Cooperative Fluctuations and Subunit Communication in Tryptophan Synthase

Abstract

Tryptophan synthase (TRPS), with linearly arrayed subunits αββα, catalyzes the last two reactions in the biosynthesis of l-tryptophan. The two reactions take place in the respective α- and β-subunits of the enzyme, and the intermediate product, indole, is transferred from the α- to the β-site through a 25 Å long hydrophobic tunnel. The occurrence of a unique ligand-mediated long-range cooperativity for substrate channeling, and a quest to understand the mechanism of allosteric control and coordination in metabolic cycles, have motivated many experimental studies on the structure and catalytic activity of the TRPS α₂β₂ complex and its mutants. The dynamics of these complexes are analyzed here using a simple but rigorous theoretical approach, the Gaussian network model. Both wild-type and mutant structures, in the unliganded and various liganded forms, are considered. The substrate binding site in the β-subunit is found to be closely coupled to a group of hinge residues (β77−β89 and β376−β379) near the β−β interface. These residues simultaneously control the anticorrelated motion of the two β−subunits, and the opening or closing of the hydrophobic tunnel. The latter process is achieved by the large amplitude fluctuations of the so-called COMM domain in the same subunit. Intersubunit communications are strengthened in the presence of external aldimines bound to the β-site. The motions of the COMM core residues are coordinated with those of the α−β hinge residues β174−β179 on the interfacial helix βH6 at the entrance of the hydrophobic tunnel. And the motions of βH6 are coupled, via helix βH1 and αL6, to those of the loop αL2 that includes the α-subunit catalytically active residue Asp60. Overall, our analysis sheds light on the molecular machinery underlying subunit communication, and identifies the residues playing a key role in the cooperative transmission of conformational motions across the two reaction sites.