Molecular Mechanisms of the Bindings between Non-Amyloid β Component Oligomers and Amylin Oligomers

The stability and dynamics of the Aβ40/Aβ42 interlaced mixed fibrils

The accumulation of fibrillar amyloid-β (Aβ) aggregates in the brain, predominantly comprising 40- and 42-residue amyloid-β (Aβ40 and Aβ42), is a major pathological hallmark of Alzheimer's disease (AD). Aβ40 and Aβ42 naturally coexist in the brain under normal physiological conditions, and their interplay is generally considered to be a critical factor in the progression of AD. In addition to forming homogeneous oligomers and fibrils, Aβ40 and Aβ42 are also reported to co-assemble into hetero-oligomers and interlaced mixed fibrils, as evidenced by solid-state nuclear magnetic resonance spectroscopy (NMR), high molecular weight mass spectrometry and cross-seeding experiments. However, the exact molecular mechanisms underlying these processes remain unclear. In this study, we have used a recently resolved structurally uniform 1:1 mixture of Aβ40/Aβ42 interlaced mixed fibril as a prototype to gain insights into the molecular-level interactions between Aβ40 and Aβ42. We employed fully atomistic molecular dynamics simulation and compared the results with a homogeneous U-shaped Aβ40 fibrillar model. Our simulations using two different force fields provide conclusive evidence that the Aβ40/Aβ42 interlaced mixed fibril is energetically more favorable than the homogeneous Aβ40 fibrillar model. Furthermore, we also show that the increase in stability observed in the mixed model stems primarily from the packing interfaces and the stacking interfaces between C-termini. Our simulation results provide valuable mechanistic insights that are not readily accessible in experiment and could have significant implications for both the pathogenesis of AD and the development of current therapeutic strategies.Communicated by Ramaswamy H. Sarma.

Interaction of Proteins Involved in Neuronal Proteinopathies

Proteinopathy is characterized by the accumulation of aggregates of a specific protein in a target organ, tissue, or cell. The aggregation of the same protein can cause different pathologies as single protein can adopt various amyloidogenic, disease-specific conformations. The conformation governs the interaction of amyloid aggregates with other proteins that are prone to misfolding and, thus, determines disease-specific spectrum of concomitant pathologies. In this regard, a detailed description of amyloid protein conformation as well as spectrum of its interaction with other proteins become a key point for drafting of precise description of the disease. The majority of clinical cases of neuronal proteinopathies is caused by the aggregation of rather limited range of amyloidogenic proteins. Here, we provided the characterization of pathologies, related to the aggregation of amyloid β peptide, tau protein, α-synuclein, TDP-43, and amylin, giving a short description of pathologies themselves, recent advances in elucidation of misfolded protein conformation, with emphasis on those protein aggregates extracted from biological samples, what is known about the interaction of this proteins, and the influence of this interaction on the progression of underlying disease and comorbidities.

Insights into Non-Proteolytic Inhibitory Mechanisms of Polymorphic Early-Stage Amyloid β Oligomers by Insulin Degrading Enzyme

Insulin degrading enzyme (IDE) has been detected in the cerebrospinal fluid media and plays a role in encapsulating and degrading the amyloid β (Aβ) monomer, thus regulating the levels of Aβ monomers. The current work illustrates a first study by which IDE encapsulates polymorphic early-stage Aβ oligomers. The main goal of this study was to investigate the molecular mechanisms of IDE activity on the encapsulated early-stage Aβ dimers: fibril-like and random coil/α-helix dimers. Our work led to several findings. First, when the fibril-like Aβ dimer interacts with IDE-C domain, IDE does not impede the contact between the monomers, but plays a role as a 'dead-end' chaperone protein. Second, when the fibril-like Aβ dimer interacts with the IDE-N domain, IDE successfully impedes the contacts between monomers. Third, the inhibitory activity of IDE on random coil/α-helix dimers depends on the stability of the dimer. IDE could impede the contacts between monomers in relatively unstable random coil/α-helix dimers, but gets hard to impede in stable dimers. However, IDE encapsulates stable dimers and could serve as a 'dead-end' chaperone. Our results examine the molecular interactions between IDE and the dimers, and between the monomers within the dimers. Hence, this study provides insights into the inhibition mechanisms of the primary nucleation of Aβ aggregation and the basic knowledge for rational design to inhibit Aβ aggregation.

Novel Amylin Analogues Reduce Amyloid-β Cross-Seeding Aggregation and Neurotoxicity

BACKGROUND

Type 2 diabetes related human islet amyloid polypeptide (hIAPP) plays a dual role in Alzheimer's disease (AD). hIAPP has neuroprotective effects in AD mouse models whereas, high hIAPP concentrations can promote co-aggregation with amyloid-β (Aβ) to promote neurodegeneration. In fact, both low and high plasma hIAPP concentration has been associated with AD. Therefore, non-aggregating hIAPP analogues have garnered interest as a treatment for AD. The aromatic amino acids F23 and I26 in hIAPP have been identified as the key residues involved in self-aggregation and Aβ cross-seeding.

OBJECTIVE

Three novel IAPP analogues with single and double alanine mutations (A1 = F23, A2 = I26, and A3 = F23 + I26) were assessed for their ability to aggregate, modulate Aβ oligomer formation, and alter neurotoxicity.

METHODS

A range of biophysical methods including Thioflavin-T, gel electrophoresis, photo-crosslinking, circular dichroism combined with cell viability assays were utilized to assess protein aggregation and toxicity.

RESULTS

All IAPP analogues showed significantly less self-aggregation than hIAPP. Co-aggregated Aβ 42-A2 and A3 also showed reduced aggregation compared to Aβ 42-hIAPP mixtures. Self- and co-oligomerized A1, A2, and A3 exhibited random coil conformations with reduced beta sheet content compared to hIAPP and Aβ 42-hIAPP aggregates. A1 was toxic at high concentrations compared to A2 and A3. However, co-aggregated Aβ 42-A1, A2, or A3 showed reduced neurotoxicity compared to Aβ 42, hIAPP, and Aβ 42-hIAPP aggregates.

CONCLUSION

These findings confirm that hIAPP analogues with non-aromatic residues at positions 23 and 26 have reduced self-aggregation and the ability to neutralize Aβ 42 toxicity. This warrants further characterization of their protective effects in pre-clinical AD models.

A new strategy to reconcile amyloid cross-seeding and amyloid prevention in a binary system of α-synuclein fragmental peptide and hIAPP

Amyloid cross-seeding and amyloid inhibition are two different research subjects being studied separately for different pathological purposes, in which amyloid cross-seeding targets to study the co-aggregation of different amyloid proteins and potential molecular links between different neurodegenerative diseases, while amyloid inhibition aims to design different molecules for preventing amyloid aggregation. While both amyloid cross-seeding and amyloid inhibition are critical for better understanding the pathological causes of different neurodegenerative diseases including Parkinson disease (PD) and Type 2 diabetes (T2D), less efforts have been made to reconcile the two phenomena. Herein, we proposed a new preventive strategy to demonstrate (a) the cross-seeding of octapeptide TKEQVTNV from α-synuclein (associated with PD) with hIAPP (associated with T2D) and (b) the cross-seeding-promoted hIAPP fibrillization and cross-seeding-reduced hIAPP toxicity. Collective results confirmed that TKEQVTNV can indeed cross-seed with hIAPP monomers and oligomers, not protofibrils, to form β-structure-rich fibrils and to accelerate hIAPP fibrillization. Moreover, such cross-seeding-induced promotion effect by TKEQVTNV also rescued the pancreatic cells from hIAPP-induced cytotoxicity by increasing cell viability and reducing cell apoptosis simultaneously. This work provides a new angle to discover amyloid fragments and use them as amyloid modulators (inhibitors or promotors) to interfere with amyloid aggregation of other amyloid proteins, as well as sequence/structure basis to explore the amyloid cross-seeding between different amyloid proteins that may help explain a potential molecular talk between different neurodegenerative diseases.

A mechanistic survey of Alzheimer's disease

Alzheimer's disease (AD) is the most common, age-dependent neurodegenerative disorder. While AD has been intensively studied from different aspects, there is no effective cure for AD, largely due to a lack of a clear mechanistic understanding of AD. In this mini-review, we mainly focus on the discussion and summary of mechanistic causes of Alzheimer's disease (AD). While different AD mechanisms illustrate different molecular and cellular pathways in AD pathogenesis, they do not necessarily exclude each other. Instead, some of them could work together to initiate, trigger, and promote the onset and development of AD. In a broader viewpoint, some AD mechanisms (e.g., amyloid aggregation mechanism, microbial infection/neuroinflammation mechanism, and amyloid cross-seeding mechanism) could also be applicable to other amyloid diseases including type II diabetes, Parkinson's disease, and prion disease. Such common mechanisms for AD and other amyloid diseases explain not only the pathogenesis of individual amyloid diseases, but also the spreading of pathologies between these diseases, which will inspire new strategies for therapeutic intervention and prevention for AD.

Advancements and future directions in research of the roles of insulin in amyloid diseases

Amyloid diseases, such as type 2 diabetes, Alzheimer's disease and Parkinson's disease are characterized by amyloid aggregates. Insulin is released from the pancreas, and it is known that insulin downstream signaling molecules are located majorly in the regions of cortex and hippocampus. Therefore, insulin plays crucial roles not only in the pancreas, but also in the brain. Recent studies have focused on the role of insulin in amyloid diseases. This review demonstrates the recent studies in which insulin affects amyloid aggregation. Specifically, molecular modeling studies provide insights into the molecular mechanisms of the effects of insulin in amyloid aggregates. Still, experimental studies are required to provide insights into the kinetics effects. This review opens new avenues for future studies on insulin molecules and amyloid aggregation.

Insights into the Mechanistic Perspective Effect of Insulin on the Nonamyloidogenic Component (NAC) and α-Synuclein Aggregation

Insulin plays important functions in the brain, such as neuroprotective effects on neurons, and it is also involved in cognitive functions (e.g., attention, learning and memory). It is proposed that a lack of insulin in the brain may initiate development of neurodegenerative diseases. Herein, we examined the effect of insulin on aggregates of α-synuclein (AS), a protein that is related to Parkinson's disease (PD), and its segment nonamyloidogenic component (NAC), which is known to play a crucial role in AS aggregation. The molecular modeling tools assist us to provide insights into the molecular mechanism of the effect of insulin on fibrillation of NAC and AS. Our research leads to three conclusions. First, the preferred interactions between insulin chain B and the "zipper domain" sequence within both NAC and AS appear at the central domain across the fibril axis or at the edge of the fibril. Second, these interactions do not disrupt the cross-β structure of NAC fibril-like oligomers but disrupt the cross-β structure of AS fibril-like oligomers. Thus, insulin does not inhibit the fibrillation of NAC but may inhibit AS fibrillation. Third, some of the polymorphic NAC and AS fibril-like oligomers bind to chain A in insulin. This is the first study that demonstrates that insulin chain A can also participate in the interactions with amyloid fibril-like oligomers. Our study proposes that insulin plays a crucial role in impeding AS aggregation in the brain and consequently could inhibit the development of PD.

Dual amyloid cross-seeding reveals steric zipper-facilitated fibrillization and pathological links between protein misfolding diseases

Amyloid cross-seeding, as a result of direct interaction and co-aggregation between different disease-causative peptides, is considered as a main mechanism for the spread of the overlapping pathology across different cells and tissues between different protein-misfolding diseases (PMDs). Despite the biomedical significance of amyloid cross-seeding in amyloidogenesis, it remains a great challenge to discover amyloid cross-seeding systems and reveal their cross-seeding structures and mechanisms. Herein, we are the first to report that GNNQQNY - a short fragment from yeast prion protein Sup35 - can cross-seed with both amyloid-β (Aβ, associated with Alzheimer's disease) and human islet amyloid polypeptide (hIAPP, associated with type II diabetes) to form β-structure-rich assemblies and to accelerate amyloid fibrillization. Dry, steric β-zippers, formed by the two β-sheets of different amyloid peptides, provide generally interactive and structural motifs to facilitate amyloid cross-seeding. The presence of different steric β-zippers in a variety of GNNQQNY-Aβ and GNNQQNY-hIAPP assemblies also explains amyloid polymorphism. In addition, alteration of steric zipper formation by single-point mutations of GNNQQNY and interactions of GNNQQNY with different Aβ and hIAPP seeds leads to different amyloid cross-seeding efficiencies, further confirming the existence of cross-seeding barriers. This work offers a better structural-based understanding of amyloid cross-seeding mechanisms linked to different PMDs.

Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis

Protein misfolding and aggregation is observed in many amyloidogenic diseases affecting either the central nervous system or a variety of peripheral tissues. Structural and dynamic characterization of all species along the pathways from monomers to fibrils is challenging by experimental and computational means because they involve intrinsically disordered proteins in most diseases. Yet understanding how amyloid species become toxic is the challenge in developing a treatment for these diseases. Here we review what computer, in vitro, in vivo, and pharmacological experiments tell us about the accumulation and deposition of the oligomers of the (Aβ, tau), α-synuclein, IAPP, and superoxide dismutase 1 proteins, which have been the mainstream concept underlying Alzheimer's disease (AD), Parkinson's disease (PD), type II diabetes (T2D), and amyotrophic lateral sclerosis (ALS) research, respectively, for many years.

Designer Amyloid Cell-Penetrating Peptides for Potential Use as Gene Transfer Vehicles

Cell-penetrating peptides are used extensively to deliver molecules into cells due to their unique characteristics such as rapid internalization, charge, and non-cytotoxicity. Amyloid fibril biomaterials were reported as gene transfer or retroviral infection enhancers; no cell internalization of the peptides themselves is reported so far. In this study, we focus on two rationally and computationally designed peptides comprised of β-sheet cores derived from naturally occurring protein sequences and designed positively charged and aromatic residues exposed at key residue positions. The β-sheet cores bestow the designed peptides with the ability to self-assemble into amyloid fibrils. The introduction of positively charged and aromatic residues additionally promotes DNA condensation and cell internalization by the self-assembled material formed by the designed peptides. Our results demonstrate that these designer peptide fibrils can efficiently enter mammalian cells while carrying packaged luciferase-encoding plasmid DNA, and they can act as a protein expression enhancer. Interestingly, the peptides additionally exhibited strong antimicrobial activity against the enterobacterium Escherichia coli.

Unique Inversion Events of Residues around the Backbone in the Turn Domain of β-Arches in Amylin Fibrils

Orientational inversion events of residues along the turn domains of amylin fibrils have been detected. This exceptional phenomenon has been observed in isolated amylin fibrils and in the cross-seeding amylin-Aβ and amylin-NAC fibrils. These new findings provide new avenues for detection of side chain flipping and side chain inversion events in turn domains and loops of various proteins.

Amyloidogenic cross-seeding of Tau protein: Transient emergence of structural variants of fibrils

Amyloid aggregates of Tau protein have been implicated in etiology of many neurodegenerative disorders including Alzheimer's disease (AD). When amyloid growth is induced by seeding with preformed fibrils assembled from the same protein, structural characteristics of the seed are usually imprinted in daughter generations of fibrils. This so-called conformational memory effect may be compromised when the seeding involves proteins with non-identical sequences leading to the emergence of distinct structural variants of fibrils (amyloid ‘strains’). Here, we investigate cross-seeding of full-length human Tau (FL Tau) with fibrils assembled from K18 and K18ΔK280 fragments of Tau in the presence of poly-L-glutamate (poly-Glu) as an enhancer of Tau aggregation. To study cross-seeding between Tau polypeptides and the role of the conformational memory effect in induction of Tau amyloid polymorphism, kinetic assays, transmission electron microscopy, infrared spectroscopy and limited proteolysis have been employed. The fastest fibrillization was observed for FL Tau monomers seeded with preformed K18 amyloid yielding daughter fibrils with unique trypsin digestion patterns. Morphological features of daughter FL Tau fibrils induced by K18 and K18ΔK280 seeds were reminiscent of the mother fibrils (i.e. straight paired fibrils and paired helical filaments (PHFs), respectively) but disappeared in the following generations which became similar to unpaired FL Tau amyloid fibrils formed de novo. The structural evolution observed in our study was accompanied by disappearance of the unique proteolysis profile originated from K18. Our findings may have implications for understanding molecular mechanisms of the emergence and stability of Tau amyloid strains.

Be positive: optimizing pramlintide from microcanonical analysis of amylin isoforms

Amylin, or human islet amyloid polypeptide (hIAPP), is a 37-residue hormone synergistic to insulin and co-secreted with it by β-cells in the pancreas. The deposition of its cytotoxic amyloid fibrils is strongly related to the progression of Type II diabetes (T2D) and islet graft failures. Notably, isoforms from some mammalian species, such as rats (rIAPP) and porcine (pIAPP), present a few key mutations preventing aggregation. This has lead to biotechnological development of drugs for adjunct therapies of T2D, such as pramlintide, a variant of hIAPP inspired by rIAPP whose proline substitutions have β-strand fibril-breaking properties. Ideally, such a drug should be formulated with insulin and co-administered, but this has been prevented by a poor solubility profile at the appropriate pH. Hopefully, this could be improved with appropriate point mutations, increasing the molecular net charge. Despite experimental progress, preliminary screening during rational drug design can greatly benefit from thermodynamic insight derived from molecular simulations. So we introduce microcanonical thermostatistics analysis of multicanonical (MUCA) simulations of wild-type amylin isoforms as a systematic assessment of protein thermostability. As a consequence of this comprehensive investigation, the most suitable single-point mutations able to optimize pramlintide are located among the wild-type amylin isoforms. In particular, we find that aggregation inhibition and increased solubility are inherited by pramlintide through further S20R substitution typical of pIAPP. Thus, we provide a consistent thermostatistical methodology to aid the design of improved adjunct therapies for T2D according to current clinical knowledge.

Insight into a New Binding Site of Zinc Ions in Fibrillar Amylin

Amylin peptides are secreted together with insulin and zinc ions from pancreatic β-cells. Under unknown conditions, the amylin peptides aggregate to produce oligomers and fibrils, and in some cases Zn²⁺ ions can bind to amylin peptides to form Zn²⁺-aggregate complexes. Consequently, these aggregates lead to the death of the β-cells and a decrease in insulin, which is one of the symptoms of type-2 diabetes (T2D). Therefore, it is crucial to investigate the binding sites of the Zn²⁺ ions in fibrillary amylin. It was previously found by in vitro and simulation studies that Zn²⁺ ion binds to two or four His residues in the turn domain of fibrillary amylin. In the current study, we present a new Zn²⁺ binding site in the N-terminus of fibrillary amylin with three different coordination modes. Our simulations showed that Zn²⁺ ions bind to polymorphic amylin fibrils with a preference to bind to four Cys residues rather than two Cys residues of two neighboring amylin monomers. The new binding site leads to conformational changes, increases the number of polymorphic states, and demonstrates the existence of competition between various binding sites. Our study provides insight into the molecular mechanisms through which Zn²⁺ ions that play a critical role in amylin aggregation can bind to amylin and promote amylin aggregation in T2D.

Coaggregation of κ-Casein and β-Lactoglobulin Produces Morphologically Distinct Amyloid Fibrils

The unfolding, misfolding, and aggregation of proteins lead to a variety of structural species. One form is the amyloid fibril, a highly aligned, stable, nanofibrillar structure composed of β-sheets running perpendicular to the fibril axis. β-Lactoglobulin (β-Lg) and κ-casein (κ-CN) are two milk proteins that not only individually form amyloid fibrillar aggregates, but can also coaggregate under environmental stress conditions such as elevated temperature. The aggregation between β-Lg and κ-CN is proposed to proceed via disulfide bond formation leading to amorphous aggregates, although the exact mechanism is not known. Herein, using a range of biophysical techniques, it is shown that β-Lg and κ-CN coaggregate to form morphologically distinct co-amyloid fibrillar structures, a phenomenon previously limited to protein isoforms from different species or different peptide sequences from an individual protein. A new mechanism of aggregation is proposed whereby β-Lg and κ-CN not only form disulfide-linked aggregates, but also amyloid fibrillar coaggregates. The coaggregation of two structurally unrelated proteins into cofibrils suggests that the mechanism can be a generic feature of protein aggregation as long as the prerequisites for sequence similarity are met.

Seed-Induced Heterogeneous Cross-Seeding Self-Assembly of Human and Rat Islet Polypeptides

Amyloid peptides can misfold and aggregate into amyloid oligomers and fibrils containing conformationally similar β-sheet structures, which are linked to the pathological hallmark of many neurodegenerative diseases. These β-sheet-rich amyloid aggregates provide common structural motifs to accelerate amyloid formation by acting as seeds. However, little is known about how one amyloid peptide aggregation will affect another one (namely, cross-seeding). In this work, we studied the cross-seeding possibility and efficiency between rat islet amyloid polypeptide (rIAPP) and human islet amyloid polypeptide (hIAPP) solution with preformed aggregates at different aggregation phases, using a combination of different biophysical techniques. hIAPP is a well-known peptide hormone that forms amyloid fibrils and induces cytotoxicity to β-cells in type 2 diabetes, whereas rIAPP is a nonaggregating and nontoxic peptide. Experimental results showed that all different preformed hIAPP aggregates can cross-seed rIAPP to promote the final fibril formation but exhibit different cross-seeding efficiencies. Evidently, hIAPP seeds preformed at a growth phase show the strongest cross-seeding potential to rIAPP, which accelerates the conformational transition from random structures to β-sheet and the aggregation process at the fibrillization stage. Homoseeding of hIAPP is more efficient in initiating and promoting aggregation than cross-seeding of hIAPP and rIAPP. Moreover, the cross-seeding of rIAPP with hIAPP at the lag phase also reduced cell viability, probably because of the formation of more toxic hybrid oligomers at the prolonged lag phase. The cross-seeding effects in this work may add new insights into the mechanistic understanding of the aggregation and coaggregation of amyloid peptides linked to different neurodegenerative diseases.

Cross-seeding between Aβ40 and Aβ42 in Alzheimer's disease

Aβ42 is the major component of parenchymal plaques in the brain of Alzheimer's patients, while Aβ40 is the major component of cerebrovascular plaques. Since Aβ40 and Aβ42 coexist in the brain, understanding the interaction between Aβ40 and Aβ42 during their aggregation is important to delineate the molecular mechanism underlying Alzheimer's disease. Here, we present a rigorous and systematic study of the cross-seeding effects between Aβ40 and Aβ42. We show that Aβ40 fibril seeds can promote Aβ42 aggregation in a concentration-dependent manner, and vice versa. Our results also suggest that seeded aggregation and spontaneous aggregation may be two separate pathways. These findings may partly resolve conflicting observations in the literature regarding the cross-seeding effects between Aβ40 and Aβ42.