Theoretical design of catalytic domain of abzyme se-scFv2F3 by introducing a catalytic triad

The single chain antibody scFv2F3 can be converted into selenium-containing Se-scFv2F3 by chemical mutation of the Ser residues. With antibody fragment 1NQB as a template, the catalytic domain of scFv2F3 was built by using homology modeling and molecular dynamics(MD) simulations. On the basis of the 3D model, we discussed the importance of Ser52 as the chemical modification site and redesigned the protein groups nearby Ser52 via introducing a catalytic triad. The following 10 ns MD results show that the designed Ser52-Trp29-Gln72 catalytic triad is stable enough and high close to the local structural features of native glutathione peroxidases(GPX). Our results may be useful for creating a new abzyme with higher catalytic efficiency and stability.