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bioRxiv · 10.1101/2025.04.07.643449

Engineering IspH for Enhanced Terpenoid Yield: Computational and Molecular Dynamics Studies

Runthala, A.·Machrela, S.·Varadharajan, V.·Selvan, S. T.·Sharma, M.·Kaur, N.·Phulara, S. C.·Ahmad, S. N.·Ghneim, H. K.
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Abstract

Terpenoids play a vital role in pharmaceuticals, biofuels, and various industries, and they are produced through the methylerythritol phosphate (MEP) pathway, with IspH catalyzing the final step. This study explores IspH homologs in Bacillus and other bacteria to aid in enzyme engineering. Sequence analysis showed a conservation range of 46-79%. Phylogenetic analysis (log-likelihood -71,581.08, bootstrap 80-100) validated the evolutionary relationships. Structural modeling revealed conserved functional motifs. Molecular docking indicated HMBPP binding affinities between -4.9 and -6.4 kcal/mol, while molecular dynamics simulations confirmed the stability of the complex (RMSD 2.02-3.45 [A], Rg 21.56-22.06 [A], with a decrease in SASA upon binding). Significant hydrogen bonds were noted with His131, Asn227, and Ser271. This thorough analysis of IspH conservation, structure, and stability, along with co-evolving residue networks, underscores the potential of Bacillus IspH variants for improved terpenoid production and lays the groundwork for targeted enzyme engineering.

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Runthala, A., Machrela, S., Varadharajan, V., Selvan, S. T., Sharma, M., Kaur, N., Phulara, S. C., Ahmad, S. N., Ghneim, H. K.. 2025-04-09. Engineering IspH for Enhanced Terpenoid Yield: Computational and Molecular Dynamics Studies. https://doi.org/10.1101/2025.04.07.643449

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