scholarly journals All-atom Molecular Dynamics model for mycobacterial plasma membrane

2019 ◽  
Author(s):  
João L. R. Scaini ◽  
Adriano V. Werhli ◽  
Vânia R. de Lima ◽  
Pedro E. A. da Silva ◽  
José Rafael Bordin ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Plasma Membrane ◽  
Multidrug Resistance ◽  
Membrane Protein ◽  
Self Assembly ◽  
Cell Envelope ◽  
Fluid Phase ◽  
Dynamics Model ◽  
Gel Phase ◽  
Im Model

AbstractPhosphatidyl-myo-inositol mannosides (PIMs) are an essential component of the cell envelope and the most predominant at the inner membrane (IM) of M. tuberculosis. In this work, we propose an Molecular Dynamics (MD) M. tuberculosis IM model composed of PIM2 lipids. The study was divided in three parts: influence of the temperature in the PIM2 membrane stability, self-assembly abilities of the PIM2 lipid and the behavior when a trans membrane protein is inserted in PIM2 membrane. Our results show that the model is able to reproduce the gel phase observed at 310 K and the transition to a fluid phase at 328.15 K. Also, the spontaneous self-assembly of randomly distributed lipids in a vesicular aggregate was observed. Finally, we observe that the PIM2 membrane is more stable than DPPC membranes when a Tap protein is inserted. Once Tap eflux pump is related to multidrug resistance of M. tuberculosis, this result indicated that the use of the proper lipid model is essential to the proper depiction and modeling of these systems.Graphical TOC Entry

scholarly journals Effect of C60 on the phase transition behavior of a lipid bilayer under high pressure

RSC Advances ◽  
2018 ◽  
Vol 8 (2) ◽  
pp. 655-661 ◽  
Author(s):  
Haiyang Yang ◽  
Zhiheng Huang ◽  
Yong Zhang
Keyword(s):  
Phase Transition ◽  
Molecular Dynamics ◽  
High Pressure ◽  
Molecular Dynamics Simulations ◽  
Fluid Phase ◽  
Coarse Grained ◽  
Phase Transition Behavior ◽  
Gel Phase ◽  
Dynamics Simulations ◽  
Pressure Phase

By employing coarse-grained molecular dynamics simulations, we obtained the temperature–pressure phase diagrams of a dipalmitoylphosphatidylcholine bilayer, which exhibits a gel phase and a fluid phase, with variation of the C60versus lipid ratios.

Coarse grained molecular dynamics model of block copolymer directed self-assembly

2013 ◽  
Author(s):  
Richard A. Lawson ◽  
Andrew J. Peters ◽  
Peter J. Ludovice ◽  
Clifford L. Henderson
Keyword(s):  
Molecular Dynamics ◽  
Block Copolymer ◽  
Self Assembly ◽  
Coarse Grained ◽  
Dynamics Model ◽  
Coarse Grained Molecular Dynamics

Simulation studies of the interactions between membrane proteins and detergents

2005 ◽  
Vol 33 (5) ◽  
pp. 910-912 ◽  
Author(s):  
P.J. Bond ◽  
J. Cuthbertson ◽  
M.S.P. Sansom
Keyword(s):  
Membrane Proteins ◽  
Membrane Protein ◽  
Self Assembly ◽  
Kinetic Mechanism ◽  
Coarse Grained ◽  
Simulation Studies ◽  
High Resolution Data ◽  
Biologically Relevant ◽  
Structure And Dynamics ◽  
Detergent Interactions

Interactions between membrane proteins and detergents are important in biophysical and structural studies and are also biologically relevant in the context of folding and transport. Despite a paucity of high-resolution data on protein–detergent interactions, novel methods and increased computational power enable simulations to provide a means of understanding such interactions in detail. Simulations have been used to compare the effect of lipid or detergent on the structure and dynamics of membrane proteins. Moreover, some of the longest and most complex simulations to date have been used to observe the spontaneous formation of membrane protein–detergent micelles. Common mechanistic steps in the micelle self-assembly process were identified for both α-helical and β-barrel membrane proteins, and a simple kinetic mechanism was proposed. Recently, simplified (i.e. coarse-grained) models have been utilized to follow long timescale transitions in membrane protein–detergent assemblies.

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