Hydrophilic neighborhood of the S4 helix in the lipid bilayer. (a) Stabilizing hydrogen-bond network of water (red) and lipid phosphates (yellow) that connect the Arg guanidinium groups (blue) to the bilayer interface. H bonds are indicated by white dots. (b) MD trajectories of the number of hydrogen-bond contacts per guanidinium group. Total number of H bonds (Top), water H bonds (Middle), and lipid phosphate groups (Bottom). These data indicate that the H-bond capacities of the guanidinium groups are saturated throughout the simulation. (c) Survival functions for water molecules in the hydrophilic neighborhood of each Arg and in the equivalent volume of bulk water (see Supporting Text). A survival function calculation taking into account the overlap of coordination shells for Arg-9, Arg-12, and Arg-15 to form a single hydrophilic neighborhood is indicated by the black curve, which is remarkably similar to the survival function for Arg-18, consistent with the idea of two similar, but independent, solvation environments. From these data, the mean residence times for waters are found to be 364 ps for Arg-9, 92 ps for Arg-12, 2,172 ps for Arg-15, and 1,130 ps for Arg-18 compared with 6 ps for bulk water.

Electrostatic potential distributions obtained by averaging 800 configurations spanning the last 8 ns of the simulation. The zero of potential is taken as the water. (a) Density map for the electrostatic potential distribution distant from the peptide (48 Å). The spatial distribution is characteristic of thermally disordered lipid bilayers, with relatively uniform contributions from the hydrocarbon core (red, yellow, green) and hydrated headgroup (blue) regions. The constant potential of the water map is shown in purple (see scale between a and b). (see also Fig. 5 and Movie 2) (b) Electrostatic potential distribution in a region centered on the peptide. The largest values of electrostatic potential (>1,000 mV) for the system are observed over a highly circumscribed region near the bilayer center (white). (c) 3D representations of two iso-potential surfaces are included in a space-filling representation similar to Fig. 1, confirming that the highest values of electrostatic potential occur in the vicinity of Arg-15 and Arg-18. The white surface (1,000 mV) surrounds the hydrophobic gap between these two residues. The purple surface (100 mV) shows the potential near the outer edge of the bilayer.

MD simulation of a model S4 voltage-sensor peptide (GGPGLGLFRLVRLLRFLRILLII-GPGG) in a palmitoyloleoylphosphatidylcholine bilayer. This model was chosen because it is the one studied by Hessa et al. (19). The simulation was carried out to understand the physical basis for the stable insertion of S4 across the ER by the translocon. (a) Cut-away view of the simulation system, showing the bilayer distortion around the peptide and the contacts between phosphate groups, water molecules, and arginine side chains. Red indicates water; yellow, phosphocholine headgroups; green, acyl chains; white, GGPG... GPGG flanks; silver, non-Arg S4 residues; blue, arginine side chains. (b) MD trajectories of the S4 helix tilt angle relative to the bilayer normal (Upper) and the S4 helix center of mass relative to the center of mass of the lipid bilayer (Lower). The average values of the tilt angle and center of mass are, respectively, 4.67 ± 0.47 (SD) degrees and –2.37 ± 0.85 (SD) Å. (c) The phospholipids in the vicinity of the S4 helix that form H bonds with the guanidinium groups (see Fig. 2). The system configuration is the same as in a, except that only the three lipids participating in the H bonds are shown. These three lipids formed a stable H-bonded complex with S4 that remained unbroken during the last 5 ns of the simulation (see Fig. 2b). One of the lipids spans the entire membrane, in a configuration akin to a lipid in a monolayer, underscoring the extreme distortion of the bilayer in the vicinity of S4.

Hydrophobic gap between Arg-15 and Arg-18. (a) Space-filling representation of the hydrophilic neighborhood of the S4 helix represented as Connolly surfaces. Red indicates water; yellow, phosphocholine headgroups; green, acyl chains; white, GGPG... GPGG flanks; silver, non-Arg S4 residues; blue, guanidinium groups. (b) MD trajectory of the hydrophobic gap, which is defined as the instantaneous distance parallel to the membrane normal, between any two H-bond forming atoms (nonhydrogens) on opposite sides of the bilayer center. The possible atoms are guanidinium nitrogens, water oxygens, and lipid phosphates. The average gap distance is 9.46 ± 0.86 (SD) Å.