Electroporation Sensitivity of Oxidized Phospholipid Bilayers

Bacterial Membranes Are More Perturbed by the Asymmetric Versus Symmetric Loading of Amphiphilic Molecules

Characterizing the biophysical properties of bacterial membranes is critical for understanding the protective nature of the microbial envelope, interaction of biological membranes with exogenous materials, and designing new antibacterial agents. Presented here are molecular dynamics simulations for two cationic quaternary ammonium compounds, and the anionic and nonionic form of a fatty acid molecule interacting with a Staphylococcus aureus bacterial inner membrane. The effect of the tested materials on the properties of the model membranes are evaluated with respect to various structural properties such as the lateral pressure profile, lipid tail order parameter, and the bilayer’s electrostatic potential. Conducting asymmetric loading of molecules in only one leaflet, it was observed that anionic and cationic amphiphiles have a large impact on the Staphylococcus aureus membrane’s electrostatic potential and lateral pressure profile as compared to a symmetric distribution. Nonintuitively, we find that the cationic and anionic molecules induce a similar change in the electrostatic potential, which points to the complexity of membrane interfaces, and how asymmetry can induce biophysical consequences. Finally, we link changes in membrane structure to the rate of electroporation for the membranes, and again find a crucial impact of introducing asymmetry to the system. Understanding these physical mechanisms provides critical insights and viable pathways for the rational design of membrane-active molecules, where controlling the localization is key.

Atomistic and Coarse Grain Simulations of the Cell Envelope of Gram-Negative Bacteria: What Have We Learned?

Bacterial membranes, and those of Gram-negative bacteria in particular, are some of the most biochemically diverse membranes known. They incorporate a wide range of lipid types and proteins of varying sizes, architectures, and functions. While simpler biological membranes have been the focus of myriad simulation studies over the years that have yielded invaluable details to complement, and often to direct, ongoing experimental studies, simulations of complex bacterial membranes have been slower to emerge. However, the past few years have seen tremendous activity in this area, leading to advances such as the development of atomistic and coarse-grain models of the lipopolysaccharide (LPS) component of the outer membrane that are compatible with widely used simulation codes. In this Account, we review our contributions to the field of molecular simulations of the bacterial cell envelope, including the development of models of both membranes and the cell wall of Gram-negative bacteria, with a predominant focus on E. coli. At the atomistic level, simulations of chemically accurate models of both membranes have revealed the tightly cross-linked nature of the LPS headgroups and have shown that penetration of solutes through these regions is not as straightforward as the route through phospholipids. The energetic differences between the two routes have been calculated. Simulations of native outer membrane proteins in LPS-containing membranes have shown that the conformational dynamics of the proteins is not only slower in LPS but also different compared to in simpler models of phospholipid bilayers. These chemically more complex and consequently biologically more relevant models are leading to details of conformational dynamics that were previously inaccessible from simulations. Coarse-grain models have enabled simulations of multiprotein systems on time scales of microseconds, leading to insights not only into the rates of protein and lipid diffusion but also into the trends in their respective directions of flow. We find that the motions of LPS molecules are highly correlated with each other but also with outer membrane proteins embedded within the membrane. We have shown that the two leaflets of the outer membrane exhibit communication, whereby regions of low disorder in one leaflet correspond to regions of high disorder in the other. The cell wall remains a comparatively neglected component, although models of the E. coli peptidoglycan are now emerging, particularly at the atomistic level. Our simulations of Braun's lipoprotein have shown that bending and tilting of this protein afford a degree of variability in the gap between the cell wall and the OM. The noncovalent interactions with the cell wall of proteins such as OmpA can further influence the width of this gap by extension or contraction of their linker domains. Overall we have shown that the dynamics of proteins, lipids, and other molecular species within the outer membrane cannot be approximated using simpler phospholipid bilayers, if one is addressing questions regarding the in vivo behavior of Gram-negative bacteria. These membranes have their own unique chemical characteristics that cannot be decoupled from their biological functions.