Structural and Thermodynamic Insight into Spontaneous Membrane-Translocating Peptides Across Model PC/PG Lipid Bilayers (original) (raw)
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Biophysical Journal, 2009
All simulations were performed using the GROMACS package (1), on a cluster of dual Opteron processors. The simulated system consists of 4 Arg-9 peptides, 92 DOPC phospholipid molecules and 8795 water molecules. The overall temperature of the water, lipids, and peptides were kept constant, coupling independently each group of molecules at 323 K with a Berendsen thermostat (2). The pressure was coupled to a Berendsen barostat at 1 atm separately in every direction (2). The temperature and pressure time constants of the coupling were 0.2 ps and 2 ps, respectively. An external electric field of 0.05 V nm -1 was included pointing towards the distal side of the bilayer to qualitatively take into account the external electrostatic potential included in the experiments (3). The integration of the equations of motion was performed using a leap frog algorithm with a time step of 2 fs. Periodic boundary conditions were implemented in all systems. A cut-off of 1 nm was implemented for the Lennard-Jones and the direct space part of the Ewald sum for Coulombic interactions. The Fourier space part of the Ewald splitting was computed using the particle-mesh Ewald method (4), with a grid length of 0.11 nm on the side and a cubic spline interpolation. Periodic boundary conditions and Ewald summations that do not include the surface term ensure system electro neutrality (5). We used the SPC/E model for water (6), the parameters from Berger et al. for the lipids , and the parameters from the GROMACS force field (1) for the peptide.
Simulations of a membrane-anchored peptide: structure, dynamics, and influence on bilayer properties
Biophysical journal, 2004
A three-dimensional structure of a model decapeptide is obtained by performing molecular dynamics simulations of the peptide in explicit water. Interactions between an N-myristoylated form of the folded peptide anchored to dipalmitoylphosphatidylcholine fluid phase lipid membranes are studied at different applied surface tensions by molecular dynamics simulations. The lipid membrane environment influences the conformational space explored by the peptide. The overall secondary structure of the anchored peptide is found to deviate at times from its structure in aqueous solution through reversible conformational transitions. The peptide is, despite the anchor, highly mobile at the membrane surface with the peptide motion along the bilayer normal being integrated into the collective modes of the membrane. Peptide anchoring moderately alters the lateral compressibility of the bilayer by changing the equilibrium area of the membrane. Although membrane anchoring moderately affects the elas...
Biophysical Journal, 2002
The membrane insertion behavior of two peptides, Magainin2 and M2␦, was investigated by applying the Monte Carlo simulation technique to a theoretical model. The model included many novel aspects, such as a new semi-empirical lipid bilayer model and a new set of semi-empirical transfer energies, which reproduced the experimental insertion behavior of Magainin2 and M2␦ without parameter fitting. Additionally, we have taken into account diminished internal (intramolecular) hydrogen bonding at the N-and C-termini of helical peptides. All simulations were carried out at 305 K, above the membrane thermal phase transition temperature, and at pH 7.0. The peptide equilibrium conformations are discussed for a range of bilayers with tail polarities varying from octanol-like to alkane-like. Probability distributions of the individual amino-acidresidue positions show the dynamic nature of these equilibrium conformations. Two different insertion mechanisms for M2␦, and a translocation mechanism for Magainin2, are described. A study of the effect of bilayer thickness on M2␦ insertion suggests a critical thickness above which insertion is unfavorable. Additionally, we did not need to use an orientational potential or array of hard cylinders to persuade M2␦ to insert perpendicular to the membrane surface. Instead, we found that diminished internal hydrogen bonding in the helical conformation anchored the termini in the headgroups and resulted in a nearly perpendicular orientation.
Variation of the Lateral Mobility of Transmembrane Peptides with Hydrophobic Mismatch
The Journal of Physical Chemistry B, 2010
A hydrophobic mismatch between protein length and membrane thickness can lead to a modification of protein conformation, function, and oligomerization. To study the role of hydrophobic mismatch, we have measured the change in mobility of transmembrane peptides possessing a hydrophobic helix of various length d π in lipid membranes of giant vesicles. We also used a model system where the hydrophobic thickness of the bilayers, h, can be tuned at will. We precisely measured the diffusion coefficient of the embedded peptides and gained access to the apparent size of diffusing objects. For bilayers thinner than d π , the diffusion coefficient decreases, and the derived characteristic sizes are larger than the peptide radii. Previous studies suggest that peptides accommodate by tilting. This scenario was confirmed by ATR-FTIR spectroscopy. As the membrane thickness increases, the value of the diffusion coefficient increases to reach a maximum at h ≈ d π. We show that this variation in diffusion coefficient is consistent with a decrease in peptide tilt. To do so, we have derived a relation between the diffusion coefficient and the tilt angle, and we used this relation to derive the peptide tilt from our diffusion measurements. As the membrane thickness increases, the peptides raise (i.e., their tilt is reduced) and reach an upright position and a maximal mobility for h ≈ d π. Using accessibility measurements, we show that when the membrane becomes too thick, the peptide polar heads sink into the interfacial region. Surprisingly, this "pinching" behavior does not hinder the lateral diffusion of the transmembrane peptides. Ultimately, a break in the peptide transmembrane anchorage is observed and is revealed by a "jump" in the D values.
The Journal of Physical Chemistry B, 2009
Some membrane-active peptides undergo drastic changes of conformation and/or orientation on water-lipid interfaces. Among the most notable examples is penetratin (pAntp), a short cell-penetrating peptide. To delineate the driving forces behind pAntp-membrane interactions, we used, in this series of two papers, a combined modeling approach that includes: (1) molecular dynamics simulations of pAntp in zwitterionic and anionic lipid bilayers, (2) free energy perturbation calculations of model residue-residue contacts, and (3) detailed analysis of spatial hydrophobic/hydrophilic properties of the peptide/membrane systems. In this first article, we consider the role of conformational plasticity of the peptide in different membrane surroundings, as well as the ability of pAntp to form stable specific residue-residue interactions and make contacts with particular lipids. It was shown that pAntp displays a complicated conformational behavior. Basic and aromatic residues of the peptide form energetically favorable pairs in water and apolar environments, which facilitate membrane insertion of the peptide and stabilization of the membrane-bound state. These residues are also capable of "trapping" lipid heads, thereby affecting their dynamics and microscopic organization of the water-lipid interface. The latter effect is much more pronounced in anionic bilayers and might be related to the initial stage of peptide-induced destabilization of lipid bilayers.
Biophysical Journal, 2009
Cell-penetrating peptides (CPPs) have recently attracted much interest due to their apparent ability to penetrate cell membranes in an energy-independent manner. Here molecular-dynamics simulation techniques were used to study the interaction of two CPPs: penetratin and the TAT peptide with 1,2-Dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and 1,2-dioleoyl-snglycero-3-phosphocholine (DOPC) phospolipid bilayers shed light on alternative mechanisms by which these peptides might cross biological membranes. In contrast to previous simulation studies of charged peptides interacting with lipid bilayers, no spontaneous formation of transmembrane pores was observed. Instead, the simulations suggest that the peptides may enter the cell by micropinocytosis, whereby the peptides induce curvature in the membrane, ultimately leading to the formation of small vesicles within the cell that encapsulate the peptides. Specifically, multiple peptides were observed to induce large deformations in the lipid bilayer that persisted throughout the timescale of the simulations (hundreds of nanoseconds). Pore formation could be induced in simulations in which an external potential was used to pull a single penetratin or TAT peptide into the membrane. With the use of umbrella-sampling techniques, the free energy of inserting a single penetratin peptide into a DPPC bilayer was estimated to bẽ 75 kJmol À1 , which suggests that the spontaneous penetration of single peptides would require a timescale of at least seconds to minutes. This work also illustrates the extent to which the results of such simulations can depend on the initial conditions, the extent of equilibration, the size of the system, and the conditions under which the simulations are performed. The implications of this with respect to the current systems and to simulations of membrane-peptide interactions in general are discussed.
Membrane Perturbation Induced by Interfacially Adsorbed Peptides
Biophysical Journal, 2004
The structural and energetic characteristics of the interaction between interfacially adsorbed (partially inserted) a-helical, amphipathic peptides and the lipid bilayer substrate are studied using a molecular level theory of lipid chain packing in membranes. The peptides are modeled as ''amphipathic cylinders'' characterized by a well-defined polar angle. Assuming two-dimensional nematic order of the adsorbed peptides, the membrane perturbation free energy is evaluated using a cell-like model; the peptide axes are parallel to the membrane plane. The elastic and interfacial contributions to the perturbation free energy of the ''peptide-dressed'' membrane are evaluated as a function of: the peptide penetration depth into the bilayer's hydrophobic core, the membrane thickness, the polar angle, and the lipid/peptide ratio. The structural properties calculated include the shape and extent of the distorted (stretched and bent) lipid chains surrounding the adsorbed peptide, and their orientational (C-H) bond order parameter profiles. The changes in bond order parameters attendant upon peptide adsorption are in good agreement with magnetic resonance measurements. Also consistent with experiment, our model predicts that peptide adsorption results in membrane thinning. Our calculations reveal pronounced, membrane-mediated, attractive interactions between the adsorbed peptides, suggesting a possible mechanism for lateral aggregation of membrane-bound peptides. As a special case of interest, we have also investigated completely hydrophobic peptides, for which we find a strong energetic preference for the transmembrane (inserted) orientation over the horizontal (adsorbed) orientation.
Coexistence of a Two-States Organization for a Cell-Penetrating Peptide in Lipid Bilayer
Biophysical Journal, 2005
Primary amphipathic cell-penetrating peptides transport cargoes across cell membranes with high efficiency and low lytic activity. These primary amphipathic peptides were previously shown to form aggregates or supramolecular structures in mixed lipid-peptide monolayers, but their behavior in lipid bilayers remains to be characterized. Using atomic force microscopy, we have examined the interactions of P (a) , a primary amphipathic cell-penetrating peptide which remains a-helical whatever the environment, with dipalmitoylphosphatidylcholine (DPPC) bilayers. Addition of P (a) at concentrations up to 5 mol % markedly modified the supported bilayers topography. Long and thin filaments lying flat at the membrane surface coexisted with deeply embedded peptides which induced a local thinning of the bilayer. On the other hand, addition of P (a) only exerted very limited effects on the corresponding liposome's bilayer physical state, as estimated from differential scanning calorimetry and diphenylhexatriene fluorescence anisotropy experiments. The use of a gel-fluid phase separated supported bilayers made of a dioleoylphosphatidylcholine/dipalmitoylphosphatidylcholine mixture confirmed both the existence of long filaments, which at low peptide concentration were preferentially localized in the fluid phase domains and the membrane disorganizing effects of 5 mol % P (a). The simultaneous two-states organization of P (a) , at the membrane surface and deeply embedded in the bilayer, may be involved in the transmembrane carrier function of this primary amphipathic peptide.