MEMBPLUGIN: studying membrane complexity in VMD

Guixà-González, Ramón; Rodríguez‐Espigares, Ismael; Ramírez-Anguita, Juan Manuel; Carrió-Gaspar, Pau; Martinez‐Seara, Hector; Giorgino, Toni; Selent, Jana

doi:10.1093/bioinformatics/btu037

Cited by 234 publications

(198 citation statements)

References 11 publications

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“…In addition, a Voronoi analysis was performed using the VMD plugin, Membplugin, 53 on each of the simulation systems in isolation, giving a value for each system for both DOPC and ceramide. These values fall in the range of a DOPC = 65.7-69.6 Å 2 and a cer = 52.7-54.7 Å 2 .…”

Section: A Area Per Lipidmentioning

confidence: 99%

Comparative atomic-scale hydration of the ceramide and phosphocholine headgroup in solution and bilayer environments

Gillams

Lorenz

McLain

2016

The Journal of Chemical Physics

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Previous studies have used neutron diffraction to elucidate the hydration of the ceramide and the phosphatidylcholine headgroup in solution. These solution studies provide bond-length resolution information on the system, but are limited to liquid samples. The work presented here investigates how the hydration of ceramide and phosphatidylcholine headgroups in a solution compares with that found in a lipid bilayer. This work shows that the hydration patterns seen in the solution samples provide valuable insight into the preferential location of hydrating water molecules in the bilayer. There are certain subtle differences in the distribution, which result from a combination of the lipid conformation and the lipid-lipid interactions within the bilayer environment. The lipid-lipid interactions in the bilayer will be dependent on the composition of the bilayer, whereas the restricted exploration of conformational space is likely to be applicable in all membrane environments. The generalized description of hydration gathered from the neutron diffraction studies thus provides good initial estimation for the hydration pattern, but this can be further refined for specific systems. Published by AIP Publishing. [http://dx

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Section: A Area Per Lipidmentioning

confidence: 99%

Comparative atomic-scale hydration of the ceramide and phosphocholine headgroup in solution and bilayer environments

Gillams

Lorenz

McLain

2016

The Journal of Chemical Physics

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“…β 2 AR in complex with agonist, antagonist and inverse agonist reached equilibrium over 10 ns MD simulations (see Figure 6A). To make sure whether the membrane keeps stable, MEMBPLUGIN [78] was employed to measure membrane thickness during MD simulations. The results showed the membrane also reached equilibrium phase over 10 ns MD simulations (see Figure S7).…”

Section: Resultsmentioning

confidence: 99%

Search for β2 Adrenergic Receptor Ligands by Virtual Screening via Grid Computing and Investigation of Binding Modes by Docking and Molecular Dynamics Simulations

et al. 2014

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We designed a program called MolGridCal that can be used to screen small molecule database in grid computing on basis of JPPF grid environment. Based on MolGridCal program, we proposed an integrated strategy for virtual screening and binding mode investigation by combining molecular docking, molecular dynamics (MD) simulations and free energy calculations. To test the effectiveness of MolGridCal, we screened potential ligands for β2 adrenergic receptor (β2AR) from a database containing 50,000 small molecules. MolGridCal can not only send tasks to the grid server automatically, but also can distribute tasks using the screensaver function. As for the results of virtual screening, the known agonist BI-167107 of β2AR is ranked among the top 2% of the screened candidates, indicating MolGridCal program can give reasonable results. To further study the binding mode and refine the results of MolGridCal, more accurate docking and scoring methods are used to estimate the binding affinity for the top three molecules (agonist BI-167107, neutral antagonist alprenolol and inverse agonist ICI 118,551). The results indicate agonist BI-167107 has the best binding affinity. MD simulation and free energy calculation are employed to investigate the dynamic interaction mechanism between the ligands and β2AR. The results show that the agonist BI-167107 also has the lowest binding free energy. This study can provide a new way to perform virtual screening effectively through integrating molecular docking based on grid computing, MD simulations and free energy calculations. The source codes of MolGridCal are freely available at http://molgridcal.codeplex.com.

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“…The increased APL values have also been observed in articaine-DMPC system. [28] The membrane thickness was calculated using MEMBPLUGIN [29], and the defined boundary layer is phosphorous atoms of POPC. The calculated membrane thickness is 37.24 ± 0.49 Å, which is slightly thicker than that of pure POPC bilayer (37.00 ± 0.44 Å).…”

Section: Area Per Lipid and Membrane Thicknessmentioning

confidence: 99%

Concentration effect of cimetidine with POPC bilayer: a molecular dynamics simulation study

Wang

Meng²

2016

Molecular Simulation

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a tianjin Key laboratory of Molecular Design and Drug Discovery, tianjin institute of Pharmaceutical research, tianjin, P.r. china; b State Key laboratory of Drug Delivery technology and Pharmacokinetics, tianjin institute of Pharmaceutical research, tianjin, P.r. china ABSTRACT All-atom molecular dynamics simulations have been performed on cimetidine in the presence of a palmitoyloleoylphosphatidylcholine (POPC) bilayer. The free energy profile of a single cimetidine molecule passing across POPC bilayer displays a minimum at the interface of bilayer and water. Ten cimetidine molecules were inserted into POPC bilayer to obtain an 8 mol % drug model, and molecular dynamics results showed that cimetidine molecules reside at the polar region of POPC bilayer with sulphur atoms directing to the hydrophobic region. By comparing the one drug model with 8 mol % drug model, one can see that the central barrier to cross the membrane increases while the free energy in bulk water decreases, indicating that the ability of cimetidine passing across the POPC bilayer weakens at increased concentration. In addition, the free energy minimum shifts closer to the hydrophobic core. Our results indicate that with the increased drug concentration, it is more difficult for cimetidine to enter and pass across POPC bilayer.

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MEMBPLUGIN: studying membrane complexity in VMD

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 234 publications

References 11 publications

Comparative atomic-scale hydration of the ceramide and phosphocholine headgroup in solution and bilayer environments

Comparative atomic-scale hydration of the ceramide and phosphocholine headgroup in solution and bilayer environments

Search for β2 Adrenergic Receptor Ligands by Virtual Screening via Grid Computing and Investigation of Binding Modes by Docking and Molecular Dynamics Simulations

Concentration effect of cimetidine with POPC bilayer: a molecular dynamics simulation study

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