Allison N. Dickey

Examining the Contributions of Lipid Shape and Headgroup Charge on Bilayer Behavior

To better understand bilayer property dependency on lipid electrostatics and headgroup size, we use atomistic molecular dynamics simulations to study negatively charged and neutral lipid membranes. We compare the negatively charged phosphatidic acid (PA), which at physiological pH and salt concentration has a negative spontaneous curvature, with the negatively charged phosphatidylglycerol (PG) and neutrally charged phosphatidylcholine (PC), both of which have zero spontaneous curvature. The PA lipids are simulated using two different sets of partial charges for the headgroup and the varied charge distribution between the two PA systems results in significantly different locations for the Na(+) ions relative to the water/membrane interface. For one PA system, the Na(+) ions are localized around the phosphate group. In the second PA system, the Na(+) ions are located near the ester carbonyl atoms, which coincides with the preferred location site for the PG Na(+) ions. We find that the Na(+) ion location has a larger effect on bilayer fluidity properties than lipid headgroup size, where the A(lipid) and acyl chain order parameter values are more similar between the PA and PG bilayers that have Na(+) ions located near the ester groups than between the two PA bilayers.

Using ergosterol to mitigate the deleterious effects of ethanol on bilayer structure.

In wine fermentations, yeast is exposed to concentrated ethanol solutions. Ergosterol, a sterol that is found in lower eukaryotic membranes, helps preserve the structural integrity of yeast membranes in stressful environmental conditions. A premature arrest in ethanol production due to unknown metabolic changes in yeasts results in undesirably large concentrations of residual sugar and may be caused by the formation of an ethanol-induced interdigitated phase. We use atomistic molecular dynamics simulations to examine the induction of the interdigitated phase in model yeast membranes that contain either 0, 10, 20, 25 mol % ergosterol in ethanol concentrations of 0, 10, 15 vol %. The 25 mol % ergosterol system shows a similar level of interdigitation for the 0 and 10 vol % ethanol solutions, indicating that ergosterol molecules in this system are able to effectively counteract the disruptive behavior of ethanol molecules. However, at a 15 vol % ethanol solution, the amount of interdigitation triples and this ethanol concentration is similar to the concentrations found in stuck fermentations. The other three ergosterol concentrations studied (0, 10, 20 mol %) show larger quantities of interdigitation in the 10 vol % ethanol solution than the 0 vol % solution. Thus, the 25 mol % ergosterol bilayer, which is representative of the ergosterol concentrations seen in yeast membranes, is unique in the systems examined in its ability to delay the onset of ethanol-induced interdigitation. The concentration of ergosterol affects the permeability of a fluid-phase bilayer, where the 10 mol % ergosterol bilayer is more permeable to ethanol than either a bilayer containing no ergosterol molecules or a bilayer containing 20/25 mol % ergosterol. This lipid permeability appears to be correlated with the existence of a lipid region whose lipids neither have direct contact with ergosterol molecules nor exhibit bulk lipid/lipid interactions.

Behavioral differences between phosphatidic acid and phosphatidylcholine in the presence of the nicotinic acetylcholine receptor.

It has been found experimentally that negatively charged phosphatidic acid (PA) lipids and cholesterol molecules stabilize the nicotinic acetylcholine receptor (nAChR) in a functional resting state that can participate in an agonist-induced conformational change. In this study, we compare phosphatidylcholine (PC) and PA lipid behavior in the presence of the nAChR to determine why PC lipids do not support a functional nAChR. For lipids that are located within 1.0 nm of the protein, both PC and PA lipids have very similar order-parameter and bilayer-thickness values, which indicate that the annular lipid properties are protein-dependent. The most significant difference between the PC and PA bilayers is the formation of a lipid domain around the protein, which is visible in the PA bilayer but not the PC bilayer. This suggests that the PA domain may help stabilize the nAChR resting state. The PA lipids in the microdomain have a decreased order compared to a homogeneous PA bilayer and the lipids near the protein attempt to increase the free space in their vicinity by residing in multiple lateral planes.

Molecular Modeling of Biomembranes: A How-to Approach

Computer Simulations have become an important complementary technique to experiment and analytical theory for scientific discoveries. Molecular Dynamics (MD) is one of the most abundant techniques of computer modeling, and is frequently used simulation methods in biomolecular applications. Its popularity may stem from its simplicity and versatile applicability. The fundamental underlying assumption of MD is that the system consists of particles that interact via the classical equations of motion, i.e., both quantum mechanical and relativistic effects are neglected. The exclusion of these effects, however, does not generally have a significant impact on the biomolecular questions being studied.