Searching for the molecular arrangement of transmembrane ceramide channels

Abstract

Ceramides have been implicated in the initiation of apoptosis by permeabilizing the mitochondrial outer membrane to small proteins, including cytochrome c. In addition, ceramides were shown to form large metastable channels in planar membranes and liposomes, indicating that these lipids permeabilize membranes directly. Here we analyze molecular models of ceramide channels and test their stability in molecular dynamics simulations. The structural units are columns of four to six ceramides H-bonded via amide groups and arranged as staves in either a parallel or antiparallel manner. Two cylindrical assemblies of 14 columns (four or six molecules per column) were embedded in a fully hydrated palmitoyloleoyl-phosphatidylcholine phospholipid bilayer, and simulated for 24 ns in total. After equilibration, the water-filled pore adopted an hourglass-like shape as headgroups of ceramides and phospholipids formed a smooth continuous interface. The structure-stabilizing interactions were both hydrogen bonds between the headgroups (including water-mediated interactions) and packing of the hydrocarbon tails. Ceramide's essential double bond reduced the mobility of the hydrocarbon tails and stabilized their packing. The six-column assembly remained stable throughout a 10-ns simulation. During simulations of four-column assemblies, pairs of columns displayed the tendency of splitting out from the channels, consistent with the previously proposed mechanism of channel disassembly.

FIGURE 1

Model of the ceramide channel and patterns of hydrogen-bonding stabilizing the assembly. (A) Structure of C₁₆ ceramide. For C₂ ceramide, the fatty acid chain indicated by a bracket is just two carbons long. Headgroup atoms capable of H-bonding are labeled in green. Color coding is as on the next panel. (B) An initial model of the ceramide channel is composed of six layers and 14 columns of C₁₆ molecules. Oxygens (red), carbons (cyan), and polar hydrogens (white) are in licorice representation. Nitrogen (blue) and oxygen of amide group are in van der Waals (VDW) spheres representation to visualize the antiparallel orientation of neighboring columns. (C) Circular hydrogen bonding occurs between the hydroxyls of neighboring ceramide molecules in the same layer. (C–E) Hydrogen bonds marked by hashing are colored according to the H-bond donor atom. (D,E) The hydrogen bonding between the amide groups is illustrated for two types of ceramide columns. An opposite orientation of the dipoles of amide groups makes these columns antiparallel to each other in the model on B. (F) Two types of arrangement of the ceramide columns in a barrel (parallel and antiparallel).

FIGURE 2

Adaptation of the lipid bilayer with the incorporated ceramide channel versus quick collapse of the introduced bilayer puncture. (A) Cross section of the initial all-atom simulation cell at the beginning of the heating process. Columns of fatty tails of the C₁₆ ceramide channel (yellow) interdigitate with the tails (cyan) of the POPC bilayer. There are initially hydrophobic tail atoms exposed to water (thin blue lines) in a rectangular gap between the polar headgroups of POPC and C₁₆. Chloride and potassium ions (orange and green VDW spheres, respectively) were distributed randomly in the bulk water. Snapshots at the end of 10-ns simulation of the six-layer (B) and four-layer (E) 14-column models show the water pathway that adopted an hourglass shape. A characteristic segregation of aliphatic tails and the continuous lipid-water boundary lined with polar groups are observed. The bilayer accommodated the channel by bending and conformational adjustment of the phospholipids (see also Fig. 4). When, instead of the ceramide channel, a round water-filled puncture of comparable size (20 Å in diameter) was introduced into the POPC membrane (C), after ∼1.8 ns of simulation under the same conditions lipid tails of the opposite walls of the puncture fused together, interrupting the water pathway (D).

FIGURE 3

Conformational adjustments in the POPC molecules surrounding the 6_L14_C C₁₆ channel. Hydrocarbon tails of POPC (cyan) are mostly expelled from the ceramide tails (yellow). Following the lenslike shape of the ceramide channels, the outer half of the fatty chains of annular POPC reaches an angle of ∼60° to bilayer normal, whereas polar POPC headgroups (blue is nitrogen, red is oxygen, tan is phosphorus) more often orient normal to bilayer and maintain the contact with the rest of the membrane headgroup region. Their attachment to the ceramide hydroxyl and amide groups is maintained through the H-bonding with oxygens belonging to glycerol or carbonyls groups (frame 2), and/or phosphate of POPC (frame 3). A smaller fraction (∼30%) of phospholipids have choline groups in tight contact with ceramide (frame 1).

FIGURE 4

The time course of the POPC-ceramide-water system development. (A) Number of contacts between the hydrophobic tails of C₁₆ and POPC. For all the plots, estimations were performed every 10 ps of simulation, except for F where pore conductivity was calculated every 500 ps. All the parameters in plots A, D, G–L are recalculated per one ceramide molecule, and in plots B and C per one ceramide in the outer layer (28 molecules per channel). Solid and shaded lines represent simulations of 6_L14_C and 4_L14_C C₁₆ channel, respectively. Time from −2 to 0 ns represents the bilayer equilibration stage with carbons of ceramide headgroups (atoms C₁–C₅ and C₂₁) restrained harmonically in the positions of the energy-minimized structure. Black and shaded circles at the time −2 ns represent the initial value of the parameter after the energy minimization. (B,C) Number of water contacts with the nonpolar atoms of ceramide (B) and annular POPC (C). (D) Number of contacts of the hydrophilic ceramide atoms with water. (E) Number of ions in the channel. (F) Estimated ion conductance of the water pathway in the channel. (G) Number of ceramide-water hydrogen bonds. (H) Number of ceramide-water-ceramide H-bond bridges. (I,J) Number of ceramide H-bonds between the amide groups (I) and between the hydroxyl groups (J). (K) Total number of ceramide-ceramide H-bonds. (L) Total number of ceramide-ceramide H-bonded connections, including direct hydrogen bonds and H-bonded C₁₆-water-C₁₆ bridges. See Methods for parameter calculation details.

FIGURE 5

An averaged shape of the ceramide molecule and tendency toward surfaces with dual curvature. Ceramide molecules from the last six nanoseconds of 6_L14_C simulation were aligned and overlapped as described in Methods. The averaged shape of the molecule (A) is illustrated by the cyan surface that encloses the space where C₁₆ atoms are found with a probability of >50%. The dark blue core visible inside shows the most rigid zone occupied with probability >80%. Fourteen alternating contours of the top projection (in the plane of the membrane) of the averaged surface are arranged into a ring (B) with negative monolayer curvature. Six side-projection contours are assembled as a bent column with positive curvature lining an hourglass-shaped conductive pathway (C).

FIGURE 6

Dipole-dipole interactions and hydrogen bonding in the simulated ceramide channels. Snapshots of the 4_L14_C (A) and 6_L14_C (B) C₁₆ simulations in the membrane show that in the stationary phase approximately one-half of the columns preserve the antiparallel orientation of column dipoles arising from the H-bonded amide groups. The original regular hydrogen-bonding pattern (C) randomizes quickly, and on average, in the 6_L14_C C₁₆ simulation approximately one-third of the bonds are dynamically maintained (D). A new pattern of hydroxyl bonding often appears, linking both layers and columns. Water (green) participates in the interceramide hydrogen bonding, acting as a bridge, and partially compensating for the lost bonds. Amide-amide and double-bond–double-bond contact interfaces between the neighboring columns are marked by the double arrows a-a and d-d, respectively.

FIGURE 7

Ordered packing of ceramide tails correlates with stability of the columns, and contact of double bond regions stabilizes packing of columns. Snapshot from the end of 6_L14_C C₁₆ simulation (A) shows that in the most stable columns (black) hydrophobic tails of ceramide are packed in highly ordered crystal-like manner, whereas damaged columns (white) occur where tails are disordered. Stable association of the pair of columns is often maintained by the tight packing of the double-bond regions (black) of the hydrophobic tails (B) and interlayer H-bonding of the hydroxyl groups. Direct intercolumn H-bonding is more extensive over the double-bond–double-bond columns packing than over the amide-amide one (marked by the double arrows d-d and a-a, respectively).