Tryptophan synthase (TRPS), with linearly arrayed subunits R R, catalyzes the last two reactions in the biosynthesis of L-tryptophan. The two reactions take place in the respective R-and -subunits of the enzyme, and the intermediate product, indole, is transferred from the R-to the -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 R 2 2 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 -subunit is found to be closely coupled to a group of hinge residues ( 77-89 and 376-379) near the -interface. These residues simultaneously control the anticorrelated motion of the two -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 -site. The motions of the COMM core residues are coordinated with those of the R-hinge residues 174-179 on the interfacial helix H6 at the entrance of the hydrophobic tunnel. And the motions of H6 are coupled, via helix H1 and RL6, to those of the loop RL2 that includes the R-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.The tryptophan synthase (TRPS) 1 R 2 2 complex is a bifunctional enzyme that catalyzes the last two reactions in the biosynthesis of L-tryptophan (L-Trp). The bacterial enzyme structure consists of two R-and two -subunits arranged in an extended R R order (Figure 1a,b). The Rand -subunits contain the respective sites for the R-and -reactions producing L-Trp: the cleavage of indole 3-glycerol phosphate (IGP) to release indole and glyceraldehyde 3-phosphate (G3P) (R-reaction) and the conversion of indole to L-Trp via a condensation reaction with L-serine ( -reaction). The latter is mediated by the cofactor pyridoxal 5′-phosphate (PLP), which forms with L-Ser a quasi-stable R-aminoacrylate intermediate, E(A-A), highly reactive toward indole. The R -reaction resulting from the combination of presents a typical example of long-range allosteric effect in that the two reactions, occurring at two topologically distinct and distant sites, are highly coordinated through a PLPdependent activation-deactivation mechanism, and the metabolite, indole, is transferred from the active site in the R-subunit to the other in the -subuni...