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1.
Amyloid fibrils formed by peptides with different sequences exhibit diversified morphologies, material properties and activities, making them valuable for developing functional bionanomaterials. However, the molecular understanding underlying the structural diversity of peptide fibrillar assembly at atomic level is still lacking. In this study, by using cryogenic electron microscopy, we first revealed the structural basis underlying the highly reversible assembly of 1GFGGNDNFG9 (referred to as hnRAC1) peptide fibril. Furthermore, by installing iodine at different sites of hnRAC1, we generated a collection of peptide fibrils with distinct thermostability. By determining the atomic structures of the iodinated fibrils, we discovered that iodination at different sites of the peptide facilitates the formation of diverse halogen bonds and triggers the assembly of entirely different structures of iodinated fibrils. Finally, based on this structural knowledge, we designed an iodinated peptide that assembles into new atomic structures of fibrils, exhibiting superior thermostability, that aligned with our design. Our work provides an in-depth understanding of the atomic-level processes underlying the formation of diverse peptide fibril structures, and paves the way for creating an amyloid “kaleidoscope” by employing various modifications and peptide sequences to fine-tune the atomic structure and properties of fibrillar nanostructures.  相似文献   

2.
Under in vitro solution conditions where the native state is destabilized, many proteins present an abnormal structure and metabolism associated with a strong tendency to self-aggregation into a polymeric amyloid fibril structure, suggesting that this ability is a generic feature of the polypeptide chains. Such structures play a key role in different pathogenesis of neurodegenerative diseases such as Alzheimer, Parkinson, or Creutzfeldt-Jakob. Here, we report the formation of amyloid fibrils in the plasma protein human serum albumin under different in vitro conditions monitored using a combination of spectrophotometric and microscopic techniques. Amyloid fibril formation, therefore, is also allowed in a protein with a high degree of structural complexity. We also infer from experimental data the existence of other protein aggregated species than fibrils, some of which seem to be formed by a structural rearrangement of the proper fibrils.  相似文献   

3.
The effect of poly(ethylene glycol) PEG crystallization on beta-sheet fibril formation is studied for a series of three peptide/PEG conjugates containing fragments modified from the amyloid beta peptide, specifically KLVFF, FFKLVFF, and AAKLVFF. These are conjugated to PEG with M n = 3300 g mol (-1). It is found, via small-angle X-ray scattering, X-ray diffraction, atomic force microscopy, and polarized optical microscopy, that PEG crystallinity in dried samples can disturb fibrillization, in particular cross-beta amyloid structure formation, for the conjugate containing the weak fibrillizer KLVFF, whereas this is retained for the conjugates containing the stronger fibrillizers AAKLVFF and FFKLVFF. For these two samples, the alignment of peptide fibrils also drives the orientation of the attached PEG chains. Our results highlight the importance of the antagonistic effects of PEG crystallization and peptide fibril formation in PEG/peptide conjugates.  相似文献   

4.
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.  相似文献   

5.
Molecular structures of diffusible amyloid intermediates, commonly observed in misfolding of amyloid proteins into fibrils, have attracted broad interest because the intermediates may be potent neurotoxins responsible for amyloid diseases such as Alzheimer's disease (AD) and because the intermediate structures provide an experimental basis for defining the misfolding pathway. However, owing to the intrinsically unstable and noncrystalline nature of the systems, traditional approaches such as X-ray crystallography and solution NMR have been ineffective for elucidating molecular-level structures of the amyloid intermediates. We present a novel approach using solid-state NMR (SSNMR) that permitted the first site-resolved structural measurement of an intermediate species in fibril formation for a 40-residue Alzheimer's beta-amyloid peptide, Abeta(1-40). In this approach, we combined detection of conformation and morphology changes by fluorescence spectroscopy and electron microscopy and quantitative structural examination for freeze-trapped intermediates by SSNMR. The results provide the initial evidence that a spherical amyloid intermediate of 15-30 nm in diameter exists prior to fibril formation of Abeta(1-40) and that the intermediate involves well-ordered beta-sheets in the C-terminal and hydrophobic core regions. The SSNMR-based approach presented here could be applied to intermediate species of diverse amyloid proteins.  相似文献   

6.
Many peptides self‐assemble to form amyloid fibrils. We previously explored the sequence propensity to form amyloid using variants of a designed peptide with sequence KFFEAAAKKFFE. These variant peptides form highly stable amyloid fibrils with varied lateral assembly and are ideal to template further assembly of non‐proteinaceous material. Herein, we show that the fibrils formed by peptide variants can be coated with a layer of silica to produce silica nanowires using tetraethyl‐orthosilicate. The resulting nanowires were characterized using electron microscopy (TEM), X‐ray fiber diffraction, FTIR and cross‐section EM to reveal a nanostructure with peptidic core. Lysine residues play a role in templating the formation of silica on the fibril surface and, using this library of peptides, we have explored the contributions of lysine as well as arginine to silica templating, and find that sequence plays an important role in determining the physical nature and structure of the resulting nanowires.  相似文献   

7.
《Chemistry & biology》1997,4(5):345-355
Background: Peptides derived from three of four putative α-helical regions of the prion protein (PrP) form amyloid in solution. These peptides serve as models for amyloidogenesis and for understanding the α helix → β strand conformational change that is responsible for the development of disease. Kinetic studies of amyloid formation usually rely on the detection of fibrils. No study has yet explored the rate of monomer peptide uptake or the presence of nonfibrillar intermediate species. We present a new electron spin resonance (ESR) method for probing the kinetics of amyloid formation. A spin label was covalently attached to a highly amyloidogenic peptide and kinetic trials were monitored by ESR.Results: Electron microscopy shows that the spin-labeled peptide forms amyloid, and ESR reveals the kinetic decay of free peptide monomer during amyloid formation. The combination of electron microscopy and ESR suggests that there are three kinetically relevant species: monomer peptide, amyloid and amorphous aggregate (peptide aggregates devoid of fibrils or other structures with long-range order). A rather surprising result is that amyloid formation requires the presence of this amorphous aggregate. This is particularly interesting because PrPSc the form of PrP associated with scrapie, is often found as an aggregate and amyloid formation is not a necessary component of prion replication or pathogenesis.Conclusions: Kinetic analysis of the time-dependent data suggests a model whereby the amorphous aggregate has a previously unsuspected dual role: it releases monomer into solution and also provides initiation sites for fibril growth. These findings suggest that the β-sheet-rich PrPSc may be stabilized by aggregation.  相似文献   

8.
Some 25 diseases are associated with proteins and peptides that assemble into amyloid fibrils composed of beta-strands connected by hydrogen bonds oriented parallel to the fiber long axis. There is mounting evidence that amyloid formation involves specific interactions between amino acid side groups, which bring together beta-sheets to form layers with buried and exposed faces. This work demonstrates how a combination of solid-state 2H and 19F NMR experiments can provide constraints on fibril architecture by probing the environment and spatial organisation of aromatic side groups. It is shown that phenylalanine rings within fibrils formed by a decapeptide fragment of the islet amyloid polypeptide, amylin, are highly motionally restrained and are situated within 6.5 A of one another. Taken together with existing structural constraints for this peptide, these results are consistent with a fibril architecture that comprises layers of two or more beta-sheets, with the aromatic residues facing into the inter-sheet space and possibly engaged in pi-pi interactions. The methods presented will be of general utility in exploring the architecture of fibrils of larger, full-length peptides and proteins, including amylin itself.  相似文献   

9.
Although amyloid fibrils are associated with numerous pathologies, their conformational stability remains largely unclear. Herein, we probe the thermal stability of various amyloid fibrils. α‐Synuclein fibrils cold‐denatured to monomers at 0–20 °C and heat‐denatured at 60–110 °C. Meanwhile, the fibrils of β2‐microglobulin, Alzheimer’s Aβ1‐40/Aβ1‐42 peptides, and insulin exhibited only heat denaturation, although they showed a decrease in stability at low temperature. A comparison of structural parameters with positive enthalpy and heat capacity changes which showed opposite signs to protein folding suggested that the burial of charged residues in fibril cores contributed to the cold denaturation of α‐synuclein fibrils. We propose that although cold‐denaturation is common to both native proteins and misfolded fibrillar states, the main‐chain dominated amyloid structures may explain amyloid‐specific cold denaturation arising from the unfavorable burial of charged side‐chains in fibril cores.  相似文献   

10.
Uncontrolled aggregation of proteins or polypeptides can be detrimental for normal cellular processes in healthy organisms. Proteins or polypeptides that form these amyloid deposits differ in their primary sequence but share a common structural motif: the (anti)parallel beta sheet. A well-accepted approach for interfering with beta-sheet formation is the design of soluble beta-sheet peptides to disrupt the hydrogen-bonding network; this ultimately leads to the disassembly of the aggregates or fibrils. Here, we describe the synthesis, spectroscopic analysis, and aggregation behavior, imaged by electron microscopy, of several backbone-modified amylin(20-29) derivatives. It was found that these amylin derivatives were not able to form fibrils and to some extent were able to inhibit fibril growth of native amylin(20-29). However, two of the amylin peptides were able to form large supramolecular assemblies, like helical ribbons and peptide nanotubes, in which beta-sheet formation was clearly absent. This was quite unexpected since these peptides have been designed as soluble beta-sheet breakers for disrupting the characteristic hydrogen-bonding network of (anti)parallel beta sheets. The increased hydrophobicity and the presence of essential amino acid side chains in the newly designed amylin(20-29) derivatives were found to be the driving force for self-assembly into helical ribbons and peptide nanotubes. This example of controlled and desired peptide aggregation may be a strong impetus for research on bionanomaterials in which special shapes and assemblies are the focus of interest.  相似文献   

11.
Alzheimer’s disease is understood to be caused by amyloid fibrils and oligomers formed by aggregated amyloid-β (Aβ) peptides. This review article presents molecular dynamics (MD) simulation studies of Aβ peptides and Aβ fragments on their aggregation, aggregation inhibition, amyloid fibril conformations in equilibrium, and disruption of the amyloid fibril by ultrasonic wave and infrared laser irradiation. In the aggregation of Aβ, a β-hairpin structure promotes the formation of intermolecular β-sheet structures. Aβ peptides tend to exist at hydrophilic/hydrophobic interfaces and form more β-hairpin structures than in bulk water. These facts are the reasons why the aggregation is accelerated at the interface. We also explain how polyphenols, which are attracting attention as aggregation inhibitors of Aβ peptides, interact with Aβ. An MD simulation study of the Aβ amyloid fibrils in equilibrium is also presented: the Aβ amyloid fibril has a different structure at one end from that at the other end. The amyloid fibrils can be destroyed by ultrasonic wave and infrared laser irradiation. The molecular mechanisms of these amyloid fibril disruptions are also explained, particularly focusing on the function of water molecules. Finally, we discuss the prospects for developing treatments for Alzheimer’s disease using MD simulations.  相似文献   

12.
Energy-based methods for calculating time-averaged peptide structures are important for rational peptide design, for defining local structure propensities in large protein chains, and for exploring the sequence determinants of amyloid formation. High-end methods are currently too slow to be practicable, and will remain so for the foreseeable future. The challenge is to create a method that runs quickly on limited computer resources and emulates reality sufficiently well. We have developed a simplified off-lattice protein model, incorporating semi-empirical physicochemical potentials, and combined it with an efficient Monte Carlo method for calculating time-averaged peptide structures. Reasonably accurate predictions are found for a set of small alpha-helical and beta-hairpin peptides, and we demonstrate a potential application in measuring local structure propensities in protein chains. Time-averaged structures have also been calculated for a set of small peptides known to form beta-amyloid fibrils. The simulations were of three interacting peptides, and in each case the time-averaged structure describes a three-stranded beta-sheet. The performance of our method in measuring the propensities of small peptides to self-associate into possible prefibrillar species compares favorably with more detailed and CPU-intensive approaches.  相似文献   

13.
Yuri Zimenkov  Liang Guo 《Tetrahedron》2004,60(34):7237-7246
We describe a model for the design of synthetic α-helical peptides that are competent for self-assembly into structurally defined supramolecular fibrils on the basis of architectural features that have been programmed into the peptide sequence. In order to test the validity of this experimental model, we have synthesized an oligopeptide YZ1 that was designed to conform to this model and to self-assemble into an α-helical fibril in which the structural sub-units that comprise the fibril corresponded to coiled coil dimers. Peptide YZ1 was prepared via conventional solid-phase peptide synthesis and was composed of 42 amino acid residues such that the sequence defined six distinct heptad repeats of a coiled coil structure. The sequence of YZ1 was designed to adopt an α-helical conformation in which the helical protomers self-associate in a parallel orientation with a staggered orientation between adjacent peptides that corresponded to an axial displacement of three heptads. The self-assembly of peptide YZ1 was examined at varying levels of structural hierarchy for compliance of the observed structures with the experimental model. Circular dichroism spectroscopy provided evidence for an α-helical coiled coil structure for YZ1 in aqueous solution, which could be reversibly denatured through thermal methods. TEM measurements indicated the formation of long aspect-ratio fibers of uniform diameter from aqueous solutions of YZ1, however the dimensions of the fibers suggested that lateral association occurred between the fibrils corresponding to the 2-stranded helical bundles. The α-helical coiled coil structure was confirmed in the solid-state for fibers derived from self-assembly of YZ1 by a combination of wide-angle X-ray diffraction and 13C CP/MAS NMR spectroscopy. SANS and synchrotron SAXS measurements on dilute aqueous solutions of YZ1 provided a fibril diameter that corresponded to the lateral dimensions estimated for a dimeric coiled coil assembly on the basis of structural determinations of model peptides.  相似文献   

14.
The aggregation of the amyloid β‐peptide into fibrils is a complex process that involves mechanisms such as primary and secondary nucleation, fibril elongation and fibril fragmentation. Some of these processes generate neurotoxic Aβ oligomers, which are involved in the development of Alzheimer's disease. Recent experimental studies have emphasized the role of the fibril as a catalytic surface for the production of highly toxic oligomers during secondary nucleation. By using molecular dynamics simulations, we show that it is the hydrophobic fibril region that causes the structural changes required for catalyzing the formation of β‐sheet‐rich Aβ1‐42 oligomers on the fibril surface. These results reveal, for the first time, the molecular basis of the secondary nucleation pathway.  相似文献   

15.
Peptides and proteins are exposed to a variety of interfaces in a physiological environment, such as cell membranes, protein nanoparticles (NPs), or viruses. These interfaces have a significant impact on the interaction, self-assembly, and aggregation mechanisms of biomolecular systems. Peptide self-assembly, particularly amyloid fibril formation, is associated with a wide range of functions; however, there is a link with neurodegenerative diseases, such as Alzheimer's disease. This review highlights how interfaces affect peptide structure and the kinetics of aggregation leading to fibril formation. In nature, many surfaces are nanostructures, such as liposomes, viruses, or synthetic NPs. Once exposed to a biological medium, nanostructures are coated with a corona, which then determines their activity. Both accelerating and inhibiting effects on peptide self-assembly have been observed. When amyloid peptides adsorb to a surface, they typically concentrate locally, which promotes aggregation into insoluble fibrils. Starting from a combined experimental and theoretical approach, models that allow for a better understanding of peptide self-assembly near hard and soft matter interfaces are introduced and reviewed. Research results from recent years are presented and relationships between biological interfaces, such as membranes and viruses, and amyloid fibril formation are proposed.  相似文献   

16.
Short peptide stretches in amyloidogenic proteins can form amyloid fibrils in vitro and have served as good models for studying amyloid fibril formation. Recently, these amyloidogenic peptides have gained considerable attention, as non-amyloid ordered structures can be obtained from these peptides by carefully tuning the conditions of self-assembly, especially pH, temperature and presence of organic solvents. We have examined the effect of surface pressure on the self-assembled structures of two amyloidogenic peptides, Pβ(2)m (Ac-DWSFYLLYYTEFT-am) and AcPHF6 (Ac-VQIVYK-am) at the air-water interface when deposited from different solvents. Both the peptides are surface-active and form Thioflavin T (ThT) positive structures at the air-water interface. There is considerable hysteresis in the compression and expansion isotherms, suggesting the occurrence of structural rearrangements during compression. Preformed Pβ(2)m fibrillar structures at the air-water interface are disrupted as peptide is compressed to lower molecular areas but restored if the film is expanded, suggesting that the process is reversible. AcPHF6, on the other hand, shows largely sheet-like structures at lower molecular areas. The solvents used for dissolution of the peptides appear to influence the nature of the aggregates formed. Our results show that like hydrostatic pressure, surface pressure can also be utilized for modulating the self-assembly of the amyloidogenic and self-assembling peptides.  相似文献   

17.
Supramolecular assembly of peptides and proteins into amyloid fibrils is of multifold interest, going from materials science to physiopathology. The binding of metal ions to amyloidogenic peptides is associated with several amyloid diseases, and amyloids with incorporated metal ions are of interest in nanotechnology. Understanding the mechanisms of amyloid formation and the role of metal ions can improve strategies toward the prevention of this process and enable potential applications in nanotechnology. Here, studies on Zn(II) binding to the amyloidogenic peptide Aβ11-28 are reported. Zn(II) modulates the Aβ11-28 aggregation, in terms of kinetics and fibril structures. Structural studies suggest that Aβ11-28 binds Zn(II) by amino acid residues Glu11 and His14 and that Zn(II) is rapidly exchanged between peptides. Structural and aggregation data indicate that Zn(II) binding induces the formation of the dimeric Zn(II)(1)(Aβ11-28)(2) species, which is the building block of fibrillar aggregates and explains why Zn(II) binding accelerates Aβ11-28 aggregation. Moreover, transient Zn(II) binding, even briefly, was enough to promote fibril formation, but the final structure resembled that of apo-Aβ11-28 amyloids. Also, seeding experiments, i.e., the addition of fibrillar Zn(II)(1)(Aβ11-28)(2) to the apo-Aβ11-28 peptide, induced aggregation but not propagation of the Zn(II)(1)(Aβ11-28)(2)-type fibrils. This can be explained by the dynamic Zn(II) binding between soluble and aggregated Aβ11-28. As a consequence, dynamic Zn(II) binding has a strong impact on the aggregation behavior of the Aβ11-28 peptide and might be a relevant and so far little regarded parameter in other systems of metal ions and amyloidogenic peptides.  相似文献   

18.
Deciphering the mechanism(s) of β-sheet mediated self-assembly is essential for understanding amyloid fibril formation and for the fabrication of polypeptide materials. Herein, we report a simple peptidomimetic that self-assembles into polymorphic β-sheet quaternary structures including protofilaments, filaments, fibrils, and ribbons that are reminiscent of the highly ordered structures displayed by the amyloidogenic peptides Aβ, calcitonin, and amylin. The distribution of quaternary structures can be controlled by and in some cases specified by manipulating the pH, buffer composition, and the ionic strength. The ability to control β-sheet-mediated assembly takes advantage of quaternary structure dependent pK(a) perturbations. Biophysical methods including analytical ultracentrifugation studies as well as far-UV circular dichroism and FT-IR spectroscopy demonstrate that linked secondary and quaternary structural changes mediate peptidomimetic self-assembly. Electron and atomic force microscopy reveal that peptidomimetic assembly involves numerous quaternary structural intermediates that appear to self-assemble in a convergent fashion affording quaternary structures of increasing complexity. The ability to control the assembly pathway(s) and the final quaternary structure(s) afforded should prove to be particularly useful in deciphering the quaternary structural requirements for amyloid fibril formation and for the construction of noncovalent macromolecular structures.  相似文献   

19.
Many unrelated proteins and peptides can assemble into amyloid or amyloid-like nanostructures, all of which share the cross-beta motif of repeat arrays of beta-strands hydrogen-bonded along the fibril axis. Yet, paradoxically, structurally polymorphic fibrils may derive from the same initial polypeptide sequence. Here, solid-state nuclear magnetic resonance (SSNMR) analysis of amyloid-like fibrils of the peptide hIAPP 20-29, corresponding to the region S (20)NNFGAILSS (29) of the human islet amyloid polypeptide amylin, reveals that the peptide assembles into two amyloid-like forms, (1) and (2), which have distinct structures at the molecular level. Rotational resonance SSNMR measurements of (13)C dipolar couplings between backbone F23 and I26 of hIAPP 20-29 fibrils are consistent with form (1) having parallel beta-strands and form (2) having antiparallel strands within the beta-sheet layers of the protofilament units. Seeding hIAPP 20-29 with structurally homogeneous fibrils from a 30-residue amylin fragment (hIAPP 8-37) produces morphologically homogeneous fibrils with similar NMR properties to form (1). A model for the architecture of the seeded fibrils is presented, based on the analysis of X-ray fiber diffraction data, combined with an extensive range of SSNMR constraints including chemical shifts, torsional angles, and interatomic distances. The model features a cross-beta spine comprising two beta-sheets with an interface defined by residues F23, A25, and L27, which form a hydrophobic zipper. We suggest that the energies of formation for fibril form containing antiparallel and parallel beta-strands are similar when both configurations can be stabilized by a core of hydrophobic contacts, which has implications for the relationship between amino acid sequence and amyloid polymorphism in general.  相似文献   

20.
De novo designed peptides, capable of undergoing a thermally triggered beta-strand-swapped self-assembly event leading to hydrogel formation were prepared. Strand-swapping peptide 1 (SSP1) incorporates an exchangeable beta-strand domain composed of eight residues appended to a nonexchangeable beta-hairpin domain. CD shows that, at pH 9 and temperatures less than 35 degrees C, this peptide adopts a random coil conformation, rendering it soluble in aqueous solution. On heating to 37 degrees C or greater, SSP1 adopts a beta-hairpin that displays an exchangeable beta-strand region. The exchangeable strand domain participates in swapping with the exchangeable domain of another peptide, affording a strand-swapped dimer. These dimers further assemble into fibrils that define the hydrogel. A second peptide (SSP2) containing an exchangeable strand composed of only four residues was also studied. Microscopy and scattering data show that the length of the exchangeable domain directly influences the fibril nanostructure and can be used as a design element to construct either twisted (SSP1) or nontwisted (SSP2) fibril morphologies. CD, FTIR, and WAXS confirm that both peptides adopt beta-sheet secondary structure when assembled into fibrils. Fibril dimensions, as measured by TEM, AFM, and SANS indicate a fibril diameter of 6.4 nm, a height of 6.0 nm, and a pitch of 50.4 nm for the twisted SSP1 fibrils. The nontwisted SSP2 fibrils are 6.2 nm in diameter and 2.5 nm in height. Oscillatory rheology, used to measure bulk hydrogel rigidity, showed that the gel composed of the nontwisted fibrils is more mechanically rigid (517 Pa at 6 rad/s) than the gel composed of twisted fibrils (367 Pa at 6 rad/s). This work demonstrates that beta-strand-swapping can be used to fabricate biomaterials with tunable fibril nanostructure and bulk hydrogel rheological properties.  相似文献   

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