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1.
Nature ; 631(8022): 913-919, 2024 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-38987603

RESUMEN

A defining pathological feature of most neurodegenerative diseases is the assembly of proteins into amyloid that form disease-specific structures1. In Alzheimer's disease, this is characterized by the deposition of ß-amyloid and tau with disease-specific conformations. The in situ structure of amyloid in the human brain is unknown. Here, using cryo-fluorescence microscopy-targeted cryo-sectioning, cryo-focused ion beam-scanning electron microscopy lift-out and cryo-electron tomography, we determined in-tissue architectures of ß-amyloid and tau pathology in a postmortem Alzheimer's disease donor brain. ß-amyloid plaques contained a mixture of fibrils, some of which were branched, and protofilaments, arranged in parallel arrays and lattice-like structures. Extracellular vesicles and cuboidal particles defined the non-amyloid constituents of ß-amyloid plaques. By contrast, tau inclusions formed parallel clusters of unbranched filaments. Subtomogram averaging a cluster of 136 tau filaments in a single tomogram revealed the polypeptide backbone conformation and filament polarity orientation of paired helical filaments within tissue. Filaments within most clusters were similar to each other, but were different between clusters, showing amyloid heterogeneity that is spatially organized by subcellular location. The in situ structural approaches outlined here for human donor tissues have applications to a broad range of neurodegenerative diseases.


Asunto(s)
Enfermedad de Alzheimer , Péptidos beta-Amiloides , Encéfalo , Microscopía por Crioelectrón , Tomografía con Microscopio Electrónico , Placa Amiloide , Proteínas tau , Humanos , Masculino , Ratones , Enfermedad de Alzheimer/patología , Enfermedad de Alzheimer/metabolismo , Péptidos beta-Amiloides/química , Péptidos beta-Amiloides/metabolismo , Péptidos beta-Amiloides/ultraestructura , Autopsia , Encéfalo/metabolismo , Encéfalo/patología , Encéfalo/ultraestructura , Vesículas Extracelulares/metabolismo , Vesículas Extracelulares/química , Vesículas Extracelulares/ultraestructura , Placa Amiloide/metabolismo , Placa Amiloide/patología , Placa Amiloide/química , Placa Amiloide/ultraestructura , Proteínas tau/química , Proteínas tau/metabolismo , Proteínas tau/ultraestructura
2.
Phys Chem Chem Phys ; 26(29): 20087-20102, 2024 Jul 24.
Artículo en Inglés | MEDLINE | ID: mdl-39007924

RESUMEN

The original etiology of Alzheimer's disease (AD) is the deposition of amyloid-beta (Aß) proteins, which starts from the aggregation of the Aß oligomers. The optimal therapeutic strategy targeting Aß oligomer aggregation is the development of AD vaccines. Despite the fact that positive progress has been made for experimental attempts at AD vaccines, the physicochemical and even structural properties of these AD vaccines remain unclear. In this study, through immunoinformatic and molecular dynamics (MD) simulations, we first designed and simulated an alternative of vaccine TAPAS and found that the structure of the alternative can reproduce the 3D conformation of TAPAS determined experimentally. Meanwhile, immunoinformatic methods were used to analyze the physicochemical properties of TAPAS, including immunogenicity, antigenicity, thermal stability, and solubility, which confirm well the efficacy and safety of the vaccine, and validate the scheme reliability of immunoinformatic and MD simulations in designing and simulating the TAPAS vaccine. Using the same scheme, we predicted the 3D conformation of the optimized ACI-24 peptide vaccine, an Aß peptide with the first 15 residues of Aß42 (Aß1-15). The vaccine was verified once to be effective against both full-length Aß1-42 and truncated Aß4-42 aggregates, but an experimental 3D structure was absent. We have also explored the immune mechanism of the vaccine at the molecular level and found that the optimized ACI-24 and its analogues can block the growth of either full-length Aß1-42 or truncated Aß4-42 pentamer by contacting the hydrophobic residues within the N-terminus and ß1 region on the contact surface of either pentamer. Additionally, residues (D1, D7, S8, H13, and Q15) were identified as the key residues of the vaccine to contact either of the two Aß oligomers. This work provides a feasible implementation scheme of immunoinformatic and MD simulations for the development of AD small peptide vaccines, validating the power of the scheme as a parallel tool to the experimental approaches and injecting molecular-level information into the understanding and design of anti-AD vaccines.


Asunto(s)
Vacunas contra el Alzheimer , Péptidos beta-Amiloides , Fragmentos de Péptidos , Vacunas de Subunidades Proteicas , Humanos , Enfermedad de Alzheimer/prevención & control , Vacunas contra el Alzheimer/química , Vacunas contra el Alzheimer/inmunología , Péptidos beta-Amiloides/química , Péptidos beta-Amiloides/inmunología , Simulación de Dinámica Molecular , Fragmentos de Péptidos/química , Fragmentos de Péptidos/inmunología , Conformación Proteica , Vacunas de Subunidades Proteicas/química , Vacunas de Subunidades Proteicas/inmunología
3.
ACS Appl Mater Interfaces ; 16(28): 35898-35911, 2024 Jul 17.
Artículo en Inglés | MEDLINE | ID: mdl-38954799

RESUMEN

Alzheimer's disease (AD) has a complex etiology and diverse pathological processes. The therapeutic effect of single-target drugs is limited, so simultaneous intervention of multiple targets is gradually becoming a new research trend. Critical stages in AD progression involve amyloid-ß (Aß) self-aggregation, metal-ion-triggered fibril formation, and elevated reactive oxygen species (ROS). Herein, red blood cell membranes (RBC) are used as templates for the in situ growth of cerium oxide (CeO2) nanocrystals. Then, carbon quantum dots (CQDs) are encapsulated to form nanocomposites (CQD-Ce-RBC). This strategy is combined with photothermal therapy (PTT) for AD therapy. The application of RBC enhances the materials' biocompatibility and improves immune evasion. RBC-grown CeO2, the first application in the field of AD, demonstrates outstanding antioxidant properties. CQD acts as a chelating agent for copper ions, which prevents the aggregation of Aß. In addition, the thermal effect induced by near-infrared laser-induced CQD can break down Aß fibers and improve the permeability of the blood-brain barrier. In vivo experiments on APP/PS1 mice demonstrate that CQD-Ce-RBC combined with PTT effectively clears cerebral amyloid deposits and significantly enhances learning and cognitive abilities, thereby retarding disease progression. This innovative multipathway approach under light-induced conditions holds promise for AD treatment.


Asunto(s)
Enfermedad de Alzheimer , Cerio , Membrana Eritrocítica , Puntos Cuánticos , Enfermedad de Alzheimer/tratamiento farmacológico , Enfermedad de Alzheimer/terapia , Enfermedad de Alzheimer/metabolismo , Animales , Cerio/química , Cerio/farmacología , Ratones , Membrana Eritrocítica/química , Puntos Cuánticos/química , Puntos Cuánticos/uso terapéutico , Humanos , Péptidos beta-Amiloides/metabolismo , Péptidos beta-Amiloides/química , Rayos Infrarrojos , Carbono/química , Carbono/farmacología , Terapia Fototérmica , Barrera Hematoencefálica/metabolismo , Barrera Hematoencefálica/efectos de los fármacos , Nanocompuestos/química , Nanocompuestos/uso terapéutico
4.
PLoS One ; 19(7): e0307213, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38990960

RESUMEN

For the study of amyloid beta (Aß) associated toxicity which is supposed to be the main pathological agent in Alzheimer's disease (AD), it is important to secure Aß peptide with appropriate biological activity. However, commercial and synthetic Aß often have some pitfalls like less cell toxicity, prompt aggregation and excess price, using recombinant technology, these issues can be resolved though the method also suffered from some problems such as low yield, aggregation and prolong time to purify. Thus, we previously developed an easy, economic and convenient method for Aß42 purification using highly expressed GroES-Ubiquitin-Aß42 fusion protein. The method was efficient, but further development was performed to improve the procedure and increase the yield. Focus was on the isolation of the fusion protein (GroES-Ubiquitin) from Aß42 peptide. After a series of systematic testing with several chemicals, we found that methanol could precipitate efficiently the fusion protein, while the Aß peptide was recovered in the supernatant. By this method, Aß peptide was easily purified without tedious chromatographic steps which are main obstacles to purify the peptide in the previous method. This method yielded ~20 mg highly pure Aß42 peptide from 1-liter bacterial culture. Different biophysical characterizations and bioactivity assays indicate that the peptide purified using this method was competitive with others which have been previously reported whereas considering the simplicity, final yield and time of purification, this method is the optimal solution.


Asunto(s)
Péptidos beta-Amiloides , Fragmentos de Péptidos , Proteínas Recombinantes de Fusión , Péptidos beta-Amiloides/aislamiento & purificación , Péptidos beta-Amiloides/química , Péptidos beta-Amiloides/metabolismo , Fragmentos de Péptidos/química , Fragmentos de Péptidos/aislamiento & purificación , Humanos , Proteínas Recombinantes de Fusión/aislamiento & purificación , Proteínas Recombinantes de Fusión/metabolismo , Proteínas Recombinantes de Fusión/química , Proteínas Recombinantes de Fusión/genética , Ubiquitina/química , Ubiquitina/metabolismo , Ubiquitina/aislamiento & purificación , Escherichia coli/genética , Escherichia coli/metabolismo , Enfermedad de Alzheimer/metabolismo
5.
J Am Chem Soc ; 146(28): 19077-19087, 2024 Jul 17.
Artículo en Inglés | MEDLINE | ID: mdl-38973199

RESUMEN

Deposition of amyloid plaques in the brains of Alzheimer's disease (AD) patients is a hallmark of the disease. AD plaques consist primarily of the beta-amyloid (Aß) peptide but can contain other factors such as lipids, proteoglycans, and chaperones. So far, it is unclear how the cellular environment modulates fibril polymorphism and how differences in fibril structure affect cell viability. The small heat-shock protein (sHSP) alpha-B-Crystallin (αBC) is abundant in brains of AD patients, and colocalizes with Aß amyloid plaques. Using solid-state NMR spectroscopy, we show that the Aß40 fibril seed structure is not replicated in the presence of the sHSP. αBC prevents the generation of a compact fibril structure and leads to the formation of a new polymorph with a dynamic N-terminus. We find that the N-terminal fuzzy coat and the stability of the C-terminal residues in the Aß40 fibril core affect the chemical and thermodynamic stability of the fibrils and influence their seeding capacity. We believe that our results yield a better understanding of how sHSP, such as αBC, that are part of the cellular environment, can affect fibril structures related to cell degeneration in amyloid diseases.


Asunto(s)
Enfermedad de Alzheimer , Péptidos beta-Amiloides , Cadena B de alfa-Cristalina , Péptidos beta-Amiloides/química , Péptidos beta-Amiloides/metabolismo , Enfermedad de Alzheimer/metabolismo , Enfermedad de Alzheimer/patología , Humanos , Cadena B de alfa-Cristalina/química , Cadena B de alfa-Cristalina/metabolismo , Cadena B de alfa-Cristalina/genética , Fragmentos de Péptidos/química , Fragmentos de Péptidos/metabolismo , Fragmentos de Péptidos/genética , Amiloide/química , Amiloide/metabolismo
6.
ACS Chem Neurosci ; 15(14): 2586-2599, 2024 Jul 17.
Artículo en Inglés | MEDLINE | ID: mdl-38979921

RESUMEN

Aß oligomers are being investigated as cytotoxic agents in Alzheimer's disease (AD). Because of their transient nature and conformational heterogeneity, the relationship between the structure and activity of these oligomers is still poorly understood. Hence, methods for stabilizing Aß oligomeric species relevant to AD are needed to uncover the structural determinants of their cytotoxicity. Here, we build on the observation that metal ions and metabolites have been shown to interact with Aß, influencing its aggregation and stabilizing its oligomeric species. We thus developed a method that uses zinc ions, Zn(II), to stabilize oligomers produced by the 42-residue form of Aß (Aß42), which is dysregulated in AD. These Aß42-Zn(II) oligomers are small in size, spanning the 10-30 nm range, stable at physiological temperature, and with a broad toxic profile in human neuroblastoma cells. These oligomers offer a tool to study the mechanisms of toxicity of Aß oligomers in cellular and animal AD models.


Asunto(s)
Péptidos beta-Amiloides , Fragmentos de Péptidos , Zinc , Péptidos beta-Amiloides/química , Péptidos beta-Amiloides/metabolismo , Humanos , Zinc/química , Fragmentos de Péptidos/química , Fragmentos de Péptidos/metabolismo , Línea Celular Tumoral , Enfermedad de Alzheimer/metabolismo , Supervivencia Celular/efectos de los fármacos
7.
J Phys Chem B ; 128(30): 7341-7349, 2024 Aug 01.
Artículo en Inglés | MEDLINE | ID: mdl-39018428

RESUMEN

The histidine behavior plays a crucial role in the structural and aggregation properties of protein folding and misfolding. Understanding the histidine behavior at the edge of the protein structure is critical for finding ways to disrupt fibril elongation and growth, but this impact remains poorly understood. In the current study, we used molecular dynamics simulations to investigate the edge substitution effect of histidine protonation on the structural and aggregation properties. Our data showed that ΔG1 contributed the most to binding affinity compared to ΔG2 and ΔG3. The different protonation states at the edge chain significantly impacted the secondary structure properties of the edge chain. Specifically, we found that such protonation behavior significantly affected specific regions, particularly the N-terminus (G9-Q15) and C-terminus (K28-A30). Further analysis confirmed that H6, H13, and H14 were directly involved in H-bonding networks with the C1_H14//C2_H13 interchain interactions critical for maintaining the interchain stability. Furthermore, we confirmed that H6, H13, and H14 were directly involved in the loss of the carbon skeleton contact in the N-terminus. Our findings indicate that the edge condition is more susceptible to changes in structural properties than the middle condition. The current study is helpful for understanding the histidine behavior hypothesis in related misfolding diseases.


Asunto(s)
Péptidos beta-Amiloides , Histidina , Simulación de Dinámica Molecular , Fragmentos de Péptidos , Protones , Histidina/química , Péptidos beta-Amiloides/química , Péptidos beta-Amiloides/metabolismo , Fragmentos de Péptidos/química , Fragmentos de Péptidos/metabolismo , Enlace de Hidrógeno , Agregado de Proteínas
8.
J Phys Chem B ; 128(29): 7022-7032, 2024 Jul 25.
Artículo en Inglés | MEDLINE | ID: mdl-39016210

RESUMEN

The interaction between iron and amyloid-beta (Aß) peptides has received significant attention in Alzheimer's disease (AD) research due to its potential implications in developing this pathology. However, the coordination preferences of iron and Aß1-42 have not been thoroughly investigated or remain unknown. This study employs a computational protocol that combines homology modeling techniques with quantum mechanics (DTF-xTB) calculations to build and evaluate several 3D models of Fe2+/3+-Aß1-42. Our results reveal well-defined complexes for both the metal and peptide moieties, and we discuss the molecular interactions stabilizing these complexes by elucidating the coordinating environments and binding preferences. These proposed models offer valuable insights into the role of iron in Alzheimer's disease (AD) pathology.


Asunto(s)
Enfermedad de Alzheimer , Péptidos beta-Amiloides , Fragmentos de Péptidos , Péptidos beta-Amiloides/química , Péptidos beta-Amiloides/metabolismo , Enfermedad de Alzheimer/metabolismo , Fragmentos de Péptidos/química , Fragmentos de Péptidos/metabolismo , Humanos , Teoría Cuántica , Modelos Moleculares , Hierro/química , Hierro/metabolismo , Compuestos Férricos/química , Compuestos Ferrosos/química
9.
Biomolecules ; 14(7)2024 Jun 28.
Artículo en Inglés | MEDLINE | ID: mdl-39062488

RESUMEN

Alzheimer's disease (AD) is a neurological disorder associated with amyloid ß-protein (Aß) assembly into toxic oligomers. In addition to the two predominant alloforms, Aß1-40 and Aß1-42, other C-terminally truncated Aß peptides, including Aß1-38 and Aß1-43, are produced in the brain. Here, we use discrete molecular dynamics (DMD) and a four-bead protein model with amino acid-specific hydropathic interactions, DMD4B-HYDRA, to examine oligomer formation of Aß1-38, Aß1-40, Aß1-42, and Aß1-43. Self-assembly of 32 unstructured monomer peptides into oligomers is examined using 32 replica DMD trajectories for each of the four peptides. In a quasi-steady state, Aß1-38 and Aß1-40 adopt similar unimodal oligomer size distributions with a maximum at trimers, whereas Aß1-42 and Aß1-43 oligomer size distributions are multimodal with the dominant maximum at trimers or tetramers, and additional maxima at hexamers and unidecamers (for Aß1-42) or octamers and pentadecamers (for Aß1-43). The free energy landscapes reveal isoform- and oligomer-order specific structural and morphological features of oligomer ensembles. Our results show that oligomers of each of the four isoforms have unique features, with Aß1-42 alone resulting in oligomers with disordered and solvent-exposed N-termini. Our findings help unravel the structure-function paradigm governing oligomers formed by various Aß isoforms.


Asunto(s)
Péptidos beta-Amiloides , Simulación de Dinámica Molecular , Isoformas de Proteínas , Péptidos beta-Amiloides/química , Péptidos beta-Amiloides/metabolismo , Isoformas de Proteínas/química , Isoformas de Proteínas/metabolismo , Humanos , Multimerización de Proteína , Enfermedad de Alzheimer/metabolismo , Fragmentos de Péptidos/química , Fragmentos de Péptidos/metabolismo
10.
J Phys Chem Lett ; 15(24): 6292-6298, 2024 Jun 20.
Artículo en Inglés | MEDLINE | ID: mdl-38855822

RESUMEN

The interaction of small Amyloid-ß (Aß) oligomers with the lipid membrane is an important component of the pathomechanism of Alzheimer's disease (AD). However, oligomers are heterogeneous in size. How each type of oligomer incorporates into the membrane, and how that relates to their toxicity, is unknown. Here, we employ a single molecule technique called Q-SLIP (Quencher-induced Step Length Increase in Photobleaching) to measure the membrane insertion of each monomeric unit of individual oligomers of Aß42, Aß40, and Aß40-F19-Cyclohexyl alanine (Aß40-F19Cha), and correlate it with their toxicity. We observe that the N-terminus of Aß42 inserts close to the center of the bilayer, the less toxic Aß40 inserts to a shallower depth, and the least toxic Aß40-F19Cha has no specific distribution. This oligomer-specific map provides a mechanistic representation of membrane-mediated Aß toxicity and should be a valuable tool for AD research.


Asunto(s)
Péptidos beta-Amiloides , Péptidos beta-Amiloides/química , Membrana Dobles de Lípidos/química , Fragmentos de Péptidos/química , Humanos , Enfermedad de Alzheimer/metabolismo , Imagen Individual de Molécula/métodos
11.
ACS Nano ; 18(24): 15416-15431, 2024 Jun 18.
Artículo en Inglés | MEDLINE | ID: mdl-38840269

RESUMEN

The accumulation of amyloid-ß (Aß) peptides is a major hallmark of Alzheimer's disease (AD) and plays a crucial role in its pathogenesis. Particularly, the structured oligomeric species rich in ß-sheet formations were implicated in neuronal organelle damage. Addressing this formidable challenge requires identifying candidates capable of inhibiting peptide aggregation or disaggregating preformed oligomers for effective antiaggregation-based AD therapy. Here, we present a dual-functional nanoinhibitor meticulously designed to target the aggregation driving force and amyloid fibril spatial structure. Leveraging the exceptional structural stability and facile tailoring capability of endohedral metallofullerene Gd@C82, we introduce desired hydrogen-binding sites and charged groups, which are abundant on its surface for specific designs. Impressively, these designs endow the resultant functionalized-Gd@C82 nanoparticles (f-Gd@C82 NPs) with high capability of redirecting peptide self-assembly toward disordered, off-pathway species, obstructing the early growth of protofibrils, and disaggregating the preformed well-ordered protofibrils or even mature Aß fibrils. This results in considerable alleviation of Aß peptide-induced neuronal cytotoxicity, rescuing neuronal death and synaptic loss in primary neuron models. Notably, these modifications significantly improved the dispersibility of f-Gd@C82 NPs, thus substantially enhancing its bioavailability. Moreover, f-Gd@C82 NPs demonstrate excellent cytocompatibility with various cell lines and possess the ability to penetrate the blood-brain barrier in mice. Large-scale molecular dynamics simulations illuminate the inhibition and disaggregation mechanisms. Our design successfully overcomes the limitations of other nanocandidates, which often overly rely on hydrophobic interactions or photothermal conversion properties, and offers a viable direction for developing anti-AD agents through the inhibition and even reversal of Aß aggregation.


Asunto(s)
Enfermedad de Alzheimer , Péptidos beta-Amiloides , Neuronas , Péptidos beta-Amiloides/metabolismo , Péptidos beta-Amiloides/antagonistas & inhibidores , Péptidos beta-Amiloides/química , Enfermedad de Alzheimer/tratamiento farmacológico , Enfermedad de Alzheimer/metabolismo , Enfermedad de Alzheimer/patología , Animales , Neuronas/efectos de los fármacos , Neuronas/metabolismo , Neuronas/patología , Humanos , Gadolinio/química , Gadolinio/farmacología , Nanopartículas/química , Fulerenos/química , Fulerenos/farmacología , Agregado de Proteínas/efectos de los fármacos , Ratones , Diseño de Fármacos , Supervivencia Celular/efectos de los fármacos , Ratas
12.
J Phys Chem B ; 128(23): 5667-5675, 2024 Jun 13.
Artículo en Inglés | MEDLINE | ID: mdl-38836448

RESUMEN

Nonspecific membrane disruption is considered a plausible mechanism for the cytotoxicity induced by ß-amyloid (Aß) aggregates. In scenarios of high local Aß concentrations, a two-step membrane fragmentation model has been proposed. Initially, membrane-embedded Aß oligomeric aggregates form, followed by membrane fragmentation. However, the key molecular-level interactions between Aß oligomeric aggregates and lipids that drive the second-stage membrane fragmentation remain unclear. This study monitors the time-dependent changes in lipid dynamics and water accessibility of model liposomes during Aß-induced membrane fragmentation. Our results indicate that lipid dynamics on the nanosecond to microsecond time scale undergo rapid acceleration upon initial incubation with membrane-incorporated Aß oligomeric aggregates, followed by a slow deceleration process. Concurrently, lipid headgroups become less accessible to water. Both observations suggest a carpet-like mechanism of membrane disruption for the Aß-induced membrane fragmentation process.


Asunto(s)
Péptidos beta-Amiloides , Péptidos beta-Amiloides/química , Péptidos beta-Amiloides/metabolismo , Liposomas/química , Liposomas/metabolismo , Agregado de Proteínas/efectos de los fármacos , Agua/química , Membrana Celular/metabolismo , Membrana Celular/química
13.
Science ; 384(6700): 1091-1095, 2024 Jun 07.
Artículo en Inglés | MEDLINE | ID: mdl-38843321

RESUMEN

Successive cleavages of amyloid precursor protein C-terminal fragment with 99 residues (APP-C99) by γ-secretase result in amyloid-ß (Aß) peptides of varying lengths. Most cleavages have a step size of three residues. To elucidate the underlying mechanism, we determined the atomic structures of human γ-secretase bound individually to APP-C99, Aß49, Aß46, and Aß43. In all cases, the substrate displays the same structural features: a transmembrane α-helix, a three-residue linker, and a ß-strand that forms a hybrid ß-sheet with presenilin 1 (PS1). Proteolytic cleavage occurs just ahead of the substrate ß-strand. Each cleavage is followed by unwinding and translocation of the substrate α-helix by one turn and the formation of a new ß-strand. This mechanism is consistent with existing biochemical data and may explain the cleavages of other substrates by γ-secretase.


Asunto(s)
Secretasas de la Proteína Precursora del Amiloide , Péptidos beta-Amiloides , Precursor de Proteína beta-Amiloide , Presenilina-1 , Humanos , Péptidos beta-Amiloides/química , Precursor de Proteína beta-Amiloide/química , Secretasas de la Proteína Precursora del Amiloide/química , Cristalografía por Rayos X , Modelos Moleculares , Fragmentos de Péptidos/metabolismo , Fragmentos de Péptidos/química , Presenilina-1/química , Conformación Proteica en Hélice alfa , Conformación Proteica en Lámina beta , Proteolisis , Especificidad por Sustrato
14.
Biomolecules ; 14(6)2024 May 23.
Artículo en Inglés | MEDLINE | ID: mdl-38927020

RESUMEN

Deposition of extracellular Amyloid Beta (Aß) and intracellular tau fibrils in post-mortem brains remains the only way to conclusively confirm cases of Alzheimer's Disease (AD). Substantial evidence, though, implicates small globular oligomers instead of fibrils as relevant biomarkers of, and critical contributors to, the clinical symptoms of AD. Efforts to verify and utilize amyloid oligomers as AD biomarkers in vivo have been limited by the near-exclusive dependence on conformation-selective antibodies for oligomer detection. While antibodies have yielded critical evidence for the role of both Aß and tau oligomers in AD, they are not suitable for imaging amyloid oligomers in vivo. Therefore, it would be desirable to identify a set of oligomer-selective small molecules for subsequent development into Positron Emission Tomography (PET) probes. Using a kinetics-based screening assay, we confirm that the triarylmethane dye Crystal Violet (CV) is oligomer-selective for Aß42 oligomers (AßOs) grown under near-physiological solution conditions in vitro. In postmortem brains of an AD mouse model and human AD patients, we demonstrate that A11 antibody-positive oligomers but not Thioflavin S (ThioS)-positive fibrils colocalize with CV staining, confirming in vitro results. Therefore, our kinetic screen represents a robust approach for identifying new classes of small molecules as candidates for oligomer-selective dyes (OSDs). Such OSDs, in turn, provide promising starting points for the development of PET probes for pre-mortem imaging of oligomer deposits in humans.


Asunto(s)
Enfermedad de Alzheimer , Péptidos beta-Amiloides , Encéfalo , Violeta de Genciana , Enfermedad de Alzheimer/diagnóstico por imagen , Enfermedad de Alzheimer/metabolismo , Enfermedad de Alzheimer/patología , Péptidos beta-Amiloides/metabolismo , Péptidos beta-Amiloides/química , Humanos , Animales , Encéfalo/diagnóstico por imagen , Encéfalo/metabolismo , Encéfalo/patología , Ratones , Violeta de Genciana/química , Amiloide/metabolismo , Amiloide/química , Tomografía de Emisión de Positrones , Femenino
15.
Int J Mol Sci ; 25(12)2024 Jun 10.
Artículo en Inglés | MEDLINE | ID: mdl-38928107

RESUMEN

Aß peptides are known to bind neural plasma membranes in a process leading to the deposit of Aß-enriched plaques. These extracellular structures are characteristic of Alzheimer's disease, the major cause of late-age dementia. The mechanisms of Aß plaque formation and deposition are far from being understood. A vast number of studies in the literature describe the efforts to analyze those mechanisms using a variety of tools. The present review focuses on biophysical studies mostly carried out with model membranes or with computational tools. This review starts by describing basic physical aspects of lipid phases and commonly used model membranes (monolayers and bilayers). This is followed by a discussion of the biophysical techniques applied to these systems, mainly but not exclusively Langmuir monolayers, isothermal calorimetry, density-gradient ultracentrifugation, and molecular dynamics. The Methodological Section is followed by the core of the review, which includes a summary of important results obtained with each technique. The last section is devoted to an overall reflection and an effort to understand Aß-bilayer binding. Concepts such as Aß peptide membrane binding, adsorption, and insertion are defined and differentiated. The roles of membrane lipid order, nanodomain formation, and electrostatic forces in Aß-membrane interaction are separately identified and discussed.


Asunto(s)
Péptidos beta-Amiloides , Membrana Dobles de Lípidos , Lípidos de la Membrana , Péptidos beta-Amiloides/metabolismo , Péptidos beta-Amiloides/química , Humanos , Membrana Dobles de Lípidos/metabolismo , Membrana Dobles de Lípidos/química , Lípidos de la Membrana/metabolismo , Lípidos de la Membrana/química , Unión Proteica , Membrana Celular/metabolismo , Enfermedad de Alzheimer/metabolismo , Animales , Fenómenos Biofísicos , Simulación de Dinámica Molecular
16.
Int J Mol Sci ; 25(12)2024 Jun 18.
Artículo en Inglés | MEDLINE | ID: mdl-38928405

RESUMEN

Intrinsically disordered proteins (IDPs) pose challenges to conventional experimental techniques due to their large-scale conformational fluctuations and transient structural elements. This work presents computational methods for studying IDPs at various resolutions using the Amber and Gromacs packages with both all-atom (Amber ff19SB with the OPC water model) and coarse-grained (Martini 3 and SIRAH) approaches. The effectiveness of these methodologies is demonstrated by examining the monomeric form of amyloid-ß (Aß42), an IDP, with and without disulfide bonds at different resolutions. Our results clearly show that the addition of a disulfide bond decreases the ß-content of Aß42; however, it increases the tendency of the monomeric Aß42 to form fibril-like conformations, explaining the various aggregation rates observed in experiments. Moreover, analysis of the monomeric Aß42 compactness, secondary structure content, and comparison between calculated and experimental chemical shifts demonstrates that all three methods provide a reasonable choice to study IDPs; however, coarse-grained approaches may lack some atomistic details, such as secondary structure recognition, due to the simplifications used. In general, this study not only explains the role of disulfide bonds in Aß42 but also provides a step-by-step protocol for setting up, conducting, and analyzing molecular dynamics (MD) simulations, which is adaptable for studying other biomacromolecules, including folded and disordered proteins and peptides.


Asunto(s)
Péptidos beta-Amiloides , Disulfuros , Proteínas Intrínsecamente Desordenadas , Simulación de Dinámica Molecular , Péptidos beta-Amiloides/química , Péptidos beta-Amiloides/metabolismo , Disulfuros/química , Proteínas Intrínsecamente Desordenadas/química , Humanos , Estructura Secundaria de Proteína , Fragmentos de Péptidos/química , Conformación Proteica
17.
J Mol Model ; 30(7): 233, 2024 Jun 28.
Artículo en Inglés | MEDLINE | ID: mdl-38937296

RESUMEN

CONTEXT: Existing researches confirmed that ß amyloid (Aß) has a high affinity for the α7 nicotinic acetylcholine receptor (α7nAChR), associating closely to Alzheimer's disease. The majority of related studies focused on the experimental reports on the neuroprotective role of Aß fragment (Aßx), however, with a lack of investigation into the most suitable binding region and mechanism of action between Aß fragment and α7nAChR. In the study, we employed four Aß1-42 fragments Aßx, Aß1-16, Aß10-16, Aß12-28, and Aß30-42, of which the first three were confirmed to play neuroprotective roles upon directly binding, to interact with α7nAChR. METHODS: The protein-ligand docking server of CABS-DOCK was employed to obtain the α7nAChR-Aßx complexes. Only the top α7nAChR-Aßx complexes were used to perform all-atom GROMACS dynamics simulation in combination with Charmm36 force field, by which α7nAChR-Aßx interactions' dynamic behavior and specific locations of these different Aßx fragments were identified. MM-PBSA calculations were also done to estimate the binding free energies and the different contributions from the residues in the Aßx. Two distinct results for the first three and fourth Aßx fragments in binding site, strength, key residue, and orientation, account for why the fourth fails to play a neuroprotective role at the molecular level.


Asunto(s)
Péptidos beta-Amiloides , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , Fragmentos de Péptidos , Unión Proteica , Receptor Nicotínico de Acetilcolina alfa 7 , Péptidos beta-Amiloides/química , Péptidos beta-Amiloides/metabolismo , Receptor Nicotínico de Acetilcolina alfa 7/química , Receptor Nicotínico de Acetilcolina alfa 7/metabolismo , Fragmentos de Péptidos/química , Fragmentos de Péptidos/metabolismo , Humanos , Sitios de Unión , Ligandos
18.
Talanta ; 277: 126362, 2024 Sep 01.
Artículo en Inglés | MEDLINE | ID: mdl-38843773

RESUMEN

Alzheimer's disease (AD), gradually recognized as an untreatable neurodegenerative disorder, has been considered to be closely associated with Aß plaques, which consist of ß-amyloid protein (Aß) and is one of the crucial pathological features of AD. There are no obvious symptoms in the initial phase of AD, and thus the therapeutic interventions are important for early diagnosis of AD. Moreover, recent researches have indicated that lipid droplets might serve as a potential ancillary biomarker, and its viscosity changes are closely associated to the pathological process of AD. Herein, two newly fluorescent probes 5QSZ and BQSZ have been developed and synthesized for identifying Aß aggregates and detecting the viscosity of lipid droplet. After selectively binding to Aß aggregates, 5QSZ and BQSZ exhibited linear and obvious fluorescence enhancements (32.58 and 36.70 folds), moderate affinity (Kd = 268.0 and 148.6 nM) and low detection limits (30.11 and 65.37 nM) in aqueous solutions. Further fluorescence staining of 5QSZ on brain tissue sections of APP/PS1 transgenic mouse exhibited the higher selectivity of 5QSZ towards Aß aggregates locating at the core of the plaques. Furthermore, 5QSZ and BQSZ displayed strong linear fluorescence emission enhancements towards viscosity changes and would be utilized to monitor variation in cellular viscosity induced by LPS or monensin. These two probes were non-cytotoxic and showed good localization in lipid droplets. Therefore, 5QSZ and BQSZ could serve as potential bi-functional fluorescent probes to image Aß aggregates and monitor the viscosity of lipid droplets, which have significant implications for the early diagnosis and progression of AD.


Asunto(s)
Péptidos beta-Amiloides , Compuestos de Boro , Colorantes Fluorescentes , Gotas Lipídicas , Agregado de Proteínas , Colorantes Fluorescentes/química , Colorantes Fluorescentes/síntesis química , Viscosidad , Compuestos de Boro/química , Compuestos de Boro/síntesis química , Animales , Gotas Lipídicas/química , Gotas Lipídicas/metabolismo , Péptidos beta-Amiloides/análisis , Péptidos beta-Amiloides/metabolismo , Péptidos beta-Amiloides/química , Ratones , Humanos , Ratones Transgénicos , Enfermedad de Alzheimer/metabolismo , Enfermedad de Alzheimer/diagnóstico , Enfermedad de Alzheimer/diagnóstico por imagen , Imagen Óptica
19.
Anal Chem ; 96(28): 11397-11403, 2024 Jul 16.
Artículo en Inglés | MEDLINE | ID: mdl-38940533

RESUMEN

Low-mass soluble ß-amyloid peptide oligomers (LSAßOs) play a crucial role in the pathogenesis of Alzheimer's disease. However, these oligomers exhibit heterogeneity in terms of structure, stability, and stoichiometry, and their abundance in biofluids is low, making accurate identification challenging. In this study, we developed a DNA nanocage-assisted method for selective sizing and sensitive quantification of LSAßOs in serum. Using LSAßO less than 10 kDa (LSAßO10kD) and less than 30 kDa (LSAßO30kD) as models, the size-matching rules between DNA nanocages and LSAßOs were investigated, and two appropriate nanocages were selected for the detection of two LSAßOs, respectively. Both nanocages were functionalized by encapsulating oligomer's aptamer and a complementary sequence within their cavities. Once the LSAßO entered the corresponding nanocage cavity, the complementary sequence was released, triggering a hybridization chain reaction on an electrochemical sensing platform. The system achieved size-selective discrimination of LSAßO10kD with a linear range of 10-150 pM and LSAßO30kD with a linear range of 15-150 pM. Real sample testing confirmed the applicability of the method for blood-based diagnosis. The DNA nanocage-assisted electrochemical analysis platform provides an accurate, highly selective, and sensitive approach for oligomer analysis, which is significant for amyloid protein research and related disease diagnosis.


Asunto(s)
Péptidos beta-Amiloides , ADN , Péptidos beta-Amiloides/análisis , Péptidos beta-Amiloides/sangre , Péptidos beta-Amiloides/química , ADN/química , Humanos , Nanoestructuras/química , Tamaño de la Partícula , Técnicas Electroquímicas/métodos , Enfermedad de Alzheimer/diagnóstico , Enfermedad de Alzheimer/metabolismo , Enfermedad de Alzheimer/sangre , Técnicas Biosensibles/métodos , Solubilidad , Aptámeros de Nucleótidos/química , Peso Molecular
20.
J Chem Inf Model ; 64(13): 5303-5316, 2024 Jul 08.
Artículo en Inglés | MEDLINE | ID: mdl-38921060

RESUMEN

The coexistence of amyloid-ß (Aß) and human islet amyloid polypeptide (hIAPP) in the brain and pancreas is associated with an increased risk of Alzheimer's disease (AD) and type 2 diabetes (T2D) due to their coaggregation and cross-seeding. Despite this, the molecular mechanisms underlying their interaction remain elusive. Here, we systematically investigated the cross-talk between Aß and hIAPP using atomistic discrete molecular dynamics (DMD) simulations. Our results revealed that the amyloidogenic core regions of both Aß (Aß10-21 and Aß30-41) and hIAPP (hIAPP8-20 and hIAPP22-29), driving their self-aggregation, also exhibited a strong tendency for cross-interaction. This propensity led to the formation of ß-sheet-rich heterocomplexes, including potentially toxic ß-barrel oligomers. The formation of Aß and hIAPP heteroaggregates did not impede the recruitment of additional peptides to grow into larger aggregates. Our cross-seeding simulations demonstrated that both Aß and hIAPP fibrils could mutually act as seeds, assisting each other's monomers in converting into ß-sheets at the exposed fibril elongation ends. The amyloidogenic core regions of Aß and hIAPP, in both oligomeric and fibrillar states, exhibited the ability to recruit isolated peptides, thereby extending the ß-sheet edges, with limited sensitivity to the amino acid sequence. These findings suggest that targeting these regions by capping them with amyloid-resistant peptide drugs may hold potential as a therapeutic approach for addressing AD, T2D, and their copathologies.


Asunto(s)
Enfermedad de Alzheimer , Péptidos beta-Amiloides , Diabetes Mellitus Tipo 2 , Polipéptido Amiloide de los Islotes Pancreáticos , Simulación de Dinámica Molecular , Enfermedad de Alzheimer/metabolismo , Diabetes Mellitus Tipo 2/metabolismo , Polipéptido Amiloide de los Islotes Pancreáticos/química , Polipéptido Amiloide de los Islotes Pancreáticos/metabolismo , Humanos , Péptidos beta-Amiloides/metabolismo , Péptidos beta-Amiloides/química , Agregado de Proteínas
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