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

Abstract

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.

FIGURE 1

The nAChR transmembrane region is composed of five subunits: α₁, β, δ, α₂, and γ. Each subunit contains four helices: M1, M2, M3, and M4 (PDB:1OED (16)).

FIGURE 2

A snapshot of the nAChR in the POPC bilayer.

FIGURE 3

Structure of a POPC lipid. The POPC choline group is replaced with a hydrogen atom in POPA.

FIGURE 4

The average RMSD values of the Cα atoms in the five subunits for helices M1–M4 in the POPC bilayer. The RMSD values are shown for the trajectory frames that include a 150 mM salt concentration. Average RMSD helix values: M1 = 0.15 nm ± 0.01, M2 = 0.25 nm ± 0.01, M3 = 0.14 nm ± 0.01, and M4 = 0.30 nm ± 0.01.

FIGURE 5

The average RMSD values of the Cα atoms in the five subunits for helices M1–M4 in the POPA bilayer. The RMSD values are shown for the trajectory frames that include a 150 mM salt concentration. Average RMSD helix values: M1 = 0.22 nm ± 0.01, M2 = 0.19 nm ± 0.01, M3 = 0.22 nm ± 0.01, and M4 = 0.39 nm ± 0.01.

FIGURE 6

The RMSF of the (A) α₁, (B) β, (C) δ, (D) α₂, and (E) γ-subunits.

FIGURE 7

The RDF for POPC and POPA ester oxygen atom O35 and the water molecule oxygen atoms. The preferred distance between POPC atom O35 and the water molecules is 0.27 nm (peak height = 2.9) and between POPA atom O35 and the water molecules is 0.29 nm (peak height = 0.56).

FIGURE 8

A lipid molecule that has a distance in the xy plane that is <1.0 nm from the protein (depicted in the figure center) is assigned to Bin 1. If the distance between a lipid molecule and the nearest protein atom is >1.0 nm, it is assigned to Bin 2 or Bin 3. Bin distance specifications: Bin 1 (<1.0 nm), shaded; Bin 2 (1.0 nm ≤ 2.0 nm), open; and Bin 3 (2.0 nm ≤), horizontal lines.

FIGURE 9

The POPC order parameter profiles for the sn-1 chains. The order parameter values are averaged over the four 2-ns time frames.

FIGURE 10

The POPA order parameter profiles for the sn-1 chains. The order parameter values are averaged over the four 2-ns time frames.

FIGURE 11

The order parameter profiles of the sn-1 chains for the POPC and POPA lipids found in the top and bottom leaflets in Bin 1. The order parameter values are averaged over the four 2-ns time segments.

FIGURE 12

Density profiles for the POPC system.

FIGURE 13

Density profiles for the POPA system.

FIGURE 14

The P atom density profile peaks for the POPC bilayer. The data for this figure comes from the 1–3 ns trajectory time frame.

FIGURE 15

The P atom density profile peaks for the POPA bilayer. The data for this figure comes from the 1–3 ns trajectory time frame.

FIGURE 16

A snapshot of the POPA lipid that lies orthogonal to the bilayer normal and forms hydrogen bonds with the M4 helix of the δ-subunit. A similarly positioned lipid is not seen in the POPC bilayer.

FIGURE 17

The bilayer thickness for Bins 1–3 in the POPC and POPA bilayers. The POPC and POPA lipids in Bin 1 converge on a thickness of 4.29–4.33 nm. Each data point is an average over the P atom density profile peaks for the four 2-ns trajectory time frames.