Computational Hydropathy Analysis of BamA Bacterial Outer Membrane Protein and Its Mutants

Outer Membrane Proteins (OMPs) are essential to the physiology of Gram-negative bacteria and are attractive targets for antimicrobial therapies. Their folding and insertion into the outer membrane are orchestrated by the β-barrel assembly machinery (BAM) complex, with BamA, its central and evolutionarily conserved component, playing a crucial role. BamA comprises five periplasmic polypeptide-transport-associated (POTRA) domains and a C-terminal transmembrane β-barrel comprising 16 antiparallel β-strands spanning ∼385 amino acids. This study focuses on the β-barrel domain, leveraging all-atom molecular dynamics (MD) simulations and the Protocol for Assigning a Residue's Character on the Hydropathy (PARCH) scale to investigate the wild-type structure and six BamA mutants previously shown to compromise bacterial viability. These mutations, including deletions and polarity-altering substitutions, target residues and loops critical for structural integrity. Our analysis reveals that local hydropathy shifts and disruption of stabilizing interactions, such as salt bridges, alter the microenvironments near mutation sites, destabilizing the β-barrel. These results provide atomistic insight into how specific mutations impair BamA function and demonstrate the utility of hydropathy-informed MD approaches in understanding membrane protein folding and stability.