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Unpicking the Cause of Stereoselectivity in Actinorhodin Ketoreductase Variants with Atomistic Simulations

preprint
submitted on 03.12.2018 and posted on 04.12.2018 by Stefano Artin Serapian, Marc van der Kamp
Ketoreductase enzymes (KRs) with a high degree of regio- and stereoselectivity are useful biocatalysts for the production of small, specific chiral alcohols from achiral ketones. Actinorhodin KR (actKR), part of a type II polyketide synthase involved in the biosynthesis of the antibiotic actinorhodin, can also turn over small ketones. In vitro studies assessing stereocontrol in actKR have found that, in the “reverse” direction, the wild-type (WT) enzyme’s mild preference for S-α-tetralol is enhanced in certain mutants (e.g. P94L); and entirely reversed in others (e.g. V151L) in favor of R-α-tetralol. Here, we employ efficient atomistic simulations to rationalize these trends in WT, P94L, and V151L actKR, using trans-1-decalone (1) as the model substrate. Three potential factors (FI-FIII) are investigated: frequency of pro-R vs. pro-S reactive poses (FI) is assessed with classical molecular dynamics (MD); binding affinity of pro-R vs. pro-S orientations (FII) is compared using the binding free energy method MM/PBSA; and differences in reaction barriers towards trans-1-decalol (FIII) are assessed by hybrid semiempirical quantum / classical (QM/MM) MD simulations with umbrella sampling, benchmarked with density functional theory. No single factor is found to dominate stereocontrol: FI largely determines the selectivity of V151L actKR, whereas FIII is more dominant in the case of P94L. It is also found that formation of S-trans-1-decalol or R-trans-1-decalol mainly arises from the reduction of the trans-1-decalone enantiomers (4aS,8aR)-1 or (4aR,8aS)-1, respectively. Our work highlights the complexity of enzyme stereoselectivity as well as the usefulness of atomistic simulations to aid the design of stereoselective biocatalysts.

Funding

BB/M026280/1

History

Email Address of Submitting Author

stefano.serapian@bristol.ac.uk

Institution

University of Bristol School of Biochemistry

Country

United Kingdom

ORCID For Submitting Author

0000-0003-0122-8499

Declaration of Conflict of Interest

Authors declare no conflict of interest.

Version Notes

Version identical to that submitted to ACS catalysis. No further updates will be made

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