Amyloid fibrils from the viewpoint of protein folding

Elossaily G, Vellapandian C, Prajapati B. Investigating the Potential Impact of Air Pollution on Alzheimer's Disease and the Utility of Multidimensional Imaging for Early Detection

Pollution is ubiquitous, and much of it is anthropogenic in nature, which is a severe risk factor not only for respiratory infections or asthma sufferers but also for Alzheimer's disease, which has received a lot of attention recently. This Review aims to investigate the primary environmental risk factors and their profound impact on Alzheimer's disease. It underscores the pivotal role of multidimensional imaging in early disease identification and prevention. Conducting a comprehensive review, we delved into a plethora of literature sources available through esteemed databases, including Science Direct, Google Scholar, Scopus, Cochrane, and PubMed. Our search strategy incorporated keywords such as "Alzheimer Disease", "Alzheimer's", "Dementia", "Oxidative Stress", and "Phytotherapy" in conjunction with "Criteria Pollutants", "Imaging", "Pathology", and "Particulate Matter". Alzheimer's disease is not only a result of complex biological factors but is exacerbated by the infiltration of airborne particles and gases that surreptitiously breach the nasal defenses to traverse the brain, akin to a Trojan horse. Various imaging modalities and noninvasive techniques have been harnessed to identify disease progression in its incipient stages. However, each imaging approach possesses inherent limitations, prompting exploration of a unified technique under a single umbrella. Multidimensional imaging stands as the linchpin for detecting and forestalling the relentless march of Alzheimer's disease. Given the intricate etiology of the condition, identifying a prospective candidate for Alzheimer's disease may take decades, rendering the development of a multimodal imaging technique an imperative. This research underscores the pressing need to recognize the chronic ramifications of invisible particulate matter and to advance our understanding of the insidious environmental factors that contribute to Alzheimer's disease.

Identification of Natural Compounds of the Apple as Inhibitors against Cholinesterase for the Treatment of Alzheimer's Disease: An In Silico Molecular Docking Simulation and ADMET Study

Alzheimer's disease (AD), the most common type of dementia in older people, causes neurological problems associated with memory and thinking. The key enzymes involved in Alzheimer's disease pathways are acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE). Because of this, there is a lot of interest in finding new AChE inhibitors. Among compounds that are not alkaloids, flavonoids have stood out as good candidates. The apple fruit, Malus domestica (Rosaceae), is second only to cranberries regarding total phenolic compound concentration. Computational tools and biological databases were used to investigate enzymes and natural compounds. Molecular docking techniques were used to analyze the interactions of natural compounds of the apple with enzymes involved in the central nervous system (CNS), acetylcholinesterase, and butyrylcholinesterase, followed by binding affinity calculations using the AutoDock tool. The molecular docking results revealed that CID: 107905 exhibited the best interactions with AChE, with a binding affinity of -12.2 kcal/mol, and CID: 163103561 showed the highest binding affinity with BuChE, i.e., -11.2 kcal/mol. Importantly, it was observed that amino acid residue Trp286 of AChE was involved in hydrogen bond formation, Van Der Walls interactions, and Pi-Sigma/Pi-Pi interactions in the studied complexes. Moreover, the results of the Molecular Dynamics Simulation (MDS) analysis indicated interaction stability. This study shows that CID: 12000657 could be used as an AChE inhibitor and CID: 135398658 as a BuChE inhibitor to treat Alzheimer's disease and other neurological disorders.

Structure-Property-Activity Relationships in Carbon Dots

Carbon dots (CDs) are one of the most versatile nanomaterials discovered in the 21st century. They possess many properties and thus hold potentials in diverse applications. While an increasing amount of attention has been given to these novel nanoparticles, the broad scientific community is actively engaged in exploring their limits. Recent studies on the fractionalization and assembly of CDs further push the limits beyond just CDs and demonstrate that CDs are both a mixture of heterogeneous fractions and promising building blocks for assembly of large carbon-based materials. With CDs moving forward toward both microscopic and macroscopic levels, a good understanding of the structure-property-activity relationships is essential to forecasting the future of CDs. Hence, in this Perspective, structure-property-activity relationships are highlighted based on the repeatedly verified findings in CDs. In addition, studies on CD fractionalization and assembly are briefly summarized in this Perspective. Eventually, these structure-property-activity relationships and controllability are essential for the development of CDs with desired properties for various applications especially in photochemistry, electrochemistry, nanomedicine, and surface chemistry. In summary, in our opinion, since 2004 until the present, history has witnessed a great development of CDs although there is still some room for more studies. Also, considering many attractive properties, structure-property-activity relationships, and the building block nature of CDs, a variety of carbon-based materials of interest can be constructed from CDs with control. They can help reduce blind trials in the development of carbon-based materials, which is of great significance in materials science, chemistry, and any fields related to the applications.

Optogenetic neuromodulation with gamma oscillation as a new strategy for Alzheimer disease: a narrative review

The amyloid hypothesis has been considered a major explanation of the pathogenesis of Alzheimer disease. However, failure of phase III clinical trials with anti-amyloid-beta monoclonal antibodies reveals the need for other therapeutic approaches to treat Alzheimer disease. Compared to its relatively short history, optogenetics has developed considerably. The expression of microbial opsins in cells using genetic engineering allows specific control of cell signals or molecules. The application of optogenetics to Alzheimer disease research or clinical approaches is increasing. When applied with gamma entrainment, optogenetic neuromodulation can improve Alzheimer disease symptoms. Although safety problems exist with optogenetics such as the use of viral vectors, this technique has great potential for use in Alzheimer disease. In this paper, we review the historical applications of optogenetic neuromodulation with gamma entrainment to investigate the mechanisms involved in Alzheimer disease and potential therapeutic strategies.

Cirsiliol mitigates Aβ fibrillation and underlying membrane-leakage associated neurotoxicity: A possible implication in the treatment of neurodegenerative disease

Protein aggregating is known as a leading pathogenic characteristic of a wide range of neurodegenerative diseases (NDs). Preventing amyloid-β (Aβ) aggregation and uncovering the associated mechanism through the application of small bioactive compounds can be considered as a useful strategy in hampering the onset of ND. In this study, we analyzed the inhibitory effects of cirsiliol, a trihydroxy-dimethoxyflavone, against human Αβ₄₂ fibrillization. Also, we explored the probable neurotoxicity of Αβ₄₂ oligomers grown with cirsiliol at different molar ratios on PC-12 cells after 24 h. The results showed that significant changes in ThT and ANS fluorescence intensities, Congo red absorbance, and ellipticity changes were modulated by co-incubation of cirsiliol with Αβ₄₂, in a concentration-dependent manner. The spectroscopy outcomes were also supported by imaging analysis, where a few Αβ₄₂ fibrillar conformations were detected with cirsiliol. In addition, cellular assays demonstrated that co-incubated Αβ₄₂ samples with cirsiliol regulated the cell mortality, LDH release, and caspase-3 activation relative to the PC-12 exposed to Aβ₄₂ oligomers alone. In conclusion, it can suggest that cirsiliol can be used as a potential candidate in the development of small molecules-based drugs for the advancement of therapeutic platforms against ND.

Structure-Activity Relationship of Carbon Nitride Dots in Inhibiting Tau Aggregation

Due to the numerous failed clinical trials of anti-amyloid drugs, microtubule associated protein tau (MAPT) now stands out as one of the most promising targets for AD therapy. In this study, we report for the first time the structure-dependent MAPT aggregation inhibition of carbon nitride dots (CNDs). CNDs have exhibited great promise as a potential treatment of Alzheimer's disease (AD) by inhibiting the aggregation of MAPT. In order to elucidate its structure-activity relationship, CNDs were separated via column chromatography and five fractions with different structures were obtained that were characterized by multiple spectroscopy methods. The increase of surface hydrophilic functional groups is consistent with the increase of polarity from fraction 1 to 5. Particle sizes (1-2 nm) and zeta potentials (~-20 mV) are similar among five fractions. With the increase of polarity from fraction 1 to 5, their MAPT aggregation inhibition capacity was weakened. This suggests hydrophobic interactions between CNDs and MAPT, validated via molecular dynamics simulations. With a zebrafish blood-brain barrier (BBB) model, CNDs were observed to cross the BBB through passive diffusion. CNDs were also found to inhibit the generation of multiple reactive oxygen species, which is an important contributor to AD pathogenesis.

Carbon Dots: A Future Blood-Brain Barrier Penetrating Nanomedicine and Drug Nanocarrier

Drug delivery across the blood-brain barrier (BBB) is one of the biggest challenges in modern medicine due to the BBB's highly semipermeable property that limits most therapeutic agents of brain diseases to enter the central nervous system (CNS). In recent years, nanoparticles, especially carbon dots (CDs), exhibit many unprecedented applications for drug delivery. Several types of CDs and CD-ligand conjugates have been reported successfully penetrating the BBB, which shows a promising progress in the application of CD-based drug delivery system (DDS) for the treatment of CNS diseases. In this review, our discussion of CDs includes their classification, preparations, structures, properties, and applications for the treatment of neurodegenerative diseases, especially Alzheimer's disease (AD) and brain tumor. Moreover, abundant functional groups on the surface, especially amine and carboxyl groups, allow CDs to conjugate with diverse drugs as versatile drug nanocarriers. In addition, structure of the BBB is briefly described, and mechanisms for transporting various molecules across the BBB and other biological barriers are elucidated. Most importantly, recent developments in drug delivery with CDs as BBB-penetrating nanodrugs and drug nanocarriers to target CNS diseases especially Alzheimer's disease and brain tumor are summarized. Eventually, future prospects of the CD-based DDS are discussed in combination with the development of artificial intelligence and nanorobots.

Study of Nanofibrils Formation of Fibroin Protein in Specific Thermal and Acidity Conditions

Background:

Amyloid fibrils are insoluble arranged aggregates of proteins that are fibrillar in structure and related to many diseases (at least 20 types of illnesses) and also create many pathologic conditions. Therefore understanding the circumstance of fibril formation is very important

Objectives:

This study aims to work on fibrillar structure formation of fibroin (as a model protein)

Material and Methods:

In this experimental study, fibroin was extracted from bombyx mori silk cocoon, and the concentration was obtained by Bradford method. The protein was incubated in a wide range of times (0 min to 7 days) in specific acidity and thermal conditions (pH=1.6, T=70 °C). The assays of UV-vis spectroscopy with congo red, field emission scanning electron microscopy, transmission electron microscopy, atomic force microscopy and circular dichroism spectroscopy were employed to monitor the fibrillation process.

Results:

Fibroin assemblies were formed upon the process of aggregation and fibril formation with a variety of morphology ranging from nanoparticles to elongated fibrils.

Conclusion:

The results showed progressive pathway of fibril formation

Probing the Nongeneralized Amyloid Inhibitory Mechanism of Hydrophobic Chaperone

Increasing prevalence of protein misfolding disorders urges the search for effective therapies. Although several antiaggregation molecules have been identified, their molecular process of aggregation and clinical trials are underway. The present study is focused on the mechanism through which phenyl butyrate (PB), a chemical chaperone, triggers inhibition of human serum albumin (HSA) fibrillation. Turbidity and Rayleigh light scattering (RLS) measurements reveal the marked presence of aggregates in HSA that were confirmed as amyloid fibrils by thioflavin T (ThT) and Congo red (CR) and were subsequently inhibited by PB in a dose dependent manner. ThT fluorescence kinetics reveals a decrease in the apparent rate constant, K_app, in the presence of PB without triggering a lag phase in HSA suggesting PB's interference with the elongation phase. Dynamic light scattering (DLS) results display a reduction in the aggregate size in the presence of PB. Isothermal titration calorimetry (ITC) data reveals strong binding of PB at site II both at 25 °C (K_b ≈ 1.94 × 10⁵ M^-1) and 65 °C (K_b ≈ 2.90 × 10⁴ M^-1), mediated by hydrogen bonding. Overall, our finding establishes that PB stabilizes partially unfolded HSA molecules through hydrogen bonding, thereby preventing establishment of hydrogen bonds between them and hindering their progression into amyloid fibrils. This is in contrast to its chaperone effect manifested with other proteins.

Panax ginseng components and the pathogenesis of Alzheimer's disease (Review)

Ginseng is one of the main representatives of traditional Chinese medicine and presents a wide range of pharmacological actions. Ginsenosides are the main class of active compounds found in ginseng. They demonstrate unique biological activity and medicinal value, namely anti-tumour, anti-inflammatory and antioxidant properties, as well as anti-apoptotic properties. Increasing levels of stress in life are responsible for the increased incidence of nervous system diseases. Neurological diseases create a huge burden on the lives and health of individuals. In recent years, studies have indicated that ginsenosides play a pronounced positive role in the prevention and treatment of neurological diseases. Nevertheless, research is still at an early stage of development, and the complex mechanisms of action involved remain largely unknown. This review aimed to shed light into what is currently known about the mechanisms of action of ginsenosides in relation to Alzheimer's disease. Scientific material and theoretical bases for the treatment of nervous system diseases with purified Panax ginseng extracts are also discussed.

Cause and consequence of Aβ - Lipid interactions in Alzheimer disease pathogenesis

Self-templating propagation of protein aggregate conformations is increasingly becoming a significant factor in many neurological diseases. In Alzheimer disease (AD), intrinsically disordered amyloid-β (Aβ) peptides undergo aggregation that is sensitive to environmental conditions. High-molecular weight aggregates of Aβ that form insoluble fibrils are deposited as senile plaques in AD brains. However, low-molecular weight aggregates called soluble oligomers are known to be the primary toxic agents responsible for neuronal dysfunction. The aggregation process is highly stochastic involving both homotypic (Aβ-Aβ) and heterotypic (Aβ with interacting partners) interactions. Two of the important members of interacting partners are membrane lipids and surfactants, to which Aβ shows a perpetual association. Aβ-membrane interactions have been widely investigated for more than two decades, and this research has provided a wealth of information. Although this has greatly enriched our understanding, the objective of this review is to consolidate the information from the literature that collectively showcases the unique phenomenon of lipid-mediated Aβ oligomer generation, which has largely remained inconspicuous. This is especially important because Aβ aggregate "strains" are increasingly becoming relevant in light of the correlations between the structure of aggregates and AD phenotypes. Here, we will focus on aspects of Aβ-lipid interactions specifically from the context of how lipid modulation generates a wide variety of biophysically and biochemically distinct oligomer sub-types. This, we believe, will refocus our thinking on the influence of lipids and open new approaches in delineating the mechanisms of AD pathogenesis. This article is part of a Special Issue entitled: Protein Aggregation and Misfolding at the Cell Membrane Interface edited by Ayyalusamy Ramamoorthy.

Computational modeling and biomarker studies of pharmacological treatment of Alzheimer's disease (Review)

Alzheimer's disease (AD) is a complex and multifactorial disease. In order to understand the genetic influence in the progression of AD, and to identify novel pharmaceutical agents and their associated targets, the present study discusses computational modeling and biomarker evaluation approaches. Based on mechanistic signaling pathway approaches, various computational models, including biochemical and morphological models, are discussed to explore the strategies that may be used to target AD treatment. Different biomarkers are interpreted on the basis of morphological and functional features of amyloid β plaques and unstable microtubule‑associated tau protein, which is involved in neurodegeneration. Furthermore, imaging and cerebrospinal fluids are also considered to be key methods in the identification of novel markers for AD. In conclusion, the present study reviews various biochemical and morphological computational models and biomarkers to interpret novel targets and agonists for the treatment of AD. This review also highlights several therapeutic targets and their associated signaling pathways in AD, which may have potential to be used in the development of novel pharmacological agents for the treatment of patients with AD. Computational modeling approaches may aid the quest for the development of AD treatments with enhanced therapeutic efficacy and reduced toxicity.

Thyroid Hormone Enhances Neurite Outgrowth in Neuroscreen 1 Cells

Objectives

Alzheimer's disease (AD) is a neurodegenerative disorder that affects millions of individuals. Moreover, hypothyroidism has been identified as one of the risk factors that may contribute to the development of AD. Here, we investigated whether there was a correlation among expression levels of proteins involved in the formation of AD lesions, neurite outgrowth, and thyroid hormone levels.

Methods

Cells were grown in media supplemented with different levels of 3,5,3'-triiodothyronine (T3) and then processed for neurite outgrowth and to prepare RNA samples. RNA samples were analysed using quantitative real-time PCR. Protein levels were measured using in cell-Western blotting analysis.

Results

By using neurite outgrowth studies, it was demonstrated that T3 treatment enhanced neurite outgrowth in NS-1 cells in a time- and dose-dependent manner. Quantitative real-time PCR studies further confirmed that NS-1 cells expressed substantial levels of TRα and significantly less TRβ, either of which could be responsible for the T3-dependent effects on neurite outgrowth. Although the overall tau protein expression was not affected in response to T3 treatment, the splicing of tau exon 10 was impacted in the direction of producing more tau molecules that excluded the exon (tau 3R).

Conclusion

The results of this study are critical not only to understand the probable link between hypothyroidism and AD but also in providing the basis for future prevention and treatment of AD in hypothyroid patients.

A Toxic Conformer of Aβ42 with a Turn at 22-23 is a Novel Therapeutic Target for Alzheimer's Disease

Immunotherapy targeting Aβ42 is drawing attention as a possible therapeutic approach for Alzheimer’s disease (AD). Considering the significance of reported oligomerized Aβ42 species, selective targeting of the oligomer will increase the therapeutic efficacy. However, what kinds of oligomers are suitable targets for immunotherapy remains unclear. We previously identified a toxic conformer of Aβ42, which has a turn structure at 22–23 (“toxic turn”), among Aβ42 conformations. This toxic conformer of Aβ42 has been reported to show rapid oligomerization and to exhibit strong neurotoxicity and synaptotoxicity. We recently developed a monoclonal antibody against the toxic conformer (24B3), which demonstrated the increase of the toxic conformer in the cerebrospinal fluid of AD patients, indicating its accumulation in AD patients’ brains. In this study, we evaluated the therapeutic efficacy of 24B3 targeting the toxic conformer in AD model mice. The intraperitoneal administration of 24B3 for 3 months improved cognitive impairment and reduced the toxic conformer levels. Notably, this treatment did not reduce the number of senile plaques. Furthermore, the single intravenous administration of 24B3 suppressed the memory deficit in AD mice. These results suggest that the toxic conformer of Aβ42 with a turn at 22–23 represents one of the promising therapeutic targets.

Concentration dependent switch in the kinetic pathway of lysozyme fibrillation: Spectroscopic and microscopic analysis

Formation of amyloid fibrils is found to be a general tendency of many proteins. Investigating the kinetic mechanisms and structural features of the intermediates and the final fibrillar state is essential to understand their role in amyloid diseases. Lysozyme, a notable model protein for amyloidogenic studies, readily formed fibrils in vitro at neutral pH in the presence of urea. It, however, showed two different kinetic pathways under varying urea concentrations when probed with thioflavin T (ThT) fluorescence. In 2M urea, lysozyme followed a nucleation-dependent fibril formation pathway which was not altered by varying the protein concentration from 2mg/ml to 8mg/ml. In 4M urea, the protein exhibited concentration dependent change in the mechanism. At lower protein concentrations, lysozyme formed fibrils without any detectable nuclei (nucleation-independent polymerization pathway). When the concentration of the protein was increased above 3mg/ml, the protein followed nucleation-dependent polymerization pathway as observed in the case of 2M urea condition. This was further verified using microscopic images of the fibrils. The kinetic parameters such as lag time, elongation rate, and fibrillation half-time, which were derived from ThT fluorescence changes, showed linear dependency against the initial protein concentration suggested that under the nucleation-dependent pathway conditions, the protein followed primary-nucleation mechanism without any significant secondary nucleation events. The results also suggested that the differences in the initial protein conformation might alter the mechanism of fibrillation; however, at the higher protein concentrations lysozyme shifted to nucleation-dependent pathway.

Identification of an aspidospermine derivative from borage extract as an anti-amyloid compound: A possible link between protein aggregation and antimalarial drugs

A number of human diseases, including Alzheimer's and Parkinson's have been linked to amyloid formation. To search for an anti-amyloidogenic product, alkaloid enriched extract from borage leaves was examined for anti-amyloidogenic activity using Hen Egg White Lysozyme (HEWL) as a model protein. After isolation of the plant extract using rHPLC, only one fraction indicated a significant bioactivity. TEM analysis confirmed a remarkable reduction of amyloid fibrils in the presence of the bioactive fraction. To identify the effective substance in the fraction, mass spectrometry, FTIR, and NMR were performed. Our analyses determined that the bioactive compound as 1-acetyl-19,21-epoxy-15,16-dimethoxyaspidospermidine-17-ol, a derivative of aspidospermine. To investigate the mechanism of the inhibition, ANS binding, intrinsic fluorescence, and amide I content were performed in the presence of the bioactive compound. All the results confirmed the role of the compound in assisting the proper folding of the protein. In addition, molecular docking indicated the aspidospermine derivative binds the amyloidogenic region of the protein. Our results show that the alkaloid extracted from borage leaves reduces protein aggregation mediating through structural elements of the protein, promoting the correct folding of lysozyme. Since a number of aspidospermine compounds have been shown to possess potent antimalarial activities, the action of compound identified in the present study suggests a possible link between protein aggregation and aspidospermine drugs.

Interaction and inhibitory influence of the azo dye carmoisine on lysozyme amyloid fibrillogenesis

The azo dye carmoisine has a significant inhibitory effect on fibrillogenesis in lysozyme.

Personalized Medicine and Resurrected Hopes for the Management of Alzheimer's Disease: A Modular Approach Based on GSK-3β Inhibitors

Alzheimer's disease (AD) is one of the most common neurological disorders with vast reaching worldwide prevalence. Research attempts to decipher what's happening to the human mind have shown that pathogenesis of AD is associated with misfolded protein intermediates displaying tertiary structure conformational changes eventually leading to forming large polymers of unwanted aggregates. The two hallmarks of AD pathological protein aggregates are extraneuronal β-amyloid (Aβ) based senile plaques and intraneuronal neurofibrillary tangles (NFTs). As such, AD is categorized as a protein misfolding neurodegenerative disease (PMND) . Therapeutic interventions interfering with the formation of these protein aggregates have been widely explored as potential pathways for thwarting AD progression. One such tactic is modulating the function of enzymes involved in the metabolic pathways leading to formation of these misfolded protein aggregates. Much evidence has shown that glycogen synthase kinase-3β (GSK-3β) plays a key role in hyperphosphorylation of tau protein leading eventually to its aggregation to form NFTs. Data presented hereby will display a plethora of information as to how to interfere with progression of AD through the route of GSK-3β activity control.

Insight into the co-solvent induced conformational changes and aggregation of bovine β-lactoglobulin

Many proteins form ordered irreversible aggregates called amyloid fibrils which are responsible for several neurodegenerative diseases. β-lactoglobulin (β-lg), an important globular milk protein, self-assembles to form amyloid-like fibrils on heating at low pH. The present study investigated the effects of two commonly used organic solvents acetonitrile (MeCN) and antimicrobial preservative benzyl alcohol (BA) on the conformation and self-assembly of β-lg at ambient condition. Both MeCN and BA induced a concentration-dependent conformational change showing exposure of hydrophobic patches, loss of tertiary structure and higher α-helical structure at moderate concentrations. In the presence of 50-80% (v/v) MeCN and 1.5-3% (v/v) BA further structural transitions from α-helical to non-native β-sheet structure were observed with a molten globule-like intermediate at 70% MeCN. These non-native β-sheet structures have high tendency to form aggregates. The formation of β-lg self-assembly was confirmed by Thioflavin T studies, Congo red assay, Rayleigh scattering and dynamic light scattering analysis. Transmission electron microscopy studies showed amyloid fibril formation in both MeCN and BA. Our results showed that BA enhances the unfolding and self-assembly of β-lg at much lower concentration than MeCN. Thus solvent composition forces the protein to achieve the non-native structures which are responsible for protein aggregation.

NOX2 As a Target for Drug Development: Indications, Possible Complications, and Progress

SIGNIFICANCE

NOX2 is important for host defense, and yet is implicated in a large number of diseases in which inflammation plays a role in pathogenesis. These include acute and chronic lung inflammatory diseases, stroke, traumatic brain injury, and neurodegenerative diseases, including Alzheimer's and Parkinson's Diseases.

RECENT ADVANCES

Recent drug development programs have targeted several NOX isoforms that are implicated in a variety of diseases. The focus has been primarily on NOX4 and NOX1 rather than on NOX2, due, in part, to concerns about possible immunosuppressive side effects. Nevertheless, NOX2 clearly contributes to the pathogenesis of many inflammatory diseases, and its inhibition is predicted to provide a novel therapeutic approach.

CRITICAL ISSUES

Possible side effects that might arise from targeting NOX2 are discussed, including the possibility that such inhibition will contribute to increased infections and/or autoimmune disorders. The state of the field with regard to existing NOX2 inhibitors and targeted development of novel inhibitors is also summarized.

FUTURE DIRECTIONS

NOX2 inhibitors show particular promise for the treatment of inflammatory diseases, both acute and chronic. Theoretical side effects include pro-inflammatory and autoimmune complications and should be considered in any therapeutic program, but in our opinion, available data do not indicate that they are sufficiently likely to eliminate NOX2 as a drug target, particularly when weighed against the seriousness of many NOX2-related indications. Model studies demonstrating efficacy with minimal side effects are needed to encourage future development of NOX2 inhibitors as therapeutic agents.

Endeavour to simplify the frustrated concept of protein-ammonium family ionic liquid interactions

Schematic representation of protein stabilization/destabilization in the presence of ionic liquids.

Intermediates caught in the act: tracing insulin amyloid fibril formation in time by combined optical spectroscopy, light scattering, mass spectrometry and microscopy

Insulin under acidic conditions. PDB-Databank structure visualized with VMD.

Pathogenic properties of Alzheimer's β-amyloid identified from structure–property patient-phenotype correlations

Direct correlation of Alzheimer patient data to a spectrum of NMR structures and chemical properties of beta amyloid (Aβ) variants allows identification of conformation-dependent disease properties.

Biochemical properties and aggregation propensity of transforming growth factor-induced protein (TGFBIp) and the amyloid forming mutants

TGFBI-associated corneal dystrophies are characterized by accumulation of insoluble deposits of the mutant protein transforming growth factor β-induced protein (TGFBIp) in the cornea. Depending on the nature of mutation, the lesions appear as granular (non-amyloid) or lattice lines (amyloid) in the Bowman's layer or in the stroma. This review article emphasizes the structural biology aspects of TGFBIp. We discuss the tinctorial properties and ultrastructure of deposits observed in granular and lattice corneal dystrophic mutants with amyloid and non-amyloid forms of other human protein deposition diseases and review the biochemical and putative functional role of the protein. Using bioinformatics tools, we identify intrinsic aggregation propensity and discuss the possible protective role of gatekeepers close to the "aggregation-prone" regions of native TGFBIp. We describe the relative aggregation rates of lattice corneal dystrophy (LCD) and granular corneal dystrophy (GCD2) mutants using the three-parameter model, which is based on intrinsic properties of polypeptide chains. The predictive power of this model is compared with two other algorithms. We conclude that the model is able to predict the aggregation rate of mutants which do not alter overall net charge of the protein. The need to understand the mechanism of corneal dystrophies from the structural biology viewpoint is emphasized.

Direct evidence for self-propagation of different amyloid-β fibril conformations

BACKGROUND

Amyloid fibrils formed by amyloid-β (Aβ) peptides are associated with Alzheimer's disease and can occur in a range of distinct morphologies that are not uniquely determined by the Aβ sequence. Whether distinct conformations of Aβ fibrils can be stably propagated over multiple cycles of seeding and fibril growth has not been established experimentally.

OBJECTIVE

The ability of the 40-residue peptide Aβ1-40 to assemble into fibrils with the conformation of the mutant Aβ1-40 peptide containing the 'Osaka' mutation E22Δ was investigated.

METHODS

Fibril formation of highly pure, recombinant Aβ1-40 in the presence of distinct, preformed seeds in vitro was recorded with thioflavin T fluorescence, and distinct fibrillar structures were identified and distinguished by fluorescence spectroscopy and electron microscopy.

RESULTS

We propagated the specific quaternary structure of Aβ1-40 E22Δ fibrils with wild-type Aβ1-40 over up to seven cycles of seeding and fibril elongation. As a result of a 10(7)-fold dilution of the initially present Aβ1-40 E22Δ seeds, the vast majority of fibrils formed after the seventh propagation cycle with Aβ1-40 did not contain a single molecule of Aβ1-40 E22Δ, but still retained the conformation of the initial Aβ1-40 E22Δ seeds. Increased critical concentrations of Aβ1-40 fibrils formed in the presence of Aβ1-40 E22Δ nuclei suggest that these fibrils are less stable than homologously seeded Aβ1-40 fibrils, consistent with a kinetically controlled mechanism of fibril formation.

CONCLUSION

The propagation of a distinct Aβ fibril conformation over multiple cycles of seeded fibril growth demonstrates the basic ability of the Aβ peptide to form amyloid strains that in turn may cause phenotypes in Alzheimer's disease.

Monodisperse carboxyl-functionalized poly(ethylene glycol)-coated magnetic poly(glycidyl methacrylate) microspheres: application to the immunocapture of β-amyloid peptides

Identification and evaluation of small changes in β-amyloid peptide (Aβ) levels in cerebrospinal fluid is of crucial importance for early detection of Alzheimer's disease. Microfluidic detection methods enable effective preconcentration of Aβ using magnetic microparticles coated with Aβ antibodies. Poly(glycidyl methacrylate) microspheres are coated with α-amino-ω-methoxy-PEG5000 /α-amino-ω-Boc-NH-PEG5000 Boc groups deprotected and NH2 succinylated to introduce carboxyl groups. Capillary electrophoresis with laser-induced fluorescence detection confirms the efficient capture of Aβ 1-40 peptides on the microspheres with immobilized monoclonal anti-Aβ 6E10. The capture specificity is confirmed by comparing Aβ 1-40 levels on the anti-IgG-immobilized particles used as a control.

Matrix metalloproteinases, new insights into the understanding of neurodegenerative disorders

Matrix metalloproteinases (MMPs) are a subfamily of zinc-dependent proteases that are responsible for degradation and remodeling of extracellular matrix proteins. The activity of MMPs is tightly regulated at several levels including cleavage of prodomain, allosteric activation, compartmentalization and complex formation with tissue inhibitor of metalloproteinases (TIMPs). In the central nervous system (CNS), MMPs play a wide variety of roles ranging from brain development, synaptic plasticity and repair after injury to the pathogenesis of various brain disorders. Following general discussion on the domain structure and the regulation of activity of MMPs, we emphasize their implication in various brain disorder conditions such as Alzheimer’s disease, multiple sclerosis, ischemia/reperfusion and Parkinson’s disease. We further highlight accumulating evidence that MMPs might be the culprit in Parkinson’s disease (PD). Among them, MMP-3 appears to be involved in a range of pathogenesis processes in PD including neuroinflammation, apoptosis and degradation of α-synuclein and DJ-1. MMP inhibitors could represent potential novel therapeutic strategies for treatments of neurodegenerative diseases.

Oxidative stress and neurodegenerative disorders

Living cells continually generate reactive oxygen species (ROS) through the respiratory chain during energetic metabolism. ROS at low or moderate concentration can play important physiological roles. However, an excessive amount of ROS under oxidative stress would be extremely deleterious. The central nervous system (CNS) is particularly vulnerable to oxidative stress due to its high oxygen consumption, weakly antioxidative systems and the terminal-differentiation characteristic of neurons. Thus, oxidative stress elicits various neurodegenerative diseases. In addition, chemotherapy could result in severe side effects on the CNS and peripheral nervous system (PNS) of cancer patients, and a growing body of evidence demonstrates the involvement of ROS in drug-induced neurotoxicities as well. Therefore, development of antioxidants as neuroprotective drugs is a potentially beneficial strategy for clinical therapy. In this review, we summarize the source, balance maintenance and physiologic functions of ROS, oxidative stress and its toxic mechanisms underlying a number of neurodegenerative diseases, and the possible involvement of ROS in chemotherapy-induced toxicity to the CNS and PNS. We ultimately assess the value for antioxidants as neuroprotective drugs and provide our comments on the unmet needs.

New insight into neurodegeneration: the role of proteomics

Recent advances within the field of proteomics, including both upstream and downstream protocols, have fuelled a transition from simple protein identification to functional analysis. A battery of proteomics approaches is now being employed for the analysis of protein expression levels, the monitoring of cellular activities and for gaining an increased understanding into biochemical pathways. Combined, these approaches are changing the way we study disease by allowing accurate and targeted, large scale protein analysis, which will provide invaluable insight into disease pathogenesis. Neurodegenerative disorders, including Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), amyotrophic lateral sclerosis (ALS), prion disease, and other diseases that affect the neuromuscular system, are a leading cause of disability in the aging population. There are no effective intervention strategies for these disorders and diagnosis is challenging as it relies primarily on clinical symptomatic features, which often overlap at early stages of disease. There is, therefore, an urgent need to develop reliable biomarkers to improve early and specific diagnosis, to track disease progression, to measure molecular responses towards treatment regimes and ultimately devise new therapeutic strategies. To accomplish this, a better understanding of disease mechanisms is needed. In this review we summarize recent advances in the field of proteomics applicable to neurodegenerative disorders, and how these advances are fueling our understanding, diagnosis, and treatment of these complex disorders.

Microcanonical thermostatistics of coarse-grained proteins with amyloidogenic propensity

The formation of fibrillar aggregates seems to be a common characteristic of polypeptide chains, although the observation of these aggregates may depend on appropriate experimental conditions. Partially folded intermediates seem to have an important role in the generation of protein aggregates, and a mechanism for this fibril formation considers that these intermediates also correspond to metastable states with respect to the fibrillar ones. Here, using a coarse-grained (CG) off-lattice model, we carry out a comparative analysis of the thermodynamic aspects characterizing the folding transition with respect to the propensity for aggregation of four different systems: two isoforms of the amyloid β-protein, the Src SH3 domain, and the human prion proteins (hPrP). Microcanonical analysis of the data obtained from replica exchange method is conducted to evaluate the free-energy barrier and latent heat in these models. The simulations of the amyloid β isoforms and Src SH3 domain indicated that the folding process described by this CG model is related to a negative specific heat, a phenomenon that can only be verified in the microcanonical ensemble in first-order phase transitions. The CG simulation of the hPrP heteropolymer yielded a continuous folding transition. The absence of a free-energy barrier and latent heat favors the presence of partially unfolded conformations, and in this context, this thermodynamic aspect could explain the reason why the hPrP heteropolymer is more aggregation-prone than the other heteropolymers considered in this study. We introduced the hydrophobic radius of gyration as an order parameter and found that it can be used to obtain reliable information about the hydrophobic packing and the transition temperatures in the folding process.

Molecular dynamics study of an insertion/duplication mutant of bacteriophage T4 lysozyme reveals the nature of α→β transition in full protein context

An α→β transition underlies the first step of disease causing amyloidogenesis in many proteins. In view of this, many studies have been carried out using peptide models to characterize these secondary structural transitions. In this paper we show that an insertion/duplication mutant 'L20' of bacteriophage T4 lysozyme (M. Sagermann, W. A. Baase and B. W. Matthews, Proc. Natl. Acad. Sci. U.S.A., 1999, 96, 6078) displays an α→β transition. We performed molecular dynamics (MD) simulation of L20, using the GROMACS package of programs and united atom GROMOS 53a6 force field for a time period of 600 ns at 300 K, in explicit water. Our MD simulation demonstrated that the transition occurs in a duplicated α-helical region inserted tandemly at the N-terminus of the 'parent' helix. We show that a C-terminal β-sheet anchors the parent helix while the loosely held N-terminal loop in the duplicate region is vulnerable to solvent attack and thus undergoes an α→β transition. Main chain-solvent interactions were seen to stabilize the observed β-structure. Thus L20 serves as a good protein model for characterization of α→β transition in a full length protein.

A Caenorhabditis elegans model system for amylopathy study

Amylopathy is a term that describes abnormal synthesis and accumulation of amyloid beta (Aβ) in tissues with time. Aβ is a hallmark of Alzheimer's disease (AD) and is found in Lewy body dementia, inclusion body myositis and cerebral amyloid angiopathy (1-4). Amylopathies progressively develop with time. For this reason simple organisms with short lifespans may help to elucidate molecular aspects of these conditions. Here, we describe experimental protocols to study Aβ-mediated neurodegeneration using the worm Caenorhabditis elegans. Thus, we construct transgenic worms by injecting DNA encoding human Aβ42 into the syncytial gonads of adult hermaphrodites. Transformant lines are stabilized by a mutagenesis-induced integration. Nematodes are age synchronized by collecting and seeding their eggs. The function of neurons expressing Aβ42 is tested in opportune behavioral assays (chemotaxis assays). Primary neuronal cultures obtained from embryos are used to complement behavioral data and to test the neuroprotective effects of anti-apoptotic compounds.

Transgenic models of Alzheimer's disease: better utilization of existing models through viral transgenesis

Animal models have been used for decades in the Alzheimer's disease (AD) research field and have been crucial for the advancement of our understanding of the disease. Most models are based on familial AD mutations of genes involved in the amyloidogenic process, such as the amyloid precursor protein (APP) and presenilin 1 (PS1). Some models also incorporate mutations in tau (MAPT) known to cause frontotemporal dementia, a neurodegenerative disease that shares some elements of neuropathology with AD. While these models are complex, they fail to display pathology that perfectly recapitulates that of the human disease. Unfortunately, this level of pre-existing complexity creates a barrier to the further modification and improvement of these models. However, as the efficacy and safety of viral vectors improves, their use as an alternative to germline genetic modification is becoming a widely used research tool. In this review we discuss how this approach can be used to better utilize common mouse models in AD research. This article is part of a Special Issue entitled: Animal Models of Disease.