Role of the fast kinetics of pyroglutamate-modified amyloid-ß oligomers in membrane binding and membrane permeability.

Membrane permeability to ions and small molecules is believed to be a critical step in the pathology of Alzheimer's disease (AD). Interactions of oligomers formed by amyloid-ß (Aß) peptides with the plasma cell membrane are believed to play a fundamental role in the processes leading to membrane permeability. Among the family of Aßs, pyroglutamate (pE)-modified Aß peptides constitute the most abundant oligomeric species in the brains of AD patients. Although membrane permeability mechanisms have been studied for full-length Aß1-40/42 peptides, these have not been sufficiently characterized for the more abundant AßpE3-42 fragment. Here we have compared the adsorbed and membrane-inserted oligomeric species of AßpE3-42 and Aß1-42 peptides. We find lower concentrations and larger dimensions for both species of membrane-associated AßpE3-42 oligomers. The larger dimensions are attributed to the faster self-assembly kinetics of AßpE3-42, and the lower concentrations are attributed to weaker interactions with zwitterionic lipid headgroups. While adsorbed oligomers produced little or no significant membrane structural damage, increased membrane permeabilization to ionic species is understood in terms of enlarged membrane-inserted oligomers. Membrane-inserted AßpE3-42 oligomers were also found to modify the mechanical properties of the membrane. Taken together, our results suggest that membrane-inserted oligomers are the primary species responsible for membrane permeability.

Antimicrobial properties of amyloid peptides.

More than two dozen clinical syndromes known as amyloid diseases are characterized by the buildup of extended insoluble fibrillar deposits in tissues. These amorphous Congo red staining deposits known as amyloids exhibit a characteristic green birefringence and cross-ß structure. Substantial evidence implicates oligomeric intermediates of amyloids as toxic species in the pathogenesis of these chronic disease states. A growing body of data has suggested that these toxic species form ion channels in cellular membranes causing disruption of calcium homeostasis, membrane depolarization, energy drainage, and in some cases apoptosis. Amyloid peptide channels exhibit a number of common biological properties including the universal U-shape ß-strand-turn-ß-strand structure, irreversible and spontaneous insertion into membranes, production of large heterogeneous single-channel conductances, relatively poor ion selectivity, inhibition by Congo red, and channel blockade by zinc. Recent evidence has suggested that increased amounts of amyloids not only are toxic to its host target cells but also possess antimicrobial activity. Furthermore, at least one human antimicrobial peptide, protegrin-1, which kills microbes by a channel-forming mechanism, has been shown to possess the ability to form extended amyloid fibrils very similar to those of classic disease-forming amyloids. In this paper, we will review the reported antimicrobial properties of amyloids and the implications of these discoveries for our understanding of amyloid structure and function.

Gap controlled plasmon-dielectric coupling effects investigated with single nanoparticle-terminated atomic force microscope probes.

Precise positioning of a plasmonic nanoparticle (NP) near a small dielectric surface is not only necessary for understanding gap-dependent interactions between a metal and dielectric but it is also a critical component in building ultrasensitive molecular rulers and force sensing devices. In this study we investigate the gap-dependent scattering of gold and silver NPs by controllably depositing them on an atomic force microscope (AFM) tip and monitoring their scattering within the evanescent field of a tin dioxide nanofiber waveguide. The enhanced distance-dependent scattering profiles due to plasmon-dielectric coupling effects show similar decays for both gold and silver NPs given the strong dependence of the coupling on the decaying power in the near-field. Experiments and simulations also demonstrate that the NPs attached to the AFM tips act as free NPs, eliminating optical interference typically observed from secondary dielectric substrates. With the ability to reproducibly place individual plasmonic NPs on an AFM tip, and optically monitor near-field plasmon-dielectric coupling effects, this approach allows a wide-variety of light-matter interactions studies to be carried out on other low-dimensional nanomaterials.

Activity and architecture of pyroglutamate-modified amyloid-ß (AßpE3-42) pores.

Among the family of Aß peptides, pyroglutamate-modified Aß (AßpE) peptides are particularly associated with cytotoxicity in Alzheimer's disease (AD). They represent the dominant fraction of Aß oligomers in the brains of AD patients, but their accumulation in the brains of elderly individuals with normal cognition is significantly lower. Accumulation of AßpE plaques precedes the formation of plaques of full-length Aß (Aß1-40/42). Most of these properties appear to be associated with the higher hydrophobicity of AßpE as well as an increased resistance to enzymatic degradation. However, the important question of whether AßpE peptides induce pore activity in lipid membranes and their potential toxicity compared with other Aß pores is still open. Here we examine the activity of AßpE pores in anionic membranes using planar bilayer electrical recording and provide their structures using molecular dynamics simulations. We find that AßpE pores spontaneously induce ionic current across the membrane and have some similar properties to the other previously studied pores of the Aß family. However, there are also some significant differences. The onset of AßpE3-42 pore activity is generally delayed compared with Aß1-42 pores. However, once formed, AßpE3-42 pores produce increased ion permeability of the membrane, as indicated by a greater occurrence of higher conductance electrical events. Structurally, the lactam ring of AßpE peptides induces a change in the conformation of the N-terminal strands of the AßpE3-42 pores. While the N-termini of wild-type Aß1-42 peptides normally reside in the bulk water region, the N-termini of AßpE3-42 peptides tend to reside in the hydrophobic lipid core. These studies provide a first step to an understanding of the enhanced toxicity attributed to AßpE peptides.

All-d-Enantiomer of ß-Amyloid Peptide Forms Ion Channels in Lipid Bilayers.

Alzheimer's disease (AD) is the most common type of senile dementia in aging populations. Amyloid ß (Aß)-mediated dysregulation of ionic homeostasis is the prevailing underlying mechanism leading to synaptic degeneration and neuronal death. Aß-dependent ionic dysregulation most likely occurs either directly via unregulated ionic transport through the membrane or indirectly via Aß binding to cell membrane receptors and subsequent opening of existing ion channels or transporters. Receptor binding is expected to involve a high degree of stereospecificity. Here, we investigated whether an Aß peptide enantiomer, whose entire sequence consists of d-amino acids, can form ion-conducting channels; these channels can directly mediate Aß effects even in the absence of receptor-peptide interactions. Using complementary approaches of planar lipid bilayer (PLB) electrophysiological recordings and molecular dynamics (MD) simulations, we show that the d-Aß isomer exhibits ion conductance behavior in the bilayer indistinguishable from that described earlier for the l-Aß isomer. The d isomer forms channel-like pores with heterogeneous ionic conductance similar to the l-Aß isomer channels, and the d-isomer channel conductance is blocked by Zn(2+), a known blocker of l-Aß isomer channels. MD simulations further verify formation of ß-barrel-like Aß channels with d- and l-isomers, illustrating that both d- and l-Aß barrels can conduct cations. The calculated values of the single-channel conductance are approximately in the range of the experimental values. These findings are in agreement with amyloids forming Ca(2+) leaking, unregulated channels in AD, and suggest that Aß toxicity is mediated through a receptor-independent, nonstereoselective mechanism.

Potential role of atomic force microscopy in systems biology.

Systems biology is a quantitative approach for understanding a biological system at its global level through systematic perturbation and integrated analysis of all its components. Simultaneous acquisition of information data sets pertaining to the system components (e.g., genome, proteome) is essential to implement this approach. There are limitations to such an approach in measuring gene expression levels and accounting for all proteins in the system. The success of genomic studies is critically dependent on polymerase chain reaction (PCR) for its amplification, but PCR is very uneven in amplifying the samples, ineffective in scarce samples and unreliable in low copy number transcripts. On the other hand, lack of amplifying techniques for proteins critically limits their identification to only a small fraction of high concentration proteins. Atomic force microscopy (AFM), AFM cantilever sensors, and AFM force spectroscopy in particular, could address these issues directly. In this article, we reviewed and assessed their potential role in systems biology.

Structural convergence among diverse, toxic beta-sheet ion channels.

Recent studies show that an array of beta-sheet peptides, including N-terminally truncated Abeta peptides (Abeta(11-42/17-42)), K3 (a beta(2)-microglobulin fragment), and protegrin-1 (PG-1) peptides form ion channel-like structures and elicit single channel ion conductance when reconstituted in lipid bilayers and induce cell damage through cell calcium overload. Striking similarities are observed in the dimensions of these toxic channels irrespective of their amino acid sequences. However, the intriguing question of preferred channel sizes is still unresolved. Here, exploiting ssNMR-based, U-shaped, beta-strand-turn-beta-strand coordinates, we modeled truncated Abeta peptide (p3) channels with different sizes (12- to 36-mer). Molecular dynamics (MD) simulations show that optimal channel sizes of the ion channels presenting toxic ionic flux range between 16- and 24-mer. This observation is in good agreement with channel dimensions imaged by AFM for Abeta(9-42), K3 fragment, and PG-1 channels and highlights the bilayer-supported preferred toxic beta-channel sizes and organization, regardless of the peptide sequence.