Sequence Coevolution Reveals an Intermediate Step in BamA Assisted Insertion of Outer Membrane Protein FadL

Abstract

A unique characteristic of outer membrane proteins (OMPs) is that they almost exclusively exist as β-barrels. In E. coli, the β-Barrel Assembly Machine (BAM) complex catalyzes insertion of OMPs from the periplasm into the outer membrane. Experimental evidence has shown that the outer membrane embedded β-barrel portion of the BAM complex BamA is essential for insertion function (1,2). However, the precise mechanism of insertion is still unknown. To better understand the interactions between BamA and its client OMPs, we explore a computational approach analyzing sequence coevolution in joint-Multiple Sequence Alignments (joint-MSAs) to determine inter-protein residue contacts between BamA and client OMPs. Our computational results using RaptroX revealed an anti-parallel contact between strand five of BamA and strand 14 of FadL. Experimentally characterizing this contact revealed that mutation does not affect the in vitro BAM-unassisted insertion of FadL into large unilamellar vesicles. However, single mutations on FadL that are hypothesized to contact the interior region of strand five of BamA affect the in vitro BAM-assisted insertion of FadL.