Molecular dynamics simulations of glyphosate in a DPPC lipid bilayer

Shedding light on the structural properties of lipid bilayers using molecular dynamics simulation: a review study

“…59 Also, hAi is related to some lipid membrane properties, such as acyl chain ordering, compressibility, and molecular packaging, among others. 60 This is one of the main objectives of the quantitative description of membranes using molecular dynamics simulations. Furthermore, in vitro studies of integral membrane proteins or peptides frequently require them to be reconstituted with membrane lipids, 10,11,13,14,61-67 where the bilayer structural dimensions involving hydrophobic matching and area per lipid are important parameters.…”

“…There are several studies that showed the time-dependent area per lipid is also a good criterion to determine if the system has reached the steady state. 60,71 Frigini and coworkers used MD simulations to study the effect of glyphosate (in its neutral and charged forms, GLYP and GLYP2-, respectively) on a fully hydrated DPPC lipid bilayer. The time evolution of the area per lipid resulting from unbiased simulations in their work is presented in Fig.…”

“…In some studies, q is considered as the time-dependent angle between a C-H bond along the acyl chain and the membrane plane normal (z-axis). 72 In the above equation, the bracket denotes the time averaging over two bonds at each group of CH 2 in all the lipids. If the united atoms force eld is used in the simulation (which is more common), it should be to reconstruct the vector C nÀ1 to C n+1 from the positions of three successive CH 2 -groups assuming tetrahedral geometry of the CH 2 -groups.…”

Effects of cholesterol on bilayers with various degrees of unsaturation of their phospholipid tails under mechanical stress

“…2 The composition of a biomembrane is complicated, and a pure phospholipid bilayer is usually employed as a simplied model of a biomembrane in simulation studies. [3][4][5][6][7][8] Mechanical stress plays an essential role in the growth, proliferation, differentiation, and apoptosis of cells. 9,10 Plenty of biomechanical experiments have indicated that a certain level of mechanical stress affects the shapes and structures of living cells.…”

All-atom Molecular Dynamics model for mycobacterial plasma membrane

“…This in silico method allow a complete control on the system properties and has been extensively applied to provide information on both their spatial organization and temporal dynamics. [12][13][14] Recent MD studies about mycobacterial membrane includes membranes based in DPPC, DOPC, POPG, POPE. [15][16][17] Nevertheless, there are no specific membrane molecular model with such uncommon and unique lipids as the observed in the M. tuberculosis.…”