Characterization of Antibiotic Peptide Pores Using Cryo-EM and Comparison to Neutron Scattering
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164 Biophysical Journal Volume 97 July 2009 164–172 Characterization of Antibiotic Peptide Pores Using Cryo-EM and Comparison to Neutron Scattering Mikyung Han,† Yuan Mei,‡ Htet Khant,† and Steven J. Ludtke†* †Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas; and ‡Department of Physics and Astronomy, Rice University, Houston, Texas ABSTRACT Magainin, a 23-residue antibiotic peptide, interacts directly with the lipid bilayer leading to cell lysis in a strongly concentration-dependent fashion. Utilizing cryo-electron microscopy, we have directly observed magainin interacting with synthetic DMPC/DMPG membranes. Visual examination shows that visibly unperturbed vesicles are often found adjacent to vesicles that are lysed or porous, demonstrating that magainin disruption is a highly stochastic process. Quantitatively, power spectra of large numbers of porous vesicles can be averaged together to produce the equivalent of an electron scattering curve, which can be related to theory, simulation, and published neutron scattering experiments. We demonstrate that magainin- induced pores in lipid vesicles have a mean diameter of ~80 A˚ , compatible with earlier reported results in multilayer stacks. In addition to establishing a connection between experiments in multilayer stacks and vesicles, this also demonstrates that computed power spectra from windowed-out regions of cryo-EM images can be compared to neutron scattering data in a mean- ingful way, even though the pores of interest cannot yet be individually identified in images. Cryo-EM offers direct imaging of systems in configurations closely related to in vivo conditions, whereas neutron scattering has a greater variety of mechanisms for specific contrast variation via D2O and deuterated lipids. Combined, the two mechanisms support each other, and provide a clearer picture of such ‘soft’ systems than either could provide alone. INTRODUCTION Magainin 2 is a 23-residue antibiotic peptide isolated from solution, and is believed to initially interact specifically the skin of Xenopus laevis (1). Unlike most commercial anti- with acidic lipids in the bacterial membrane through electro- biotics, which interact with specific protein targets, magainin static interactions (22). Association with the lipid-water 2 and other peptides in this class have been shown to interact interface induces folding into a single-domain, amphipathic directly with the lipid bilayer (2,3). Peptides in this class are a-helix oriented parallel to the surface of the bilayer. This ubiquitous, with hundreds of identified members (4) over surface adsorption causes local thinning of the bilayer a wide range of species, and they play a critical role in the (13,23). Once a critical concentration of surface-adsorbed early stages of host defense (5). Magainin 2 lyses a wide peptides is achieved, the peptides spontaneously rotate 90, range of both Gram-negative and gram-positive bacteria at forming the boundary of an aqueous pore (Fig. 1)(18,24). concentrations two-orders-of-magnitude lower than those It was previously shown by neutron scattering (12) that the required to lyse red blood cells (6,7). Magainin has also pores formed by magainin were larger than anticipated been demonstrated to lyse a range of cancer cells (8,9)at (~71 A˚ diameter), and hypothesized that the lipid bilayer concentrations at which normal tissue is unaffected. For itself was also involved in channel formation, with magainin these reasons, peptides in this class are under active develop- acting as basically a stabilizing agent for a natural transient ment by the pharmaceutical industry. Because they interact membrane defect. However, much of the work leading to directly with the lipid bilayer, it is believed that bacteria these previous conclusions was performed using multilayer will be largely unable to develop resistance to this class of stacks of lipid bilayers rather than lipid vesicles. That is, antibiotics. many bilayers are forced into close contact in these experi- A wide range of techniques have been used to elucidate ments, and it was unknown what implications this might magainin’s interaction with the lipid bilayer, including have, since, in vivo, the peptides would be interacting with fluorescence leakage experiments (10), oriented circular isolated vesiclelike membranes. However, the fact that in dichroism (11), in-plane neutron and x-ray scattering and some cases interactions between neighboring layers or pore- lamellar x-ray diffraction (12,13), solid-state nuclear pore correlation were observed in the multilayer stack exper- magnetic resonance (14,15), Raman spectroscopy (16), and iments (25) implied that there may be some differences simulation (17), just to name a few. Several reviews are between the two systems. available with a more complete history of this active field Cryo-EM and neutron/x-ray scattering have been used (18–21). Magainin exists as a disordered chain in aqueous together in a cooperative approach in several cases (26–28), and in fact, x-ray solution scattering curves are a highly accurate method for CTF amplitude correction in Submitted October 29, 2008, and accepted for publication April 27, 2009. cryo-EM single particle reconstructions (29,30). *Correspondence: [email protected] Editor: Edward H. Egelman. Ó 2009 by the Biophysical Society 0006-3495/09/07/0164/9 $2.00 doi: 10.1016/j.bpj.2009.04.039 Visualizing Peptide Pores with Cryo-EM 165 For comparison with previous neutron scattering experiments, we desired a high surface density of pores. The 400-mM concentration used here would correspond to a lipid/peptide molar ratio of ~25:1 if all magainin were associated with the lipid vesicles. Lipid concentration was determined by phosphorus analysis after extrusion (34). Vitrification Before vitrification, all specimen preparation was carried out at 33C, well above the 24C phase transition of the DMPC/DMPG mixture (35). It has been previously demonstrated that the vitrification process of the thin films on a TEM grid is so rapid (~10,000CsÀ1), that the system effectively remains in a snapshot of its solution conformation (36,37). Previous exper- iments with lipid-dense systems have demonstrated that lipid preparations vitrified from higher than the phase-transition temperature will not change state upon vitrification (38). Vitrification was performed in LN2 cooled liquid ethane using standard procedures on a Vitrobot (FEI, Hillsboro, OR). FIGURE 1 Schematic of possible modes of interaction between amphi- pathic peptides and lipid bilayers. At low concentration, peptides adsorb Electron cryo-microscopy to the surface of the lipid bilayer. At higher concentrations, a fraction of peptide molecules rotate to form pores. If the peptide is oriented perpendic- All specimens were imaged on a JEM2010F electron microscope (JEOL, ular to the membrane, two models must be considered: the barrel-stave chan- Peabody, MA) equipped with a field emission gun operated at 200 keV. nels or the toroidal channels. Previous neutron scattering evidence led to the Images were collected at 50 K magnification, and defocus ranged from 1.2 À1 hypothesis of the toroidal form for magainin channels based on arguments to 3.4 mm, putting the first zero crossing of the CTF at q ¼ 0.2–0.4 A˚ , about the amount of peptide available for pore formation. respectively. Images were collected on a 4 K Â 4 K charge-coupled device (CCD) camera (model No. US4000, Gatan, Pleasanton, CA) giving images at 2.2 A˚ /pixel. MATERIALS AND METHODS Image analysis Data conventions Images of vesicles were manually selected (Fig. 2); in the presence of magai- Throughout this article, we make use of momentum transfer, q, as tradition- nin, 69 CCD frames produced 304 magainin-perturbed vesicle images; for the ally used in the scattering and physics communities in preference to the control experiment with no magainin, 64 CCD frames yielded 537 vesicle spatial frequency, s, traditionally used in cryo-EM. The relationship is images. Power spectra were determined by computing the two-dimensional simply s ¼ q/2p. Spatial frequency is simply the reciprocal of the real-space fast Fourier transform (FFT) of each masked image, rotationally averaging periodicity of the oscillation. That is, a sinusoidal oscillation with a real- the results, then averaging the one-dimensional power spectra from the set space wavelength of 10 nm would have a spatial frequency of s ¼ 0.1 nmÀ1. of images. The image analysis was performed using the EMAN software package (39). Vesicles from CCD frames were selected using the EMAN Materials command ‘‘boxer’’ with a 320 Â 320 box size. Each image was normalized such that the mean density around the edge was zero, then padded with zeroes 1,2-Dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1,2-dimyris- to 640 Â 640 pixels using the EMAN command ‘‘proc2d’’. The central region toyl-sn-glycero-3-[phospho-rac-(1-glycerol)] (DMPG) were purchased from of each vesicle was masked using a circular mask (radius ¼ 150 pixels). Next, Avanti Polar Lipids (Alabaster, AL). Magainin 2 was purchased from Sigma- the squared modulus of the FFT was computed for each image to produce an Aldrich Chemical (St. Louis, MO). estimated power spectrum. The masking process eliminates the strong signal produced by the bilayer edge of each vesicle, and limits the curvature of the Sample preparation vesicle surface area under consideration. To reduce noise levels, many such power spectra are then averaged together from many images. The final two- Liposomes were prepared by mixing a 1:1 ratio of DMPC/DMPG in chloro- dimensional spectrum is then rotationally averaged to produce a one-dimen- form/methanol (1:1) and allowing the solvent to evaporate under a dry argon sional power spectrum. This aggregate process is completed using the gas flow. The films were kept under light vacuum overnight to remove re- ‘‘fftavg’’ program in EMAN (39). The error bars are simply the standard maining traces of organic solvent. The resulting dried lipid films were deviation of the mean value at each spatial frequency.