Intermolecular packing and alignment in an ordered beta-hairpin antimicrobial peptide aggregate from 2D solid-state NMR

The aggregation and packing of a membrane-disruptive beta-hairpin antimicrobial peptide, protegrin-1 (PG-1), in the solid state are investigated to understand its oligomerization and hydrogen-bonding propensity. Incubation of PG-1 in phosphate buffer saline produced well-ordered nanometer-scale aggregates, as indicated by 13C and 15N NMR line widths, chemical shifts, and electron microscopy. Two-dimensional 13C and 1H spin diffusion experiments using C-terminus strand and N-terminus strand labeled peptides indicate that the beta-hairpin molecules in these ordered aggregates are oriented parallel to each other with like strands lining the intermolecular interface. In comparison, disordered and lyophilized peptide samples are randomly packed with both parallel and antiparallel alignments. The PG-1 aggregates show significant immobilization of the Phe ring near the beta-turn, further supporting the structural ordering. The intermolecular packing of PG-1 found in the solid state is consistent with its oligomerization in lipid bilayers. This solid-state aggregation approach may be useful for determining the quaternary structure of peptides in general and for gaining insights into the oligomerization of antimicrobial peptides in lipid bilayers in particular.     

Why Is the C-terminus of Abeta(1-42) more unfolded than that of Abeta(1-40)? Clues from hydrophobic interaction

Abeta(1-40) and Abeta(1-42) are the main forms of amyloid beta (Abeta) peptides in the brain of Alzheimer's patients; however, the latter possesses much stronger aggregation and deposition propensity than the former, which is partially attributed to the more unfolded C-terminus of Abeta(1-42) than that of Abeta(1-40). To explore the physical basis underlying the different dynamic behaviors of both Abeta peptides, parallel molecular dynamics (MD) simulations on Abeta(1-40) and Abeta(1-42) were performed to investigate their thermal unfolding processes. It is revealed that the addition of residues 41 and 42 in Abeta(1-42) disrupts the C-terminal hydrophobic core, which triggers the unraveling of the C-terminal helix of Abeta(1-42). This conclusion is supported by the MD simulation on the I41A mutant of Abeta(1-42), in which the C-terminal helix possesses relatively higher conformational stability than that of wild type Abeta(1-42) owing to the change in hydrophobic interaction patterns.     

Phage display affords peptides that modulate beta-amyloid aggregation

As the population ages, the need to develop methods to understand and intercept the processes responsible for protein aggregation diseases is becoming more urgent. The aggregation of the protein beta-amyloid (Abeta) has been implicated in Alzheimer's Disease (AD); however, whether the toxic species is a large, insoluble aggregate or some lower order form is not yet known. Agents that can modulate the aggregation state of Abeta could resolve this controversy by facilitating our understanding of the consequences of aggregation and its underlying mechanism. To date, however, ligands that bind to specific forms of Abeta have not been identified. To address this deficiency, we tested whether phage display could yield such ligands by screening libraries against Abeta in two different states: monomeric or highly aggregated. Intriguingly, the peptides selected had different effects on Abeta aggregation. Peptides selected for binding to monomeric Abeta did not perturb aggregation, but those selected using highly aggregated Abeta increase the rate of aggregation drastically. The latter also alter the morphology of the resulting aggregate. The ability of a peptide to promote aggregation correlated with its affinity for the N-terminal 10 residues of Abeta. This result indicates that the mechanism by which the peptides influence aggregation is related to their affinity for the Abeta N-terminus. Thus, the identification of compounds that bind to this Abeta section can afford agents that affect aggregation. Moreover, the data suggest that endogenous ligands that interact with the N-terminal region can influence the propensity of Abeta to form aggregates and the morphology of those that form. Our data highlight the utility of phage display for identifying ligands that bind to target proteins in different states, and they indicate that such agents can be used to perturb protein aggregation.     

Alzheimer amyloid beta(1-40) peptide: interactions with cationic gemini and single-chain surfactants

The aggregation of amyloid beta-peptide [Abeta(1-40)] into fibril is a key pathological process associated with Alzheimer's disease. The effect of cationic gemini surfactant hexamethylene-1,6-bis-(dodecyldimethylammonium bromide) [C(12)H(25)(CH(3))(2)N(CH(2))(6)N(CH(3))(2)C(12)H(25)]Br(2) (designated as C(12)C(6)C(12)Br(2)) and single-chain cationic surfactant dodecyltrimethylammonium bromide (DTAB) on the Alzheimer amyloid beta-peptide Abeta(1-40) aggregation behavior was studied by microcalorimetry, circular dichroism (CD), and atomic force microscopy (AFM) measurements at pH 7.4. Without addition of surfactant, 0.5 g/L Abeta(1-40) mainly exists in dimeric state. It is found that the addition of the monomers of C(12)C(6)C(12)Br(2) and DTAB may cause the rapid aggregation of Abeta(1-40) and the fibrillar structures are observed by CD spectra and the AFM images. Due to the repulsive interaction among the head groups of surfactants and the formation of a small hydrophobic cluster of surfactant molecules, the fibrillar structure is disrupted again as the surfactant monomer concentration is increased, whereas globular species are observed in the presence of micellar solution. Different from single-chain surfactant, C(12)C(6)C(12)Br(2) has a much stronger interaction with Abeta(1-40) to generate larger endothermic energy at much lower surfactant concentration and has much stronger ability to induce the aggregation of Abeta(1-40).     

Micellization of surfactin and its effect on the aggregate conformation of amyloid beta(1-40)

The aggregation of amyloid beta-peptide (Abeta(1-40)) into fibrils is a key pathological process associated with Alzheimer's disease. This work has investigated the micellization process of biosurfactant surfactin and its effect on the aggregation behavior of Abeta(1-40). The results show that surfactin has strong self-assembly ability to form micelles and the micelles tend to form larger aggregates. Surfactin adopts a beta-turn conformation at low micelle concentration but a beta-sheet conformation at high micelle concentration. The effect of surfactin on the Abeta(1-40) aggregation behavior exhibits a strong concentration-dependent fashion. Below the critical micelle concentration of surfactin, the electrostatic binding of surfactin monomers on Abeta(1-40) causes Abeta(1-40) molecules to unfold. Assisted by the hydrophobic interaction among surfactin monomers on the Abeta(1-40) chain, the conformation of Abeta(1-40) transfers to the beta-sheet structure, which promotes the formation of fibrils. At low surfactin micelle concentration, besides the electrostatic force and hydrophobic interaction, hydrogen bonds formed between surfactin micelles and adjacent Abeta(1-40) peptide chains may promote the ordered organization of these Abeta(1-40) peptide chains, thus leading to the formation of beta-sheets and fibrils to a great extent. At high surfactin micelle concentration, the separating of Abeta(1-40) chains by the excessive surfactin micelles and the aggregation of the complexes of Abeta(1-40) with surfactin micelles inhibit the formation of beta-sheets and fibrils.     

Hydrogen exchange studies on Alzheimer's amyloid-beta peptides by mass spectrometry using matrix-assisted laser desorption/ionization and electrospray ionization

The conformation and aggregation behavior of synthetic Alzheimer's amyloid peptides (Abeta) has been investigated using hydrogen-deuterium exchange measured by electrospray ionization mass spectrometry and matrix-assisted laser desorption/ionization mass spectrometry. Mass spectrometric fragmentation of deuterated Abeta peptides was carried out by collision-induced dissociation, inlet fragmentation, and post-source decay. In contrast to the C-terminally truncated peptides Abeta(1-40) and Abeta(1-36) showing full hydrogen-deuterium exchange, Abeta(1-42) and the pyroglutamyl peptide Pyr(3)-Abeta(3-42) produced more complex signal patterns resulting from the formation of beta-sheet-structured oligomers having 18-20 strongly protected protons. Using mass spectrometric fragmentation the results show that the reduced isotope exchange of Abeta(1-42) can be attributed to the central part of the chain comprising residues 8-23. This confirms involvement of the hydrophobic binding domain LVFFA in the course of Abeta aggregation and demonstrates that hydrogen-deuterium exchange in combination with mass spectrometry is well suited for structural analysis of monomeric and reversibly associated amyloid peptides using picomole quantities of material.     

Morphological Characterization of the Molecular Superstructure of Polyphenylene Ethynylene Derivatives

Two different polyphenylene ethynylene derivatives, one partly hydrophobic and one hydrophilic, were investigated with a combination of X-ray and light scattering techniques and hydrodynamic techniques, as well as scanning force microscopy and transmission electron microscopy to elucidate their molecular structure and aggregation behavior in tetrahydrofuran and water, respectively. It turns out that both polymers possess a rod-like molecular architecture which, however, is the basis of a cascade of aggregation steps. Both, electron microscopy and X-ray analysis support the concept of a primary back-to-back aggregation of polymer chains into cylindrically shaped aggregates with high anisometry. The thickness of these aggregates was between 4.0 and 4.5 nm. The aggregates of the hydrophobic polymer further associate into fibrils and these fibrils form clusters of globular shape, though with high internal anisometry. Copyright 1999 Academic Press.     

Modulation of fibrillogenesis of amyloid beta(1-40) peptide with cationic gemini surfactant

Modulation of the fibrillogenesis of amyloid peptide Abeta(1-40) with the cationic gemini surfactant hexamethylene-1,6-bis(dodecyldimethylammonium bromide) (C(12)C(6)C(12)Br(2)) has been studied. Both UV-vis and AFM results show that C(12)C(6)C(12)Br(2) monomers can promote the fibrillogenesis of Abeta(1-40) while its micelles inhibit this process. The electrostatic/hydrophobic force balance plays important roles in determining the Abeta(1-40) aggregation style and the secondary structures. When the surfactant positive charges are close to the Abeta(1-40) negative charges in number, the hydrophobic interaction is highly enhanced in the system. Both the nucleation rate and the lateral association between fibrils are greatly promoted. However, when the surfactant positive charges are in excess of the Abeta(1-40) negative charges, the electrostatic interaction is strengthened. In this case, the lateral association is inhibited and the alpha-helix to beta-sheet transition in the secondary structure is prevented. Simultaneously, another assembly pathway is induced to give the amorphous aggregates. Moreover, the size and surface roughness of the Abeta(1-40) aggregates also vary upon increasing C(12)C(6)C(12)Br(2) concentration.     

An application of 1H nuclear magnetic resonance to the determination of hydrophobic interactions in peptides

Intermolecular hydrophobic interactions between the indole or phenyl moieties of the peptides containing L -tryptophan (L -Trp) or L -phenylalanine (L -Phe) residues and the apolar isopropyl groups of the peptides containing L -leucine (L -Leu) or L -valine (L -Val) in aqueous solutions have been detected by ¹H NMR by monitoring the observed changes in the proton magnetic resonance parameters of the methyl resonances of the peptides containing L -Leu or L -Val residues. The ¹H NMR data indicate that intermolecular hydrophobic interactions are responsible for the observed changes in the proton magnetic resonance parameters of the methyl resonances. For example, when a solution of glycylglycylleucine (Gly-Gly-L -Leu) in deuterium oxide was mixed with glycylglycyltryptophan (Gly-Gly-L -Trp), the methyl protons of Gly-Gly-L -Leu exhibited large diamagnetic ring current shifts. However, when glycylglycylglycine (Gly-Gly-Gly) was substituted for Gly-Gly-L -Trp in the NMR experiment, the methyl resonances did not show any upfield or downfield shift, thereby demonstrating that the observed upfield shifts are not due to bulk susceptibility differences between solutions. The C-terminus peptides containing L -Leu or L -Val residues bind to the aromatic L -Trp or L -Phe peptides better than the N-terminus L -Leu or L -Val peptides. The C-terminus Gly-Gly-L -Leu binds better than the C-terminus glycylglycylvaline (Gly-Gly-L -Val). The strength and specificity of hydrophobic interactions in several small peptides are discussed.     

Mechanisms of the interaction of alpha-helical transmembrane peptides with phospholipid bilayers

The synthetic peptide acetyl-K(2)-G-L(24)-K(2)-A-amide (P(24)) and its analogs have been successfully utilized as models of the hydrophobic transmembrane alpha-helical segments of integral membrane proteins. The central polyleucine region of these peptides was designed to form a maximally stable, very hydrophobic alpha-helix which will partition strongly into the hydrophobic environment of the lipid bilayer core, while the dilysine caps were designed to anchor the ends of these peptides to the polar surface of the lipid bilayer and to inhibit the lateral aggregation of these peptides. Moreover, the normally positively charged N-terminus and the negatively charged C-terminus have both been blocked in order to provide a symmetrical tetracationic peptide, which will more faithfully mimic the transbilayer region of natural membrane proteins and preclude favorable electrostatic interactions. In fact, P(24) adopts a very stable alpha-helical conformation and transbilayer orientation in lipid model membranes. The results of our recent studies of the interaction of this family of alpha-helical transmembrane peptides with phospholipid bilayers are summarized here.     

Stimulatory and inhibitory effects of alkyl bromide surfactants on beta-amyloid fibrillogenesis

Beta-amyloid peptide (Abeta), in fibrillar form, is the primary constituent of senile plaques, a defining feature of Alzheimer's disease. In solution assays, fibril formation exhibits a lag time, interpreted as a nucleation/condensation-dependent process. The kinetics of fibrillogenesis is controlled by two key parameters: nucleation and elongation rate constants. We characterized the time course of Abeta fibril formation by measuring the scattering caused by peptide aggregates. We report here the interaction of Abeta with three alkylammonium bromides (dodecyl, tetradecyl, and hexadecyl) at supra- and submicellar concentrations and their influence on the kinetic constants. We observed a dual behavior: surfactants promoted or retarded fibril formation in a concentration-dependent manner. Below a determined surfactant concentration (close to the corresponding critical micellar concentration in medium without peptide), surfactants favor aggregation, presumably by means of electrostatic interactions that destabilize the native conformation. Beyond such concentration, the stabilizing effects of the monomer predominate. As a general rule, surfactants delay but do not completely inhibit aggregation.     

Requirements for prediction of peptide retention time in reversed-phase high-performance liquid chromatography: hydrophilicity/hydrophobicity of side-chains at the N- and C-termini of peptides are dramatically affected by the end-groups and location

The value of reversed-phase high-performance liquid chromatography (RP-HPLC) and the field of proteomics would be greatly enhanced by accurate prediction of retention times of peptides of known composition. The present study investigates the hydrophilicity/hydrophobicity of amino acid side-chains at the N- and C-termini of peptides while varying the functional end-groups at the termini. We substituted all 20 naturally occurring amino acids at the N- and C-termini of a model peptide sequence, where the functional end-groups were N(alpha)-acetyl-X- and N(alpha)-amino-X- at the N-terminus and -X-C(alpha)-carboxyl and -X-C(alpha)-amide at the C-terminus. Amino acid coefficients were subsequently derived from the RP-HPLC retention behaviour of these peptides and compared to each other as well as to coefficients determined in the centre of the peptide chain (internal coefficients). Coefficients generated from residues substituted at the C-terminus differed most (between the -X-C(alpha)-carboxyl and -X-C(alpha)-amide peptide series) for hydrophobic side-chains. A similar result was seen for the N(alpha)-acetyl-X- and N(alpha)-amino-X- peptide series, where the largest differences in coefficient values were observed for hydrophobic side-chains. Coefficients derived from substitutions at the C-terminus for hydrophobic amino acids were dramatically different compared to internal coefficients for hydrophobic side-chains, ranging from 17.1 min for Trp to 4.8 min for Cys. In contrast, coefficients derived from substitutions at the N-terminus showed relatively small differences from the internal coefficients. Subsequent prediction of peptide retention time, within an error of just 0.4 min, was achieved by a predictive algorithm using a combination of internal coefficients and coefficients for the C-terminal residues. For prediction of peptide retention time, the sum of the coefficients must include internal and terminal coefficients.     

A DNA G-quadruplex converts SOD1 into fibrillar aggregates

Nucleic acids with G4 elements play a role in the formation of aggregates involved in intracellular phase transitions. Our previous studies suggest that different forms of DNA could act as an accelerating template in Cu/Zn superoxide dismutase (SOD1) aggregation. Here, we examined the regulation of formation and cytotoxicity of the SOD1 aggregates by single-stranded 12-mer deoxynucleotide oligomers (dN)₁₂ (N = A, T, G, C; ssDNAs) under acidic conditions. The ssDNAs can be divided into two groups based on their roles in SOD1 binding, exposure of hydrophobic clusters in SOD1, accelerated formation, morphology and cytotoxicity of SOD1 aggregates. G-quadruplexes convert SOD1 into fibrillar aggregates as a template, a fact which was observed for the first time in the nucleic acid regulation of protein aggregation. Moreover, the fibrillar or fibril-like SOD1 species with a G-quadruplex provided by (dG)₁₂ were less toxic than the amorphous species with (dN)₁₂ (N = A, T). This study not only indicates that both morphology and cytotoxicity of protein aggregates can be regulated by the protein-bound DNAs, but also help us understand roles of nucleic aid G-quadruplexes in the formation of aggregates and membraneless organelles involved in intracellular phase transitions.     

Amyloid fibril polymorphism is under kinetic control

Self-assembly of proteins into amyloid aggregates displays a broad diversity of morphologies, both at the protofibrillar and final fibrillar species. These polymorphic species can coexist at fixed experimental conditions, and their relative abundance can be controlled by changing the solvent composition, or stirring the solution. However, the extent to which external conditions regulate the equilibrium of morphologically distinct species is still unknown. Here we investigate the nucleation of distinct fibril morphologies using computer simulations of a simplified model of an amyloid polypeptide. Counterintuitively, the energetically less favorable fibril morphologies nucleate more frequently than the morphologies of higher stability for models with low aggregation propensity. The free-energy profiles of the aggregation process indicate that the nucleation barrier determines the population fractions of different fibril morphologies, i.e., amyloid polymorphism is under kinetic control.     

Design of peptides that form amyloid-like fibrils capturing amyloid beta1-42 peptides

Amyloid beta-peptide (Abeta) plays a critical role in Alzheimer's disease (AD). The monomeric state of Abeta can self-assemble into oligomers, protofibrils, and amyloid fibrils. Since the fibrils and soluble oligomers are believed to be responsible for AD, the construction of molecules capable of capturing these species could prove valuable as a means of detecting these potentially toxic species and of providing information pertinent for designing drugs effective against AD. To this aim, we have designed short peptides with various hydrophobicities based on the sequence of Abeta14-23, which is a critical region for amyloid fibril formation. The binding of the designed peptides to Abeta and the amplification of the formation of peptide amyloid-like fibrils coassembled with Abeta are elucidated. A fluorescence assay utilizing thioflavin T, known to bind specifically to amyloid fibrils, revealed that two designed peptides (LF and VF, with the leucine and valine residues, respectively, in the hydrophobic core region) could form amyloid-like fibrils effectively by using mature Abeta1-42 fibrils as nuclei. Peptide LF also coassembled with soluble Abeta oligomers into peptide fibrils. Various analyses, including immunostaining with gold nanoparticles, enzyme-linked immunosorbent assays, and size-exclusion chromatography, confirmed that the LF and VF peptides formed amyloid-like fibrils by capturing and incorporating Abeta1-42 aggregates into their peptide fibrils. In this system, small amounts of mature Abeta1-42 fibrils or soluble oligomers could be transformed into peptide fibrils and detected by amplifying the amyloid-like fibrils with the designed peptides.     

Formation and stabilization model of the 42-mer Abeta radical: implications for the long-lasting oxidative stress in Alzheimer's disease

Amyloid fibrils mainly consist of 40-mer and 42-mer peptides (Abeta40, Abeta42). Abeta42 is believed to play a crucial role in the pathogenesis of Alzheimer's disease because its aggregative ability and neurotoxicity are considerably greater than those of Abeta40. The neurotoxicity of Abeta peptides involving the generation of free radicals is closely related to the S-oxidized radical cation of Met-35. However, the cation's origin and mechanism of stabilization remain unclear. Recently, structural models of fibrillar Abeta42 and Abeta40 based on systematic proline replacement have been proposed by our group [Morimoto, A.; et al. J. Biol. Chem. 2004, 279, 52781] and Wetzel's group [Williams, A. D.; et al. J. Mol. Biol. 2004, 335, 833], respectively. A major difference between these models is that our model of Abeta42 has a C-terminal beta-sheet region. Our biophysical study on Abeta42 using electron spin resonance (ESR) suggests that the S-oxidized radical cation of Met-35 could be generated by the reduction of the tyrosyl radical at Tyr-10 through a turn structure at positions 22 and 23, and stabilized by a C-terminal carboxylate anion through an intramolecular beta-sheet at positions 35-37 and 40-42 to form a C-terminal core that would lead to aggregation. A time-course analysis of the generation of radicals using ESR suggests that stabilization of the radicals by aggregation might be a main reason for the long-lasting oxidative stress of Abeta42. In contrast, the S-oxidized radical cation of Abeta40 is too short-lived to induce potent neurotoxicity because no such stabilization of radicals occurs in Abeta40.     

Direct Nanospectroscopic Verification of the Amyloid Aggregation Pathway

The aggregation pathways of neurodegenerative peptides determine the disease etiology, and their better understanding can lead to strategies for early disease treatment. Previous research has allowed modelling of hypothetic aggregation pathways. However, their direct experimental observation has been elusive owing to methodological limitations. Herein, we demonstrate that nanoscale chemical mapping by tip‐enhanced Raman spectroscopy of single amyloid fibrils at various stages of aggregation captures the fibril formation process. We identify changes in TERS/Raman marker bands for Aβ_1‐42, including the amide III band (above 1255 cm^?1 for turns/random coil and below 1255 cm^?1 for β‐sheet conformation). The spatial distribution of β‐sheets in aggregates is determined, allowing verification of a particular fibrillogenesis pathway, starting from aggregation of monomers to meta‐stable oligomers, which then rearrange to ordered β‐sheets, already at the oligomeric or protofibrillar stage.     

Self-assembly of beta-sheet forming peptides into chiral fibrillar aggregates

The authors introduce a novel mid-resolution off-lattice coarse-grained model to investigate the self-assembly of beta-sheet forming peptides. The model retains most of the peptide backbone degrees of freedom as well as one interaction center describing the side chains. The peptide consists of a core of alternating hydrophobic and hydrophilic residues, capped by two oppositely charged residues. Nonbonded interactions are described by Lennard-Jones and Coulombic terms. The influence of different levels of "hydrophobic" and "steric" forces between the side chains of the peptides on the thermodynamics and kinetics of aggregation was investigated using Langevin dynamics. The model is simple enough to allow the simulation of systems consisting of hundreds of peptides, while remaining realistic enough to successfully lead to the formation of chiral, ordered beta tapes, ribbons, as well as higher order fibrillar aggregates.     

Peptide tic-tac-toe: heterotrimeric coiled-coil specificity from steric matching of multiple hydrophobic side chains

Specific coiled-coil heterotrimers result from steric matching of hydrophobic core side chains. A 2:1 heterotrimer is formed by peptides containing alanine or cyclohexylalanine, respectively, at a central core residue. Detailed thermodynamic analysis reveals that the designed complex is considerably more stable than the corresponding alanine homotrimer (deltaT(m) = 25 degrees C, deltadeltaG(unf) = 4.5 kcal/mol), while control complexes with naphthylalanine or cyclopropylalanine peptides are much less stable. However, the cyclohexylalanine homotrimer is of comparable stability to the 2:1 complex, prompting an investigation of multiply substituted peptides. A specific 1:1:1 heterotrimer is formed from three independent peptide strands, each bearing one large (cyclohexylalanine) and two small (alanine) side chains at the same three core positions but in different order. The combined impact of three substitutions improves specificity to the point where each pure peptide and all pairwise equimolar mixtures form significantly less stable complexes (deltaTm = 22-24 degrees C). The capacity for specific complex formation governed by multiple unnatural core side chains should facilitate design of numerous new peptide assemblies.     

Capillary electrophoresis studies on the aggregation process of beta-amyloid 1-42 and 1-40 peptides

The possibility to monitor, in solution, the steps of beta-amyloid (Abeta) nucleation and therefore to describe this dynamic process by using capillary electrophoresis and under optimized experimental conditions is described. Striking differences in the electrophoretic patterns of Abeta 1-42 and Abeta 1-40 over time are here shown, and different aggregation states are elucidated, which reflect the very diverse oligomerization behavior of two very similar peptides. The isolation of one aggregated species of high molecular weight by ultracentrifugation allowed us to assess its role as toxic oligomer. The perturbation of the existing equilibrium among the identified species by the addition of small molecules can in principle interfere with the aggregation process of the peptides and ultimately prevent the plaque formation in vitro.