Molecular Dynamics Simulations Reveal the Conformational Flexibility of Lipid II and Its Loose Association with the Defensin Plectasin in the Staphylococcus aureus Membrane

Abstract

Lipid II is critical for peptidoglycan synthesis, which is the main component of the bacterial cell wall. Lipid II is a relatively conserved and important part of the cell wall biosynthesis pathway and is targeted by antibiotics such as the lantibiotics, which achieve their function by disrupting the biosynthesis of the cell wall. Given the urgent need for development of novel antibiotics to counter the growing threat of bacterial infection resistance, it is imperative that a thorough molecular-level characterization of the molecules targeted by antibiotics be achieved. To this end, we present a molecular dynamics simulation study of the conformational dynamics of Lipid II within a detailed model of the Staphylococcus aureus cell membrane. We show that Lipid II is able to adopt a range of conformations, even within the packed lipidic environment of the membrane. Our simulations also reveal dimerization of Lipid II mediated by cations. In the presence of the defensin peptide plectasin, the conformational lability of Lipid II allows it to form loose complexes with the protein, via a number of different binding modes.

Flotillin mediated membrane fluidity controls peptidoglycan synthesis and MreB movement

“…It has recently been shown that modulation of either MreBCD or PBP1 levels is sufficient to alter the shape of B. subtilis cells 41 , underscoring the importance of both systems. In the absence of flotillins, the activity of the MreBCD component is strongly reduced – as evidenced by the reduction of MreB speed – and the overall rigidity of the membrane is increased which results in a less favourable environment for the peptidoglycan precursor LipidII, which prefers more liquid, disordered membrane phases 11,12,42 . To compensate, membrane fluidity and peptidoglycan synthesis activity is increased at division sites in flotillin mutants, which is sufficient to keep the overall cell shape intact, although cells are elongated.…”

“…In the absence of flotillins, the activity of the MreBCD component is strongly reduced – as evidenced by the reduction of MreB speed – and the overall rigidity of the membrane is increased. This results in a less favourable environment for the peptidoglycan precursor LipidII, which prefers more liquid, disordered membrane phases 14,15,47 . Our data indicate that the reduction in elongasome activity, which does not impact the growth rate itself, is compensated by increased peptidoglycan synthesis activity around division sites in flotillin mutants, which is sufficient to keep the overall cell shape intact, although cells are elongated.…”

“…Inward membrane curvature serves as a localization trigger for MreB and the elongasome, and enhanced local synthesis at bulges straightens out the membrane sufficient to convey a rod shape to spherical cells 8,9 . Interestingly, MreB localizes to and organizes regions of increased membrane fluidity (RIF) 10 , which in turn is linked to the presence of LipidII, which favours a more fluid membrane and promotes local membrane disorder 11,12 . Inhibition of LipidII synthesis by genetic or chemical means results in a dissolution of membrane structures observed with the dye FM 4-64 and release of MreB from the membrane 13-16 .…”

“…In Bacillus subtilis , the motion of MreB along the membrane is associated with elongasome activity 10,11 and the velocity of MreB patches is related to growth rate 12 , indicating that MreB motion can be used as a marker for elongasome activity. Interestingly, MreB localizes to and organizes regions of increased membrane fluidity (RIF) 13 , which in turn is linked to the presence of LipidII, which favours a more fluid membrane and promotes local membrane disorder 14,15 . Inhibition of LipidII synthesis by genetic or chemical means results in a dissolution of membrane structures observed with the dye FM 4-64 and release of MreB from the membrane 10,11,16,17 .…”

Structure-based modelling and dynamics of MurM, aStreptococcus pneumoniaepenicillin resistance determinant that functions at the cytoplasmic membrane interface

“…However, in a related study we were able to solve the X-ray structure of the isofunctional homologue of MurM from S. aureus (FemX), which we have used here as a template for homology modelling of MurM. Using this MurM homology model we have successfully identified the Lipid II binding site, and used molecular dynamics (MD) simulations to investigate interactions between MurM and both membrane phospholipids and its Lipid II substrate (Witzke et al, 2016). We subsequently, studied the effects of these membrane embedded phospholipids, on the enzymatic activity of MurM in vitro, corroborating our in silico analysis.…”