Amphipathic antimicrobial peptides--from biophysics to therapeutics?

Amphipathic peptides are accommodated within the diffuse gradient of polarity that characterizes the interfacial regions of phospholipid bilayer membranes. Interfacial membrane interactions are key to the diverse biological functions and activities of these peptides, which encompass a large class of antimicrobial peptides, including the helical peptides magainin, melittin, and RTA3 derived from the commensal bacterium Streptococcus mitis. For these peptides in vitro efficacy (high antimicrobial activity with minimal mammalian cell toxicity, equivalent to high potential therapeutic index; PTI), can be broadly understood in relation to the thermodynamics of interfacial binding and membrane disruption in membranes having surface charges that correspond to bacterial and mammalian cell membranes, respectively. Peptides with disrupted amphipathicity resulting from a positively charged amino acid residue on the non-polar helix face, can have greatly enhanced PTI, although a balance of amphipathicity, hydrophobicity and positive charge is required for retention of high antimicrobial activity. These observations are illustrated with recent examples from the literature, and studies on RTA3 and magainin analogues from our laboratories. Despite the identification and optimisation of peptides with very good PTI, a focus on addressing toxicity upon systemic administration and poor in vivo efficacy is likely to be required to translate growing understanding of the relationships between peptide interfacial activity and effects on cells, into novel systemic therapeutics.

Observation of pyridine aggregation in aqueous solution using neutron scattering experiments and MD simulations

Neutron diffraction with isotopic substitution (NDIS) experiments have been used to examine the structuring of aqueous solutions of pyridine. A new method is described for extracting the structure factors relating to intermolecular correlations from neutron scattering experiments on liquid solutions of complex molecular species. This approach performs experiments at different concentrations and exploits the intramolecular coordination number concentration invariance (ICNCI) to separate the internal and intermolecular contributions to the total intensities. The ability of this method to deconvolute molecular and intermolecular correlations is tested and demonstrated using simulated neutron scattering results predicted from molecular dynamics simulations of aqueous solutions of the polyatomic solute pyridine in which the inter- and intramolecular terms are known. The method is then implemented using neutron scattering measurements on solutions of pyridine. The results confirm that pyridine shows a significant propensity to aggregate in solution and demonstrate the prospects for the future application of the ICNCI approach to the study of large polyatomic solutes using next-generation neutron sources and detectors.

Preferential interactions of guanidinum ions with aromatic groups over aliphatic groups

Small angle neutron scattering (SANS) and molecular dynamics (MD) simulations were used to characterize the long-range structuring (aggregation) of aqueous solutions of isopropanol (IPA) and pyridine and the effect on structuring of guanidinium chloride (GdmCl). These solutes serve as highly soluble analogs of the nonpolar aliphatic (IPA) and aromatic (pyridine) side chains of proteins. SANS data showed that isopropanol and pyridine both form clusters in water resulting from interaction between nonpolar groups of the solutes, with pyridine aggregation producing longer-range structuring than isopropanol in 3 m solutions. Addition of GdmCl at 3 m concentration considerably reduced pyridine aggregation but had no effect on isopropanol aggregation. MD simulations of these solutions support the conclusion that long-range structuring involves hydrophobic solute interactions and that Gdm(+) interacts with the planar pyridine group to suppress pyridine-pyridine interactions in solution. Hydrophobic interactions involving the aliphatic groups of isopropanol were unaffected by GdmCl, indicating that the planar and weakly hydrated Gdm(+) cation cannot make productive interactions with the highly curved or "lumpy" aliphatic groups of this solute. These observations support the conclusion that the effects of Gdm(+) ions on protein-stabilizing interactions involving aromatic amino acid side chains make significant contributions to the denaturant activity of GdmCl, whereas interactions with the "lumpy" aliphatic side chains are likely to be less important.

hERG1a/1b heteromeric currents exhibit amplified attenuation of inactivation in variant 1 short QT syndrome

Potassium channels encoded by hERG (human ether-à-go-go-related gene) underlie the cardiac rapid delayed rectifier K⁺ current (I_Kr) and hERG mutations underpin clinically important repolarization disorders. Virtually all electrophysiological investigations of hERG mutations have studied exclusively the hERG1a isoform; however, recent evidence indicates that native I_Kr channels may be comprised of hERG1a together with the hERG1b variant, which has a shorter N-terminus. Here, for the first time, electrophysiological effects were studied of a gain-of-function hERG mutation (N588K; responsible for the ‘SQT1’ variant of the short QT syndrome) on current (I_hERG1a/1b) carried by co-expressed hERG1a/1b channels. There were no significant effects of N588K on I_hERG1a/1b activation or deactivation, but N588K I_hERG1a/1b showed little inactivation up to highly positive voltages (⩽+80 mV), a more marked effect than seen for hERG1a expressed alone. I_hERG1a/1b under action potential voltage-clamp, and the effects on this of the N588K mutation, also showed differences from those previously reported for hERG1a. The amplified attenuation of I_hERG inactivation for the N588K mutation reported here indicates that the study of co-expressed hERG1a/1b channels should be considered when investigating clinically relevant hERG channel mutations, even if these reside outside of the N-terminus region.

The reversal by sulfate of the denaturant activity of guanidinium

Guanidinium (Gdm+) chloride is a powerful protein denaturant, whereas the sulfate dianion (SO42-) is a strong stabilizer of folded protein states; Gdm2SO4 is effectively neutral in its effects on protein stability. While the "neutralizing" effects of protein-stabilizing solutes on the activity of denaturants can be broadly interpreted in terms of additive effects of the solutes, recent experimental and simulation studies support a role for hetero-ion interactions in the effect of sulfate on Gdm+ denaturation [Mason, P. E.; et al. J. Phys. Chem. B 2005, 109, 24185-24196]. Here we describe an experimental strategy for testing this mechanism that involves spectroscopic analysis of the separate effects of alkali metal sulfates (Na2SO4, Rb2SO4), GdmCl, and Gdm2SO4 on the folded populations of several peptides chosen to dissect specific noncovalent contributions to the conformational stability of proteins [alanine-based helical peptides stabilized by hydrogen bonds, tryptophan zipper (trpzip) peptides stabilized largely by cross-strand indole-indole interactions]. While the trpzip peptides are highly sensitive to GdmCl denaturation, they are unaffected by NaCl, Na2SO4, or Gdm2SO4, indicating that the reversal of the denaturant activity of Gdm+ by sulfate in this case is not due to competing stabilizing (sulfate) and destabilizing (Gdm+) interactions. Gdm2SO4 was found to retain considerable denaturant activity against alanine-based alpha-helical peptides. The differences in the effects of Gdm2SO4 on the two peptide types can be understood in terms of the different mechanisms of Gdm+ denaturation of trpzip peptides and helical peptides, respectively, and the specific nature of Gdm+ and SO42- ionic "clustering" that differentially affects the ability of Gdm+ to make the molecular interactions with the peptides that underlie its denaturant activity.

Nanometer-scale ion aggregates in aqueous electrolyte solutions: guanidinium carbonate

Neutron diffraction with isotopic substitution (NDIS) experiments and molecular dynamics (MD) simulations have been used to characterize the structure of aqueous guanidinium carbonate (Gdm2CO3) solutions. The MD simulations found very strong hetero-ion pairing in Gdm2CO3 solution and were used to determine the best structural experiment to demonstrate this ion pairing. The NDIS experiments confirm the most significant feature of the MD simulation, which is the existence of strong hetero-ion pairing between the Gdm+ and CO3(2-) ions. The neutron structural data also support the most interesting feature of the MD simulation, that the hetero-ion pairing is sufficiently strong as to lead to nanometer-scale aggregation of the ions. The presence of such clustering on the nanometer length scale was then confirmed using small-angle neutron scattering experiments. Taken together, the experiment and simulation suggest a molecular-level explanation for the contrasting denaturant properties of guanidinium salts in solution.

The interaction of guanidinium ions with a model peptide

In addition to promoting unfolded protein states, the denaturants urea and guanidinium (Gdm(+)) accumulate at the surface of folded proteins at subdenaturing concentrations, a phenomenon that correlates with their denaturant activities. The enhanced accumulation of Gdm(+) relative to urea indicates different binding modes, or additional binding sites, for Gdm(+), and we recently proposed potential binding modes to protein functional groups for Gdm(+) based on the determination of the weak hydration properties of this complex cation. Here we describe molecular dynamics simulations of a model helical peptide, melittin, in a 3 M solution of GdmCl, to identify potential interactions with amino-acid side chains in a nondenatured polypeptide surface. The simulations indicate that Gdm(+) can interact with a number of planar amino-acid side chains (Arg, Trp, Gln) in a stacking manner, as well as more weakly with hydrophobic surfaces composed of aliphatic side chains, and that these interactions result in enhanced number densities of Gdm(+) at certain locations on the peptide surface. These observations provide molecular scale insight into the accumulation of Gdm(+) at protein surfaces that has previously been observed experimentally.

Neutron Diffraction and Simulation Studies of CsNO3 and Cs2CO3 Solutions

Neutron diffraction with isotopic substitution (NDIS) experiments and molecular dynamics (MD) simulations have been used to study the structuring in aqueous solution of two cesium salts, cesium carbonate, and cesium nitrate. As was previously found for guanidinium salts of carbonate, mesoscopic-scale clusters were seen to form in the Cs2CO3 solution both in the MD simulations and in the diffraction experiments. No such large scale ion clusters were found in the CsNO3 solutions in either the modeling or experiments. The results are dominated by the strength and geometry of the direct first-neighbor interactions, which explain the differences in the clustering behavior between the two solutions without need to refer to longer-range water-water structuring.

Insight into indole interactions from alkali metal chloride effects on a tryptophan zipper beta-hairpin peptide

Weakly solvated, low charge density, alkali metal cations (K+ and Rb+) destabilize tryptophan zipper (trpzip) peptides with an effectiveness (for Rb+) similar to that of the protein denaturant urea. An analysis of alkali metal cation effects on polypeptides stabilized predominantly either by hydrogen bonds or by the classical hydrophobic effect indicates that the alkali metals attenuate stabilizing interactions involving the tryptophan indole groups. Destabilization does not result from electrolyte screening of the electrostatic component of the indole-indole interaction, but is likely to involve direct interaction of the low charge density cation with the indole group in a cation-pi interaction. The observations highlight a general simplicity in the nature of molecular interactions in solution, in which stabilizing contributions to polypeptide and protein structures are attenuated by solutes of a complementary nature.

Erythromycin block of the HERG K+ channel: Accessibility to F656 and Y652

The HERG potassium channel might have a non-canonical drug binding site, distinct from the channel's inner cavity, that could be responsible for elements of closed-state pharmacological inhibition of the channel. The macrolide antibiotic erythromycin is a drug that may block unconventionally because of its size. Here we used whole-cell patch-clamp recording at 37 degrees C from heterologously expressed HERG channels in a mammalian cell line to show that erythromycin either produces a rapid open-state-dependent HERG channel inhibition, or components of both open-state-dependent and closed-state-dependent inhibition. Alanine-substitution of HERG's canonical determinants of blockade revealed that Y652 was not important as a molecular determinant of blockade, and that mutation of F656 resulted in only weak attenuation of inhibition. In computer models of the channel, erythromycin could make several direct contacts with F656, but not with Y652, in the open-state model, and erythromycin was unable to fit into a closed-state channel model.

Nanometer-Scale Ion Aggregates in Aqueous Electrolyte Solutions: Guanidinium Sulfate and Guanidinium Thiocyanate

Neutron diffraction experiments and molecular dynamics simulations are used to study the structure of aqueous solutions of two electrolytes: guanidinium sulfate (a mild protein conformation stabilizer) and guanidinium thiocyanate (a powerful denaturant). The MD simulations find the unexpected result that in the Gdm2SO4 solution the ions aggregated into mesoscopic (nanometer-scale) clusters, while no such aggregation is found in the GdmSCN solution. The neutron diffraction studies, the most direct experimental probe of solution structure, provide corroborating evidence that the predicted very strong ion pairing does occur in solutions of 1.5 m Gdm2SO4 but not in 3 m solutions of GdmSCN. A mechanism is proposed as to how this mesoscopic solution structure affects solution denaturant properties and suggests an explanation for the Hofmeister ordering of these solutions in terms of this ion pairing and the ability of sulfate to reverse the denaturant power of guanidinium.

Dissecting Contributions to the Denaturant Sensitivities of Proteins

Understanding the molecular basis for protein denaturation by urea and guanidinium chloride (GdmCl) should accommodate the observation that, on a molar basis, GdmCl is generally 2-2.5-fold more effective as a protein denaturant than urea. Previous studies [Smith, J. S., and Scholtz, J. M. (1996) Biochemistry 35, 7292-7297] have suggested that the effects of GdmCl on the stability of alanine-based helical peptides can be separated into denaturant and salt effects, since adding equimolar NaCl to urea enhanced urea-induced unfolding to an extent that was close to that of Gdm. We reinvestigated this observation using an alanine-based helical peptide (alahel) that lacks side chain electrostatic contributions to stability, and compared the relative denaturant sensitivities of this peptide with that of tryptophan zipper peptides (trpzip) whose native conformations are stabilized largely by cross-strand indole ring interactions. In contrast to the observations of Smith and Scholtz, GdmCl was only slightly more powerful as a denaturant of alahel than urea in salt-free buffer (the denaturant m value m(GdmCl)/m(urea) ratio = 1.4), and the denaturation of alahel by urea exhibited only a small dependence on NaCl or KCl. The trpzip peptides were much more sensitive to GdmCl than to urea (m(GdmCl)/m(urea) = 3.5-4). These observations indicate that the m(GdmCl)/m(urea) ratio of 2-2.5 for proteins results from a combination of effects on the multiple contributions to protein stability, for which GdmCl may be only slightly more effective than urea (e.g., hydrogen bonds) or considerably more effective than urea (e.g., indole-indole interactions).

The Structure of Aqueous Guanidinium Chloride Solutions

The combination of neutron diffraction with isotopic substitution (NDIS) experiments and molecular dynamics (MD) simulations to characterize the structuring in an aqueous solution of the denaturant guanidinium chloride is described. The simulations and experiments were carried out at a concentration of 3 m at room temperature, allowing for an examination of any propensity for ion association in a realistic solution environment. The simulations satisfactorily reproduced the principal features of the neutron scattering and indicate a bimodal hydration of the guanidinium ions, with the N-H groups making well-ordered hydrogen bonds in the molecular plane, but with the planar faces relatively deficient in interactions with water. The most striking feature of these solutions is the rich ion-ion ordering observed around the guanidinium ion in the simulations. The marked tendency of the guanidinium ions to stack parallel to their water-deficient surfaces indicates that the efficiency of this ion as a denaturant is due to its ability to simultaneously interact favorably with both water and hydrophobic side chains of proteins.

The low-potency, voltage-dependent HERG blocker propafenone--molecular determinants and drug trapping

The molecular determinants of high-affinity human ether-a-go-go-related gene (HERG) potassium channel blockade by methanesulfonanilides include two aromatic residues (Phe656 and Tyr652) on the inner helices (S6) and residues on the pore helices that face into the inner cavity, but determinants for lower-affinity HERG blockers may be different. In this study, alanine-substituted HERG channel mutants of inner cavity residues were expressed in Xenopus laevis oocytes and were used to characterize the HERG channel binding site of the antiarrhythmic propafenone. Propafenone's blockade of HERG was strongly dependent on residue Phe656 but was insensitive or weakly sensitive to mutation of Tyr652, Thr623, Ser624, Val625, Gly648, or Val659 and did not require functional inactivation. Homology models of HERG based on KcsA and MthK crystal structures, representing the closed and open forms of the channel, respectively, suggest propafenone is trapped in the inner cavity and is unable to interact exclusively with Phe656 in the closed state (whereas exclusive interactions between propafenone and Phe656 are found in the open-channel model). These findings are supported by very slow recovery of wild-type HERG channels from block at -120 mV, but extremely rapid recovery of D540K channels that reopen at this potential. The experiments and modeling suggest that the open-state propafenone binding-site may be formed by the Phe656 residues alone. The binding site for propafenone (which may involve pi-stacking interactions with two or more Phe656 side-chains) is either perturbed or becomes less accessible because of closed-channel gating. This provides further evidence for the existence of gating-induced changes in the spatial location of Phe656 side chains.

Preferential closed channel blockade of HERG potassium currents by chemically synthesised BeKm-1 scorpion toxin

The scorpion toxin peptide BeKm-1 was synthesised by fluorenylmethoxycarbonyl solid phase chemistry and folded by air oxidation. The peptide's effects on heterologous human ether-a-go-go-related gene potassium current (I(HERG)) in HEK293 cells were assessed using 'whole-cell' patch clamp. Blockade of I(HERG) by BeKm-1 was concentration-dependent, temperature-dependent, and rapid in onset and reversibility. Blockade also exhibited inverse voltage dependence, inverse dependence on duration of depolarisation, and reverse use- and frequency-dependence. Blockade by BeKm-1 and recombinant ergtoxin, another scorpion toxin known to block HERG, differed in their recovery from HERG current inactivation elicited by strong depolarisation and in their ability to block HERG when the channels were already activated. We conclude that synthetic BeKm-1 toxin blocks HERG preferentially through a closed (resting) state channel blockade mechanism, although some open channel blockade also occurs.

Effect of protein kinase A-mediated phosphorylation on the structure and association properties of the enteropathogenic Escherichia coli Tir virulence protein

Enteropathogenic Escherichia coli virulence is dependent on delivery of the translocated intimin receptor protein (Tir) into host cells. Tir phosphorylation on a single tyrosine (Tyr-474) is essential in mediating cytoskeletal rearrangement correlated with disease. Tir is also phosphorylated on other residues, with cAMP-dependent kinase (PKA) modification shown to play a role in Tir function. However, the mechanism by which nontyrosine phosphorylation affects Tir function remains unclear. In this study, analytical ultracentrifugation, SDS and native gel electrophoresis revealed that both Tir and its C-terminal domain (residues 385-550 of Tir that include the PKA substrate sites) exist in an equilibrium of monomers, dimers, and in the case of Tir, higher oligomers. PKA phosphorylation (1:300, PKA/C-Tir, mol/mol) shifted the equilibrium of C-Tir, but not Tir, predominantly to the dimeric state, whereas, at 100-fold higher concentrations of PKA the phosphorylated C-Tir was largely monomeric. This monomeric state was also produced at the lower PKA concentration and physiological ionic strength. Phosphorylation-mediated effects were achieved without significant changes in secondary structure as determined by circular dichroism spectroscopy. The data presented indicate that PKA-mediated phosphorylation induces changes in the association properties of the C-terminal domain of Tir that may facilitate Tir-Tir interactions and subsequently C-Tir-host protein interactions in vivo.

The hydration structure of guanidinium and thiocyanate ions: implications for protein stability in aqueous solution

Neutron diffraction experiments were carried out on aqueous solutions containing either guanidinium or thiocyanate ions. The first-order difference method of neutron diffraction and isotopic substitution was applied, and the hydration structures of two of nature's strongest denaturant ions were determined. Each ion is shown to interact weakly with water: Guanidinium has no recognizable hydration shell and is one of the most weakly hydrated cations yet characterized. Hydration of thiocyanate is characterized by a low coordination number involving around one hydrogen-bonded water molecule and approximately two water molecules weakly interacting through "hydration bonds." The weak hydration of these denaturant ions strongly supports suggestions that a major contribution to the denaturant effect is the preferential interaction of the denaturant with the protein surface. By contrast, solute species such as many sugars and related polyols that stabilize proteins are strongly hydrated and are thus preferentially retained in the bulk solvent and excluded from the protein surface.

Enhanced membrane permeabilization and antibacterial activity of a disulfide-dimerized magainin analogue

A cysteine substitution analogue of magainin-2 amide (magainin-F12W, N22C; denoted here as mag-N22C), and a disulfide-linked dimer prepared by air oxidation [(mag-N22C)(2)], were compared in their ability to release carboxyfluorescein (CF) from 100-nm large unilamellar vesicles (LUV) and to kill the Gram negative bacteria Stenotrophomonas maltophilia and Escherichia coli. The disulfide-dimerized peptide showed enhanced permeabilization and antimicrobial activity, when compared with the monomeric peptide, that was particularly marked at very low peptide concentrations. The enhanced CF-releasing activity of the dimer at low concentrations in vesicles results from (i) enhanced binding to negatively charged membrane surfaces and (ii) a low concentration dependence for permeabilization in the dimer compared to the monomer. The unique properties of the dimeric peptide suggest a role for structural diversity of antimicrobial peptides in frog skin, including the recent identification of a heterodimer composed of disulfide-linked amphipathic helical peptides [Batista et al. (2001) FEBS Lett. 494, 85-89]. Disulfide-dimerization of pore-forming, positively charged, amphipathic helical peptides may be a useful general approach to the generation of peptide antimicrobials having activity at very low concentrations.

Structure, location, and lipid perturbations of melittin at the membrane interface

Melittin is arguably the most widely studied amphipathic, membrane-lytic alpha-helical peptide. Although several lines of evidence suggest an interfacial membrane location at low concentrations, melittin's exact position and depth of penetration into the hydrocarbon core are unknown. Furthermore, the structural basis for its lytic action remains largely a matter of conjecture. Using a novel x-ray absolute-scale refinement method, we have now determined the location, orientation, and likely conformation of monomeric melittin in oriented phosphocholine lipid multilayers. Its helical axis is aligned parallel to the bilayer plane at the depth of the glycerol groups, but its average conformation differs from the crystallographic structure. As observed earlier for another amphipathic alpha-helical peptide, the lipid perturbations induced by melittin are remarkably modest. Small bilayer perturbations thus appear to be a general feature of amphipathic helices at low concentrations. In contrast, a dimeric form of melittin causes larger structural perturbations under otherwise identical conditions. These results provide direct structural evidence that self-association of amphipathic helices may be the crucial initial step toward membrane lysis.