Mechanistic docking in terpene synthases using EnzyDock

Renana Schwartz, Shani Zev, Dan T. Major

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

Abstract

Terpene Synthases (TPS) catalyze the formation of multicyclic, complex terpenes and terpenoids from linear substrates. Molecular docking is an important research tool that can further our understanding of TPS multistep mechanisms and guide enzyme design. Standard docking programs are not well suited to tackle the unique challenges of TPS, like the many chemical steps which form multiple stereo-centers, the weak dispersion interactions between the isoprenoid chain and the hydrophobic region of the active site, description of carbocation intermediates, and finding mechanistically meaningful sets of docked poses. To address these and other unique challenges, we developed the multistate, multiscale docking program EnzyDock and used it to study many TPS and other enzymes. In this review we discuss the unique challenges of TPS, the special features of EnzyDock developed to address these challenges and demonstrate its successful use in ongoing research on the bacterial TPS CotB2.

Original languageEnglish
Title of host publicationMethods in Enzymology
PublisherAcademic Press Inc.
Chapter10
Pages265-292
Volume699
DOIs
StatePublished - 2024

Publication series

NameMethods in Enzymology
ISSN (Print)0076-6879
ISSN (Electronic)1557-7988

Bibliographical note

Publisher Copyright:
© 2024

Keywords

  • Docking
  • EnzyDock
  • QM/MM
  • Terpene Synthases

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