Predicting Productive Binding Modes for Substrates and Carbocation Intermediates in Terpene Synthases-Bornyl...

Area of Science:

• Enzymology
• Biochemistry
• Computational Chemistry

Background:

• Terpene synthases (TPS) are crucial enzymes converting isoprenoid diphosphates into complex terpene natural products.
• Their active sites, typically nonpolar, facilitate carbocation chemistry, but predicting substrate binding and reaction pathways is challenging.
• Accurate prediction of binding modes is essential for understanding TPS mechanisms and for enzyme engineering.

Purpose of the Study:

• To develop and validate a computational method, TerDockin, for predicting substrate and carbocation binding modes within TPS active sites.
• To provide a foundational tool for understanding the intricate reaction mechanisms of terpene synthases.
• To facilitate the rational engineering of terpene synthases for novel applications.

Main Methods:

• TerDockin employs a series of protocols to predict the orientation of substrate and carbocation carbon skeletons relative to the diphosphate group.
• The method was applied to bornyl diphosphate synthase as a case study.
• Predicted binding modes were compared against existing experimental data, including isotope labeling and stereoselectivity studies.

Main Results:

• TerDockin successfully predicted binding modes for bornyl diphosphate synthase that align with all available experimental evidence.
• The method's predictions were consistent with stereoselectivity and isotope labeling results.
• The computational predictions mirrored key findings from more intensive QM/MM molecular dynamics simulations.

Conclusions:

• TerDockin offers a valuable and efficient computational approach for predicting substrate and intermediate binding in terpene synthases.
• This method serves as an effective starting point for more complex computational investigations.
• The TerDockin approach lays the groundwork for the rational design and engineering of terpene synthase enzymes.