Parallel Β-sheet Research Articles

Structural Insights into the Amyloid Fibril Polymorphism Using an Isotope-Edited Vibrational Circular Dichroism Study at the Amino Acid Residue Level.

Polymorphism is common in both in vitro and in vivo amyloid fibrils formed by the same peptide/protein. However, the differences in their self-assembled structures at the amino acid level remain poorly understood. In this study, we utilized isotope-edited vibrational circular dichroism (VCD) on a well-known amyloidogenic peptide fragment (N22FGAIL27) of human islet amyloid polypeptide (IAPf) to investigate the structural polymorphism. Two individual isotope-labeled IAPf peptides were used, with a 13C label on the carbonyl group of phenylalanine (IAPf-F) and glycine (IAPf-G). We compared the amyloid-like nanofibril of IAPf induced by solvent casting (fibril B) with our previous report on the same IAPf peptide fibril but with a different fibril morphology (fibril A) formed in an aqueous buffer solution. Fibril B consisted of entangled, laterally fused amyloid-like nanofibrils with a relatively shorter diameter (15-50 nm) and longer length (several microns), while fibril A displayed nanofibrils with a higher diameter (30-60 nm) and shorter length (500 nm-2 μm). The isotope-edited VCD analysis indicated that fibrils B consisted of anti-parallel β-sheet arrangements with glycine residues in the registry and phenylalanine residues out of the registry, which was significantly different from fibrils A, where a mixture of parallel β-sheet and turn structure with the registry at phenylalanine and glycine residues was observed. The VCD analysis, therefore, suggests that polymorphism in amyloid-like fibrils can be attributed to the difference in the packing/arrangement of the individual β-strands in the β-sheet and the difference in the amino acid registry. Our findings provide insights into the structural aspects of fibril polymorphism related to various amyloid diseases and may aid in designing amyloid fibril inhibitors for therapeutic purposes.

Structural Space of the Duffy Antigen/Receptor for Chemokines' Intrinsically Disordered Ectodomain 1 Explored by Temperature Replica-Exchange Molecular Dynamics Simulations.

Plasmodium vivax malaria affects 14 million people each year. Its invasion requires interactions between the parasitic Duffy-binding protein (PvDBP) and the N-terminal extracellular domain (ECD1) of the host's Duffy antigen/receptor for chemokines (DARC). ECD1 is highly flexible and intrinsically disordered, therefore it can adopt different conformations. We computationally modeled the challenging ECD1 local structure. With T-REMD simulations, we sampled its dynamic behavior and collected its most representative conformations. Our results suggest that most of the DARC ECD1 domain remains in a disordered state during the simulated time. Globular local conformations are found in the analyzed local free-energy minima. These globular conformations share an α-helix spanning residues Ser18 to Ser29 and in many cases they comprise an antiparallel β-sheet, whose β-strands are formed around residues Leu10 and Ala49. The formation of a parallel β-sheet is almost negligible. So far, progress in understanding the mechanisms forming the basis of the P. vivax malaria infection of reticulocytes has been hampered by experimental difficulties, along with a lack of DARC structural information. Our collection of the most probable ECD1 structural conformations will help to advance modeling of the DARC structure and to explore DARC-ECD1 interactions with a range of physiological and pathological ligands.

Self-Assembly of Insulin-Derived Chimeric Peptides into Two-Component Amyloid Fibrils: The Role of Coulombic Interactions.

Canonical amyloid fibrils are composed of covalently identical polypeptide chains. Here, we employ kinetic assays, atomic force microscopy, infrared spectroscopy, circular dichroism, and molecular dynamics simulations to study fibrillization patterns of two chimeric peptides, ACC1-13E8 and ACC1-13K8, in which a potent amyloidogenic stretch derived from the N-terminal segment of the insulin A-chain (ACC1-13) is coupled to octaglutamate or octalysine segments, respectively. While large electric charges prevent aggregation of either peptide at neutral pH, stoichiometric mixing of ACC1-13E8 and ACC1-13K8 triggers rapid self-assembly of two-component fibrils driven by favorable Coulombic interactions. The low-symmetry nonpolar ACC1-13 pilot sequence is crucial in enforcing the fibrillar structure consisting of parallel β-sheets as the self-assembly of free poly-E and poly-K chains under similar conditions results in amorphous antiparallel β-sheets. Interestingly, ACC1-13E8 forms highly ordered fibrils also when paired with nonpolypeptide polycationic amines such as branched polyethylenimine, instead of ACC1-13K8. Such synthetic polycations are more effective in triggering the fibrillization of ACC1-13E8 than poly-K (or poly-E in the case of ACC1-13K8). The high conformational flexibility of these polyamines makes up for the apparent mismatch in periodicity of charged groups. The results are discussed in the context of mechanisms of heterogeneous disease-related amyloidogenesis.

Concentration-Regulated Fibrillation of Soy Protein: Structure and In Vitro Digestion.

The impact of protein types, heating temperatures, and times on protein fibrillation has been widely studied. However, there is little understanding of the influence of protein concentration (PC) on the protein fibril assembly. In this work, the structure and in vitro digestibility of soy protein amyloid fibrils (SAFs) were investigated at pH 2.0 and different PCs. Significant increases in fibril conversion rate and parallel β-sheets proportion were observed in SAFs upon increasing the PC from 2 to 8% (w/v). The AFM images showed that curly fibrils were prone to form at 2-6% PCs, while rigid, straight fibrils developed at higher PCs (≥8%). As evidenced in XRD results, increasing PC led to a more stable structure of SAFs with enhanced thermal stability and lower digestibility. Moreover, positive correlations among PC, β-sheet content, persistence length, enthalpy, and total hydrolysis were established. These findings would provide valuable insights into concentration-regulated protein fibrillation.

Atomic Insight on Inhibition of Fibrillization of Dipeptides by Replacement of Phenylalanine with Tryptophan.

Tryptophan (Trp) conjugates destabilize amyloid fibrils responsible for amyloidoses. However, the mechanism of such destabilization is obscure. Herein the self-assembly of four synthesized Trp-containing dipeptides Boc-xxx-Trp-OMe (xxx: Val, Leu, Ile, and Phe) has been investigated and compared with the existing report on their Phe congeners. Two among them are the C-terminal tryptophan analogs of Boc-Val-Phe-OMe (VF, Aβ18-19) and Boc-Phe-Phe-OMe (FF, Aβ19-20), part of the central hydrophobic region of amyloid-β (Aβ1-42). While Boc-Val-Trp-OMe (VW), Boc-Leu-Trp-OMe (LW), Boc-Ile-Trp-OMe (IW), and Boc-Phe-Trp-OMe (FW) displayed a spherical morphology in FESEM and AFM images, the corresponding phenylalanine-containing dipeptides displayed various fibrous structures. Single-crystal X-ray diffraction (SC-XRD) indicated that peptides VW and IW exhibited structures containing parallel β-sheet, cross-β-structure, sheet-like layer structure, and helical arrangement in the solid state. Interestingly, peptide FW displayed inverse γ-turn conformation (similar to open-turn structure), antiparallel β-sheet structure, columnar structure, supramolecular nanozipper structure, sheet-like layer arrangement, and helical architecture in the solid state. The open-turn conformation and nanozipper structure formation by FW may be the first example of a dipeptide that forms such structures. The minute but consistent differences in molecular packing at the atomic level between Trp and Phe congeners may be responsible for their remarkably different supramolecular structure generation. This molecular-level structural analysis may be helpful for the de novo design of peptide nanostructures and therapeutics. Similar studies by the Debasish Haldar group are reported, but they investigated the inhibition of fibrillization of dipeptides by tyrosine and interactions are expectedly different.

IR microspectroscopic investigation of the interaction of some losartan salts with human stratum corneum protein and its effect on losartan transdermal permeation.

The interaction of pharmacologically active drugs with SC biochemical components is underestimated in pharmaceutical research. The aim of this research was to illustrate that some drugs intended for transdermal delivery could interact with the protein component of SC. Such interactions could be in favor of or opposition to their percutaneous absorption. IR microspectroscopy was used to delineate possible interaction of SC keratin with three losartan salts LOS-K, LOS-DEA and LOS-AML salts in addition to AML-BES salt. The results of PCA, combined with comparisons of average second derivative spectra of SC samples treated with these salts and the control SC, showed that LOS-DEA did not interact with SC, thus providing base line permeation of losartan. AML-BES, LOS-AML and LOS-K salts modified the conformational structure of keratin. The disorganization effect on the α-helical structure and induced formation of parallel β-sheets and random coils were in the order of AML-BES˃LOS-AML˃LOS-K. The order of the impact of treatments which resulted in increased formation of β-turns was AML-BES˃LOS-AML. The formation of antiparallel β-sheets was manifested by LOS-AML. Thus, the overall effect of these salts on the SC protein was AML-BES˃LOS-AML˃LOS-K. The impact of LOS-K was associated with improved permeation whereas the impact of LOS-AML was associated with hindered permeation of both losartan and amlodipine. There is a possibility that losartan and amlodipine when present in combination inside SC, their binding to the protein is enhanced leading to being retained within SC.

Molecular dynamics simulation of the interaction of a raspberry polygalacturonase (RiPG) with a PG inhibiting protein (RiPGIP) isolated from ripening raspberry (Rubus idaeus cv. Heritage) fruit as a model to understand proteins interaction during fruit softening

Polygalacturonase (PG) is an important hydrolytic enzyme involved in pectin disassembly and the subsequent textural changes during fruit ripening. Although the interaction of fungal PGs with other proteins has been documented, the interaction of plant PGs with other plant proteins has not yet been studied. In this study, the molecular mechanisms involved in raspberry fruit ripening, particularly the polygalacturonase (RiPG) interaction with polygalacturonase inhibiting protein (RiPGIP) and substrate, were investigated with a structural approach. The 3D model of RiPG2 and RiPGIP3 was built using a comparative modeling strategy and validated using molecular dynamics (MD) simulations. The RiPG2 model structure comprises 11 complete coils of right-handed parallel β-helix architecture, with an average of 27 amino acid residues per turn. The structural model of the RiPGIP3 displays a typical structure of LRR protein, with the right-handed superhelical fold with an extended parallel β-sheet. The conformational interaction between the RiPG2 protein and RiPGIP3 showed that RiPGIP3 could bind to the enzyme and thereby leave the active site cleft accessible to the substrate. All this evidence indicates that RiPG2 enzyme could interact with RiPGIP3 protein. It can be a helpful model for evaluating protein-protein interaction as a potential regulator mechanism of hydrolase activity during pectin disassembly in fruit ripening.

Characterization of Freeze-Thaw Treatments Upon Binders in Ancient Chinese Wall Paintings by X-Ray Diffraction (XRD) and Attenuated Total Reflection – Fourier Transform Infrared (ATR-FTIR) Spectroscopy

This study investigated the physico-chemical properties of the binders used in ancient Chinese wall paintings under repeated freeze–thaw cycles. Gum Arabic, cow bone, and fish bladder glue samples were prepared before and after three, six, and nine freeze–thaw cycles. The surface morphology, crystallinity, and spectral characteristics were characterized using scanning electron microscopy (SEM), X-ray diffraction (XRD), and attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy. The secondary structures of the protein binders were also analyzed before and after thaw–freeze cycles. The results show that the surface morphologies of the gum Arabic, cow bone, and fish bladder glue gradually changed from undulating to smooth as the number of freeze–thaw cycles increased. The intensities of the XRD peaks and crystallinity of the binders gradually decreased after six freeze–thaw cycles. ATR-FTIR spectroscopy indicated that no significant changes occurred in the original chemical compositions of the binders after multiple freeze–thaw cycles. The wavenumbers of the characteristic peaks remained unchanged but the intensities of the peaks changed significantly. Analysis of the secondary protein structures indicated that the α-helix contents of the cow bone and fish bladder glue samples decreased significantly, whereas the parallel β-sheet and random coil contents increased.

A double point mutation of SOD1 targeting net charge promotes aggregation under destabilizing conditions: Correlation of charge distribution and ALS-provoking mutation

A progressive neurodegenerative illness such as amyotrophic lateral sclerosis (ALS) is characterized by the misfolding and aggregation of human CuZn superoxide dismutase (hSOD1) into amyloid aggregates. Thus, designing strategies for the choice of WT-SOD1 and double mutant (G12D/G138E) with an increased net negative charge can be a good idea to elucidate the pathological mechanism of SOD1 in ALS under some destabilizing conditions. Consequently, we show evidence that protein charge, together with other destabilizing conditions, plays an important role in ALS disease. To achieve this purpose, we use methods, such as spectroscopy and transmission electron microscopy (TEM) to monitor the formation of amyloid aggregation. The specific activity of WT-SOD1 was approximately 1.72 times higher than that of the double mutant. Under amyloidogenic circumstances, structural properties such as local, secondary, oligomeric, and fibrillar structures were explored. The double mutant's far-UV CD spectra displayed a broad minimum peak in the region 213 to 218 nm, suggesting the production of β-rich amyloid fibrils. FTIR spectra of the double mutant samples at different incubation times showed a low-frequency peak around 1630–1640 cm-1, attributed to a parallel β-sheet. Moreover, CR-binding assay and TEM analysis revealed and confirmed that mutation with an increased repulsive charge promotes the formation of fibrous aggregates. Consequently, ALS mutations with a higher repulsive charge are the apparent exceptions that validate the rule. This findings revealed that the double mutant increases protein aggregation through a novel mechanism, likely involving destabilization of structure and a change in the net negative charge.

Lipids uniquely alter the secondary structure and toxicity of amyloid beta 1-42 aggregates.

Abrupt aggregation of amyloid β1-42 (Aβ) peptide is a hallmark of Alzheimer's disease (AD), a severe pathology that affects more than 44million people worldwide. A growing body of evidence suggests that lipids can uniquely alter rates of Aβ1-42 aggregation. However, it remains unclear whether lipids only alter rates of protein aggregation or also uniquely modify the secondary structure and toxicity of Aβ1-42 oligomers and fibrils. In this study, we investigated the effect of phosphatidylcholine (PC), cardiolipin (CL), and cholesterol (Chol) on Aβ1-42 aggregation. We found that PC, CL and Chol strongly accelerated the rate of fibril formation compared to the rate of Aβ1-42 aggregation in the lipid-free environment. Furthermore, anionic CL enabled the strongest acceleration of Aβ1-42 aggregation compared to zwitterionic PC and uncharged Chol. We also found that PC, CL and Chol uniquely altered the secondary structure of early-, middle- and late-stage Aβ1-42 aggregates. Specifically, CL and Chol drastically increased the amount of parallel β-sheet in Aβ1-42 oligomers and fibrils grown in the presence of these lipids. This caused a significant increase in the toxicity of Aβ:CL and Aβ:Chol compared to the toxicity of Aβ:PC and Aβ1-42 aggregates formed in the lipid-free environment. These results demonstrate that toxicity of Aβ aggregates correlates with the amount of their β-sheet content, which, in turn, is determined by the chemical structure of lipids present at the stage of Aβ1-42 aggregation.

Effect of nanoparticles on the aggregation and amyloid formation of amyloid-beta peptide.

Nanoparticles are becoming more and more important in medicine and biotechnology. Moreover, due to environmental pollution, the human body is exposed to nanoparticles in the everyday life. Nanomaterials can also affect the aggregation processes of proteins. The Aβ peptides are known for forming amyloid aggregates in the brain in Alzheimer's disease. We used in-house expressed recombinant Aβ(1-42) to study the structure, aggregation kinetics and cytotoxicity of the peptide. We characterized nanoparticles of different materials and studied their effects on the structure and aggregation of Aβ. We followed amyloid formation by monitoring Thioflavin T fluorescence in the presence of nanoparticles. We observed that nanoparticles typically reduce the lag time of aggregation. We found that polystyrene particles bind monomers to a certain saturation point and allow only excess monomers to form fibrils. Calcium fluoride (CaF2) nanoparticles do not bind monomers in a similar fashion, but do influence the secondary structure composition of the resulting amyloid fibrils. We used CD spectroscopy and the BeStSel method to determine the secondary structure composition of the different forms of Aβ. While the main characteristics of Aβ fibrils formed alone is parallel β-sheet, in the presence of CaF2, Aβ forms significant amount of antiparallel β-structure as well. We also conducted cytotoxicity experiments to investigate if nanoparticles alter the toxic effect of Aβ on mouse hippocampal cells. Our preliminary findings suggest that studied particles might reduce cytotoxicity of Aβ if applied in very low concentrations.

Stabilization of small Aβ oligomers in SDS micelles.

Aβ fibrillation is a slow process without seeding or assisted nucleation. It was observed previously that SDS micelles promote Aβ40 fibrillation and stabilize Aβ42 small oligomers (in the dimer to tetramer range). Here we characterized small oligomers in SDS micelles by molecular dynamics simulations and solid-state NMR spectroscopy. Parallel β-sheets formed by the C-terminal region (Ala30 to the C-terminus, or C-strand) of Aβ40 and Aβ42 tetramers are unstable in SDS micelles, due to fraying starting at Gly37 and Gly38. In contrast, an antiparallel β-sheet formed by four Aβ42 C-strands is stable, with the tails of SDS molecules inserted next to the β-sheet in the voids above Gly33 of one strand and Gly37 and Gly38 one of the next strand. This deep insertion allows the SDS tails to form hydrophobic interactions with numerous nearby nonpolar sidechains. Measurements of intermolecular 13C-13C dipolar couplings show that the SDS-stabilized antiparallel tetramer is an on-pathway intermediate for a 150-kD oligomer formed on dialysis. These observations have implications for the stimulation of endogenous Aβ aggregation at cellular interfaces.

Analysis of gelatin secondary structure in gelatin/keratin-based biomaterials

The possibility of using protein-based materials as cellular scaffold strongly depends on protein conformation, and several attempts have been made by researchers to obtain scaffold with morphology miming the extracellular matrix. It is widely recognized that the secondary structure of proteins affects the mechanical and biological properties of protein-based scaffolds. However, few studies have been published, and an exhaustive explanation is still missing. In this work the study of the gelatin structure in gelatin-based materials and the investigation of the possible correlations between structure, mechanical and biological features is reported.We have examined how the secondary structure of gelatin is affected (i) by the process used to obtain the biomaterials (solvent casting vs. electrospinning), (ii) by the concentration of cross linker (3-(Glycidyloxypropyl)trimethoxysilane) (GPTMS), and (iii) by the raw keratin extract added. Gelatin electrospun materials have shown a content of ordered structure higher than gelatin casted films, likely due to the random coil – α-helix transition occuring during electrospinning. GPTMS gives a decrease of ordered structures in gelatin casted films (random structure increasing from 20% to 60%), while it does not affect the percentage of ordered structure in electrospun samples. In the gelatin/keratin electrospun biomaterials, the presence of keratin produces a decrease of α-helix content from 31% to 2–15% and an increase of β-structures, promoting the conversion from antiparallel to parallel β-sheet. The structure of gelatin affects the mechanical performances of biomaterials. In gelatin/keratin electrospun biomaterials we have found a positive correlation between failure strain and helix conformation and a negative correlation with β-structures. Elastic modulus has opposite correlations. All gelatin-based biomaterials have been tested as scaffold for pre-osteoblastic cells showing good biocompatibility for both casted films and electrospun biomaterials.

A structural basis for prion strain diversity

Recent cryogenic electron microscopy (cryo-EM) studies of infectious, ex vivo, prion fibrils from hamster 263K and mouse RML prion strains revealed a similar, parallel in-register intermolecular β-sheet (PIRIBS) amyloid architecture. Rungs of the fibrils are composed of individual prion protein (PrP) monomers that fold to create distinct N-terminal and C-terminal lobes. However, disparity in the hamster/mouse PrP sequence precludes understanding of how divergent prion strains emerge from an identical PrP substrate. In this study, we determined the near-atomic resolution cryo-EM structure of infectious, ex vivo mouse prion fibrils from the ME7 prion strain and compared this with the RML fibril structure. This structural comparison of two biologically distinct mouse-adapted prion strains suggests defined folding subdomains of PrP rungs and the way in which they are interrelated, providing a structural definition of intra-species prion strain-specific conformations.

β-Sheet Structure Formation within Binary Blends of Two Spider Silk Related Peptides.

Intrinsically disordered proteins (IDPs) play an important role in molecular biology and medicine because their induced folding can lead to so-called conformational diseases, where β-amyloids play an important role. Still, the molecular folding process into the different substructures, such as parallel/antiparallel or extended β-sheet/crossed β-sheet is not fully understood. The recombinant spider silk protein eADF4(Cx) consisting of repeating modules C, which are composed of a crystalline (pep-c) and an amorphous peptide sequence (pep-a), can be used as a model system for IDP since it can assemble into similar structures. In this work, blend films of the pep-c and pep-a sequences were investigated to modulate the β-sheet formation by varying the molar fraction of pep-c and pep-a. Dichroic Fourier-transform infrared spectroscopy (FTIR), circular dichroism, spectroscopic ellipsometry, atomic force microscopy, and IR nanospectroscopy were used to examine the secondary structure, the formation of parallel and antiparallel β-sheets, their orientation, and the microscopic roughness and phase formation within peptide blend films upon methanol post-treatment. New insights into the formation of filament-like structures in these silk blend films were obtained. Filament-like structures could be locally assigned to β-sheet-rich structures. Further, the antiparallel or parallel character and the orientation of the formed β-sheets could be clearly determined. Finally, the ideal ratio of pep-a and pep-c sequences found in the fibroin 4 of the major ampullate silk of spiders could also be rationalized by comparing the blend and spider silk protein systems.

Nanoscale insights into the local structural rearrangements of amyloid-β induced by bexarotene.

A better understanding of the abnormal protein aggregation and the effect of anti-aggregation agents on the fibrillation pathways and the secondary structure of aggregates can determine strategies for the early treatment of dementia. Herein, we present a combination of experimental and theoretical studies providing new insights into the influence of the anti-aggregation drug bexarotene on the secondary structure of individual amyloid-β aggregates and its primary aggregation. The molecular rearrangements and the spatial distribution of β-sheets within individual aggregates were monitored at the nanoscale with infrared nanospectroscopy. We observed that bexarotene limits the parallel β-sheets formation, known to be highly abundant in fibrils at later phases of the amyloid-β aggregation composed of in-register cross-β structure. Moreover, we applied molecular dynamics to provide molecular-level insights into the investigated system. Both theoretical and experimental results revealed that bexarotene slows down the protein aggregation process via steric effects, largely prohibiting the antiparallel to parallel β-sheet rearrangement. We also found that bexarotene interacts not only via the single hydrogen bond formation with the peptide backbone but also with the amino acid side residue via a hydrophobic effect. The studied model of the drug-amyloid-β interaction contributes to a better understanding of the inhibition mechanism of the amyloid-β aggregation by the small molecule drugs. However, our nanoscale findings need to meet in vivo research requiring different analytical approaches.

Forced amyloidogenic cooperativity of structurally incompatible peptide segments: Fibrillization behavior of highly aggregation-prone A-chain fragment of insulin coupled to all-L, and alternating L/D octaglutamates

Aggregation of proteins into amyloid fibrils is driven by interactions between relatively small amyloidogenic segments. The interplay between aggregation-prone and aggregation-resistant fragments within a single polypeptide chain remains obscure. Here, we examine fibrillization behavior of two chimeric peptides, ACC1–13E8 and ACC1–13E8(L/D), in which the highly amyloidogenic fragment of insulin (ACC1–13) is extended by an octaglutamate segment composed of all-L (E8), or alternating L/D residues (E8(L/D)). As separate entities, ACC1–13 readily forms fibrils with the infrared features of parallel β-sheet while E8 forms antiparallel β-sheets with the distinct infrared characteristics. This contrasts with the profoundly aggregation-resistant E8(L/D), although L/D patterns have been hypothesized as compatible with aggregated α-sheets. ACC1–13E8 and ACC1–13E8(L/D) are found to be equally prone to fibrillization at low pH, or in the presence of Ca2+ ions. Fibrillar states of both ACC1–13E8 and ACC1–13E8(L/D) reveal the infrared features of highly ordered parallel β-sheet without evidence of β2-aggregates (ACC1–13E8) or α-sheets (ACC1–13E8(L/D)). Hence, the preferred structural pattern of ACC1–13 overrides the tendency of E8 to form antiparallel β-sheets and enforces the fibrillar order in E8(L/D). We demonstrate how the powerful amyloid stretch determines the overall amyloid structure forcing non-amyloidogenic fragments to participate in its native amyloid pattern.

Cryo-EM of prion strains from the same genotype of host identifies conformational determinants.

Prion strains in a given type of mammalian host are distinguished by differences in clinical presentation, neuropathological lesions, survival time, and characteristics of the infecting prion protein (PrP) assemblies. Near-atomic structures of prions from two host species with different PrP sequences have been determined but comparisons of distinct prion strains of the same amino acid sequence are needed to identify purely conformational determinants of prion strain characteristics. Here we report a 3.2 Å resolution cryogenic electron microscopy-based structure of the 22L prion strain purified from the brains of mice engineered to express only PrP lacking glycophosphatidylinositol anchors [anchorless (a) 22L]. Comparison of this near-atomic structure to our recently determined structure of the aRML strain propagated in the same inbred mouse reveals that these two mouse prion strains have distinct conformational templates for growth via incorporation of PrP molecules of the same sequence. Both a22L and aRML are assembled as stacks of PrP molecules forming parallel in-register intermolecular β-sheets and intervening loops, with single monomers spanning the ordered fibril core. Each monomer shares an N-terminal steric zipper, three major arches, and an overall V-shape, but the details of these and other conformational features differ markedly. Thus, variations in shared conformational motifs within a parallel in-register β-stack fibril architecture provide a structural basis for prion strain differentiation within a single host genotype.

Nanoscale Infrared Spectroscopy Identifies Parallel to Antiparallel β-Sheet Transformation of Aβ Fibrils.

Spontaneous aggregation of amyloid beta (Aβ) proteins leading to the formation of oligomers and eventually into fibrils has been identified as a key pathological signature of Alzheimer's disease. The structure of late-stage aggregates have been studied in depth by conventional structural biology techniques, including nuclear magnetic resonance, X-ray crystallography, and infrared spectroscopy; however, the structure of early-stage aggregates is less known due to their transient nature. As a result, the structural evolution of amyloid aggregates from early oligomers to mature fibrils is still not fully understood. Here, we have applied atomic force microscopy-infrared nanospectroscopy to investigate the aggregation of Aβ 16-22, which spans the amyloidogenic core of the Aβ peptide. Our results demonstrate that Aβ 16-22 involves a structural transition from oligomers with parallel β-sheets to antiparallel fibrils through disordered and possibly helical intermediate fibril structures, contrary to the known aggregation pathway of full-length Aβ.

Nanoscale Characterization of Parallel and Antiparallel β-Sheet Amyloid Beta 1-42 Aggregates.

Abrupt aggregation of amyloid beta (Aβ) peptide is strongly associated with Alzheimer's disease. In this study, we used atomic force microscopy-infrared (AFM-IR) spectroscopy to characterize the secondary structure of Aβ oligomers, protofibrils and fibrils formed at the early (4 h), middle (24 h), and late (72 h) stages of protein aggregation. This innovative spectroscopic approach allows for label-free nanoscale structural characterization of individual protein aggregates. Using AFM-IR, we found that at the early stage of protein aggregation, oligomers with parallel β-sheet dominated. However, these species exhibited slower rates of fibril formation compared to the oligomers with antiparallel β-sheet, which first appeared in the middle stage. These antiparallel β-sheet oligomers rapidly propagated into fibrils that were simultaneously observed together with parallel β-sheet fibrils at the late stage of protein aggregation. Our findings showed that aggregation of Aβ is a complex process that yields several distinctly different aggregates with dissimilar toxicities.