Molecular dynamics simulation of transmembrane polypeptide orientational fluctuations

Abstract

The orientation and motion of a model lysine-terminated transmembrane polypeptide were investigated by molecular dynamics simulation. Recent 2H NMR studies of synthetic polypeptides with deuterated alanine side chains suggest that such transmembrane polypeptides undergo fast, axially symmetric reorientation about the bilayer normal but have a preferred average azimuthal orientation about the helix axis. In this work, interactions that might contribute to this behavior were investigated in a simulated system consisting of 64 molecules of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and one alpha-helical polypeptide with the sequence acetyl-KK-(LA)11-KK-amide. In one simulation, initiated with the peptide oriented along the bilayer normal, the system was allowed to evolve for 8.5 ns at 1 atm of pressure and a temperature of 55 degrees C. A second simulation was initiated with the peptide orientation chosen to match a set of experimentally observed alanine methyl deuteron quadrupole splittings and allowed to proceed for 10 ns. Simulated alanine methyl group orientations were found to be inequivalent, a result that is consistent with 2H NMR observations of specifically labeled polypeptides in POPC bilayers. Helix tilt varied substantially over the durations of both simulations. In the first simulation, the peptide tended toward an orientation about the helix axis similar to that suggested by experiment. In the second simulation, orientation about the helix axis tended to return to this value after an excursion. These results provide some insight into how interactions at the bilayer surface can constrain reorientation about the helix axis while accommodating large changes in helix tilt.

FIGURE 1

Root mean squared displacement (RMSD) of bilayer coordinates during the initial 600-ps bilayer simulation before insertion of the peptide.

FIGURE 2

(A) Average orientational order parameter profile for the POPC saturated chain in Simulation 1 with (•) and without (○) the polypeptide present. (B) Average orientational order parameter profile for the POPC unsaturated chain in Simulation 1 with (•) and without (○) the polypeptide present.

FIGURE 3

Peptide dihedral angles ψ (○) and ϕ (•) versus residue position along the helix backbone averaged over the trajectory for the simulation in which the peptide is initially oriented along the bilayer normal.

FIGURE 4

Axes used to define polypeptide tilt and azimuthal orientation. The polypeptide backbone is represented as a ribbon with the side chain of alanine 14 shown explicitly. Axis 1 is the bilayer normal. Axis 2 is the helix axis. The tilt, τ, is the angle between Axis 1 and Axis 2. Axis 3, the cross product of the bilayer normal and helix axis, provides a reference direction for the azimuthal orientation. Axis 4 is directed along the methyl group symmetry axis of alanine 14. Axis 5 is the projection of Axis 4 onto the plane perpendicular to the helix axis. The azimuthal orientation, ρ, is measured between Axis 5 and Axis 3. The polypeptide is shown in the orientation that gives the best fit to observed methyl deuteron splittings for alanines 8, 10, 12, 14, 16, 18, and 20. This is also the starting orientation for Simulation 2.

FIGURE 5

The time dependence of selected polypeptide orientational parameters obtained from the trajectory of Simulation 1 (peptide helix axis initially oriented along the bilayer normal). Angles shown are (A) the tilt (τ) of the helix axis with respect to the bilayer normal, (B) the azimuthal orientation (ρ) about the helix axis, (C) shows the angle (θ₁₂) between the C-CH₃ bond axis of alanine residue 12 and the bilayer normal, and (D) the angle (θ₁₄) between the C-CH₃ bond axis of alanine residue 14 and the bilayer normal.

FIGURE 6

(A) The time dependence of the helix tilt (τ) derived from the trajectory of Simulation 1 (peptide helix axis initially oriented along the bilayer normal). (B) The time dependence of for Simulation 1. (C) The time dependence of for Simulation 1. Here θ_n is the instantaneous angle between the bilayer normal and the methyl group axis for the alanine residue n and .

FIGURE 7

The time dependence of selected polypeptide orientational parameters obtained from the trajectory of Simulation 2 (initial orientation of the peptide corresponds to the best fit to observed alanine methyl deuteron quadrupole splittings). Angles shown are (A) the tilt (τ) of the helix axis with respect to the bilayer normal, (B) the azimuthal orientation (ρ) about the helix axis, (C) shows the angle (θ₁₂) between the C-CH₃ bond axis of alanine residue 12 and the bilayer normal and (D) the angle (θ₁₄) between the C-CH₃ bond axis of alanine residue 14 and the bilayer normal.

FIGURE 8

(A) The time dependence of the helix tilt (τ) derived from the trajectory of Simulation 2 (initial orientation of the peptide corresponds to the best fit to observed alanine methyl deuteron quadrupole splittings). (B) The time dependence of for Simulation 2. (C) The time dependence of for Simulation 2. Here θ_n is the instantaneous angle between the bilayer normal and the methyl group axis for the alanine residue n and .

FIGURE 9

Comparison of lysine α-carbon positions with average phosphorus positions along the z axis from the two molecular dynamics trajectories. Top panels show α-carbon positions for lysine residues 1 and 26 obtained from the trajectories of Simulation 1 (A) and Simulation 2 (C). Bottom panels show the α-carbon positions for lysine residues 2 and 25 obtained from the trajectories of Simulation 1 (B) and Simulation 2 (D). In all panels, the finer traces show the average positions of the phosphorus atoms on either side of the bilayer.

FIGURE 10

Comparison of lysine side-chain nitrogen positions with average phosphorus positions along the z axis from the two molecular dynamics trajectories. Top panels show side-chain nitrogen positions for lysine residues 1 and 26 obtained from the trajectories of Simulation 1 (A) and Simulation 2 (C). Bottom panels show side-chain nitrogen positions for lysine residues 2 and 25 obtained from the trajectories of Simulation 1 (B) and Simulation 2 (D). In all panels, the finer traces show the average positions of the phosphorus atoms on either side of the bilayer.