Contributors: Chester
Autodock Vina binding affinities
[Attachments: GH10-cellobiose.pdbqt, GH1-cellobiose.pdbqt]
Top-ranked cellobiose docking scores:
| Domain | ΔG (kcal/mol) |
|---|---|
| GH10/Cex | −6.6 |
| GH1 | −6.4 |
The 0.2 kcal/mol difference falls within Vina’s known error margin (±0.5–1.0 kcal/mol) — not interpretable as a meaningful difference between domains.
Calibration check — Vina overestimation confirmed
The experimentally measured ΔG for xylobiose in Cex (its preferred natural substrate) is −3.29 kcal/mol (K_i = 4800 µM, Notenboom et al. 2000). Vina predicts −6.6 kcal/mol for cellobiose in the same enzyme — a ~3.3 kcal/mol overestimate.
This demonstrates Vina substantially overestimates binding strength in this system. Absolute Vina scores must not be used as substitutes for experimental ΔG measurements; they are valid only for within-receptor, within-ligand pose ranking and convergence assessment.
MSA planning
Next step: characterise conserved sequences across other GH10-domain enzymes (using Cex as representative of CxnA’s GH10 domain) ahead of mutagenesis. This enables a before/after comparison of key sites post-epPCR, and produces the .aln file needed downstream for ConSurf.
Approach: BlastP to find best hits; top 15 selected (following lecture convention). Clustal W alignment with Cex as reference, output as .aln file — using the clustal_w_alignment script.