1,721,149 research outputs found
A computational swiss army knife approach to unravelling the secrets of proton movement through SERCA
No full textMovement of arginine through OprD: The energetics of permeation and the role of lipopolysaccharide in directing arginine to the protein
No full textThe outer membrane channel OprD from Pseudomonas aeruginosa transports basic amino acids and clinically relevant carbapenem antibiotics. Understanding the molecular basis of substrate permeation across this channel will therefore lead to better therapeutic designs to treat infections. Using umbrella sampling simulations, we calculated the potential of mean force (PMF) for the arginine permeation pathway through OprD. The PMF reveals a deep free energy well of ~6 kT around the putative substrate binding site followed by a shallower well of ~4 kT close to the most constricted region of the pore. Despite becoming partially dehydrated during translocation, some water molecules are retained to shield the guanidinium side chain of arginine from the ladder of basic residues in the protein. Sugars of the lipopolysaccharide headgroups form contacts with arginine and could potentially play an important role in transferring substrate from the external medium to OprD. The PMF through bulk membrane shows a large energetic barrier of ~45 kT within the hydrophobic core of the membrane, suggesting that spontaneous translocation without OprD is highly unlikely. This significant energetic penalty is likely caused by the extensive distortion of the lower leaflet of the outer membrane as phospholipid headgroups sink inwards to interact with charged groups of arginine. Our results provide quantitative insights into solute permeation across bacterial outer membrane
Atomistic molecular-dynamics simulations enable prediction of the Arginine Permeation Pathway through OccD1/OprD from pseudomonas aeruginosa
No full textPseudomonas aeruginosa is a Gram-negative bacterium that does not contain large, nonspecific porins in its outer membrane. Consequently, the outer membrane is highly impermeable to polar solutes and serves as a barrier against the penetration of antimicrobial agents. This is one of the reasons why such bacteria are intrinsically resistant to antibiotics. Polar molecules that permeate across the outer membrane do so through substrate-specific channels proteins. To design antibiotics that target substrate-channel proteins, it is essential to first identify the permeation pathways of their natural substrates. In P. aeruginosa, the largest family of substrate-specific proteins is the OccD (previously reported under the name OprD) family. Here, we employ equilibrium and steered molecular-dynamics simulations to study OccD1/OprD, the archetypical member of the OccD family. We study the permeation of arginine, one of the natural substrates of OccD1, through the protein. The combination of simulation methods allows us to predict the pathway taken by the amino acid, which is enabled by conformational rearrangements of the extracellular loops of the protein. Furthermore, we show that arginine adopts a specific orientation to form the molecular interactions that facilitate its passage through part of the protein. We predict a three-stage permeation process for arginine
Molecular simulations of gram-negative bacterial membranes come of age
No full textGram-negative bacteria are protected by a multicompartmental molecular architecture known as the cell envelope that contains two membranes and a thin cell wall. As the cell envelope controls influx and efflux of molecular species, in recent years both experimental and computational studies of such architectures have seen a resurgence due to the implications for antibiotic development. In this article we review recent progress in molecular simulations of bacterial membranes. We show that enormous progress has been made in terms of the lipidic and protein compositions of bacterial systems. The simulations have moved away from the traditional setup of one protein surrounded by a large patch of the same lipid type toward a more bio-logically representative viewpoint. Simulations with multiple cell envelope components are also emerging. We review some of the key method developments that have facilitated recent progress, discuss some current limitations, and offer a perspective on future directions.</p
To infect or not to infect: molecular determinants of bacterial outer membrane vesicle internalization by host membranes
No full textOuter membrane vesicles (OMVs) are spherical liposomes that are secreted by almost all forms of Gram-negative bacteria. The nanospheres contribute to bacterial pathogenesis by trafficking molecular cargo from bacterial membranes to target cells at the host-pathogen interface. We have simulated the interaction of OMVs with host cell membranes to understand why OMV uptake depends on the length of constituent lipopolysaccharide macromolecules. Using coarse-grained molecular dynamics simulations, we show that lipopolysaccharide lipid length affects OMV shape at the host-pathogen interface: OMVs with long (smooth-type) lipopolysaccharide lipids retain their spherical shape when they interact with host cell membranes, whereas OMVs with shorter (rough-type) lipopolysaccharide lipids distort and spread over the host membrane surface. In addition, we show that OMVs preferentially coordinate domain-favoring ganglioside lipids within host membranes to enhance curvature and affect the local lipid composition. We predict that these differences in shape preservation affect OMV internalization on long timescales: spherical nanoparticles tend to be completely enveloped by host membranes, whereas low sphericity nanoparticles tend to remain on the surface of cells
Conformational dynamics and putative substrate extrusion pathways of the N-glycosylated outer membrane factor CmeC from Campylobacter jejuni
No full textInput files for and trajectory files from the simulation of of the outer membrane factor CmeC from Campylobacter jejuni in a representative outer membrane model. Preprint with details of the simulations and results can be found here: https://doi.org/10.1101/2022.08.31.50606
Binding From both sides: TolR and full-length OmpA bind and maintain the local structure of the E. coli cell wall
No full textWe present a molecular modeling and simulation study of the E. coli cell envelope, with a particular focus on the role of TolR, a native protein of the E. coli inner membrane in interactions with the cell wall. TolR has been proposed to bind to peptidoglycan, but the only structure of this protein thus far is in a conformation in which the putative peptidoglycan binding domain is not accessible. We show that a model of the extended conformation of the protein in which this domain is exposed, binds peptidoglycan largely through electrostatic interactions. Non-covalent interactions of TolR and OmpA with the cell wall, from the inner membrane and outer membrane sides respectively, maintain the position of the cell wall even in the absence of Braun’s lipoprotein. The charged residues that mediate the cell-wall interactions of TolR in our simulations, are conserved across a number of species of Gram-negative bacteria
Binding From both sides: TolR and full-length OmpA bind and maintain the local structure of the E. coli cell wall.
No full textWe present a molecular modelling and simulation study of the E. coli cell envelope, with a particular focus on the role of TolR, a native protein of the E. coli inner membrane in interactions with the cell wall. TolR has been proposed to bind to peptidoglycan, but the only structure of this protein thus far is in a conformation in which the putative peptidoglycan binding domain is not accessible. We show that a model of the extended conformation of the protein in which this domain is exposed, binds peptidoglycan largely through electrostatic interactions. Non-covalent interactions of TolR and OmpA with the cell wall, from the inner membrane and outer membrane sides respectively, maintain the position of the cell wall even in the absence of Braun’s lipoprotein. The charged residues that mediate the cell-wall interactions of TolR in our simulations, are conserved across a number of species of Gram-negative bacteria.</span
Atomistic and coarse grain simulations of the cell envelope of Gram-negative bacteria: what have we learned?
No full textBacterial 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
Molecular crowding alters the interactions of polymyxin lipopeptides within the periplasm of <i>E. coli</i>: insights from molecular dynamics
No full textThe cell envelope of Gram-negative bacteria is a crowded tripartite architecture that separates the cell interior from the external environment. Two membranes encapsulate the aqueous periplasm, which contains the cell wall. Little is known about the mechanisms via which antimicrobial peptides move through the periplasm from the outer membrane to their site of action, the inner membrane. We utilize all-atom molecular dynamics to study two antimicrobial peptides, polymyxins B1 and E, within models of the E. coli periplasm crowded to different extents. In a simple chemical environment, both PMB1 and PME bind irreversibly to the cell wall. The presence of specific macromolecules leads to competition with the polymyxins for cell wall interaction sites, resulting in polymyxin dissociation from the cell wall. Chemical complexity also impacts interactions between polymyxins and Braun’s lipoprotein; thus, the interaction modes of lipoprotein antibiotics within the periplasm are dependent upon the nature of the other species present.</p
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