On the orientation of a designed transmembrane peptide: toward the right tilt angle?
The orientation of the transmembrane peptide WALP23 under small hydrophobic mismatch has been assessed through long-time-scale molecular dynamics simulations of hundreds of nanoseconds. Each simulation gives systematically large tilt angles (>30 degrees). In addition, the peptide visits various azimuthal rotations that mostly depend on the initial conditions and converge very slowly. In contrast, small tilt angles as well as a well-defined azimuthal rotation were suggested by recent solid-state 2H NMR studies on the same system. To optimally compare our simulations with NMR data, we concatenated the different trajectories in order to increase the sampling. The agreement with 2H NMR quadrupolar splittings is spectacularly better when these latter are back-calculated from the concatenated trajectory than from any individual simulation. From these ensembled-average quadrupolar splittings, we then applied the GALA method as described by Strandberg et al. (Biophys J. 2004, 86, 3709-3721), which basically derives the peptide orientation (tilt and azimuth) from the splittings. We find small tilt angles (6.5 degrees), whereas the real observed tilt in the concatenated trajectory presents a higher value (33.5 degrees). We thus propose that the small tilt angles estimated by the GALA method are the result of averaging effects, provided that the peptide visits many states of different azimuthal rotations. We discuss how to improve the method and suggest some other experiments to confirm this hypothesis. This work also highlights the need to run several and rather long trajectories in order to predict the peptide orientation from computer simulations.
Ozdirekcan
Suat
S
Department of Chemical Biology and Organic Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
Etchebest
Catherine
C
Killian
J Antoinette
JA
Fuchs
Patrick F J
PF
D015060:1,2-Dipalmitoylphosphatidylcholine / Q000737:chemistry; D000465:Algorithms; D003198:Computer Simulation; D004134:Dimyristoylphosphatidylcholine / Q000737:chemistry; D008051:Lipid Bilayers / Q000737:chemistry*; D008565:Membrane Proteins / Q000737:chemistry*; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods; D013816:Thermodynamics
D008051:Lipid Bilayers; D008565:Membrane Proteins; D015060:1,2-Dipalmitoylphosphatidylcholine; D004134:Dimyristoylphosphatidylcholine