Amyloid Sequences Research Articles

Ac-LPFFD-Th: A Trehalose-Conjugated Peptidomimetic as a Strong Suppressor of Amyloid-β Oligomer Formation and Cytotoxicity.

The inhibition of amyloid formation is a promising therapeutic approach for the treatment of neurodegenerative diseases. Peptide-based inhibitors, which have been widely investigated, are generally derived from original amyloid sequences. Most interestingly, trehalose, a nonreducing disaccharide of α-glucose, is effective in preventing the aggregation of numerous proteins. We have determined that the development of hybrid compounds could provide new molecules with improved properties that might synergically increase the potency of their single moieties. In this work, the ability of Ac-LPFFD-Th, a C-terminally trehalose-conjugated derivative, to slow down the Aβ aggregation process was investigated by means of different biophysical techniques, including thioflavin T fluorescence, dynamic light scattering, ESI-MS, and NMR spectroscopy. Moreover, we demonstrate that Ac-LPFFD-Th modifies the aggregation features of Aβ and protects neurons from Aβ oligomers' toxic insult.

Efficient MoS2 Exfoliation by Cross-β-Amyloid Nanotubes for Multistimuli-Responsive and Biodegradable Aqueous Dispersions.

Herein, we report the efficient exfoliation of MoS2 in aqueous medium by short cationic peptide nanotubes featuring the nucleating core (17) LVFFA(21) of β-amyloid (Aβ 1-42), a sequence associated with Alzheimer's disease. The role of morphology, length, and nature of the amyloid surface on exfoliation/dispersions of MoS2 were investigated through specific mutations of the amyloid sequences. Notably, owing to the properties of both the constituents, self-assembled soft nanostructures and MoS2 , the hybrid dispersions responded reversibly to various stimuli, including temperature, pH, and light. Addition of a protease resulted in loss of the dispersions, which are otherwise stable for months at ambient conditions. The design flexibility of the peptide sequences, along with the stimuli-responsiveness and biodegradability, can complement the applications of MoS2 in diverse fields.

Efficient MoS2 Exfoliation by Cross‐β‐Amyloid Nanotubes for Multistimuli‐Responsive and Biodegradable Aqueous Dispersions

AbstractHerein, we report the efficient exfoliation of MoS2 in aqueous medium by short cationic peptide nanotubes featuring the nucleating core 17LVFFA21 of β‐amyloid (Aβ 1–42), a sequence associated with Alzheimer's disease. The role of morphology, length, and nature of the amyloid surface on exfoliation/dispersions of MoS2 were investigated through specific mutations of the amyloid sequences. Notably, owing to the properties of both the constituents, self‐assembled soft nanostructures and MoS2, the hybrid dispersions responded reversibly to various stimuli, including temperature, pH, and light. Addition of a protease resulted in loss of the dispersions, which are otherwise stable for months at ambient conditions. The design flexibility of the peptide sequences, along with the stimuli‐responsiveness and biodegradability, can complement the applications of MoS2 in diverse fields.

The Human Disease-Associated Aβ Amyloid Core Sequence Forms Functional Amyloids in a Fungal Adhesin.

ABSTRACTThere is increasing evidence that many amyloids in living cells have physiological functions. On the surfaces of fungal cells, amyloid core sequences in adhesins can aggregate into 100- to 1,000-nm-wide patches to form high-avidity adhesion nanodomains on the cell surface. The nanodomains form through interactions that have amyloid-like properties: binding of amyloid dyes, perturbation by antiamyloid agents, and interaction with homologous sequences. To test whether these functional interactions are mediated by typical amyloid interactions, we substituted an amyloid core sequence, LVFFA, from human Aβ protein for the native sequence IVIVA in the 1,419-residue Candida albicans adhesin Als5p. The chimeric protein formed cell surface nanodomains and mediated cellular aggregation. The native sequence and chimeric adhesins responded similarly to the amyloid dye thioflavin T and to amyloid perturbants. However, unlike the native protein, the nanodomains formed by the chimeric protein were not force activated and formed less-robust aggregates under flow. These results showed the similarity of amyloid interactions in the amyloid core sequences of native Als5p and Aβ, but they also highlighted emergent properties of the native sequence. Also, a peptide composed of the Aβ amyloid sequence flanked by amino acids from the adhesin formed two-dimensional sheets with sizes similar to the cell surface patches of the adhesins. These results inform an initial model for the structure of fungal cell surface amyloid nanodomains.

Untangling a Repetitive Amyloid Sequence: Correlating Biofilm-Derived and Segmentally Labeled Curli Fimbriae by Solid-State NMR Spectroscopy.

Curli are functional bacterial amyloids produced by an intricate biogenesis machinery. Insights into their folding and regulation can advance our understanding of amyloidogenesis. However, gaining detailed structural information of amyloids, and their tendency for structural polymorphisms, remains challenging. Herein we compare high-quality solid-state NMR spectra from biofilm-derived and recombinantly produced curli and provide evidence that they adopt a similar, well-defined β-solenoid arrangement. Curli subunits consist of five sequence repeats, resulting in severe spectral overlap. Using segmental isotope labeling, we obtained the unambiguous sequence-specific resonance assignments and secondary structure of one repeat, and demonstrate that all repeats are most likely structurally equivalent.

Quantitative Analyses of Force-Induced Amyloid Formation in Candida albicans Als5p: Activation by Standard Laboratory Procedures.

Candida albicans adhesins have amyloid-forming sequences. In Als5p, these amyloid sequences cluster cell surface adhesins to create high avidity surface adhesion nanodomains. Such nanodomains form after force is applied to the cell surface by atomic force microscopy or laminar flow. Here we report centrifuging and resuspending S. cerevisiae cells expressing Als5p led to 1.7-fold increase in initial rate of adhesion to ligand coated beads. Furthermore, mechanical stress from vortex-mixing of Als5p cells or C. albicans cells also induced additional formation of amyloid nanodomains and consequent activation of adhesion. Vortex-mixing for 60 seconds increased the initial rate of adhesion 1.6-fold. The effects of vortex-mixing were replicated in heat-killed cells as well. Activation was accompanied by increases in thioflavin T cell surface fluorescence measured by flow cytometry or by confocal microscopy. There was no adhesion activation in cells expressing amyloid-impaired Als5pV326N or in cells incubated with inhibitory concentrations of anti-amyloid dyes. Together these results demonstrated the activation of cell surface amyloid nanodomains in yeast expressing Als adhesins, and further delineate the forces that can activate adhesion in vivo. Consequently there is quantitative support for the hypothesis that amyloid forming adhesins act as both force sensors and effectors.

Cross‐β Amyloid Nanohybrids Loaded With Cytochrome C Exhibit Superactivity in Organic Solvents

AbstractThe present study reports the development of a unique class of Cytochrome C (CytC)‐loaded cross‐beta amyloid nanohybrids. The peroxidase activity of the bound CytC increased up to two orders of magnitude in organic solvents compared to the activity of unbound CytC in water. The amyloid sequences used in the study feature the nucleating core 17LVFF21 of the beta amyloid (Aβ), which assembled to form homogenous fibers and nanotubes. The morphology and exposed surface of the amyloid nanohydrids critically modulated the CytC activity. A CytC–Ac‐KLVFFAE‐NH2 hybrid featuring nanofiber morphology showed 308‐fold higher activity than unbound CytC in water, which increased to 450‐fold with the nanotube morphology of CytC–Ac‐KLVFFAL‐NH2. Notably, activity declined substantially when the exposed surface charge was detuned by replacing lysine with histidine, thus underpinning the importance of surface charge. This enzyme–amyloid nanohybrid system could facilitate the technological application of enzymes.

Cross-β Amyloid Nanohybrids Loaded With Cytochrome C Exhibit Superactivity in Organic Solvents.

The present study reports the development of a unique class of Cytochrome C (CytC)-loaded cross-beta amyloid nanohybrids. The peroxidase activity of the bound CytC increased up to two orders of magnitude in organic solvents compared to the activity of unbound CytC in water. The amyloid sequences used in the study feature the nucleating core (17) LVFF(21) of the beta amyloid (Aβ), which assembled to form homogenous fibers and nanotubes. The morphology and exposed surface of the amyloid nanohydrids critically modulated the CytC activity. A CytC-Ac-KLVFFAE-NH2 hybrid featuring nanofiber morphology showed 308-fold higher activity than unbound CytC in water, which increased to 450-fold with the nanotube morphology of CytC-Ac-KLVFFAL-NH2 . Notably, activity declined substantially when the exposed surface charge was detuned by replacing lysine with histidine, thus underpinning the importance of surface charge. This enzyme-amyloid nanohybrid system could facilitate the technological application of enzymes.

Monoclonal Antibodies against Aβ42 Fibrils Distinguish Multiple Aggregation State Polymorphisms in Vitro and in Alzheimer Disease Brain

Amyloidogenic proteins generally form intermolecularly hydrogen-bonded β-sheet aggregates, including parallel, in-register β-sheets (recognized by antiserum OC) or antiparallel β-sheets, β-solenoids, β-barrels, and β-cylindrins (recognized by antiserum A11). Although these groups share many common properties, some amyloid sequences have been reported to form polymorphic structural variants or strains. We investigated the humoral immune response to Aβ42 fibrils and produced 23 OC-type monoclonal antibodies recognizing distinct epitopes differentially associated with polymorphic structural variants. These mOC antibodies define at least 18 different immunological profiles represented in aggregates of amyloid-β (Aβ). All of the antibodies strongly prefer amyloid aggregates over monomer, indicating that they recognize conformational epitopes. Most of the antibodies react with N-terminal linear segments of Aβ, although many recognize a discontinuous epitope consisting of an N-terminal domain and a central domain. Several of the antibodies that recognize linear Aβ segments also react with fibrils formed from unrelated amyloid sequences, indicating that reactivity with linear segments of Aβ does not mean the antibody is sequence-specific. The antibodies display strikingly different patterns of immunoreactivity in Alzheimer disease and transgenic mouse brain and identify spatially and temporally unique amyloid deposits. Our results indicate that the immune response to Aβ42 fibrils is diverse and reflects the structural polymorphisms in fibrillar amyloid structures. These polymorphisms may contribute to differences in toxicity and consequent effects on pathological processes. Thus, a single therapeutic monoclonal antibody may not be able to target all of the pathological aggregates necessary to make an impact on the overall disease process.

De novo design of self-assembled hexapeptides as β-amyloid (Aβ) peptide inhibitors.

The ability of peptides to construct specific secondary structures provides a useful function for biomaterial design that cannot be achieved with traditional organic molecules and polymers. Inhibition of amyloid formation is a promising therapeutic approach for the treatment of neurodegenerative diseases. Existing peptide-based inhibitors are mainly derived from original amyloid sequences, which have very limited sequence diversity and activity. It is highly desirable to explore other peptide-based inhibitors that are not directly derived from amyloid sequences. Here, we develop a hybrid high-throughput computational method to efficiently screen and design hexapeptide inhibitors against amyloid-β (Aβ) aggregation and toxicity from the first principle. Computationally screened/designed inhibitors are then validated for their inhibition activity using biophysical experiments. We propose and demonstrate a proof-of-concept of the "like-interacts-like" design principle that the self-assembling peptides are able to interact strongly with conformationally similar motifs of Aβ peptides and to competitively reduce Aβ-Aβ interactions, thus preventing Aβ aggregation and Aβ-induced toxicity. Such a de novo design can also be generally applicable to design new peptide inhibitors against other amyloid diseases, beyond traditional peptide inhibitors with homologous sequences to parent amyloid peptides.

Structural and Energetic Insight into the Cross-Seeding Amyloid Assemblies of Human IAPP and Rat IAPP

The misfolding and aggregation of human islet amyloid polypeptide (hIAPP or amylin) into small oligomers and large amyloid fibrils is believed to be responsible for the dysfunction and death of pancreatic β-cells in diabetes type II. However, rat IAPP (rIAPP), which differs from the hIAPP by only 6 of 37 residues, lacks the ability to form amyloid fibrils and to induce cell death. Little is known about the cross-sequence interactions and cross-seeding structures between hIAPP and rIAPP peptides. Herein using explicit-solvent molecular dynamics (MD) simulations, we modeled and simulated different heteroassemblies formed by the amyloidogenic hIAPP and the nonamyloidogenic rIAPP peptides. Simulations showed that the U-shaped hIAPP monomer and oligomers can interact with conformationally similar rIAPP to form stable complexes and to coassemble into heterogeneous structures. Stable heterointeractions between hIAPP and rIAPP were shown to arise from hydrophobic contacts and hydrogen bonds at the interface, particularly at N- and C-terminal β-sheet regions. Because of the enhanced interpeptide interactions at the interface, upon binding to hIAPP oligomers, the β-sheet population of rIAPP was greatly increased as compared to that of rIAPP alone. More importantly, the conformational energies of rIAPP monomers at the bound state were observed to be consistently higher than those of rIAPP monomers at the unbound state. However, rIAPP monomers enable one to adopt different conformations and follow different pathways for associating with hIAPP from the high energy of the bound state to the low energy of the unbound state, without encountering any large and abrupt energy barrier. In parallel, AFM study of cross-aggregation of hIAPP and rIAPP provided additional evidence that hIAPP can seed with rIAPP to form hybrid fibrils at all concentrations similar to pure hIAPP fibrils. This work demonstrates the existence of cross-interactions between the two different IAPP peptides, which provides an improved fundamental understanding of the cross-seeding of different amyloid sequences toward amyloid aggregation and toxicity mechanisms.

Between Amyloids and Aggregation Lies a Connection with Strength and Adhesion

We tell of a journey that led to discovery of amyloids formed by yeast cell adhesins and their importance in biofilms and host immunity. We begin with the identification of the adhesin functional amyloid-forming sequences that mediate fiber formation in vitro. Atomic force microscopy and confocal microscopy show 2-dimensional amyloid “nanodomains” on the surface of cells that are activated for adhesion. These nanodomains are arrays of adhesin molecules that bind multivalent ligands with high avidity. Nanodomains form when adhesin molecules are stretched in the AFM or under laminar flow. Treatment with antiamyloid perturbants or mutation of the amyloid sequence prevents adhesion nanodomain formation and activation. We are now discovering biological consequences. Adhesin nanodomains promote formation and maintenance of biofilms, which are microbial communities. Also, in abscesses within candidiasis patients, we find adhesin amyloids on the surface of the fungi. In both human infection and a Caenorhabditis elegans infection model, the presence of fungal surface amyloids elicits anti-inflammatory responses. Thus, this is a story of how fungal adhesins respond to extension forces through formation of cell surface amyloid nanodomains, with key consequences for biofilm formation and host responses.

Peptide Detection of Fungal Functional Amyloids in Infected Tissue

Many fungal cell adhesion proteins form functional amyloid patches on the surface of adhering cells. The Candida albicans Agglutinin-like sequence (Als) adhesins are exemplars for this phenomenon, and have amyloid forming sequences that are conserved between family members. The Als5p amyloid sequence mediates amyloid fibril formation and is critical for cell adhesion and biofilm formation, and is also present in the related adhesins Als1p and Als3p. We have developed a fluorescent peptide probe containing the conserved Als amyloid-forming sequence. This peptide bound specifically to yeast expressing Als5p, but not to cells lacking the adhesin. The probe bound to both yeast and hyphal forms of C. albicans. Δals1/Δals3 single and double deletion strains exhibited reduced fluorescence, indicating that probe binding required expression of these proteins. Additionally, the Als peptide specifically stained fungal cells in abscesses in autopsy sections. Counterstaining with calcofluor white showed colocalization with the amyloid peptide. In addition, fungi in autopsy sections derived from the gastrointestinal tract showed colocalization of the amyloid-specific dye thioflavin T and the fluorescent peptide. Collectively, our data demonstrate that we can exploit amyloid sequence specificity for detection of functional amyloids in situ.

Distinct Roles of sAPP-α and sAPP-β in Regulating U251 Cell Differentiation

Sequential cleavages of APP by β-secretase and γ-secretase release β-amyloid (Aβ) and one secreted form of APP (sAPP-β) in Alzheimer' s disease (AD). Alternatively, in non-pathological situations, APP is predominantly cleaved by α-secretase within the amyloid sequence, to release the other soluble form of APP, sAPP-α. However, the functions of the two types of sAPP are still unclear. We performed this study to compare the function of sAPP-α and sAPP-β in differentiation of the glioma cell line U251. We found that sAPP-α suppressed astrocytic differentiation and promoted neuronal differentiation in U251 cells. Additionally, sAPP-α enhanced U251 terminal differentiation into a cholinergic-like neuronal phenotype. In contrast, sAPP-β suppressed neuronal differentiation and promoted the astrocytic differentiation of U251 cells. These findings could not only enrich the knowledge of the potential physiological function of sAPP-α and sAPP-β, but also indicate that they may be connected to the pathological mechanism of AD. Furthermore, these findings suggest that new strategies, such as increasing the level of sAPP-α and/or decreasing the level of sAPP-β in brain, or transplanting stem cells with increased sAPP-α and/or decreased sAPP-β, may have potential value for AD treatment.

Exploring the sequence-structure relationship for amyloid peptides.

Amyloid fibril formation is associated with misfolding diseases, as well as fulfilling a functional role. The cross-β molecular architecture has been reported in increasing numbers of amyloid-like fibrillar systems. The Waltz algorithm is able to predict ordered self-assembly of amyloidogenic peptides by taking into account the residue type and position. This algorithm has expanded the amyloid sequence space, and in the present study we characterize the structures of amyloid-like fibrils formed by three peptides identified by Waltz that form fibrils but not crystals. The structural challenge is met by combining electron microscopy, linear dichroism, CD and X-ray fibre diffraction. We propose structures that reveal a cross-β conformation with ‘steric-zipper’ features, giving insights into the role for side chains in peptide packing and stability within fibrils. The amenity of these peptides to structural characterization makes them compelling model systems to use for understanding the relationship between sequence, self-assembly, stability and structure of amyloid fibrils.

Bacterial curli protein promotes the conversion of PAP248-286 into the amyloid SEVI: cross-seeding of dissimilar amyloid sequences.

Fragments of prostatic acid phosphatase (PAP248-286) in human semen dramatically increase HIV infection efficiency by increasing virus adhesion to target cells. PAP248-286 only enhances HIV infection in the form of amyloid aggregates termed SEVI (Semen Enhancer of Viral Infection), however monomeric PAP248-286 aggregates very slowly in isolation. It has therefore been suggested that SEVI fiber formation in vivo may be promoted by exogenous factors. We show here that a bacterially-produced extracellular amyloid (curli or Csg) acts as a catalytic agent for SEVI formation from PAP248-286 at low concentrations in vitro, producing fibers that retain the ability to enhance HIV (Human Immunodeficiency Virus) infection. Kinetic analysis of the cross-seeding effect shows an unusual pattern. Cross-seeding PAP248-286 with curli only moderately affects the nucleation rate while significantly enhancing the growth of fibers from existing nuclei. This pattern is in contrast to most previous observations of cross-seeding, which show cross-seeding partially bypasses the nucleation step but has little effect on fiber elongation. Seeding other amyloidogenic proteins (IAPP (islet amyloid polypeptide) and Aβ1−40) with curli showed varied results. Curli cross-seeding decreased the lag-time of IAPP amyloid formation but strongly inhibited IAPP elongation. Curli cross-seeding exerted a complicated concentration dependent effect on Aβ1−40 fibrillogenesis kinetics. Combined, these results suggest that the interaction of amyloidogenic proteins with preformed fibers of a different type can take a variety of forms and is not limited to epitaxial nucleation between proteins of similar sequence. The ability of curli fibers to interact with proteins of dissimilar sequences suggests cross-seeding may be a more general phenomenon than previously supposed.

Designing Self Assembling Beta Helices

Amyloid fibers are unusually stable structures that self-assemble from soluble proteins. The fibers are typically composed of parallel β-sheets that run along the long fiber axis while the β-strands run perpendicular (cross-β) to the fiber axis. β-helices are a parallel β-sheet motif that have similar properties to amyloid fibers. In this work, we explore the utility of the β-helix as a building block to capture and test attributes of amyloid fibers relevant to the design of self-assembling nanostructures. We have isolated and characterized a five-rung portion of the triple-stranded, homotrimeric β-helix, GP5, of the bacteriophage T4. In order to construct a self-assembling β-helix, we have developed a small library based on amyloid sequence analysis and applied it to the five-rung helix. Specific changes targeting internal interactions of the helix have been made. The mutations in these positions have been selected to allow for greater control of self-assembly and hold the promise of breaking the homomeric assembly into a heteromeric construction. A split adenylate kinase selection assay has been developed to monitor self-assembly of these alternative structures.

Unzipping a Functional Microbial Amyloid

Bacterial and fungal species produce some of the best-characterized functional amyloids, that is, extracellular fibres that play key roles in mediating adhesion and biofilm formation. Yet, the molecular details underlying their mechanical strength remain poorly understood. Here, we use single-molecule atomic force microscopy to measure the mechanical properties of amyloids formed by Als cell adhesion proteins from the pathogen Candida albicans. We show that stretching Als proteins through their amyloid sequence yields characteristic force signatures corresponding to the mechanical unzipping of β-sheet interactions formed between surface-arrayed Als proteins. The unzipping probability increases with contact time, reflecting the time necessary for optimal inter β-strand associations. These results demonstrate that amyloid interactions provide cohesive strength to a major adhesion protein from a microbial pathogen, thereby strengthening cell adhesion. We suggest that such functional amyloids may represent a generic mechanism for providing mechanical strength to cell adhesion proteins. In nanotechnology, these single-molecule manipulation experiments provide new opportunities to understand the molecular mechanisms driving the cohesion of functional amyloid-based nanostructures.

Selenomethionine Incorporation into Amyloid Sequences Regulates Fibrillogenesis and Toxicity

BackgroundThe capacity of a polypeptide chain to engage in an amyloid formation process and cause a conformational disease is contained in its sequence. Some of the sequences undergoing fibrillation contain critical methionine (Met) residues which in vivo can be synthetically substituted by selenomethionine (SeM) and alter their properties.Methodology/Principal FindingsUsing peptide synthesis, biophysical techniques and cell viability determinations we have studied the effect of the substitution of methionine (Met) by selenomethionine (SeM) on the fibrillogenesis and toxic properties of Aβ40 and HuPrP(106–140). We have found that the effects display site-specificity and vary from inhibition of fibrillation and decreased toxicity ([SeM35]Aβ40, [SeM129]HuPrP(106–140) and [SeM134]HuPrP(106–140)), retarded assembly, modulation of polymer shape and retention of toxicity ([SeM112]HuPrP(106–140) to absence of effects ([SeM109]HuPrP(106–140)).Conclusions/SignificanceThis work provides direct evidence that the substitution of Met by SeM in proamyloid sequences has a major impact on their self-assembly and toxic properties, suggesting that the SeM pool can play a major role in dictating the allowance and efficiency of a polypeptide chain to undergo toxic polymerization.

Exploring the sequence determinants of amyloid structure using position-specific scoring matrices

Protein aggregation results in beta-sheet-like assemblies that adopt either a variety of amorphous morphologies or ordered amyloid-like structures. These differences in structure also reflect biological differences; amyloid and amorphous beta-sheet aggregates have different chaperone affinities, accumulate in different cellular locations and are degraded by different mechanisms. Further, amyloid function depends entirely on a high intrinsic degree of order. Here we experimentally explored the sequence space of amyloid hexapeptides and used the derived data to build Waltz, a web-based tool that uses a position-specific scoring matrix to determine amyloid-forming sequences. Waltz allows users to identify and better distinguish between amyloid sequences and amorphous beta-sheet aggregates and allowed us to identify amyloid-forming regions in functional amyloids.