Structural bioinformatics studies of bacterial outer membrane beta-barrel transporters and their AlphaFold2 predicted water-soluble QTY variants

Abstract

Beta-barrel outer membrane proteins (OMP) are integral components of Gram-negative bacteria, eukaryotic mitochondria, and chloroplasts. They play essential roles in various cellular processes including nutrient transport, membrane stability, host-pathogen interactions, antibiotic resistance and more. The advent of AlphaFold2 for accurate protein structure predictions transformed structural bioinformatic studies. We previously used a QTY code to convert hydrophobic alpha-helices to hydrophilic alpha-helices in over 50 membrane proteins with all alpha-helices. The QTY code systematically replaces hydrophobic leucine (L), isoleucine (I), valine (V), and phenylalanine (F) with hydrophilic glutamine (Q), threonine (T), and tyrosine (Y). We here present a structural bioinformatic analysis of five outer membrane beta-barrel proteins with known molecular structures, including a) BamA, b) Omp85 (also called Sam50), c) FecA, d) Tsx, and e) OmpC. We superposed the structures of five native beta-barrel outer membrane proteins and their AlphaFold2-predicted corresponding QTY variant structures. The superposed structures of OMPs and their QTY variants exhibit remarkable structural similarity, as evidenced by residue mean square distance (RMSD) values between 0.206Å to 0.414Å despite the replacement of at least 22% (Transmembrane variation) of the amino acids in the transmembrane regions. We also show that native outer membrane proteins and QTY variants have different hydrophobicity patches. Our study provides important insights into the differences between hydrophobic and hydrophilic beta-barrels and validates the QTY code for studying beta-barrel membrane proteins and perhaps other hydrophobic aggregated proteins. Our findings demonstrate that the QTY code can be used as a simple tool for designing hydrophobic proteins in various biological contexts.