Enhancing functional proteins through multimodal inverse folding with ABACUS-T.

Area of Science:

• Protein engineering
• Computational biology
• Biotechnology

Background:

• Structure-based protein redesign aims to enhance stability but often reduces function.
• Existing inverse folding models struggle to balance stability and activity.
• Need for advanced models that incorporate diverse biological data for accurate protein engineering.

Purpose of the Study:

• Introduce ABACUS-T, a multimodal inverse folding model.
• Improve precision in protein sequence redesign while minimizing functional compromise.
• Demonstrate enhanced stability and retained/improved function in redesigned proteins.

Main Methods:

• Developed ABACUS-T, integrating atomic sidechains, ligand interactions, protein language models, multiple backbone conformations, and multiple sequence alignment (MSA) data.
• Applied ABACUS-T to redesign proteins including an allose binding protein, endo-1,4-β-xylanase, TEM β-lactamase, and OXA β-lactamase.
• Evaluated redesigned proteins for binding affinity, conformational changes, enzyme activity, substrate selectivity, and thermostability.

Main Results:

• Redesigned allose binding protein showed 17-fold higher affinity, retaining conformational change.
• Endo-1,4-β-xylanase and TEM β-lactamase maintained or surpassed wild-type activity.
• OXA β-lactamase exhibited altered substrate selectivity.
• All redesigned proteins demonstrated significantly increased thermostability (∆T_m ≥ 10°C).
• Enhancements were achieved with few sequences, each containing numerous simultaneous mutations.

Conclusions:

• ABACUS-T effectively enhances protein structural stability and functional activity.
• The model's multimodal approach overcomes limitations of existing inverse folding methods.
• ABACUS-T is a promising tool for reengineering functional proteins in biotechnology.