Evaluation of the hybrid resolution PACE model for the study of folding, insertion, and pore formation of membrane associated peptides

Abstract

The PACE force field presents an attractive model for conducting molecular dynamics simulations of membrane-protein systems. PACE is a hybrid model, in which lipids and solvents are coarse-grained consistent with the MARTINI mapping, while proteins are described by a united atom model. However, given PACE is linked to MARTINI, which is widely used to study membranes, the behavior of proteins interacting with membranes has only been limitedly examined in PACE. In this study, PACE is used to examine the behavior of several peptides in membrane environments, namely WALP peptides, melittin and influenza hemagglutinin fusion peptide (HAfp). Overall, we find PACE provides an improvement over MARTINI for modeling helical peptides, based on the membrane insertion energetics for WALP16 and more realistic melittin pore dynamics. Our studies on HAfp, which forms a helical hairpin structure, do not show the hairpin structure to be stable, which may point toward a deficiency in the model. © 2017 Wiley Periodicals, Inc.

Keywords: WALP; coarse-grained models; hybrid resolution models; influenza hemagglutinin fusion peptide; melittin; membranes.

Figure 1

Folding of WALP16 and WALP19 from solution. a) Initial structure for the WALP16 folding simulation. b) WALP16 and WALP19 (c) membrane bound centroid structures. d) Normalized contact probability for WALP16 during the initial membrane binding (first 1.3 μs) phase of simulation. e–f) Helical probabilities for WALP16 (e) and WALP19 (f) for when the peptide in solution and membrane bound. Helical probabilities were computed over 5 μs of data. The simulations were divided into 1 μs blocks from which the mean probabilities and standard errors (represented by the errorbars), were computed. TRP residues are shown in yellow in (b) and (c). Membrane coloring: tails=silver, glycerol=cyan, phosphate=red, choline=blue.

Figure 2

WALP folding from a TM state. a) Initial configuration for WALP16 TM folding simulation. WALP16 initially folds to a TM helix (b), but transitions to a surface bound helical hairpin (c) after ~4 μs. WALP19 (d) and WALP23 (e) remain in a TM helical state for the full 10 μs simulations. f) Tilt angle distributions for WALP peptides. Distributions were calculated between 500 ns and 10 μs for WALP19 and WALP23 and between 500 ns and 4 μs for WALP16.

Figure 3

WALP16 insertion energetics. a) The PMF of WALP16 membrane insertion shows equal free energy minima at the TM and interface states. Centroid structures from the umbrella sampling windows corresponding to minima and maxima are indicated by roman numerals and shown below. b) The peptide end-to-end distance and helicity for the umbrella sampling window when the center of mass separation was restrained to 0 nm (TM) and 1.5 nm (interfacial). Data was analyzed between 200–1000 ns, the helicity values are smoothed over 5 ns, to remove the discreteness of the helicity values.

Figure 4

TM melittin tetramer in PACE and MARTINI. Water (solid lines) and phosphate (dashed lines) number density in PACE (a) and MARTINI (b) for each μs of the simulations. The water density is multiplied by four to account of the CG water mapping. Densities were computed using 100 slabs. c) Density of water at the center of the bilayer using 11 slabs, again multiplied by 4. d–f) Snapshots from the PACE simulation at various time points, CG waters are represented as cyan spheres and lipid phosphate groups as red spheres.

Figure 5

HAFP Analysis. a) Centroid structure from simulation initiated in hairpin conformation on the membrane. b). Kink angles for simulations started from hairpin structure in solution and on membrane. c) NMR determined structure, the H-bonds involving GLY12 and the distance between ASP19 and GLU11 are shown. d) Structure at 10 ns, for simulation starting in hairpin on the membrane. Distances between ASP19 and GLU11 side chain oxygens as well as H-bonds involving GLU11 and GLY12 are shown. e) Distance of first 10ns of membrane bound simulations of the distance pairs denoted in subfigures (c) and (d).