466 research outputs found
The effects of model membrane complexity for the <i>E.coli</i> cell envelope
No full textTo overcome resistance to antibiotics in bacteria, such as Escherichia coli, further understanding of the nature of the cell envelope is required. Molecular dynamics has provided a powerful tool into investigations of the dynamics and structure of biological systems of varying complexity. In this thesis, coarse-grained simulations were used to probe the behaviour of the outer membrane and the proteins within, relative to typical phospholipid membranes. In the first chapter, nanopores of varying sizes, shapes and chemistry were studied in the context of symmetric and asymmetric bacterial membranes. It was found that communication between leaflets played a significant role in lipid sorting of larger lipids. Following this, a broad study of the protein-lipid interactions between a range of different proteins and outer membrane models was carried out. The interactions between a protein and any given outer membrane model were found to have a unique fingerprint. The stability of the lipids in outer and inner membranes were then investigated by measuring the free energy of lipid extraction. The results concluded that there was little similarity between the extraction of different lipopolysaccharide lipids, as well as repeats of the same lipid. A further study on the effects of a membrane protein on the stability of local and bulk lipids was carried out for the inner membrane. In the final chapter, the use of sparse lipopolysaccharide densities and Hamiltonian Replica Exchange Molecular Dynamics were investigated to enhance lipopolysaccharide mixing
Communication between the leaflets of asymmetric membranes revealed from coarse-grain molecular dynamics simulations
No full textWe use coarse-grain molecular simulations to investigate the structural and dynamics differences between an asymmetric and a symmetrical membrane, both containing beta barrel transmembrane proteins. We find in where the dynamics of the two leaflets differ greatly, the slowest leaflet dominates the structural effects and importance of protein-lipid interactions.</p
Outer membrane proteins OmpA, FhuA, OmpF, EstA, BtuB, and OmpX have unique lipopolysaccharide fingerprints
No full textThe outer membrane of Gram-negative bacteria has a highly complex asymmetrical architecture, containing a mixture of phospholipids in the inner leaflet and almost exclusively lipopolysaccharide (LPS) molecules in the outer leaflet. In E. coli, the outer membrane contains a wide range of proteins with a β barrel architecture, that vary in size from the smallest having eight strands to larger barrels composed of 22 strands. Here we report coarse-grained molecular dynamics simulations of six proteins from the E. coli outer membrane OmpA, OmpX, BtuB, FhuA, OmpF, and EstA in a range of membrane environments, which are representative of the in vivo conditions for different strains of E. coli. We show that each protein has a unique pattern of interaction with the surrounding membrane, which is influenced by the composition of the protein, the level of LPS in the outer leaflet, and the differing mobilities of the lipids in the two leaflets of the membrane. Overall we present analyses from over 200 μs of simulation for each protein.</p
The role of O-antigen in the response to mechanical stress of the E. coli outer membrane: Insights from coarse-grained MD simulations
No full textLipopolysaccharide (LPS) is an important component of the outer membrane of Gram-negative bacteria, contributing to the structural integrity of the bacterial cell wall and conferring resistance to chemical attack. The rough variant of LPS contains a conserved lipid A domain and a complete core saccharide section, whereas the smooth variant additionally contains a terminal O-antigen chain. In the following, smooth LPS lipids are simulated in multicomponent membrane models using coarse-grained molecular dynamics. The simulations reveal that the lipid environment of smooth LPS lipids affects the orientation and clustering of their O-antigen chains. When the outer membrane leaflets contain smooth LPS lipids alone, the O-antigen chains are packed tightly, leading to strong cohesive intermolecular interactions. When the outer leaflets incorporate interstitial phospholipids and rough LPS variants, the O-antigen chains are tilted and less tightly bound. The different packing of terminal O-antigen chains affects lipid mobility and the mechanical strength of the Gram-negative membrane models. Gram-negative membranes with outer leaflets of smooth LPS alone can withstand surface tensions (150 mN m–1) that cause the membrane models with rough LPS lipids and comparable phospholipid bilayers to rupture much more readily
Molecular dynamics simulations of bacterial outer membrane lipid extraction: Adequate sampling?
No full textThe outer membrane of Gram-negative bacteria is almost exclusively composed of lipopolysaccharide in its outer leaflet, whereas the inner leaflet contains a mixture of phospholipids. Lipopolysaccharide diffuses at least an order of magnitude slower than phospholipids, which can cause issues for molecular dynamics simulations in terms of adequate sampling. Here, we test a number of simulation protocols for their ability to achieve convergence with reasonable computational effort using the MARTINI coarse-grained force-field. This is tested in the context both of potential of mean force (PMF) calculations for lipid extraction from membranes and of lateral mixing within the membrane phase. We find that decoupling the cations that cross-link the lipopolysaccharide headgroups from the extracted lipid during PMF calculations is the best approach to achieve convergence comparable to that for phospholipid extraction. We also show that lateral lipopolysaccharide mixing/sorting is very slow and not readily addressable even with Hamiltonian replica exchange. We discuss why more sorting may be unrealistic for the short (microseconds) timescales we simulate and provide an outlook for future studies of lipopolysaccharide-containing membranes. </p
It is complicated: curvature, diffusion and lipid sorting within the two membranes of Escherichia coli
No full textThe 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
Modelling and Simulation on Shearer Self-adaptive Memory Cutting
No full textAbstractAutomation of shearer is the key point to realize the fully mechanized coal face. According to the complicated geological condition in our country, this paper built a shearer self-adaptive memory cutting model based on fuzzy control theory. This model contains shearer positioning system and fuzzy control system which can get the message of shearer's position and attitude at any point, trace the memorial cutting path automatically, judge whether the shearer cuts rocks based on fuzzy control theory and find the optimal scheme. The author simulated the working environment in laboratory and factory, did experiment to test whether the model can adapt complicated geological condition in the coal mine. The simulation results show that the model can realize the shearer memory cutting and discriminate the abnormal state, then adjust the drawing speed and drum height self-adaptively which can satisfy the control requirements under the complicated geological condition
Think Global: Act Local - Ensuring an Equitable Transition to Open Science
No full textShearer\u27s presentation Think Global: Act Local - Ensuring an Equitable Transition to Open Science will focus on how open science promises to offer unprecedented access to the full corpus of research, breaking down access barriers for many researchers. However, there is a risk in the transition to open science - new barriers will be erected and a significant portion of researchers/authors will again be excluded from the system because of the predominance of pay to publish models. This presentation will examine the systemic factors including the transition to open science and discuss potential avenues for ensuring diversity, equity, and inclusivity across the scholarly publishing ecosystem. Shearer has been working in the area of open access, open science, scholarly communications, and research data management for over 20 years. She is the author of numerous publications and delivered many presentations at international events. Most recently, she was the lead author of the paper Fostering Bibliodiversity in Scholarly Communications: A Call for Action (April 2020). She participates in the work of numerous other organizations to advance open science around the world and is also a Research Associate with the Canadian Association of Research Libraries (CARL) and has been instrumental in many of CARL’s activities related to open science, including the launch of the Portage Initiative in Canada, a national research data management network
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