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Predicting the functions and specificity of triterpenoid synthases: a mechanism-based multi-intermediate docking approach

Tian B, Wallrapp FH, Holiday GL, Chow J, Babbitt PC, Poulter CD, Jacobson MP (2014) PLoS Comput Biol, 10, e1003874. PMCID: PMC4191879

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.

Abstract

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.

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Figure 1: Example structures of TPSs: a) limonene synthase (PDB: 2ONH) [8]; b) squalene-hopene cyclase (PDB: 1SQC) [9], [10].

Figure 2: Example reactions of TPSs: a) limonene synthase; b) squalene-hopene cyclase.

Figure 3: Reaction channels for triterpenoid synthase and triterpenoid synthase-like enzymes [54], [71].

Figure 4: Sequence similarity network of triterpenoid synthase and triterpenoid synthase-like proteins colored by reaction channels.

Figure 5: Illustration of the key dihedral angle C16-C17-C18-H18 that determines the conversion of I1 to I2: a) A-I1; b) B-I1.

Figure 6: Carbocationic intermediate docking scores (MM/GBSA) along the reaction coordinates of a) 1SQC and b) 1W6K.

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).

Figure 8: Intermediates and products of Channel C.

Figure 9: Docking score (MM/GBSA) of 9 carbocationic intermediates for 22 triterpenoid synthase homology models that follow channel C.

Figure 10: Key intermediates involved in the reaction channel leading to the hopanyl cation (A-I4), and products derived from these.

Figure 11:Example of constraints and restraints used during docking (residue numbering is for 1W6K).

Figure 12:A hypothetical example output of the carbocation docking.

Reprinted with permission from Biochemistry.
© 2011 American Chemical Society.