For protein families where sequence identity alone does not provide clear delineations between distinct functions, such as in the case of the terpenoid synthases (TS, an important enzyme class in biosynthesis of natural products), computational strategies are needed for accurate prediction of product specificity. This study from the Computation Core and IS Bridging Project acts as "proof of concept" for the strategy of docking multiple carbocation intermediates to experimental or modeled TS structures in order to predict reaction pathways, and thus, end-point products. A clear benefit to this approach is the reduced computational cost relative to established techniques for modeling enzyme reactions, such as QM/MM, thus allowing medium-throughput application.
Terpenoid synthases construct the carbon skeletons of tens of thousands of natural products. To predict functions and specificity of triterpenoid synthases, a mechanism-based, multi-intermediate docking approach is proposed. In addition to enzyme function prediction, other potential applications of the current approach, such as enzyme mechanistic studies and enzyme redesign by mutagenesis, are discussed.
Figure 7: a) Superimposed view of the product lanosterol in the 1W6K crystal structure (grey) and the docking pose of C-I6 (the product precursor carbocation, c.f. Figure 6b; in orange); b) The docking poses of the second representative intermediates: A-I2 (blue), B-I2 (red) and C-I2 (lime), as well as lanosterol in the 1W6K crystal structure (grey, c.f. Figure 6b).
Reprinted with permission from Biochemistry.
© 2011 American Chemical Society.