Comparing PET-active lipase surfaces with the SASA calculator
Researchers used ProteinIQ's SASA calculator to compare active-site accessibility in lipases investigated for PET hydrolysis.
- Authors
- Rubén Muñoz-Tafalla, José M. González-Romero, Paula Vidal, Laura Fernandez-Lopez, et al.
- Published in
- Microbial Biotechnology · 2026-08 · Barcelona Supercomputing Center and ICP-CSIC
- ProteinIQ in this study
- ProteinIQ's SASA calculator supplied surface-accessibility measurements for predicted lipase structures compared in the study's supporting information.
- Tools used
- Sasa Calculator
Two enzymes can carry similar catalytic machinery while presenting very different surfaces to a substrate. Understanding that difference helps researchers connect a protein's structure to what it does in an experiment.
The challenge: look beyond sequence similarity
A team at the Barcelona Supercomputing Center and ICP-CSIC searched genomes from 18,082 extremophilic microorganisms for enzymes that could hydrolyse PET. Their study combined genome mining, structural modelling, simulations, and laboratory tests to investigate true lipases as candidates beyond familiar PETases.
Comparing sequences alone could not explain how a substrate would reach the catalytic site. The team also needed to describe the geometry and accessibility of the predicted structures, including whether an active site lay in an exposed groove or a deeper pocket.
The solution: measure surface accessibility
The supporting information links directly to ProteinIQ's SASA calculator for solvent-accessible surface area measurements. Figure S5 compares LipBv's open groove with LipSh1's deeper cavity, combining these measurements with pocket volume and hydrophobicity calculated using Fpocket.
SASA describes the surface a solvent-sized probe can reach. It adds a numerical measure of exposure to visual inspection of a structure, helping researchers examine differences that can be difficult to judge from a single molecular view.
ProteinIQ makes that calculation available in the browser. A researcher can upload a PDB structure, choose a probe radius, and inspect results for the whole structure, individual chains, or individual residues. Residue-level results are useful when the question concerns a particular region rather than the protein's total exposed area.
For a similar analysis, the practical benefit is access to a ready-to-use calculation without installing a local SASA package or writing a script to process coordinates. The researcher still needs to choose appropriate structures and compare them under consistent settings. SASA measures exposure in the supplied coordinates; it does not by itself predict substrate binding or catalytic activity.
The outcome: structural context for experimental results
Of six lipases experimentally characterised, LipBv and LipSh1 showed PET-hydrolysing activity. Their contrasting active-site architectures helped the team interpret the results, with ProteinIQ contributing the surface-accessibility measurements to that comparison.
The enzymes broaden the set of candidates for further investigation, but the paper does not claim they outperform the best engineered PETases. Experiments with bottle-grade PET or commercial films remain a next step toward assessing industrial relevance. Read the published study.
For other enzyme-discovery projects, the same calculation can help turn a visual observation about a protein surface into a comparison that can be inspected alongside experimental data.
