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. 2008 Dec;95(11):5021-9.
doi: 10.1529/biophysj.108.133579. Epub 2008 Aug 1.

Free-energy Profiles of Membrane Insertion of the M2 Transmembrane Peptide From Influenza A Virus

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Free-energy Profiles of Membrane Insertion of the M2 Transmembrane Peptide From Influenza A Virus

In-Chul Yeh et al. Biophys J. .
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Abstract

The insertion of the M2 transmembrane peptide from influenza A virus into a membrane has been studied with molecular-dynamics simulations. This system is modeled by an atomically detailed peptide interacting with a continuum representation of a membrane bilayer in aqueous solution. We performed replica-exchange molecular-dynamics simulations with umbrella-sampling techniques to characterize the probability distribution and conformation preference of the peptide in the solution, at the membrane interface, and in the membrane. The minimum in the calculated free-energy surface of peptide insertion corresponds to a fully inserted, helical peptide spanning the membrane. The free-energy profile also shows that there is a significant barrier for the peptide to enter into this minimum in a nonhelical conformation. The sequence of the peptide is such that hydrophilic amino acid residues at the ends of the otherwise primarily hydrophobic peptide create a trapped, U-shaped conformation with the hydrophilic residues associated with the aqueous phase and the hydrophobic residues embedded in the membrane. Analysis of the free energy shows that the barrier to insertion is largely enthalpic in nature, whereas the membrane-spanning global minimum is favored by entropy.

Figures

FIGURE 1
FIGURE 1
(a) Snapshots of the M2 transmembrane peptide (M2-TMP) (sequence: SSDPLVVAASIIGILHLILWILDRL) from the REMD simulations in the implicit solvent at 300 K. The initial [time (t) = 0 ns] helical conformation corresponds to the experimentally determined structure. (b) The RMSD distribution of the M2-TMP in aqueous solution without the membrane obtained from the WHAM analysis on the last 2 ns of trajectories from the REMD simulation. The RMSDs are calculated with respect to the initial helical conformation. (c) The distribution of pairwise RMSD of 400 structures randomly selected from the last 2 ns of the 300-K trajectory. This distribution was calculated by forming all possible pairs between the 400 structures and calculating the RMSD for each pair. Almost half of the structures (199 out of 400) belonged to a cluster in which all members were within an RMSD of 2 Å from each other. This set includes the last configuration of the M2-TMP at 4 ns shown in a. The second-largest cluster (38 members) contains the configuration of the M2-TMP at 3.625 ns, shown in a.
FIGURE 2
FIGURE 2
Two different starting configurations of the fully extended M2-TMP. (a) The M2-TMP is preinserted perpendicularly into the membrane. (b) The M2-TMP is initially placed outside but parallel to the membrane surface.
FIGURE 3
FIGURE 3
PMF surfaces at 300 K calculated from the conformations generated by REMD simulations of the M2-TMP. (a) PMF surface as a function of the RMSD and tilt angle of the M2-TMP initially preinserted into the membrane. (b) PMF surface as a function of the RMSD and Z-position of M2-TMP initially preinserted into the membrane. A membrane-spanning configuration of the peptide is shown in atomic detail at right. The hydrophilic residues are drawn with atomic van der Waals spheres and are shown located at both sides of the membrane. (c) PMF surface as a function of the RMSD and Z-position of the M2-TMP initially placed outside of the membrane at a distance of 45 Å away from the membrane center. The minimum of the PMF is set to 0 by normalizing the probability distribution with the maximum probability. Here, a representative, trapped peptide conformation is shown with the hydrophilic residues at both ends of the peptide at the interface and the hydrophobic middle residues solvated in the membrane core.
FIGURE 4
FIGURE 4
PMF at 300 K of the M2-TMP calculated from REMD simulations combined with the center-of-mass Z-positional restraints. The peptide center-of-mass Z-position is restrained at various locations extending from the center of the membrane to the point where Z = 15 Å at 0.5-Å intervals. The final PMF surface is pieced together from restrained simulations by the WHAM analysis. (a) PMF surface as a function of the M2-TMP's Z-position and RMSD with respect to the experimental helical conformation. The overall global minimum is seen as the dark red area in the lower left-hand corner and corresponds to a helical conformation spanning the membrane with the appropriate experimental tilt angle. (b) 1D energy profiles obtained by averaging the 2D probability distributions over all RSMD values. The PMF profile as a function of the Z-position of the M2-TMP clearly shows the overall hydrophobic attraction of the solvated peptide to the membrane, but it also shows a barrier to full penetration into the membrane core. The averaged potential energy (formula image) profile shows that the partially inserted trapped peptide is stabilized by the enthalpic component outside the membrane core, and that these states are more energetically favorable than a fully inserted peptide at Z = 0 Å. The entropic contribution (formula image) to the free-energy surface was calculated from the difference between the PMF and the ensemble average potential energy (PMF formula image). This graph clearly shows that the trapped states outside the membrane core are disfavored whereas the fully inserted peptide (which is experimentally observed) is favored. The statistical uncertainties in the PMF and the average potential energy profiles are twice the standard deviation estimated by the WHAM error analysis.

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