Transformation of transmembrane proteins into soluble forms using protein language models

Abstract

Redesigning insoluble proteins into soluble forms is crucial for advancing studies on protein structure, function, and interactions. Redesigning proteins in vitro without the aid of computational tools would necessitate substantial time and resources. This project aims to redesign the transmembrane domain of Outer Membrane Protein A (OmpA) from Escherichia coli into a soluble form using computational tools such as ProteinMPNN, Protein-Sol and AlphaFold 3. Hydrophobic surface residues and its were identified on OmpA and redesigned using ProteinMPNN. The sequences generated were then ran through Protein-Sol and AlphaFold to predict its solubility and structure. The results indicate a theoretical increase in solubility of up to 35% and demonstrate that the redesigned protein can achieve a β-barrel structure, characteristic of OmpA, with high confidence, as predicted by computational software. However, experimental validation is required to confirm these in silico findings.