Fusogenic Alzheimer's peptide fragment Abeta (29-42) in interaction with lipid bilayers: secondary structure, dynamics, and specific interaction with phosphatidyl ethanolamine polar heads as revealed by solid-state NMR

Exploring interactions between lipids and amyloid-forming proteins: A review on applying fluorescence and NMR techniques

A hallmark of Alzheimer's, Parkinson's, and other amyloid diseases is the assembly of amyloid proteins into amyloid aggregates or fibrils. In many cases, the formation and cytotoxicity of amyloid assemblies are associated with their interaction with cell membranes. Despite studied for many years, the characterization of the interaction is challenged for reasons on the multiple aggregation states of amyloid-forming proteins, transient and weak interactions in the complex system. Although several strategies such as computation biology, spectroscopy, and imaging methods have been performed, there is an urgent need to detail the molecular mechanism in different time scales and high resolutions. This review highlighted the recent applications of fluorescence, solution and solid-state NMR in exploring the interactions between amyloid protein and membranes attributing to their advantages of high sensitivity and atomic resolution.

Computational Modeling and Validation of Thermally Induced Electrical Capacitance Changes for Lipid Bilayer Membranes Irradiated by Pulsed Lasers

Neural stimulation has widespread applications in investigating brain functions, restoring impaired neural functions, and treating numerous neurological/psychiatric diseases. Use of infrared pulses to stimulate neurons (infrared neural stimulation) offers a direct and non-invasive technique. Recent research has demonstrated that transient heating associated with the absorption of infrared light by the local aqueous medium around the cell membrane can stimulate nerves. One mechanism for this stimulation is due to a thermally induced increase in the membrane electrical capacitance, which causes cell depolarization as well as action potential production under certain physiological conditions. A theoretical and computational model helps better understand the mechanism of thermally induced electrical capacitance changes and optimize the stimulus parameters. In this article, we develop the existing theoretical models for membrane electrical capacitance and its thermally induced changes. We improve the formulation of Gouy-Chapman-Stern theory by Genet et al. and Shapiro et al. with the addition of a diffuse layer to the electrical double layer and by modifying the relation of Stern layer capacitance, to calculate the membrane capacitive charge and capacitive current. We also present a new method to calculate the membrane electrical capacitance and the rate of its thermally induced changes. In our calculations, two new factors are considered including the temperature dependence of the surface charge density and the hydrophobic core dielectric constant of the lipid bilayer. Our developed model predicts rates of 0.3 and 0.26%/°C for the thermally induced capacitance changes of the artificial lipid bilayer under two different sets of conditions previously reported by Shapiro et al. and Carvalho-de-Souza et al., respectively. Our model is in very good agreement with the corresponding experimental values given by these groups. The presented model is also able to calculate the membrane capacitive currents and investigate the voltage dependence of this current.

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

Alzheimer's disease (AD) is the most common type of senile dementia in aging populations. Amyloid β (Aβ)-mediated dysregulation of ionic homeostasis is the prevailing underlying mechanism leading to synaptic degeneration and neuronal death. Aβ-dependent ionic dysregulation most likely occurs either directly via unregulated ionic transport through the membrane or indirectly via Aβ 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 Aβ peptide enantiomer, whose entire sequence consists of d-amino acids, can form ion-conducting channels; these channels can directly mediate Aβ 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-Aβ isomer exhibits ion conductance behavior in the bilayer indistinguishable from that described earlier for the l-Aβ isomer. The d isomer forms channel-like pores with heterogeneous ionic conductance similar to the l-Aβ isomer channels, and the d-isomer channel conductance is blocked by Zn(2+), a known blocker of l-Aβ isomer channels. MD simulations further verify formation of β-barrel-like Aβ channels with d- and l-isomers, illustrating that both d- and l-Aβ 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 Aβ toxicity is mediated through a receptor-independent, nonstereoselective mechanism.

Molecular dynamics simulations of low-ordered alzheimer β-amyloid oligomers from dimer to hexamer on self-assembled monolayers

Accumulation of small soluble oligomers of amyloid-β (Aβ) in the human brain is thought to play an important pathological role in Alzheimer's disease. The interaction of these Aβ oligomers with cell membrane and other artificial surfaces is important for the understanding of Aβ aggregation and toxicity mechanisms. Here, we present a series of exploratory molecular dynamics (MD) simulations to study the early adsorption and conformational change of Aβ oligomers from dimer to hexamer on three different self-assembled monolayers (SAMs) terminated with CH(3), OH, and COOH groups. Within the time scale of MD simulations, the conformation, orientation, and adsorption of Aβ oligomers on the SAMs is determined by complex interplay among the size of Aβ oligomers, the surface chemistry of the SAMs, and the structure and dynamics of interfacial waters. Energetic analysis of Aβ adsorption on the SAMs reveals that Aβ adsorption on the SAMs is a net outcome of different competitions between dominant hydrophobic Aβ-CH(3)-SAM interactions and weak CH(3)-SAM-water interactions, between dominant electrostatic Aβ-COOH-SAM interactions and strong COOH-SAM-water interactions, and between comparable hydrophobic and electrostatic Aβ-OH-SAM interactions and strong OH-SAM-water interactions. Atomic force microscopy images also confirm that all of three SAMs can induce the adsorption and polymerization of Aβ oligomers. Structural analysis of Aβ oligomers on the SAMs shows a dramatic increase in structural stability and β-sheet content from dimer to trimer, suggesting that Aβ trimer could act as seeds for Aβ polymerization on the SAMs. This work provides atomic-level understanding of Aβ peptides at interface.

Lipid composition influences the release of Alzheimer's amyloid β-peptide from membranes

The behavior of the amyloid β-peptide (Aβ) within a membrane environment is integral to its toxicity and the progression of Alzheimer's disease. Ganglioside GM1 has been shown to enhance the aggregation of Aβ, but the underlying mechanism is unknown. Using atomistic molecular dynamics simulations, we explored the interactions between the 40-residue alloform of Aβ (Aβ(40) ) and several model membranes, including pure palmitoyloleoylphosphatidylcholine (POPC) and palmitoyloleoylphosphatidylserine (POPS), an equimolar mixture of POPC and palmitoyloleoylphosphatidylethanolamine (POPE), and lipid rafts, both with and without GM1, to understand the behavior of Aβ(40) in various membrane microenvironments. Aβ(40) remained inserted in POPC, POPS, POPC/POPE, and raft membranes, but in several instances exited the raft containing GM1. Aβ(40) interacted with GM1 largely through hydrogen bonding, producing configurations containing β-strands with C-termini that, in some cases, exited the membrane and became exposed to solvent. These observations provide insight into the release of Aβ from the membrane, a previously uncharacterized process of the Aβ aggregation pathway.

Polymorphic structures of Alzheimer's β-amyloid globulomers

Background

Misfolding and self-assembly of Amyloid-β (Aβ) peptides into amyloid fibrils is pathologically linked to the development of Alzheimer's disease. Polymorphic Aβ structures derived from monomers to intermediate oligomers, protofilaments, and mature fibrils have been often observed in solution. Some aggregates are on-pathway species to amyloid fibrils, while the others are off-pathway species that do not evolve into amyloid fibrils. Both on-pathway and off-pathway species could be biologically relevant species. But, the lack of atomic-level structural information for these Aβ species leads to the difficulty in the understanding of their biological roles in amyloid toxicity and amyloid formation.

Methods and Findings

Here, we model a series of molecular structures of Aβ globulomers assembled by monomer and dimer building blocks using our peptide-packing program and explicit-solvent molecular dynamics (MD) simulations. Structural and energetic analysis shows that although Aβ globulomers could adopt different energetically favorable but structurally heterogeneous conformations in a rugged energy landscape, they are still preferentially organized by dynamic dimeric subunits with a hydrophobic core formed by the C-terminal residues independence of initial peptide packing and organization. Such structural organizations offer high structural stability by maximizing peptide-peptide association and optimizing peptide-water solvation. Moreover, curved surface, compact size, and less populated β-structure in Aβ globulomers make them difficult to convert into other high-order Aβ aggregates and fibrils with dominant β-structure, suggesting that they are likely to be off-pathway species to amyloid fibrils. These Aβ globulomers are compatible with experimental data in overall size, subunit organization, and molecular weight from AFM images and H/D amide exchange NMR.

Conclusions

Our computationally modeled Aβ globulomers provide useful insights into structure, dynamics, and polymorphic nature of Aβ globulomers which are completely different from Aβ fibrils, suggesting that these globulomers are likely off-pathway species and explaining the independence of the aggregation kinetics between Aβ globulomers and fibrils.

Transformation of amyloid β(1-40) oligomers into fibrils is characterized by a major change in secondary structure

Alzheimer's disease (AD) is a neurodegenerative disorder occurring in the elderly. It is widely accepted that the amyloid beta peptide (Aβ) aggregation and especially the oligomeric states rather than fibrils are involved in AD onset. We used infrared spectroscopy to provide structural information on the entire aggregation pathway of Aβ(1-40), starting from monomeric Aβ to the end of the process, fibrils. Our structural study suggests that conversion of oligomers into fibrils results from a transition from antiparallel to parallel β-sheet. These structural changes are described in terms of H-bonding rupture/formation, β-strands reorientation and β-sheet elongation. As antiparallel β-sheet structure is also observed for other amyloidogenic proteins forming oligomers, reorganization of the β-sheet implicating a reorientation of β-strands could be a generic mechanism determining the kinetics of protein misfolding. Elucidation of the process driving aggregation, including structural transitions, could be essential in a search for therapies inhibiting aggregation or disrupting aggregates.

Alzheimer Abeta(1-42) monomer adsorbed on the self-assembled monolayers

Amyloid-beta (Abeta) peptide aggregation on the cell membranes is a key pathological event responsible for neuron cell death in Alzheimer's disease (AD). We present a collection of molecular docking and molecular dynamics simulations to study the conformational dynamics and adsorption behavior of Abeta monomer on the self-assembled monolayer (SAM), in comparison to Abeta structure in bulk solution. Two distinct Abeta conformations (i.e., alpha-helix and beta-hairpin) are selected as initial structures to mimic different adsorption states, whereas four SAM surfaces with different end groups in hydrophobicity and charge distribution are used to examine the effect of surface chemistry on Abeta structure and adsorption. Simulation results show that alpha-helical monomer displays higher structural stability than beta-hairpin monomer on all SAMs, suggesting that the preferential conformation of Abeta monomer could be alpha-helical or random structure when bound to surfaces. Structural stability and adsorption behavior of Abeta monomer on the SAMs originates from competitive interactions between Abeta and SAM and between SAM and interfacial water, which involve the conformation of Abeta, the surface chemistry of SAM, and the structure and dynamics of interfacial waters. The relative net binding affinity of Abeta with the SAMs is in the favorable order of COOH-SAM > NH(2)-SAM > CH(3)-SAM > OH-SAM, highlighting the importance of electrostatic and hydrophobic interactions for driving Abeta adsorption at the SAMs, but both interactions contribute differently to each Abeta-SAM complex. This work provides parallel insights into the understanding of Abeta structure and aggregation on cell membrane.

Simultaneous single-molecule fluorescence and conductivity studies reveal distinct classes of Abeta species on lipid bilayers

The extracellular senile plaques prevalent in brain tissue in Alzheimer's disease (AD) are composed of amyloid fibrils formed by the Abeta peptide. These fibrils have been traditionally believed to be featured in neurotoxicity; however, numerous recent studies provide evidence that cytotoxicity in AD may be associated with low-molecular weight oligomers of Abeta that associate with neuronal membranes and may lead to membrane permeabilization and disruption of the ion balance in the cell. The underlying mechanism leading to disruption of the membrane is the subject of many recent studies. Here we report the application of single-molecule optical detection, using fluorescently labeled human Alphabeta40, combined with membrane conductivity measurements, to monitor the interaction of single-oligomeric peptide structures with model planar black lipid membranes (BLMs). In a qualitative study, we show that the binding of Alphabeta to the membrane can be described by three distinctly different behaviors, depending on the Alphabeta monomer concentration. For concentrations much below 10 nM, there is uniform binding of monomers over the surface of the membrane with no evidence of oligomer formation or membrane permeabilization. Between 10 nM and a few hundred nanomolar, the uniform monomer binding is accompanied by the presence of peptide species ranging from dimers to small oligomers. The dimers are not found to permeabilize the membrane, but the larger oligomers lead to permeabilization with individual oligomers producing ion conductances of <10 pS/pore. At higher concentrations, perhaps beyond physiologically relevant concentrations, larger extended and dynamic structures are found with large conductances (hundreds of picosiemens), suggesting a major disruption of the membrane.

Comparative molecular dynamics study of Abeta adsorption on the self-assembled monolayers

The adsorption and aggregation of the amyloid-beta (Abeta) peptides on the cell membrane plays a causal role in the pathogenesis of Alzheimer's disease. Here, we report all-atom molecular dynamics (MD) simulations to study the interactions of Abeta oligomer with self-assembled monolayers (SAMs) terminated with hydrophobic CH(3) and hydrophilic OH functional groups, with particular interests in how surface chemistry and Abeta orientation affect the adsorption behavior of Abeta. Simulation results show that the CH(3)-SAM has a stronger binding affinity to Abeta than the OH-SAM does, although both surfaces can induce Abeta adsorption. Regardless of the characteristics of the surface, the hydrophobic C-terminal region is more likely to be adsorbed on the SAMs, indicating a preferential orientation and interface for Abeta adsorption. Structural and energetic comparison among six Abeta-SAM systems further reveals that Abeta orientation, SAM surface hydrophobicity, and interfacial waters all determine Abeta adsorption behavior on the surface, highlighting the importance of hydrophobic interactions at the interface. This work may provide parallel insights into the interactions of Abeta with lipid bilayers.

Study of the specific lipid binding properties of Abeta 11-22 fragment at endosomal pH

Increasing evidence implicates interactions between Abeta peptide and lipids in the development of Alzheimer's disease. More generally, Abeta peptide interactions with membranes seem to depend on the composition of the lipid bilayer and the structural features of the peptide. One key parameter should be pH, since one site of intracellular Abeta peptide production and/or accumulation is likely to be endosomes. This intracellular endosomal accumulation was suggested to contribute to disease progression. In this paper, we report a study on the 11-22 amphiphilic domain of Abeta in interaction with model membrane; this region contains most of the charged residues of the N-terminal domain of Abeta. We show that the peptide charge, and more precisely the protonation state of histidines 13 and/or 14, is important for the interaction with lipids. Hence, it is only at endosomal pH that a conformational change of the peptide is observed in the presence of negatively charged lipid vesicles, that is, when both lipid headgroups and histidines can interact through electrostatic interactions. Specific interactions of the fragment with phosphatidylserine and to a lesser extent with phosphatidylcholine, but not phosphatidylethanolamine, are further evidenced by the Langmuir monolayer technique. From our results, we suggest that the protonation state of His residues could have a role in the pathogenic surface interaction of the whole Abeta peptide with membranes.

Membrane-targeted strategies for modulating APP and Abeta-mediated toxicity

Alzheimer's disease (AD) is a progressive neurodegenerative disease characterized by numerous pathological features including the accumulation of neurotoxic amyloid-β (Aβ) peptide. There is currently no effective therapy for AD, but the development of therapeutic strategies that target the cell membrane is gaining increased interest. The amyloid precursor protein (APP) from which Aβ is formed is a membrane-bound protein, and Aβ production and toxicity are both membrane mediated events. This review describes the critical role of cell membranes in AD with particular emphasis on how the composition and structure of the membrane and its specialized regions may influence toxic or benign Aβ/APP pathways in AD. The putative role of copper (Cu) in AD is also discussed, and we highlight how targeting the cell membrane with Cu complexes has therapeutic potential in AD.

Induction of negative curvature as a mechanism of cell toxicity by amyloidogenic peptides: the case of islet amyloid polypeptide

The death of insulin-producing beta-cells is a key step in the pathogenesis of type 2 diabetes. The amyloidogenic peptide Islet Amyloid Polypeptide (IAPP, also known as amylin) has been shown to disrupt beta-cell membranes leading to beta-cell death. Despite the strong evidence linking IAPP to the destruction of beta-cell membrane integrity and cell death, the mechanism of IAPP toxicity is poorly understood. In particular, the effect of IAPP on the bilayer structure has largely been uncharacterized. In this study, we have determined the effect of the amyloidogenic and toxic hIAPP(1-37) peptide and the nontoxic and nonamyloidogenic rIAPP(1-37) peptide on membranes by a combination of DSC and solid-state NMR spectroscopy. We also characterized the toxic but largely nonamyloidogenic rIAPP(1-19) and hIAPP(1-19) fragments. DSC shows that both amyloidogenic (hIAPP(1-37)) and largely nonamyloidogenic (hIAPP(1-19) and rIAPP(1-19)) toxic versions of the peptide strongly favor the formation of negative curvature in lipid bilayers, while the nontoxic full-length rat IAPP(1-37) peptide does not. This result was confirmed by solid-state NMR spectroscopy which shows that in bicelles composed of regions of high curvature and low curvature, nontoxic rIAPP(1-37) binds to the regions of low curvature while toxic rIAPP(1-19) binds to regions of high curvature. Similarly, solid-state NMR spectroscopy shows that the toxic rIAPP(1-19) peptide significantly disrupts the lipid bilayer structure, whereas the nontoxic rIAPP(1-37) does not have a significant effect. These results indicate IAPP may induce the formation of pores by the induction of excess membrane curvature and can be used to guide the design of compounds that can prevent the cell-toxicity of IAPP. This mechanism may be important to understand the toxicity of other amyloidogenic proteins. Our solid-state NMR results also demonstrate the possibility of using bicelles to measure the affinity of biomolecules for negatively or positively curved regions of the membrane, which we believe will be useful in a variety of biochemical and biophysical investigations related to the cell membrane.

Disordered proteins: biological membranes as two-dimensional aggregation matrices

Aberrant folded proteins and peptides are hallmarks of amyloidogenic diseases. However, the molecular processes that cause these proteins to adopt non-native structures in vivo and become cytotoxic are still largely unknown, despite intense efforts to establish a general molecular description of their behavior. Clearly, the fate of these proteins is ultimately linked to their immediate biochemical environment in vivo. In this review, we focus on the role of biological membranes, reactive interfaces that not only affect the conformational stability of amyloidogenic proteins, but also their aggregation rates and, probably, their toxicity. We first provide an overview of recent work, starting with findings regarding the amphiphatic amyloid-beta protein (Abeta), which give evidence that membranes can directly promote aggregation, and that the effectiveness in this process can be related to the presence of specific neuronal ganglioside lipids. In addition, we discuss the implications of recent research (medin as an detailed example) regarding putative roles of membranes in the misfolding behavior of soluble, non-amphiphatic proteins, which are attracting increasing interest. The potential role of membranes in exerting the toxic action of misfolded proteins will also be highlighted in a molecular context. In this review, we discuss novel NMR-based approaches for exploring membrane-protein interactions, and findings obtained using them, which we use to develop a molecular concept to describe membrane-mediated protein misfolding as a quasi-two-dimensional process rather than a three-dimensional event in a biochemical environment. The aim of the review is to provide researchers with a general understanding of the involvement of membranes in folding/misfolding processes in vivo, which might be quite universal and important for future research concerning amyloidogenic and misfolding proteins, and possible ways to prevent their toxic actions.

Membrane interactions and the effect of metal ions of the amyloidogenic fragment Abeta(25-35) in comparison to Abeta(1-42)

Abeta(1-42) peptide, found as aggregated species in Alzheimer's disease brain, is linked to the onset of Alzheimer's disease. Many reports have linked metals to inducing Abeta aggregation and amyloid plaque formation. Abeta(25-35), a fragment from the C-terminal end of Abeta(1-42), lacks the metal coordinating sites found in the full-length peptide and is neurotoxic to cortical cortex cell cultures. We report solid-state NMR studies of Abeta(25-35) in model lipid membrane systems of anionic phospholipids and cholesterol, and compare structural changes to those of Abeta(1-42). When added after vesicle formation, Abeta(25-35) was found to interact with the lipid headgroups and slightly perturb the lipid acyl-chain region; when Abeta(25-35) was included during vesicle formation, it inserted deeper into the bilayer. While Abeta(25-35) retained the same beta-sheet structure irrespective of the mode of addition, the longer Abeta(1-42) appeared to have an increase in beta-sheet structure at the C-terminus when added to phospholipid liposomes after vesicle formation. Since the Abeta(25-35) fragment is also neurotoxic, the full-length peptide may have more than one pathway for toxicity.

Solid-state NMR as a method to reveal structure and membrane-interaction of amyloidogenic proteins and peptides

It is important to understand the Amyloid fibril formation in view of numerous medical and biochemical aspects. Structural determination of amyloid fibril has been extensively studied using electron microscopy. Subsequently, solid state NMR spectroscopy has been realized to be the most important means to determine not only microscopic molecular structure but also macroscopic molecular packing. Molecular structure of amyloid fibril was first predicted to be parallel beta-sheet structure, and subsequently, was further refined for Abeta(1-40) to be cross beta-sheet with double layered in register parallel beta-sheet structure by using solid state NMR spectroscopy. On the other hand, anti-parallel beta-sheet structure has been reported to short fragments of Abeta-amyloid and other amyloid forming peptides. Kinetic study of amyloid fibril formation has been studied using a variety of methods, and two-step autocatalytic reaction mechanism used to explain fibril formation. Recently, stable intermediates or proto-fibrils have been observed by electron microscope (EM) images. Some of the intermediates have the same microscopic structure as the matured fibril and subsequently change to matured fibrils. Another important study on amyloid fibril formation is determination of the interaction with lipid membranes, since amyloid peptide are cleaved from amyloid precursor proteins in the membrane interface, and it is reported that amyloid lipid interaction is related to the cytotoxicity. Finally it is discussed how amyloid fibril formation can be inhibited. Firstly, properly designed compounds are reported to have inhibition ability of amyloid fibril formation by interacting with amyloid peptide. Secondly, it is revealed that site directed mutation can inhibit amyloid fibril formation. These inhibitors were developed by knowing the fibril structure determined by solid state NMR.

The N-terminal 12 Residue Long Peptide of HIV gp41 is the Minimal Peptide Sufficient to Induce Significant T-cell-like Membrane Destabilization in Vitro

Here, we predicted the minimal N-terminal fragment of gp41 required to induce significant membrane destabilization using IMPALA. This algorithm is dedicated to predict peptide interaction with a membrane. We based our prediction of the minimal fusion peptide on the tilted peptide theory. This theory proposes that some protein fragments having a peculiar distribution of hydrophobicity adopt a tilted orientation at a hydrophobic/hydrophilic interface. As a result of this orientation, tilted peptides should disrupt the interface. We analysed in silico the membrane-interacting properties of gp41 N-terminal peptides of different length derived from the isolate BRU and from an alignment of 710 HIV strains available on the Los Alamos National Laboratory. Molecular modelling results indicated that the 12 residue long peptide should be the minimal fusion peptide. We then assayed lipid-mixing and leakage of T-cell-like liposomes with N-terminal peptides of different length as first challenge of our predictions. Experimental results confirmed that the 12 residue long peptide is necessary and sufficient to induce membrane destabilization to the same extent as the 23 residue long fusion peptide. In silico analysis of some fusion-incompetent mutants presented in the literature further revealed that they cannot insert into a modelled membrane correctly tilted. According to this work, the tilted peptide model appears to explain at least partly the membrane destabilization properties of HIV fusion peptide.