binding protein, supporting the idea that anything that might change the conformation even slightly (e.g., a cofactor or substrate analog) could have a dramatic effect.
