Molecular Dynamics Study on the Effects of Chain Branching on the Physical Properties of Lipid Bilayers:  2. Permeability

Abstract

We studied the effects of chain branching on the water and nonionic (neutral) solute permeability of lipid bilayers in a molecular dynamics simulation comparing two bilayers: dipalmitoylphosphatidylcholine (DPPC) and diphytanoylphosphatidylcholine (DPhPC). The calculated free energy profiles of several neutral solute and water molecules across the lipid membranes showed that chain branching caused no significant changes in the solubility of these molecules inside the membrane core. However, an analysis of the cavity distribution in each of these bilayer systems demonstrated that the branch-chained DPhPC bilayer had, compared with the straight-chained DPPC bilayer, a relatively small and discrete free volume distribution in the hydrophobic part. This suggests that small penetrants have a lower rate of diffusion inside branch-chained lipid bilayers. Actually, water molecules showed lower local diffusion coefficients inside the DPhPC membrane than inside the DPPC membrane. The low penetrant mobility of the former must correlate with the slower dynamics of the branched DPhPC chains. Thus, we conclude that chain branching effects on the permeability are, as far as neutral small penetrants are concerned, attributable mainly to the reduction of chain dynamics. The effects of chain branching on proton permeability are also discussed in the context of the proton-wire hypothesis.

On the Electroporation Thresholds of Lipid Bilayers: Molecular Dynamics Simulation Investigations

“…It is unlikely that such an increase in the local membrane lateral tension affects greatly the U EPthres . Shinoda et al (2004b) performed an extensive study of water permeability in both membranes that may provide a rationale for the increased electroporation threshold as we go from DPPC to DPhPC. Indeed, the authors show from analyses of local diffusion coefficients that water molecules have considerably reduced mobility in the DPhPC membrane interior compared with the DPPC membrane interior.…”

“…Compared to simple phosphatidylcholine lipids, archaeal lipids have a special headgroup formed of sugar moieties but also methyl branches in the lipid tails and ether linkages instead of ester linkages between the headgroup and the carbonyl region (Ulrih et al 2009). Comparison between dipalmitoylphosphatidylcholine (DPPC)-, diphytanoyl-phosphocholine-ester (DPhPC-ester)-and diphytanoyl-phosphocholine-ether (DPhPC-ether)-based bilayers show, for instance, that branched chains increase the stability and decrease the permeability (Shinoda et al 2003(Shinoda et al , 2004b of the membrane, which are related to the slower conformational motion of the lipid tails. The difference in ester and ether linkage affects, on the other hand, the headgroup hydration and the membrane electrostatic potential.…”

Molecular dynamics study on thermal dehydration process of epsomite (MgSO4·7H2O)

“…Shinoda et al [31] argued that the diffusion coefficient of water was not sensitive to the choice of duration in the range of 2 -10 ps in lipid bilayer systems. Meanwhile, Taylor et al [32] selected 2 ps in his study of nanometer water films.…”

Free energy profiles for penetration of methane and water molecules into spherical sodium dodecyl sulfate micelles obtained using the thermodynamic integration method combined with molecular dynamics calculations

“…Here, the methane and water molecules are called "solubilized" or "penetrating" molecules. Let r be the distance between the center of mass of the penetrating molecule and that of the SDS micelle, and let G(r) be the Gibbs free energy of the whole system, where the distance is constrained to r. The Gibbs free energy of transfer G(r) of the penetrating molecule from a reference distance r 0 to r may be calculated as [28][29][30] …”