Mechanism of Substrate Activation by Tryptophan Hydroxylase: A Computational Study

Abstract

Serotonin is a hormone that is responsible for mood regultion in the brain; however, details on its biosynthetic mechanism remain controversial. Tryptophan hydroxylase catalyzes the first step in the serotonin biosynthesis in the human body, where it regio- and stereoselectively hydroxylates a free tryptophan (Trp) amino acid at the C₅-position. In this work, we present a computational study ranging from molecular dynamics (MD) to quantum mechanics (QM) methods, focused on the mechanism of tryptophan hydroxylase. An MD simulation on an enzyme structure with the substrate, co-substrate and dioxygen bound reveals a tightly bound conformation of substrate and co-substrate, while the protein's three-dimensional structure stays virtually intact during the simulation. Subsequently, large active-site cluster models containing more than 200 atoms were created, and oxygen atom transfer reactions were studied. The calculations predict that the co-factor tetrahydrobiopterin binds covalently to the iron center and react with a dioxygen molecule to form an iron(IV)-oxo species and pterin-4a-carbinolamine in a stepwise manner with small energy barriers (<5 kcal mol⁻¹) along an exergonic pathway. However, the rate-determining step, is Trp activation through a C−O activation transition state, followed by a rapid proton relay to produce 5-hydroxy-L-Trp.