Lateral Gate Opening of BAM Complex Studied by Free Energy Calculations and the String Method

Abstract

In Gram-negative bacteria, important functions such as the import of nutrients and export of virulence factors are performed by β-barrel outer membrane proteins (OMPs). These proteins are inserted and folded with the aid of the β-barrel assembly machinery (BAM). Structures of the BAM complex display two distinct conformations: a lateral-closed state and a lateral-open state. In the lateral-open state, the first and last β-strand of the BamA β-barrel separates, producing a “lateral gate” and exposing the β-barrel lumen to the outer membrane. The motion is accompanied by a significant rotation of the five polypeptide transport associated (POTRA) domains and the four accessory proteins around the barrel. Here we studied the transition between the two conformations using molecular dynamics simulations. We examined the relationship between the lateral gate opening and the rotational angle of the POTRA domains and accessory proteins using free energy calculations. We also found the minimum-energy transition pathway between the two conformations using the string method. Important contact points between the POTRA domains and the accessory proteins were found, showing how their rotation translates into the regulation of lateral gate opening.