QM/MM modelling of ketosteroid isomerase reactivity indicates that active site closure is integral to catalysis

Marc W. van der Kamp, Robin Chaudret, Adrian J. Mulholland*

*Corresponding author for this work

Research output: Contribution to journalArticle (Academic Journal)peer-review

24 Citations (Scopus)

Abstract

Ketosteroid isomerase (5-3-keto steroid isomerase or steroid -isomerase) is a highly efficient enzyme at the centre of current debates on enzyme catalysis. We have modelled the reaction mechanism of the isomerization of 3-oxo-5-steroids into their 4-conjugated isomers using high-level combined quantum mechanics/molecular mechanics (QM/MM) methods, and semi-empirical QM/MM molecular dynamics simulations. Energy profiles were obtained at various levels of QM theory (AM1, B3LYP and SCS-MP2). The high-level QM/MM profile is consistent with experimental data. QM/MM dynamics simulations indicate that active site closure and desolvation of the catalytic Asp38 occur before or during formation of dienolate intermediates. These changes have a significant effect on the reaction barrier. A low barrier to reaction is found only when the active site is closed, poising it for catalysis. This conformational change is thus integral to the whole process. The effects on the barrier are apparently largely due to changes in solvation. The combination of high-level QM/MM energy profiles and QM/MM dynamics simulation shows that the reaction involves active site closure, desolvation of the catalytic base, efficient isomerization and re-opening of the active site. These changes highlight the transition between the ligand binding/releasing form and the catalytic form of the enzyme. The results demonstrate that electrostatic interactions (as a consequence of pre-organization of the active site) are crucial for stabilization during the chemical reaction step, but closure of the active site is essential for efficient catalysis to occur.

Original languageEnglish
Pages (from-to)3120-3131
Number of pages12
JournalFEBS Journal
Volume280
Issue number13
DOIs
Publication statusPublished - Jul 2013

Bibliographical note

© 2013 The Authors Journal compilation © 2013 FEBS.

Keywords

  • conformational change
  • desolvation
  • enzyme catalysis
  • enzyme dynamics
  • quantum mechanics
  • molecular mechanics
  • ACETYL-COA DEPROTONATION
  • BARRIER HYDROGEN-BOND
  • AB-INITIO QM/MM
  • DELTA(5)-3-KETOSTEROID ISOMERASE
  • CITRATE SYNTHASE
  • MOLECULAR-DYNAMICS
  • 3-OXO-DELTA(5)-STEROID ISOMERASE
  • 3-OXO-DELTA-5-STEROID ISOMERASE
  • TRIOSEPHOSPHATE ISOMERASE
  • TRANSITION-STATE

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