Novel allosteric effectors of the tryptophan synthase α2β2 complex identified by computer-assisted molecular modeling

Anna Marabotti, Pietro Cozzini, Andrea Mozzarelli

Research output: Contribution to journalArticlepeer-review


Tryptophan synthase is a pyridoxal 5'-phosphate-dependent α2β2 complex catalyzing the formation of L-tryptophan. The functional properties of one subunit are allosterically regulated by ligands of the other subunit. Molecules tailored for binding to the α-active site were designed using as a starting model the three-dimensional structure of the complex between the enzyme from Salmonella typhimurium and the substrate analog indole-3-propanol phosphate. On the basis of molecular dynamics simulations, indole-3-acetyl-X, where X is glycine, alanine, valine and aspartate, and a few other structurally related compounds were found to be good candidates for ligands of the α-subunit. The binding of the designed compounds to the α-active site was evaluated by measuring the inhibition of the α-reaction of the enzyme from Salmonella typhimurium. The inhibition constants were found to vary between 0.3 and 1.7 mM. These α-subunit ligands do not bind to the β- subunit, as indicated by the absence of effects on the rate of the β- reaction in the isolated β2 dimer. A small inhibitory effect on the activity of the α2β2 complex was caused by indole-3-acetyl-glycine and indole-3-acetyl-aspartate whereas a small stimulatory effect was caused by indole-3-acetamide. Furthermore, indole-3-acetyl-glycine, indole-3-acetyl- aspartate and indole-3-acetamide perturb the equilibrium of the catalytic intermediates formed at the β-active site, stabilizing the α-aminoacrylate Schiff base. These results indicate that (i) indole-3-acetyl-glycine, indole- 3-acetyl-aspartate and indole-3-acetamide bind to the α-subunit and act as allosteric effectors whereas indole-3-acetyl-valine and indole-3-acetyl- alanine only bind to the α-subunit, and (ii) the terminal phosphate present in the already known allosteric effectors of tryptophan synthase is not strictly required for the transmission of regulatory signals. (C) 2000 Elsevier Science B.V.

Original languageEnglish
Pages (from-to)287-299
Number of pages13
JournalBiochimica et Biophysica Acta (BBA)/Protein Structure and Molecular
Issue number2
Publication statusPublished - Feb 9 2000


  • Allosteric effector
  • Enzymology
  • Ligand design
  • Molecular modeling
  • Pyridoxal 5'-phosphate

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Structural Biology
  • Biophysics


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