Understanding Complex Mechanisms of Enzyme Reactivity: The Case of Limonene-1,2-Epoxide Hydrolases

Silvia Rinaldi, Marc W. Van Der Kamp, Kara E. Ranaghan, Adrian J. Mulholland*, Giorgio Colombo

*Corresponding author for this work

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

19 Citations (Scopus)
389 Downloads (Pure)


Limonene-1,2-epoxide hydrolases (LEHs), a subset of the epoxide hydrolase family, present interesting opportunities for the mild, regio- and stereo- selective hydrolysis of epoxide substrates. However, moderate enantioselectivity for non-natural ligands, combined with narrow substrate specificity, has so far limited the use of LEHs as general biocatalytic tools. A detailed molecular understanding of the structural and dynamic determinants of activity may complement directed evolution approaches to expand the range of applicability of these enzymes. Herein, we have combined quantum mechanics/molecular mechanics (QM/MM) free energy calculations for the reaction with MD simulations of the enzyme internal dynamics, and the calculation of binding affinities (using the WaterSwap method) for various representatives of the enzyme conformational ensemble, to show that the presence of natural or non-natural substrates differentially modulates the dynamic and catalytic behavior of LEH. The cross-talk between the protein and the ligands favors the selection of specific substrate-dependent interactions in the binding site, priming reactive complexes to select different preferential reaction pathways. The knowledge gained via our combined approach provides a molecular rationale for LEH substrate preferences. The comprehensive strategy we present here is general and broadly applicable to other cases of enzyme-substrate selectivity and reactivity.

Original languageEnglish
Pages (from-to)5698-5707
Number of pages10
JournalACS Catalysis
Issue number7
Early online date14 May 2018
Publication statusPublished - 6 Jul 2018


  • binding affinity
  • biocatalysis
  • catalytic mechanism
  • free energy landscape
  • internal dynamics
  • QM/MM and MD calculations
  • stereoselective epoxide hydrolysis
  • substrate specificity


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