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

Abstract

Structure-based sequence redesign or inverse folding can significantly enhance structural stability but often compromises functional activity when performed using existing models. Here, we introduce ABACUS-T, a multimodal inverse folding model that improves precision and minimizes functional loss. ABACUS-T unifies several important features into one framework: detailed atomic sidechains and ligand interactions, a pre-trained protein language model, multiple backbone conformational states, and evolutionary information from multiple sequence alignment (MSA). Redesigned proteins show notable improvements: an allose binding protein achieves 17-fold higher affinity while retaining conformational change; redesigned endo-1,4-β-xylanase and TEM β-lactamase maintain or surpass wild-type activity; and OXA β-lactamase gains altered substrate selectivity. All achieve substantially increase thermostability (∆T_m ≥ 10 °C). In each test case, these enhancements are achieved by testing only a few sequences, each containing dozens of simultaneously mutated residues. ABACUS-T thus offers a promising tool for reengineering functional proteins in biotechnological applications.