CHARMM-GUI <i>Membrane Builder</i>: Past, Current, and Future Developments and Applications

Feng, Shasha; Park, Soohyung; Choi, Yeol Kyo; Im, Wonpil

doi:10.1021/acs.jctc.2c01246

Cited by 14 publications

(10 citation statements)

References 309 publications

(543 reference statements)

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“…For the simulations containing oxidized lipids, parameters and topologies from the recently updated CHARMM-GUI library were used . We employed PoxnoPC (1-palmitoyl-2-(9′-oxo-nonanoyl)- sn -glycero-3-phosphocholine), a stable oxidation product of POPC bearing a carbonyl group at the end of the truncated sn-2 chain.…”

Section: Methodsmentioning

confidence: 99%

“…For the simulations containing oxidized lipids, parameters and topologies from the recently updated CHARMM-GUI library were used. 70 We employed PoxnoPC (1-palmitoyl-2-(9′-oxo-nonanoyl)-snglycero-3-phosphocholine), a stable oxidation product of POPC bearing a carbonyl group at the end of the truncated sn-2 chain. Two systems comprising a membrane with 67% PoxnoPC and 33% POPC lipids were built, and 8 BV-1 molecules in light conformation were added to one of them, four per layer.…”

mentioning

confidence: 99%

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Nanoactuator for Neuronal Optoporation

Pfeffer,

DiFrancesco,

Marchesi

et al. 2024

ACS Nano

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Light-driven modulation of neuronal activity at high spatial-temporal resolution is becoming of high interest in neuroscience. In addition to optogenetics, nongenetic membranetargeted nanomachines that alter the electrical state of the neuronal membranes are in demand. Here, we engineered and characterized a photoswitchable conjugated compound (BV-1) that spontaneously partitions into the neuronal membrane and undergoes a charge transfer upon light stimulation. The activity of primary neurons is not affected in the dark, whereas millisecond light pulses of cyan light induce a progressive decrease in membrane resistance and an increase in inward current matched to a progressive depolarization and action potential firing. We found that illumination of BV-1 induces oxidation of membrane phospholipids, which is necessary for the electrophysiological effects and is associated with decreased membrane tension and increased membrane fluidity. Time-resolved atomic force microscopy and molecular dynamics simulations performed on planar lipid bilayers revealed that the underlying mechanism is a light-driven formation of pore-like structures across the plasma membrane. Such a phenomenon decreases membrane resistance and increases permeability to monovalent cations, namely, Na + , mimicking the effects of antifungal polyenes. The same effect on membrane resistance was also observed in nonexcitable cells. When sustained light stimulations are applied, neuronal swelling and death occur. The light-controlled pore-forming properties of BV-1 allow performing "on-demand" light-induced membrane poration to rapidly shift from cell-attached to perforated wholecell patch-clamp configuration. Administration of BV-1 to ex vivo retinal explants or in vivo primary visual cortex elicited neuronal firing in response to short trains of light stimuli, followed by activity silencing upon prolonged light stimulations. BV-1 represents a versatile molecular nanomachine whose properties can be exploited to induce either photostimulation or spacespecific cell death, depending on the pattern and duration of light stimulation.

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Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

Nanoactuator for Neuronal Optoporation

Pfeffer,

DiFrancesco,

Marchesi

et al. 2024

ACS Nano

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“…We employed the CHARMM36 all-atom force field , for simulating LPS molecules and the different membrane systems (Table ). The initial structures for LPS molecules and the membranes were constructed from the CHARMM-GUI interface. − The temperature (310 K) was maintained using a Nosé–Hoover thermostat with a coupling constant of 1 ps . Isotropic pressure coupling was used to control pressure (1 bar) in bulk water simulations, while the semi-isotropic pressure coupling was employed for membrane systems to separately maintain pressure components along the lateral and normal directions in the membrane.…”

Section: Simulation Methodologymentioning

confidence: 99%

Martini-3 Coarse-Grained Models for the Bacterial Lipopolysaccharide Outer Membrane of Escherichia coli

Vaiwala,

Ayappa

2023

J. Chem. Theory Comput.

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The outer lipopolysaccharide (LPS) membrane of Gram-negative bacteria forms the main barrier for transport of antimicrobial molecules into the bacterial cell. In this study we develop coarse-grained models for the outer membrane of Escherichia coli in the Martini-3 framework. The coarse-grained model force field was parametrized and validated using all-atom simulations of symmetric membranes of lipid A and rough LPS as well as a complete asymmetric membrane of LPS with the Oantigen. The bonded parameters were obtained using an iterative refinement procedure with target bonded distributions obtained from all-atom simulations. The membrane thickness, area of the LPS, and density distributions for the different regions as well as the water and ion densities in Martini-3 simulations show excellent agreement with the all-atom data. Additionally the solvent accessible surface area for individual molecules in water was found to be in good agreement. The binding of calcium ions with phosphate and carboxylate moieties of LPS is accurately captured in the Martini-3 model, indicative of the integrity of the highly negatively charged LPS molecules in the outer membranes of Gram-negative bacteria. The melting transition of the coarse-grained lipid A membrane model was found to occur between 300 and 310 K, and the model captured variations in area per LPS, order parameter, and membrane thickness across the melting transition. Our study reveals that the proposed Martini-3 models for LPS are able to capture the physicochemical balance of the complex sugar architecture of the outer membrane of Escherichia coli. The coarse-grained models developed in this study would be useful for determining membrane protein interactions and permeation of potential antimicrobials through bacterial membranes at mesoscopic spatial and temporal scales.

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“…The need for transparency is even more important, given that the field of MD simulations has significantly lowered the entry barrier, making them increasingly routine and readily utilized as a “black box”. Tools like CHARMM-GUI and Martinize exemplify how simulations can be set up and run within mere minutes or hours, which is a stark and positive change from just a few years ago. Similarly, the accessibility of force field parameters in various simulation packages has been improved.…”

Section: Coupling Molecular Dynamics and Artificial Intelligencementioning

confidence: 99%