Engineering IspH for Enhanced Terpenoid Yield: Computational and Molecular Dynamics Studies
Bibliographic record
Abstract
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 Å, Rg 21.56-22.06 Å, 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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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.003 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".