Identification of specific sphingolipid-bama interactions using coarse-grained molecular dynamics simulation of the C. crescentus outer membrane.

Abstract

Sphingolipids (SLs) have been primarily studied in eukaryotic cell membranes, where they modulate fundamental cellular processes ranging from apoptosis to cytoskeletal reorganization. It has recently been discovered that many bacteria also synthesize sphingolipids, but their role in bacterial membranes is poorly understood. One example of a gram-negative bacteria with sphingolipids in its outer membrane is C. crescentus. Previous studies showed that the absence of SLs in the outer membrane increases resistance to cationic polymyxin antibiotics, permeability, and susceptibility to antimicrobials like bacitracin while inducing an unfolded-protein stress response. The machinery responsible for the folding of many outer membrane proteins (OMPs) is the β-barrel assembly machinery (BAM complex). In the present study, we used coarse-grained molecular dynamics (CG-MD) simulations to understand the possible interactions between SLs and the BAM complex to determine if SLs regulate BamA activity by direct interaction. The C. crescentus BamA protein was homology modeled in two conformations: open- and closed-gate. Martini models of the rough lipopolysaccharide (RLPS), smooth lipopolysaccharide (SLPS), and anionic SLs of C. crescentus were built. We carried out CG-MD simulations of BamA embedded in a model of a C. crescentus bacterial membrane in the closed and open conformations. Afterward, the density distribution of SLs with respect to BamA was analyzed, using the CG-MD analysis toolkit Nougat from Brannigan Lab.