A complex cell envelope, composed of a mixture of lipid types including complex lipopolysaccharides, protects bacteria from the external environment. Clearly, the proteins embedded within the various components of the cell envelope have an intricate relationship with their local environment. Therefore, to obtain meaningful results, molecular simulations need to mimic as far as possible this chemically heterogeneous system. However, setting up such systems for computational studies is far from trivial, and consequently the vast majority of simulations of outer membrane proteins still rely on oversimplified phospholipid membrane models. This work presents an update of CHARMM-GUI Martini Maker for coarse-grained modeling and simulation of complex bacterial membranes with lipopolysaccharides. The qualities of the outer membrane systems generated by Martini Maker are validated by simulating them in bilayer, vesicle, nanodisc, and micelle environments (with and without outer membrane proteins) using the Martini force field. We expect this new feature in Martini Maker to be a useful tool for modeling large, complicated bacterial outer membrane systems in a user-friendly manner.

Carbon fullerenes are emerging as effective devices for different biomedical applications, including the transportation of nanosized drugs and the extraction of harmful oxidants and radicals. It has been proposed that fullerenes could be used as novel antibacterial agents, given the realization that the nanoparticles can kill pathogenic Gram-negative bacteria. To explore this at the molecular level, we simulated C 60 fullerenes with bacterial membranes using the coarse-grain (CG) molecular dynamics (MD) Martini force field. We find that pristine C 60 has a limited tendency to penetrate (incomplete core) Re mutant lipopolysaccharide (LPS) leaflets, but the translocation of C 60 fullerenes into (complete core) Ra mutant LPS leaflets is not thermodynamically favored. Moreover, we show that the permeability of Re LPS bilayers depends sensitively on system temperature, the charge of ambient ions, and the prevalence of POPE defect domains. The different permeabilities are rationalized in terms of transitory head group pore formation, which underpins the translocation of C 60 into the lipid core. The Re LPS lipids readily form transient micropores when they are linked with monovalent cations, or when they are heated to a high temperature. POPE lipids are shown to be particularly adept at forming these transient surface cavities, and their inclusion into Re LPS membranes facilitates the formation of particularly large pores that are tunneled by C 60 aggregates of significant size (~ 5 nm wide). After inserting into the lipid core, the aggregates dissociate, and the disbanded nanoparticles migrate to the interface between separate POPE and LPS domains, where they weaken the boundaries between the coexisting lipid fractions and thereby promoting lipid mixing.

In the following molecular simulations are used to reveal unexpected behavior within bacterial membranes. We show that lipopolysaccharide molecules found in these membranes form viscous amorphous solids when they are interlinked with monovalent and divalent cations. The bilayers exhibit both liquid and glassy characteristics, due to the co-existence of both liquid and crystalline domains in the bilayer. Polymyxin B1 (PMB1), a potent antimicrobial peptide, is shown to increase order within the LPS bilayers by inducing the formation of crystalline patches.Crucially we are able to decompose the energetics of insertion into their enthalpic and entropic components. The present coarse-grain (CG) molecular dynamics (MD) study provides unprecedented insights into the antibacterial action of antimicrobial peptides, thus paving the way for development of novel therapeutic agents to treat multiple drug resistant Gram-negative bacteria.

Plasma membranes (PMs) contain hundreds of different lipid species that contribute differently to overall bilayer properties. By modulation of these properties, membrane protein function can be affected. Furthermore, inhomogeneous lipid mixing and domains of lipid enrichment/depletion can sort proteins and provide optimal local environments. Recent coarse-grained (CG) Martini molecular dynamics efforts have provided glimpses into lipid organization of different PMs: an “Average” and a “Brain” PM. Their high complexity and large size require long simulations (∼80 μs) for proper sampling. Thus, these simulations are computationally taxing. This level of complexity is beyond the possibilities of all-atom simulations, raising the question—what complexity is needed for “realistic” bilayer properties? We constructed CG Martini PM models of varying complexity (63 down to 8 different lipids). Lipid tail saturations and headgroup combinations were kept as consistent as possible for the “tissues’” (Average/Brain) at three levels of compositional complexity. For each system, we analyzed membrane properties to evaluate which features can be retained at lower complexity and validate eight-component bilayers that can act as reliable mimetics for Average or Brain PMs. Systems of reduced complexity deliver a more robust and malleable tool for computational membrane studies and allow for equivalent all-atom simulations and experiments.

The cell envelope of Gram-negative bacteria is composed of two membranes separated by a soluble region. Here, we report microsecond time scale coarse-grained molecular dynamics simulations of models of the Escherichia coli cell envelope that incorporate both membranes and various native membrane proteins. Our results predict that both the inner and outer membranes curve in a manner dependent on the size of the embedded proteins. The tightly cross-linked lipopolysaccharide molecules (LPS) of the outer membrane cause a strong coupling between the movement of proteins and lipids. While the flow of phospholipids is more random, their diffusion is nevertheless influenced by nearby proteins. Our results reveal protein-induced lipid sorting, whereby cardiolipin is significantly enriched within the vicinity of the water channel AqpZ and the multidrug efflux pump AcrBZ. In summary, our results provide unprecedented details of the intricate relationship between both membranes of E. coli and the proteins embedded within them.

Highlights d Structure of an RND transporter with an allosteric modulator in a membrane environment d Cooperation of lipid and small protein in allosterically modulating transport activity

Bacteria are protected by complex molecular architectures known as the cell envelope. The cell envelope is composed of regions with distinct chemical compositions and physical properties; namely membranes and a cell wall. To develop novel antibiotics to combat pathogenic bacteria, molecular level knowledge of the structure, dynamics and interplay between the chemical components of the cell envelope that surrounds bacterial cells is imperative. In addition, conserved molecular patterns associated with the bacterial envelope are recognized by receptors as part of the mammalian defensive response to infection, and an improved understanding of bacteria-host interactions would facilitate the search for novel immunotherapeutics. This Perspective introduces an emerging area of computational biology; multiscale molecular dynamics simulations of chemically complex models of bacterial lipids and membranes. We discuss progress to date, and identify areas for future development that will enable the study of aspects of the membrane components that are as yet unexplored by computational methods.Bacteria are divided into two categories, Gramnegative and Gram positive, both of which include pathogens that are harmful to humans. Gram-negative bacteria have cell envelopes composed of two membranes, separated by a region known as the periplasm. The outer membrane (OM) is asymmetric in nature; the two leaflets differ in their compositions. The inner membrane contains a symmetric arrangement of phospholipids. In contrast, Gram-positive bacteria contain only one membrane, which is similar in composition to the inner membrane of Gram-negative bacteria. Both types of bacteria have a cell wall, which is composed of the biopolymer peptidoglycan. The combination of membrane plus cell wall gives rise to the characteristic semi-permeable properties of the cell envelope. To be effective, antibiotics must either cause bacterial cell death or inhibit cell growth. In both cases they must interact with the cell envelope, as they must either (i) disrupt the cell envelope, such that the cell contents leak out, or (ii) cross the cell envelope to gain access to the interior of the cell, where they may interfere with essential cellular process such as DNA replication and metabolism. The emergence of antimicrobial resistance is recognized as a major threat to human health. 1 It is thus imperative to have a detailed knowledge of the structure-dynamics-function relationships of the cell wall and membranes, in order to develop new antibiotics under reduced pressure of resistance. Furthermore, molecules derived from the cell membrane and wall are utilized by the mammalian innate immune system to mount a defensive response. 2 Over-amplification of such pathways can lead to sepsis, which remains the primary cause of death due to infection, highlighting the need for an improved understanding of the molecular mechanisms of immunostimulation. Due to the numerous molecular components involved, studying biological membranes in an in vivo condition rema...

Cinnamycin is a lantibiotic peptide, which selectively binds to and permeabilizes membranes containing phosphatidylethanolamine (PE) lipids. As PE is a major component of many bacterial cell membranes, cinnamycin has considerable potential for destroying these. In this study, molecular dynamics simulations are used to elucidate the structure of a lipid–cinnamycin complex and the origin of selective lipid binding. The simulations reveal that cinnamycin selectively binds to PE by forming an extensive hydrogen-bonding network involving all three hydrogen atoms of the primary ammonium group of the PE head group. The substitution of a single hydrogen atom with a methyl group on the ammonium nitrogen destabilizes this hydrogen-bonding network. In addition to binding the primary ammonium group, cinnamycin also interacts with the phosphate group of the lipid through a previously uncharacterized phosphate-binding site formed by the backbone Phe10-Abu11-Phe12-Val13 moieties (Abu = 1-α-aminobutyric acid). In addition, hydroxylation of Asp15 at Cβ plays a role in selective binding of PE due to its tight interaction with the charged amine of the lipid head group. The simulations reveal that the position and orientation of the peptide in the membrane depend on the type of lipid to which it binds, suggesting a reason for why cinnamycin selectively permeabilizes PE-containing membranes.