Structure of beta-crystallite assemblies formed by Alzheimer beta-amyloid protein analogues: analysis by x-ray diffraction

Simple fluorinated moiety insertion on Aβ 16-23 peptide for stain-free TEM imaging

Peptide aggregation and fibre formation are one of the major underlying causes of several neurodegenerative disorders such as Alzheimer's disease. During the past decades the characterisation of these fibres has been widely studied in an attempt to further understand the nature of the related diseases and in an effort to develop treatments. Transmission electron microscopy (TEM) is one of the most commonly used techniques to identify these fibres, but requires the use of a radioactive staining agent. The procedure we report overcomes this drawback through simple addition of a fluorinated moiety to a short Amyloid β sequence via solid phase peptide synthesis (SPPS). This method is synthetically straightforward, widely applicable to different aggregation-prone sequences and, above all, allows for stain-free TEM imaging with improved quality compared to standard imaging procedures. The presence of the fluorinated moiety does not cause major changes in the fibre structure or aggregation, but rather serves to dissipate the microscope's electron beam, thus allowing for high contrast and straightforward imaging by TEM.

Breakdown of hierarchical architecture in cellulose during dilute acid pretreatments

Cellulose is an attractive candidate as a feedstock for sustainable bioenergy because of its global abundance. Pretreatment of biomass has significant influence on the chemical availability of cellulose locked in recalcitrant microfibrils. Optimizing pretreatment depends on an understanding of its impact on the microscale and nanoscale molecular architecture. X-ray scattering experiments have been performed on native and pre-treated maize stover and models of cellulose architecture have been derived from these data. Ultra small-angle, very small-angle and small-angle X-ray scattering (USAXS, VSAXS and SAXS) probe three different levels of architectural scale. USAXS and SAXS have been used to study cellulose at two distinct length scales, modeling the fibrils as ~30 Å diameter rods packed into ~0.14 μm diameter bundles. VSAXS is sensitive to structural features at length scales between these two extremes. Detailed analysis of diffraction patterns from untreated and pretreated maize using cylindrical Guinier plots and the derivatives of these plots reveals the presence of substructures within the ~0.14 μm diameter bundles that correspond to grouping of cellulose approximately 30 nm in diameter. These sub-structures are resilient to dilute acid pretreatments but are sensitive to pretreatment when iron sulfate is added. These results provide evidence of the hierarchical arrangement of cellulose at three length scales and the evolution of these arrangements during pre-treatments.

Rapid detection of Aβ aggregation and inhibition by dual functions of gold nanoplasmic particles: catalytic activator and optical reporter

One of the primary pathological hallmarks of Alzheimer's diseases (AD) is amyloid-β (Aβ) aggregation and its extracellular accumulation. However, current in vitro Aβ aggregation assays require time-consuming and labor-intensive steps, which delay the process of drug discovery and understanding the mechanism of Aβ induced neurotoxicity. Here, we propose a rapid detection method for studying Aβ aggregation and inhibition under an optimized acidic perturbation condition by dual functions of gold nanoplasmonic particles (GNPs): (1) catalytic activator and (2) optical reporter. Because of roles of GNPs as effective nucleation sites for fast-catalyzing Aβ aggregation and colorimetric optical reporters for tracking Aβ aggregation, we accomplished the fast aggregation assay in less than 1 min by the naked eyes. Our detection method is based on spontaneous clustering of unconjugated (unmodified) GNPs along with the aggregated Aβ network under an aggregation-promoting condition. As a proof-of-concept demonstration, we employed the acidic perturbation permitting rapid cooperative assemblies of GNPs and Aβ peptides via their surface charge modulation. Under the optimized acidic perturbation condition around pH 2 to 3, we characterized the concentration-dependent colorimetric responses for aggregation at physiologically relevant Aβ concentration levels (from 100 μM to 10 nM). We also demonstrated the GNP/acidic condition-based rapid inhibition assay of Aβ aggregation by using well-known binding reagents such as antibody and serum albumin. The proposed methodology can be a powerful alternative method for screening drugs for AD as well as studying molecular biophysics of protein aggregations, and further extended to explore other protein conformational diseases such as neurodegenerative disease.

Distinct β-sheet structure in protein aggregates determined by ATR-FTIR spectroscopy

Attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR) was used to study the conformation of aggregated proteins in vivo and in vitro. Several different protein aggregates, including amyloid fibrils from several peptides and polypeptides, inclusion bodies, folding aggregates, soluble oligomers, and protein extracts from stressed cells, were examined in this study. All protein aggregates demonstrate a characteristic new β structure with lower-frequency band positions. All protein aggregates acquire this new β band following the aggregation process involving intermolecular interactions. The β sheets in some proteins arise from regions of the polypeptide that are helical or non β in the native conformation. For a given protein, all types of the aggregates (e.g., inclusion bodies, folding aggregates, and thermal aggregates) showed similar spectra, indicating that they arose from a common partially folded species. All of the aggregates have some nativelike secondary structure and nonperiodic structure as well as the specific new β structure. The new β could be most likely attributed to stronger hydrogen bonds in the intermolecular β-sheet structure present in the protein aggregates.

Binding mechanism of inositol stereoisomers to monomers and aggregates of Aβ(16-22)

Alzheimer's disease (AD) is a severe neurodegenerative disease with no cure. A potential therapeutic approach is to prevent or reverse the amyloid formation of Aβ42, a key pathological hallmark of AD. We examine the molecular basis for stereochemistry-dependent inhibition of the formation of Aβ fibrils in vitro by a polyol, scyllo-inositol. We present molecular dynamics simulations of the monomeric, disordered aggregate, and protofibrillar states of Aβ(16-22), an amyloid-forming peptide fragment of full-length Aβ, successively with and without scyllo-inositol and its inactive stereoisomer chiro-inositol. Both stereoisomers bind monomers and disordered aggregates with similar affinities of 10-120 mM, whereas binding to β-sheet-containing protofibrils yields affinities of 0.2-0.5 mM commensurate with in vitro inhibitory concentrations of scyllo-inositol. Moreover, scyllo-inositol displays a higher binding specificity for phenylalanine-lined grooves on the protofibril surface, suggesting that scyllo-inositol coats the surface of Aβ protofibrils and disrupts their lateral stacking into amyloid fibrils.

Specific domains of Aβ facilitate aggregation on and association with lipid bilayers

A hallmark of Alzheimer's disease, a late-onset neurodegenerative disease, is the deposition of neuritic amyloid plaques composed of aggregated forms of the β-amyloid peptide (Aβ). Aβ forms a variety of nanoscale, toxic aggregate species ranging from small oligomers to fibrils. Aβ and many of its aggregate forms strongly interact with lipid membranes, which may represent an important step in several toxic mechanisms. Understanding the role that specific regions of Aβ play in regulating its aggregation and interaction with lipid membranes may provide insights into the fundamental interaction between Aβ and cellular surfaces. We investigated the interaction and aggregation of several Aβ fragments (Aβ1-11, Aβ1-28, Aβ10-26, Aβ12-24, Aβ16-22, Aβ22-35, and Aβ1-40) in the presence of supported model total brain lipid extract (TBLE) bilayers. These fragments represent a variety of chemically unique domains within Aβ, that is, the extracellular domain, the central hydrophobic core, and the transmembrane domain. Using scanning probe techniques, we elucidated aggregate morphologies for these different Aβ fragments in free solution and in the presence of TBLE bilayers. These fragments formed a variety of oligomeric and fibrillar aggregates under free solution conditions. Exposure to TBLE bilayers resulted in distinct aggregate morphologies compared to free solution and changes in bilayer stability dependent on the Aβ sequence. Aβ10-26, Aβ16-22, Aβ22-35, and Aβ1-40 aggregated into a variety of distinct fibrillar aggregates and disrupted the bilayer structure, resulting in altered mechanical properties of the bilayer. Aβ1-11, Aβ1-28, and Aβ12-24 had minimal interaction with lipid membranes, forming only sparse oligomers.

Synthesis and characterization of designed BMHP1-derived self-assembling peptides for tissue engineering applications

The importance of self-assembling peptides (SAPs) in regenerative medicine is becoming increasingly recognized. The propensity of SAPs to form nanostructured fibers is governed by multiple forces including hydrogen bonds, hydrophobic interactions and π-π aromatic interactions among side chains of the amino acids. Single residue modifications in SAP sequences can significantly affect these forces. BMHP1-derived SAPs is a class of biotinylated oligopeptides, which self-assemble in β-structured fibers to form a self-healing hydrogel. In the current study, selected modifications in previously described BMHP1-derived SAPs were designed in order to investigate the influence of modified residues on self-assembly kinetics and scaffold formation properties. The Fourier transform infrared spectroscopy (FTIR) and X-ray diffraction (XRD) analysis demonstrated the secondary structure (β-sheet) formation in all modified SAP sequences, whereas atomic force microscopy (AFM) analysis further confirmed the presence of nanofibers. Furthermore, the fiber shape and dimension analysis by AFM showed flattened and twisted fiber morphology ranging from ∼8 nm to ∼70 nm. The mechanical properties of the pre-assembled and post assembled solution were investigated by rheometry. The shear-thinning behavior and rapid re-healing properties of the pre-assembled solutions make them a preferable choice for injectable scaffolds. The wide range of stiffnesses (G')--from ∼1000 to ∼27,000 Pa--exhibited by the post-assembled scaffolds demonstrated their potential for a variety of tissue engineering applications. The extra cellular matrix (ECM) mimicking (physically and chemically) properties of SAP scaffolds enhanced cell adhesion and proliferation. The capability of the scaffold to facilitate murine neural stem cell (mNSC) proliferation was evaluated in vitro: the increased mNSCs adhesion and proliferation demonstrated the potential of newly synthesized SAPs for regenerative medicine approaches.

Self-assembly of Aβ-based peptide amphiphiles with double hydrophobic chains

Two peptide-amphiphiles (PAs), 2C(12)-Lys-Aβ(12-17) and C(12)-Aβ(11-17)-C(12), were constructed with two alkyl chains attached to a key fragment of amyloid β-peptide (Aβ(11-17)) at different positions. The two alkyl chains of 2C(12)-Lys-Aβ(12-17) were attached to the same terminus of Aβ(12-17), while the two alkyl chains of C(12)-Aβ(11-17)-C(12) were separately attached to each terminus of Aβ(11-17). The self-assembly behavior of both the PAs in aqueous solutions was studied at 25 °C and at pHs 3.0, 4.5, 8.5, and 11.0, focusing on the effects of the attached positions of hydrophobic chains to Aβ(11-17) and the net charge quantity of the Aβ(11-17) headgroup. Cryogenic transmission electron microscopy and atomic force microscopy show that 2C(12)-Lys-Aβ(12-17) self-assembles into long stable fibrils over the entire pH range, while C(12)-Aβ(11-17)-C(12) forms short twisted ribbons and lamellae by adjusting pHs. The above fibrils, ribbons, and lamellae are generated by the lateral association of nanofibrils. Circular dichroism spectroscopy suggests the formation of β-sheet structure with twist and disorder to different extents in the aggregates of both the PAs. Some of the C(12)-Aβ(11-17)-C(12) molecules adopt turn conformation with the weakly charged peptide sequence, and the Fourier transform infrared spectroscopy indicates that the turn content increases with the pH increase. This work provides additional basis for the manipulations of the PA's nanostructures and will lead to the development of tunable nanostructure materials.

X-ray fibre diffraction studies of amyloid fibrils

Amyloid fibrils are polymeric assemblies of normally soluble proteins or peptides. To investigate their structure, it is generally not possible to use conventional methods of crystallography and solution nuclear magnetic resonance. To examine the repeating crystalline structure along the fibre axis, X-ray fibre diffraction has been a useful tool. Here we discuss the methods by which amyloid-like fibrils may be prepared to form a sample suitable for structural analysis and describe how data may be collected and then analysed to arrive at a potential model structure.

Amyloid structure: conformational diversity and consequences

Many, perhaps most, proteins, are capable of forming self-propagating, β-sheet (amyloid) aggregates. Amyloid-like aggregates are found in a wide range of diseases and underlie prion-based inheritance. Despite intense interest in amyloids, structural details have only recently begun to be revealed as advances in biophysical approaches, such as hydrogen-deuterium exchange, X-ray crystallography, solid-state nuclear magnetic resonance (SSNMR), and cryoelectron microscopy (cryoEM), have enabled high-resolution insights into their molecular organization. Initial studies found that despite the highly divergent primary structure of different amyloid-forming proteins, amyloids from different sources share many structural similarities. With higher-resolution information, however, it has become clear that, on the molecular level, amyloids comprise a wide diversity of structures. Particularly surprising has been the finding that identical polypeptides can fold into multiple, distinct amyloid conformations and that this structural diversity can lead to distinct heritable prion states or strains.

Differential effects of Phe19 and Phe20 on fibril formation by amyloidogenic peptide A beta 16-22 (Ac-KLVFFAE-NH2)

The sequence KLVFFAE (A beta 16-22) in Alzheimer's beta-amyloid is thought to be a core beta-structure that could act as a template for folding other parts of the polypeptide or molecules into fibrillar assemblies rich in beta-sheet. To elucidate the mechanism of the initial folding process, we undertook combined X-ray fiber/powder diffraction and infrared (IR) spectroscopy to analyze lyophilized A beta 16-22 and solubilized/dried peptide containing nitrile probes at F19 and/or F20. Solubilized/dried wild-type (WT) A beta 16-22 and the peptide containing cyanophenylalanine at F19 (19CN) or at F20 (20CN) gave fiber patterns consistent with slab-like beta-crystallites that were cylindrically averaged around the axis parallel to the polypeptide chain direction. The WT and 19CN assemblies showed 30-A period arrays arising from the stacking of the slabs along the peptide chain direction, whereas the 20CN assemblies lacked any such stacking. The electron density projection along the peptide chain direction indicated similar side-chain dispositions for WT and 20CN, but not for 19CN. These X-ray results and modeling imply that in the assembly of WT A beta 16-22 the F19 side chain is localized within the intersheet space and is involved in hydrophobic contact with amino acids across the intersheet space, whereas the F20 side chain localized near the slab surface is less important for the intersheet interaction, but involved in slab stacking. IR observations for the same peptides in dilute solution showed a greater degree of hydrogen bonding for the nitrile groups in 20CN than in 19CN, supporting this interpretation.

Preparation and characterization of toxic Abeta aggregates for structural and functional studies in Alzheimer's disease research

The amyloid cascade hypothesis, supported by strong evidence from genetics, pathology and studies using animal models, implicates amyloid-beta (Abeta) oligomerization and fibrillogenesis as central causative events in the pathogenesis of Alzheimer's disease (AD). Today, significant efforts in academia, biotechnology and the pharmaceutical industry are devoted to identifying the mechanisms by which the process of Abeta aggregation contributes to neurodegeneration in AD and to the identity of the toxic Abeta species. In this paper, we describe methods and detailed protocols for reproducibly preparing Abeta aggregates of defined size distribution and morphology, including monomers, protofibrils and fibrils, using size exclusion chromatography. In addition, we describe detailed biophysical procedures for elucidating the structural features, aggregation kinetics and toxic properties of the different Abeta aggregation states, with special emphasis on protofibrillar intermediates. The information provided by this approach allows for consistent correlation between the properties of the aggregates and their toxicity toward primary neurons and/or cell lines. A better understanding of the molecular and structural basis of Abeta aggregation and toxicity is crucial for the development of effective strategies aimed at prevention and/or treatment of AD. Furthermore, the identification of specific aggregation states, which correlate with neurodegeneration in AD, could lead to the development of diagnostic tools to detect and monitor disease progression. The procedures described can be performed in as little as 1 day, or may take longer, depending on the exact toxicity assays used.

Mechanisms of enzymatic degradation of amyloid Beta microfibrils generating nanofilaments and nanospheres related to cytotoxicity

Amyloid beta (Abeta) fibrils are found in the brain tissue of persons with Alzheimer's disease (AD), where they accumulate as plaques. One way to reduce the level of accumulation of Abeta in the brain and potentially treat AD is with Abeta-degrading enzymes such as neprilysin (NEP) and insulin-degrading enzyme (IDE). However, enzymatic responses and degradation mechanisms of Abeta fibrils (crystalline-state Abeta) have not been investigated, particularly with respect to how to avoid cytotoxicity of the degradation products to neuronal cells. Thus, insight into mechanisms of enzymatic degradation of Abeta fibrils would be instructive as a route to elucidating different structural features related to degradation and to cytotoxicity. We report mechanisms of enzymatic degradation of Abeta with cross-beta structures and show the series of steps involved in the digestion of Abeta microfibrils to nanospheres or nanofilaments by protease XIV or alpha-chymotrypsin, respectively. These degradation products, which contained almost the same secondary structures, exhibited different cytotoxicities, indicating that relationships between nanoassembled structures and cytotoxicity of Abeta peptides are more significant than the beta-sheet content. In addition, the enzymatic digestion at the Lys28 loop region linking the two beta-sheets in Abeta fibrils is suggested as a key target related to cytotoxicity, a feature that can be selectively targeted on the basis of the choice of protease.

Natural and synthetic prion structure from X-ray fiber diffraction

A conformational isoform of the mammalian prion protein (PrP(Sc)) is the sole component of the infectious pathogen that causes the prion diseases. We have obtained X-ray fiber diffraction patterns from infectious prions that show cross-beta diffraction: meridional intensity at 4.8 A resolution, indicating the presence of beta strands running approximately at right angles to the filament axis and characteristic of amyloid structure. Some of the patterns also indicated the presence of a repeating unit along the fiber axis, corresponding to four beta-strands. We found that recombinant (rec) PrP amyloid differs substantially from highly infectious brain-derived prions, both in structure as demonstrated by the diffraction data, and in heterogeneity as shown by electron microscopy. In addition to the strong 4.8 A meridional reflection, the recPrP amyloid diffraction is characterized by strong equatorial intensity at approximately 10.5 A, absent from brain-derived prions, and indicating the presence of stacked beta-sheets. Synthetic prions recovered from transgenic mice inoculated with recPrP amyloid displayed structural characteristics and homogeneity similar to those of naturally occurring prions. The relationship between the structural differences and prion infectivity is uncertain, but might be explained by any of several hypotheses: only a minority of recPrP amyloid possesses a replication-competent conformation, the majority of recPrP amyloid has to undergo a conformational maturation to acquire replication competency, or inhibitory forms of recPrP amyloid interfere with replication during the initial transmission.

Amyloid-beta fibrillogenesis: structural insight and therapeutic intervention

Structural insight into the conformational changes associated with aggregation and assembly of fibrils has provided a number of targets for therapeutic intervention. Solid-state NMR, hydrogen/deuterium exchange and mutagenesis strategies have been used to probe the secondary and tertiary structure of amyloid fibrils and key intermediates. Rational design of peptide inhibitors directed against key residues important for aggregation and stabilization of fibrils has demonstrated effectiveness at inhibiting fibrillogenesis. Studies on the interaction between Abeta and cell membranes led to the discovery that inositol, the head group of phosphatidylinositol, inhibits fibrillogenesis. As a result, scyllo-inositol is currently in clinical trials for the treatment of AD. Additional small-molecule inhibitors, including polyphenolic compounds such as curcumin, (-)-epigallocatechin gallate (EGCG), and grape seed extract have been shown to attenuate Abeta aggregation through distinct mechanisms, and have shown effectiveness at reducing amyloid levels when administered to transgenic mouse models of AD. Although the results of ongoing clinical trials remain to be seen, these compounds represent the first generation of amyloid-based therapeutics, with the potential to alter the progression of AD and, when used prophylactically, alleviate the deposition of Abeta.

POLYMERIC NANOMATERIALS IN BIOMINERALIZATION

Hierarchical synthesis of well-defined nanoparticles and structures is one of the challenges in materials science. Conventional methods have limitations in controlling the size of the crystals as well as their orientation. Biominerals have inspired research to explore bottom-up approaches to the design of novel nanomaterials by utilizing polymeric nanomaterials as templates to synthesize nanoparticles with well-defined morphologies and structures. Here in this review, the role of synthetic and natural polymeric nanomaterials with controlled architecture and selected affinities in the design of biomimetic materials over the years are discussed.

Protein Misfolding and Aggregation

Interest in the problem of protein misfolding and aggregation has exploded in recent years for two reasons: (1) the sharp rise in the number and volume of therapeutic proteins produced commercially and (2) the recognition of the central role of protein aggregates in degenerative diseases. The systematic study of protein aggregation presents major challenges to both the experimentalist and the theoretician. Much of the work retains an empirical flavor due to the experimental complexities; the sensitivity of protein aggregation to the slightest change in protein amino acid composition, solvent properties, or protein concentration; and the lack of robust theoretical models of misfolding and aggregation. Novel experimental and computational approaches are being developed, and we anticipate substantial progress will be made in the near future. Several presentations describing the latest advances in protein misfolding and aggregation were given at the American Chemical Society meeting (BIOT division) held in September, 2006 in San Francisco.

The effect of a DeltaK280 mutation on the unfolded state of a microtubule-binding repeat in Tau

Tau is a natively unfolded protein that forms intracellular aggregates in the brains of patients with Alzheimer's disease. To decipher the mechanism underlying the formation of tau aggregates, we developed a novel approach for constructing models of natively unfolded proteins. The method, energy-minima mapping and weighting (EMW), samples local energy minima of subsequences within a natively unfolded protein and then constructs ensembles from these energetically favorable conformations that are consistent with a given set of experimental data. A unique feature of the method is that it does not strive to generate a single ensemble that represents the unfolded state. Instead we construct a number of candidate ensembles, each of which agrees with a given set of experimental constraints, and focus our analysis on local structural features that are present in all of the independently generated ensembles. Using EMW we generated ensembles that are consistent with chemical shift measurements obtained on tau constructs. Thirty models were constructed for the second microtubule binding repeat (MTBR2) in wild-type (WT) tau and a DeltaK280 mutant, which is found in some forms of frontotemporal dementia. By focusing on structural features that are preserved across all ensembles, we find that the aggregation-initiating sequence, PHF6*, prefers an extended conformation in both the WT and DeltaK280 sequences. In addition, we find that residue K280 can adopt a loop/turn conformation in WT MTBR2 and that deletion of this residue, which can adopt nonextended states, leads to an increase in locally extended conformations near the C-terminus of PHF6*. As an increased preference for extended states near the C-terminus of PHF6* may facilitate the propagation of beta-structure downstream from PHF6*, these results explain how a deletion at position 280 can promote the formation of tau aggregates.

Amyloid fibrils: abnormal protein assembly

Amyloid refers to the abnormal fibrous, extracellular, proteinaceous deposits found in organs and tissues. Amyloid is insoluble and is structurally dominated by beta-sheet structure. Unlike other fibrous proteins it does not commonly have a structural, supportive or motility role but is associated with the pathology seen in a range of diseases known as the amyloidoses. These diseases include Alzheimer's, the spongiform encephalopathies and type II diabetes, all of which are progressive disorders with associated high morbidity and mortality. Not surprisingly, research into the physicochemical properties of amyloid and its formation is currently intensely pursued. In this chapter we will highlight the key scientific findings and discuss how the stability of amyloid fibrils impacts on bionanotechnology.

Insight into the kinetic of amyloid beta (1-42) peptide self-aggregation: elucidation of inhibitors' mechanism of action

The initial transition of amyloid beta (1-42) (Abeta42) soluble monomers/small oligomers from unordered/alpha-helix to a beta-sheet-rich conformation represents a suitable target to design new potent inhibitors and to obtain effective therapeutics for Alzheimer's disease. Under optimized conditions, this reliable and reproducible CD kinetic study showed a three-step sigmoid profile that was characterized by a lag phase (prevailing unordered/alpha-helix conformation), an exponential growth phase (increasing beta-sheet secondary structure) and a plateau phase (prevailing beta-sheet secondary structure). This kinetic analysis brought insight into the inhibitors' mechanism of action. In fact, an increase in the duration of the lag phase can be related to the formation of an inhibitor-Abeta complex, in which the non-amyloidogenic conformation is stabilized. When the exponential rate is affected exclusively, such as in the case of Congo red and tetracycline, then the inhibitor affinity might be higher for the pleated beta-sheet structure. Finally, by adding the inhibitor at the end of the exponential phase, the soluble protofibrils can be disrupted and the Abeta amyloidogenic structure can revert into monomers/small oligomers. Congo red and tetracycline preferentially bind to amyloid in the beta-sheet conformation because both decreased the slope of the exponential growth, even if to a different extent, whereas no effect was observed for tacrine and galantamine. Some very preliminary indications can be derived about the structural requirements for binding to nonamyloidogenic or beta-sheet amyloid secondary structure for the development of potent antiaggregating agents. On these premises, memoquin, a multifunctional molecule that was designed to become a drug candidate for the treatment of Alzheimer's disease, was investigated under the reported circular dichroism assay and its anti-amyloidogenic mechanism of action was elucidated.

Amyloid peptides and proteins in review

Amyloids are filamentous protein deposits ranging in size from nanometres to microns and composed of aggregated peptide beta-sheets formed from parallel or anti-parallel alignments of peptide beta-strands. Amyloid-forming proteins have attracted a great deal of recent attention because of their association with over 30 diseases, notably neurodegenerative conditions like Alzheimer's, Huntington's, Parkinson's, Creutzfeldt-Jacob and prion disorders, but also systemic diseases such as amyotrophic lateral sclerosis (Lou Gehrig's disease) and type II diabetes. These diseases are all thought to involve important conformational changes in proteins, sometimes termed misfolding, that usually produce beta-sheet structures with a strong tendency to aggregate into water-insoluble fibrous polymers. Reasons for such conformational changes in vivo are still unclear. Intermediate aggregated state(s), rather than precipitated insoluble polymeric aggregates, have recently been implicated in cellular toxicity and may be the source of aberrant pathology in amyloid diseases. Numerous in vitro studies of short and medium length peptides that form amyloids have provided some clues to amyloid formation, with an alpha-helix to beta-sheet folding transition sometimes implicated as an intermediary step leading to amyloid formation. More recently, quite a few non-pathological amyloidogenic proteins have also been identified and physiological properties have been ascribed, challenging previous implications that amyloids were always disease causing. This article summarises a great deal of current knowledge on the occurrence, structure, folding pathways, chemistry and biology associated with amyloidogenic peptides and proteins and highlights some key factors that have been found to influence amyloidogenesis.

Role of different regions of alpha-synuclein in the assembly of fibrils

Elucidating the details of the assembly of amyloid fibrils is a key step to understanding the mechanism of amyloid deposition diseases including Parkinson's disease. Although several models have been proposed, based on analyses of polypeptides and short peptides, a detailed understanding of the structure and mechanism of alpha-synuclein fibrillation remains elusive. In this study, we used trypsin and endoproteinase GluC to digest intact alpha-synuclein fibrils and to analyze the detailed morphology of the resultant fibrils/remnants. We also created three mutants of alpha-synuclein, in which the N-terminal and C-terminal regions were removed, both individually and in combination, and investigated the detailed morphology of the fibrils from these mutants. Our results indicate that the assembly of mature alpha-synuclein fibrils is hierarchical: protofilaments --> protofibrils --> mature fibrils. There is a core region of approximately 70 amino acids, from residues approximately 32 to 102, which comprises the beta-rich core of the protofilaments and fibrils. In contrast, the two terminal regions show no evidence of participating in the assembly of the protofilament core but play a key role in the interactions between the protofilaments, which is necessary for the fibril maturation.

Refined fibril structures: the hydrophobic core in Alzheimer's amyloid beta-protein and prion as revealed by X-ray diffraction

From the wide-angle, equatorial X-ray data of a beta-amyloid analogue, we previously calculated the electron density of the constituent beta-crystallite, which assembles as multimers (four to six crystallites) in building the amyloid fibre. In the scattering region where the spacing d < approximately 10 A, the observed reflections were indexed by an orthogonal lattice with a unit cell having a = 9.44 A, b = 6.92 A and c = 10.76 A. The phases were initially derived from the atomic coordinates of the beta-keratin backbone and were optimized by including new peaks (as point atom or sphere) in the subsequent Fourier iteration. The R-factor between the observed and calculated amplitudes was refined to 35%. In further developing our analysis, we have now applied an alternative constraint to the optimization by eliminating the negative electron densities, and found that the R-factor decreased to 19% after three iterations. The refined electron density map fits phenylalanine, indicating that the amyloid core likely comes from the hydrophobic Leu-Val-Phe-Phe residues. We have applied the same type of optimization, using beta-silk as an initial phase model, to the hydrophobic H1 domain of the prion protein for which the monoclinic unit cell constants are a = 9.51 A, b = 7.06 A, c = 15.94 A and beta = 88.4 degrees. The R-factor decreased to 11% from 64% after two iterations. The electron density map shows a silk-like quarter-staggered arrangement of beta-sheets which, in the intersheet direction, have circular peaks in one beta-sheet and elongated peaks in the alternating beta-sheet. These peaks were interpreted as arising from the C-terminal alanine-rich domain and N-terminal hydrophobic residues. Skeletal atomic models for these core regions support this interpretation.

Cytoplasmic domain of zebrafish myelin protein zero: adhesive role depends on beta-conformation

Solution spectroscopy studies on the cytoplasmic domain of human myelin protein zero (P0) (hP0-cyt) suggest that H-bonding between beta-strands from apposed molecules is likely responsible for the tight cytoplasmic apposition in compact myelin. As a follow-up to these findings, in the current study we used circular dichroism and x-ray diffraction to analyze the same type of model membranes previously used for hP0-cyt to investigate the molecular mechanism underlying the zebrafish cytoplasmic apposition. This space is significantly narrower in teleosts compared with that in higher vertebrates, and can be accounted for in part by the much shorter cytoplasmic domain in the zebrafish protein (zP0-cyt). Circular dichroism measurements on zP0-cyt showed similar structural characteristics to those of hP0-cyt, i.e., the protein underwent a beta-->alpha structural transition at lipid/protein (L/P) molar ratios >50, and adopted a beta-conformation at lower L/P molar ratios. X-ray diffraction was carried out on lipid vesicle solutions with zP0-cyt before and after dehydration to study the effect of protein on membrane lipid packing. Solution diffraction revealed the electron-density profile of a single membrane bilayer. Diffraction patterns of dried samples suggested a multilamellar structure with the beta-folded P0-cyt located at the intermembrane space. Our findings support the idea that the adhesive role of P0 at the cytoplasmic apposition in compact myelin depends on the cytoplasmic domain of P0 being in the beta-conformation.

Simulation protocols for coherent femtosecond vibrational spectra of peptides

Two algorithms for simulating the response of peptides to sequences of IR pulses are developed and applied to N-methyl acetamide (NMA) and a 17 residue alpha-helical peptide (YKKKH17) in D(2)O. A fluctuating vibrational-exciton Hamiltonian for the amide I mode is constructed from molecular dynamics trajectories. Coupling with the environment is described using a density functional theory electrostatic map. The cumulant expansion of Gaussian fluctuation incorporates motional narrowing due to fast frequency fluctuations and is adequate for NMA and for isotopically labeled bands in large peptides. Real-space truncation of the scattering matrix of the nonlinear exciton equations significantly reduces the computational cost, making it particularly attractive for slow fluctuations in large globular proteins.

The Structure of the Alzheimer Amyloid β 10-35 Peptide Probed through Replica-Exchange Molecular Dynamics Simulations in Explicit Solvent

The conformational states sampled by the Alzheimer amyloid beta (10-35) (Abeta 10-35) peptide were probed using replica-exchange molecular dynamics (REMD) simulations in explicit solvent. The Abeta 10-35 peptide is a fragment of the full-length Abeta 40/42 peptide that possesses many of the amyloidogenic properties of its full-length counterpart. Under physiological temperature and pressure, our simulations reveal that the Abeta 10-35 peptide does not possess a single unique folded state. Rather, this peptide exists as a mixture of collapsed globular states that remain in rapid dynamic equilibrium with each other. This conformational ensemble is dominated by random coil and bend structures with insignificant presence of an alpha-helical or beta-sheet structure. The 3D structure of Abeta 10-35 is seen to be defined by a salt bridge formed between the side-chains of K28 and D23. This salt bridge is also observed in Abeta fibrils and our simulations suggest that monomeric conformations of Abeta 10-35 contain pre-folded structural motifs that promote rapid aggregation of this peptide.

Controlling amyloid growth in multiple dimensions

The great progress made in defining the structure of protein and peptide amyloid assemblies, particularly the arrangement of peptides in beta-sheets, is counterbalanced by the still poor understanding of the higher organization of beta-sheets within the fibril and overall fibril/fibril associations. The assembly pathway and basis of amyloid toxicity may well depend on these higher-order structural features. For example, significant evidence points to association between sheets as the rate limiting step in fibril assembly, and a critical metal binding site has now been identified that involves residues from different individual sheets. Here we review experiments that are identifying some of the issues associated with sheet-sheet association by investigating simple model peptides derived from the central core of the Abeta peptide implicated in Alzheimer's disease. These peptides transit between fibril/ribbon/nanotube morphologies in response to assembly conditions, laying the foundation for understanding the folding landscape for these higher order assemblies, revealing potential targets for therapeutic intervention, and opening strategies for the design of highly ordered peptide self-assembled microscale morphologies.

Alzheimer's beta-amyloid: insights into fibril formation and structure from Congo red binding

We consider here the chemistry of Congo red (CR), its binding equilibrium to Alzheimer's beta-amyloid, and the kinetics of beta-amyloid formation. Spectroscopic UV/V is measurements for the pH- and time-dependence binding of CR to Abeta analogues are analysed by Scatchard binding and the theory of nucleation-dependent fibril formation. CR likely binds electrostatically to the imidazolium sidechains of histidine residues that are exposed at the surface of amyloid fibrils. As revealed by atomic models of the Abeta protofilament, such as the nanotube beta-helix and parallel beta-sheet, the regular arrangement of histidines likely acts as a template for the end-to-end J-aggregation of CR molecules, which produces a red shift in UV/V is absorption.

Molecular alignment within beta-sheets in Abeta(14-23) fibrils: solid-state NMR experiments and theoretical predictions

We report investigations of the molecular structure of amyloid fibrils formed by residues 14-23 of the beta-amyloid peptide associated with Alzheimer's disease (Abeta(14-23)), using solid-state nuclear magnetic resonance (NMR) techniques in conjunction with electron microscopy and atomic force microscopy. The NMR measurements, which include two-dimensional proton-mediated (13)C-(13)C exchange and two-dimensional relayed proton-mediated (13)C-(13)C exchange spectra, show that Abeta(14-23) fibrils contain antiparallel beta-sheets with a registry of backbone hydrogen bonds that aligns residue 17+k of each peptide molecule with residue 22-k of neighboring molecules in the same beta-sheet. We compare these results, as well as previously reported experimental results for fibrils formed by other beta-amyloid fragments, with theoretical predictions of molecular alignment based on databases of residue-specific alignments in antiparallel beta-sheets in known protein structures. While the theoretical predictions are not in exact agreement with the experimental results, they facilitate the design of experiments by suggesting a small number of plausible alignments that are readily distinguished by solid-state NMR.

Linker histone H1 binds to disease associated amyloid-like fibrils

Alzheimer's disease (AD) and Parkinson's disease (PD) are the two most prevalent neurodegenerative diseases of the central nervous system. These two diseases share a common feature in that a normally soluble peptide (amyloid-beta) or protein (alpha-synuclein) aggregates into an ordered fibrillar structure. As well as structural similarities observed between fibrillar aggregates related to these diseases, common pathological processes of increased oxidative injury, excitotoxicity and altered cell cycle are also evident. It was the aim of this study to identify novel interacting proteins to the amyloid-like motif and therefore identify common potential pathways between neurodegenerative diseases that share biophysical properties common to classical amyloid fibrils. Optimal ageing of recombinant proteins to form amyloid-like fibrils was determined by electron microscopy, Congo red birefringement and photo-induced cross-linking. Using pull-down assays the strongest detected interacting protein to the amyloid-like motifs of amyloid-beta, alpha-synuclein and lysozyme was identified as histone H1. The interaction with the amyloid-like motif was confirmed by techniques including surface plasmon resonance and immunohistochemistry. Histone H1 is known to be an integral part of chromatin within the nucleus, with a primary role of binding DNA that enters and exits from the nucleosome, and facilitating the shift in equilibrium of chromatin towards a more condensed form. However, phosphorylated histone H1 is predominantly present in the cytoplasm and as yet the functional significance of this translocation is unknown. This study also found that histone H1 is localised within the cytoplasm of neurons and astrocytes from areas affected by disease as well as amyloid plaques, supporting the hypothesis that histone H1 favoured binding to an ordered fibrillar motif. We conclude that the binding of histone H1 to a general amyloid-like motif indicates that histone H1 may play an important common role in diseases associated with amyloid-like fibrils.

Matrix metalloproteinase-9 degrades amyloid-beta fibrils in vitro and compact plaques in situ

The pathological hallmark of Alzheimer disease is the senile plaque principally composed of tightly aggregated amyloid-beta fibrils (fAbeta), which are thought to be resistant to degradation and clearance. In this study, we explored whether proteases capable of degrading soluble Abeta (sAbeta) could degrade fAbeta as well. We demonstrate that matrix metalloproteinase-9 (MMP-9) can degrade fAbeta and that this ability is not shared by other sAbeta-degrading enzymes examined, including endothelin-converting enzyme, insulin-degrading enzyme, and neprilysin. fAbeta was decreased in samples incubated with MMP-9 compared with other proteases, assessed using thioflavin-T. Furthermore, fAbeta breakdown with MMP-9 but not with other proteases was demonstrated by transmission electron microscopy. Proteolytic digests of purified fAbeta were analyzed with matrix-assisted laser desorption ionization time-of-flight mass spectrometry to identify sites of Abeta that are cleaved during its degradation. Only MMP-9 digests contained fragments (Abeta(1-20) and Abeta(1-30)) from fAbeta(1-42) substrate; the corresponding cleavage sites are thought to be important for beta-pleated sheet formation. To determine whether MMP-9 can degrade plaques formed in vivo, fresh brain slices from aged APP/PS1 mice were incubated with proteases. MMP-9 digestion resulted in a decrease in thioflavin-S (ThS) staining. Consistent with a role for endogenous MMP-9 in this process in vivo, MMP-9 immunoreactivity was detected in astrocytes surrounding amyloid plaques in the brains of aged APP/PS1 and APPsw mice, and increased MMP activity was selectively observed in compact ThS-positive plaques. These findings suggest that MMP-9 can degrade fAbeta and may contribute to ongoing clearance of plaques from amyloid-laden brains.

Molecular Interactions of Dendrimers with Amyloid Peptides: pH Dependence

The formation of amyloid plaques is a key pathological event in neurodegenerative disorders, such as prion and Alzheimer's diseases. Dendrimers are considered promising therapeutic agents in these disorders. In the present work, we have studied the effect of polypropyleneimine dendrimers on the formation of amyloid fibrils as a function of pH in order to gain further insight in the aggregation mechanism and its inhibition. Amyloid fibrils from prion peptide PrP 185-208 and Alzheimer's peptide Abeta 1-28 were produced in vitro, and their formation was monitored using the dye thioflavin T (ThT). The results showed that the level of protonation of His, Glu, and Asp residues is important for the final effect, especially at low dendrimer concentration when their inhibiting capacity depends on the pH. At the highest concentrations, dendrimers were very effective against fibril formations for both prion and Alzheimer's peptides.