Structural dynamics of the Ca2+-regulated cutinase towards structure-based improvement of PET degradation activity

Abstract

We previously revealed the structural basis of Ca²⁺ dependent regulation of a polyethylene terephthalate (PET)-degrading enzyme, Cut190, and proposed a unique reaction cycle in which the enzyme repeatedly binds and releases Ca²⁺. Here, we report crystal structures of Cut190 mutants with high thermal stability complexed with PET-like ligands that contain aromatic rings. The structural information has allowed us to perform further computational analyses using a PET-trimer bound model. Our multicanonical molecular dynamics simulations and subsequent analyses of the free energy landscapes revealed a novel intermediate form that occurs during the enzymatic reaction cycle. Furthermore, the computational analyses were used to investigate the effect of the point mutations F77L and F81L in the Ca²⁺-binding site, which showed that the former stabilizes the engaged and open forms to improve transition between the open and active forms, while the latter extremely increases the open form. Subsequent experiments showed that the F77L mutation increased the activity, while the F81L mutation decreased the activity. Our computational analysis has enabled us to explore the dynamics of Cut190 on a completely new level, providing key insights into how the balance between the various conformations influences the reaction cycle and ultimately how to improve the reaction cycle.

Keywords: Crystal structure; Multicanonical molecular dynamics; Rational design.