Computer evaluation of protein segments removal effects from naphthalene 1,2-dioxygenase enzyme on polycyclic aromatic hydrocarbons interaction

Abstract

A novel computer approach for in silico molecular modification was here developed and applied to the bacterial enzyme naphthalene 1,2-dioxygenase. A complete set of small deletions was obtained modifying the crystal structure file of the enzyme dimer form, therefore conformational analysis and substrate interaction simulations methods were performed to describe molecule behavior related to different levels of modification. The analysis of interaction zones between all dimers of the examer structure permitted to extend these evaluations to the natural form present on bacterial cells. Four candidates for the biosynthesis of shorter molecules were individuated this way.