Computational Study of Conformational Transitions in the Active Site of Tosyl-α-chymotrypsin

Themis Lazaridis, Michael E. Paulaitis

Research output: Contribution to journalArticlepeer-review

Abstract

The motion of the tosyl group covalently bound in the active site of α-chymotrypsin has been studied using an empirical force Held. A previously developed method employing an adiabatic projection of the potential energy hypersurface onto a small number of essential degrees of freedom has been used to determine multidimensional reaction paths for the rotation of the tosyl aromatic ring within and its movement out of the specificity pocket of the enzyme. The conformation of the specificity pocket was found to change under stochastic boundary, molecular dynamics simulations. The shape of the paths and the height of the calculated energy barriers were affected substantially by this conformational change. The free-energy profile for tosyl-ring rotation was also determined by free-energy perturbation in the presence and absence of explicit solvent water and in both cases was found to be lower than the energy barrier, indicating a positive activation entropy. On the basis of the calculated energy and free-energy barriers, the mobility of the bound inhibitor was found to be much lower than that observed in NMR experiments on the same system. Our calculations also indicate that the time scales for movement of the tosyl ring out of the pocket are much slower than that for rotation in the pocket. This result implies that the measured NMR correlation times for ring rotation are an average of correlation times for rotation in the pocket and in solution.

Original languageEnglish (US)
Pages (from-to)1546-1556
Number of pages11
JournalJournal of the American Chemical Society
Volume116
Issue number4
DOIs
StatePublished - Feb 1 1994
Externally publishedYes

ASJC Scopus subject areas

  • Catalysis
  • Chemistry(all)
  • Biochemistry
  • Colloid and Surface Chemistry

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