Accelerated molecular dynamics (aMD) is an enhanced sampling technique that expedites conformational space sampling by reducing the barriers separating various low-energy states of a system. Here, we present the first application of the aMD method on lipid membranes. Altogether, ∼1.5 μs simulations were performed on three systems: a pure POPC bilayer, a pure DMPC bilayer, and a mixed POPC:DMPC ...

Aggregation at the neuronal cell membrane's lipid bilayer surface is implicated in amyloid-β (Aβ) toxicity associated with Alzheimer's disease; however, structural and mechanistic insights into the process remain scarce. We have identified a conserved binding mode of Aβ40 on lipid bilayer surfaces with a conserved helix containing the self-recognition site (K16-E22).

Imidazolium-based ionic surfactants with hydrocarbon tails of different sizes were simulated with lipid bilayers at different salt concentrations. Starting with the random position of ionic surfactants outside the bilayer, surfactants with long tails mostly insert into the bilayer, while those with short tails show the insertion of fewer surfactant molecules, indicating the effect of the tail l...

Artificial lipid bilayer on solid substrate plays an important role as an interface between nanotechnology and biology. In this study, grid structures were patterned on Au-Nb-glass substrate and artificial bilayer was prepared on these structures. The fluidity was checked using fluorescence recovery after photobleaching (FRAP), and neuronal adhesion was monitored on such structure using EphrinA...

We investigate the interactions between lipid bilayers and amphiphilic peptides using a solvent-free coarse-grained simulation technique. In our model, each lipid is represented by one hydrophilic and three hydrophobic beads. The amphiphilic peptide is modeled as a hydrophobic-hydrophilic cylinder with hydrophilic caps. We find that with increasing peptide-lipid attraction the preferred state o...

Many drugs are amphiphiles that, in addition to binding to a particular target protein, adsorb to cell membrane lipid bilayers and alter intrinsic bilayer physical properties (e.g., bilayer thickness, monolayer curvature, and elastic moduli). Such changes can modulate membrane protein function by altering the energetic cost (DeltaG(bilayer)) of bilayer deformations associated with protein confo...

Previous attempts to simulate phospholipid bilayers using the General Amber Force Field (GAFF) yielded many bilayer characteristics in agreement with experiment, however when using a tensionless NPT ensemble the bilayer is seen to compress to an undesirable extent resulting in low areas per lipid and high order parameters in comparison to experiment. In this work, the GAFF Lennard-Jones paramet...

A microfabricated silicon device for studying artificial lipid bilayer systems is described. The experimental apparatus employed enabled the simultaneous acquisition of electrical and optical data. Reconstitution of channel-forming proteins into a artificial lipid bilayer formed across an aperture in the silicon device is demonstrated.