Characterization of lipid membrane dynamics by simulation: I. Torsion angle motions of the linear chains

Abstract

The torsion angle motions, generated from molecular dynamics (MD) simulations, of the two aliphatic chains of 1,2‐dimyristoyl‐sn‐glycero‐3‐phosphatidylcholine (DMPC) in its lipid monolayer were evaluated by comparing these motions to those of an equivalent isolated (free) n‐alkane chain, and the same n‐alkane chain in its crystal lattice. The time‐dependent autocorrelation and (1,2)‐, (1,3)‐, (1,4)‐, and (1,5)‐cross‐correlation functions were constructed to analyze the torsion angle motions. It was found that the torsion angle motions of the DMPC lipid monolayer aliphatic chains are intermediate to those of the free n‐alkane chain and the same n‐alkane chain in its crystal lattice, particularly for short correlation times. The torsion angle motions of the aliphatic chains of DMPC are also found to be essentially independent of the charge state on the head group. The linear aliphatic chains of a DMPC lipid monolayer behave most like the isolated n‐alkane chains with respect to torsion angle flexibility, even though the pairs of aliphatic chains of each DMPC are part of an ordered monolayer assembly. The aliphatic chains of the DMPC molecules in their monolayer exhibit at least two types of wave motions. One of the wave motions is the same in form, though somewhat more diffuse, as a traveling wave found in n‐alkane crystals. The other wave motion involves major torsion angle transitions, and has some characteristics of the soliton properties observed in n‐alkane crystals near their respective melt transition temperatures. © 1997 John Wiley & Sons, Inc.

Permeability of Psoralen Derivatives in Lipid Membranes

“…Several models have been proposed for the passive diffusion of molecules across biological membranes (42). In the free volume model, the bilayer interior is compared to a soft polymer and the molecules make a diffusive step when they jump from one free volume pocket to another.…”

“…5-MOP. The permeation process is usually described by three steps, involving the solvation of the molecule into the bilayer, diffusion through the membrane interior and across the bilayer middle, and finally the return of the molecule to the environment surrounding the bilayer (42). Since in the constrained dynamic simulations our starting point already contained the molecules inside the lipid bilayer (although close to the water/lipid interface), the calculated permeability coefficients do not contain the first and last steps of the process.…”

Atomic force microscopy investigation of the dependence of cellular elastic moduli on glutaraldehyde fixation

“…The principal change in mechanical properties resulting from glutaraldehyde fixation is due to cross‐linking of F‐actin filaments (Hopwood, 1972; Johnson, 1987), which other studies demonstrate to be the primary source of elastic rigidity in fibroblast cells (Rotsch & Radmacher, 2000). Because the cell thickness (up to ∼3 µm for the RDX2C2 cells) is much less than the diffusion length ∼ 50 µm of glutaraldehyde (where we conservatively estimate the diffusivity of glutaraldehyde in the cell as D ∼10 −7 cm 2 s −1 , typical of other small molecules in cellular membranes (Jin & Hopfinger, 1996), and t = 60 s is the fixation period), we expect the glutaraldehyde concentration in the cell to fully equilibrate with the surrounding fixative solution during the fixation process. Previous real‐time studies of the effects of glutaraldehyde fixation on cell elasticity have demonstrated saturation of the elastic modulus within a similar period of time (Hoh & Schoenenberger, 1994).…”

Strategies toward predicting peptide cellular permeability from computed molecular descriptors

“…Such modeling may even need to go beyond isotropic environment models (e.g. explicit molecular representations of solvent environment) to more accurately reflect anisotropic conditions experienced during solute transport (70–76). The importance of conformational‐energy‐weighted (or unweighted) averaging of computed descriptors should then be placed in the context of selecting the most appropriate solvation treatment for molecular modeling.…”