The membranes of Gram-negative bacteria: progress in molecular modelling and simulation

Khalid, Syma; Berglund, Nils; Holdbrook, Daniel A.; Leung, Yuk Ming; Parkin, Jamie

doi:10.1042/bst20140262

Cited by 23 publications

(28 citation statements)

References 34 publications

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“…5). Similar simulations of large outer membrane systems were also reported by Khalid et al (66). These large systems create new issues in term of analysis and visualization to decipher the intricate interdependency of proteins and lipids.…”

Section: Protein-protein Interactions In the Outer Membranesupporting

confidence: 61%

“…With these models and methods it is now possible to study protein and lipid diffusion, and the interdependence of the protein-protein interactions and the effects of membrane curvature on these phenomena (64)(65)(66). Future work in this area will include adding coarse-grained models of the LPS component of the outer membrane, and extending the system sizes such that life-size models of outer membrane vesicles can be studied.…”

Section: Discussionmentioning

confidence: 96%

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Molecular Simulations of Gram-Negative Bacterial Membranes: A Vignette of Some Recent Successes

Parkin

Chavent

Khalid

2015

Biophysical Journal

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In the following review we use recent examples from the literature to discuss progress in the area of atomistic and coarse-grained molecular dynamics simulations of selected bacterial membranes and proteins, with a particular focus on Gram-negative bacteria. As structural biology continues to provide increasingly high-resolution data on the proteins that reside within these membranes, simulations have an important role to play in linking these data with the dynamical behavior and function of these proteins. In particular, in the last few years there has been significant progress in addressing the issue of biochemical complexity of bacterial membranes such that the heterogeneity of the lipid and protein components of these membranes are now being incorporated into molecular-level models. Thus, in future we can look forward to complementary data from structural biology and molecular simulations combining to provide key details of structure-dynamics-function relationships in bacterial membranes.

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Section: Protein-protein Interactions In the Outer Membranesupporting

confidence: 61%

Section: Discussionmentioning

confidence: 96%

Molecular Simulations of Gram-Negative Bacterial Membranes: A Vignette of Some Recent Successes

Parkin

Chavent

Khalid

2015

Biophysical Journal

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“…It is promising to see that over the past few years much progress has been made on that front. There are now force field parameters for a wider range of lipids including sterols, ceramides, sphingomyelin, and cardiolipins enabling simulations of more complex membranes . In particular the presence of cholesterol, which is known to increase the rigidity of membranes, will likely affect the membrane‐binding properties of peptides.…”

Section: Discussionmentioning

confidence: 99%

Molecular simulations of venom peptide‐membrane interactions: Progress and challenges

Deplazes

2018

Peptide Science

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Because of their wide range of biological activities venom peptides are a valuable source of lead molecules for the development of pharmaceuticals, pharmacological tools and insecticides. Many venom peptides work by modulating the activity of ion channels and receptors or by irreversibly damaging cell membranes. In many cases, the mechanism of action is intrinsically linked to the ability of the peptide to bind to or partition into membranes. Thus, understanding the biological activity of these venom peptides requires characterizing their membrane binding properties. This review presents an overview of the recent developments and challenges in using biomolecular simulations to study venom peptide‐membrane interactions. The review is focused on (i) gating modifier peptides that target voltage‐gated ion channels, (ii) venom peptides that inhibit mechanosensitive ion channels, and (iii) pore‐forming venom peptides. The methods and approaches used to study venom peptide‐membrane interactions are discussed with a particular focus on the challenges specific to these systems and the type of questions that can (and cannot) be addressed using state‐of‐the‐art simulation techniques. The review concludes with an outlook on future aims and directions in the field.

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“…As an alternative, the construction and simulation of in silico molecular models can help understand cell envelope processes and cellular behaviour [9]. Specifically, agent-based models (ABM) have shown great potential to simulate biological events [10][11][12][13][14].…”

Section: Introductionmentioning

confidence: 99%

Application of agent-based modelling to assess single-molecule transport across the cell envelope of E. coli

Maia

Pérez-Rodríguez

Pérez-Pérez

et al. 2019

Computers in Biology and Medicine

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A B S T R A C TMotivation: Single cells often show stochastic behaviour and variations in the physiological state of individual cells affect the behaviour observed in cell populations. This may be partially explained by variations in the concentration and spatial location of molecules within and in the vicinity of each cell. Methods: This paper introduces an agent-based model that represents single-molecule transport through the cellular envelope of Escherichia coli at the micrometre scale. This model enables broader observation of molecular transport throughout the different membrane layers and the study of the effect of molecular concentration in cellular noise. Simulations considered various low molecular weight molecules, i.e. ampicillin, bosentan, coumarin, saquinavir, and terbutaline, and a gradient of molecular concentrations. The model ensured stochasticity in the location of the agents, using diffusing spherical particles with physical dimensions. Results: Simulation results were validated against theoretical and experimental data. For example, theoretically, ampicillin molecules take 0.6 s to cross the entire cell envelope, and computational simulations took 0.68 s, 0.68 s, 0.70 s, and 0.69 s, for concentrations of 1.44 μM, 13.21 μM, 26.4 μM and 105.61 μM, respectively. Replicate standard deviation decreased with growing initial concentrations of the molecules. In turn, no clear relationship could be observed between molecular size and variability. Conclusions: This work presented a novel agent-based model to study the effect of the initial concentration of low molecular weight molecules on cellular noise. Cellular noise during molecule diffusion was found to be concentration-dependent and size-independent. The new model holds considerable potential for future, more complex analyses, when emerging experimental data may enable modelling of membrane transport mechanisms.

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The membranes of Gram-negative bacteria: progress in molecular modelling and simulation

Cited by 23 publications

References 34 publications

Molecular Simulations of Gram-Negative Bacterial Membranes: A Vignette of Some Recent Successes

Molecular Simulations of Gram-Negative Bacterial Membranes: A Vignette of Some Recent Successes

Molecular simulations of venom peptide‐membrane interactions: Progress and challenges

Application of agent-based modelling to assess single-molecule transport across the cell envelope of E. coli

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