Molecular dynamics simulations of pore formation in stretched phospholipid/cholesterol bilayers

Shigematsu, Taiki; Koshiyama, Kenichiro; Wada, Shigeo

doi:10.1016/j.chemphyslip.2014.05.005

Cited by 31 publications

(31 citation statements)

References 38 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For the estimation of KA, the trajectories in the pre-equilibrating stage obtained from our previous study (Shigematsu et al, 2014) are used.…”

Section: Discussionmentioning

confidence: 99%

“…The trajectories during the latter 50 ns are used for the analysis of the bilayers at equilibrium. Details of MD simulation parameters are summarized in the supplementary material of our previous study (Shigematsu et al, 2014) and the same parameters are used in our current investigation. All MD calculations are performed with the GROMACS molecular dynamics simulation codes (Berendsen et al, 1995;Hess and Kutzner, 2008).…”

Section: Initial Systemsmentioning

confidence: 99%

“…From the trajectory of the bilayer at equilibrium taken from our previous study (Shigematsu et al, 2014), the averaged system box areas on the x-y plain A0 are 65.4, 48.7, and 39.2 nm 2 for the bilayers containing cholesterol at 0, 20, and 40 mol%, respectively. The corresponding areas per molecule are 0.65, 0.49, and 0.39 nm 2 , respectively, which are in good agreement with those obtained from MD simulations reported by other groups (Chiu et al, 2002;Saito and Shinoda, 2011).…”

Section: Estimation Of Line Tensionmentioning

confidence: 99%

“…The initial configurations are taken from our previous study (Shigematsu et al, 2014). The systems were equilibrated at a temperature of 323 K and a pressure of 0.1 MPa for at least 100 ns in our previous study (Shigematsu et al, 2014). The trajectories during the latter 50 ns are used for the analysis of the bilayers at equilibrium.…”

Section: Initial Systemsmentioning

confidence: 99%

“…DPPC, cholesterol, and water molecules are represented by the united atom force fields for DPPC (Berger et al, 1997), for cholesterol (Höltje et al, 2001), and the simple point charge model for water (Berendsen et al, 1981). The initial configurations are taken from our previous study (Shigematsu et al, 2014). The systems were equilibrated at a temperature of 323 K and a pressure of 0.1 MPa for at least 100 ns in our previous study (Shigematsu et al, 2014).…”

Section: Initial Systemsmentioning

confidence: 99%

See 4 more Smart Citations

Line tension of the pore edge in phospholipid/cholesterol bilayer from stretch molecular dynamics simulation

Shigematsu

Koshiyama

Wada

2015

JBSE

Self Cite

View full text Add to dashboard Cite

The line tension of the pore in a phospholipid bilayer is important for pore-mediated molecular transport techniques. To understand the cholesterol effects on the line tension of the pore edge at the molecular level, we perform molecular dynamics simulations of phospholipid bilayers with a pore containing cholesterol in different concentrations (0, 20, and 40 mol%). The bilayer with a pore is prepared by using an equibiaxial stretching simulation. The stretched bilayer with a pore is subsequently compressed and the pore spontaneously closes when the applied areal strain of the bilayer is below a certain value. Using the pore closure areal strain and a free energy model of a stretched bilayer with a pore, the upper and lower limits of the line tensions for the bilayers containing cholesterol at 0, 20, and 40 mol% are estimated to be 17.0-48.2, 54.5-100, and 170-261 pN, respectively. The increasing tendency of the line tension qualitatively agrees with that observed experimentally. The pores in the cholesterol-containing bilayers are lined with several cholesterol molecules, which might increase the bending rigidity of the pore edge, and result in the higher line tension of the cholesterol-containing bilayer. The considerable dependency of the line tension on the bilayer compositions might be useful to explain the large variations of the transduction efficiency observed with sonoporation treatment.

show abstract

“…For the estimation of KA, the trajectories in the pre-equilibrating stage obtained from our previous study (Shigematsu et al, 2014) are used.…”

Section: Discussionmentioning

confidence: 99%