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1.
Science ; 384(6700): 1091-1095, 2024 Jun 07.
Article in English | MEDLINE | ID: mdl-38843321

ABSTRACT

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.


Subject(s)
Amyloid Precursor Protein Secretases , Amyloid beta-Peptides , Amyloid beta-Protein Precursor , Presenilin-1 , Humans , Amyloid Precursor Protein Secretases/metabolism , Amyloid Precursor Protein Secretases/chemistry , Amyloid beta-Protein Precursor/metabolism , Amyloid beta-Protein Precursor/chemistry , Substrate Specificity , Presenilin-1/chemistry , Presenilin-1/metabolism , Amyloid beta-Peptides/metabolism , Amyloid beta-Peptides/chemistry , Proteolysis , Peptide Fragments/metabolism , Peptide Fragments/chemistry , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Crystallography, X-Ray , Models, Molecular
2.
Protein Sci ; 33(6): e5008, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38723181

ABSTRACT

One of the most important attributes of anti-amyloid antibodies is their selective binding to oligomeric and amyloid aggregates. However, current methods of examining the binding specificities of anti-amyloid ß (Aß) antibodies have limited ability to differentiate between complexes that form between antibodies and monomeric or oligomeric Aß species during the dynamic Aß aggregation process. Here, we present a high-resolution native ion-mobility mass spectrometry (nIM-MS) method to investigate complexes formed between a variety of Aß oligomers and three Aß-specific IgGs, namely two antibodies with relatively high conformational specificity (aducanumab and A34) and one antibody with low conformational specificity (crenezumab). We found that crenezumab primarily binds Aß monomers, while aducanumab preferentially binds Aß monomers and dimers and A34 preferentially binds Aß dimers, trimers, and tetrameters. Through collision induced unfolding (CIU) analysis, our data indicate that antibody stability is increased upon Aß binding and, surprisingly, this stabilization involves the Fc region. Together, we conclude that nIM-MS and CIU enable the identification of Aß antibody binding stoichiometries and provide important details regarding antibody binding mechanisms.


Subject(s)
Amyloid beta-Peptides , Antibodies, Monoclonal, Humanized , Ion Mobility Spectrometry , Amyloid beta-Peptides/chemistry , Amyloid beta-Peptides/immunology , Amyloid beta-Peptides/metabolism , Antibodies, Monoclonal, Humanized/chemistry , Antibodies, Monoclonal, Humanized/immunology , Antibodies, Monoclonal, Humanized/metabolism , Ion Mobility Spectrometry/methods , Humans , Mass Spectrometry/methods , Protein Binding , Antibodies, Monoclonal/chemistry , Antibodies, Monoclonal/immunology , Protein Multimerization
3.
Biomolecules ; 14(5)2024 May 15.
Article in English | MEDLINE | ID: mdl-38785993

ABSTRACT

Despite the extensive research conducted on Alzheimer's disease (AD) over the years, no effective drug for AD treatment has been found. Therefore, the development of new drugs for the treatment of AD is of the utmost importance. We recently reported the proteolytic activities of JAL-TA9 (YKGSGFRMI) and ANA-TA9 (SKGQAYRMA), synthetic peptides of nine amino acids each, derived from the Box A region of Tob1 and ANA/BTG3 proteins, respectively. Furthermore, two components of ANA-TA9, ANA-YA4 (YRMI) at the C-terminus end and ANA-SA5 (SKGQA) at the N-terminus end of ANA-TA9, exhibited proteolytic activity against amyloid-ß (Aß) fragment peptides. In this study, we identified the active center of ANA-SA5 using AEBSF, a serine protease inhibitor, and a peptide in which the Ser residue of ANA-SA5 was replaced with Leu. In addition, we demonstrate the proteolytic activity of ANA-SA5 against the soluble form Aß42 (a-Aß42) and solid insoluble form s-Aß42. Furthermore, ANA-SA5 was not cytotoxic to A549 cells. These results indicate that ANA-SA5 is a promising Catalytide and a potential candidate for the development of new peptide drugs targeting Aß42 for AD treatment.


Subject(s)
Amyloid beta-Peptides , Proteolysis , Amyloid beta-Peptides/metabolism , Amyloid beta-Peptides/chemistry , Humans , Proteolysis/drug effects , Alzheimer Disease/drug therapy , Alzheimer Disease/metabolism , Peptide Fragments/chemistry , Peptide Fragments/pharmacology , Peptide Fragments/metabolism , Peptides/chemistry , Peptides/pharmacology , Cell Line, Tumor
4.
Int J Mol Sci ; 25(9)2024 May 02.
Article in English | MEDLINE | ID: mdl-38732194

ABSTRACT

An imbalance between production and excretion of amyloid ß peptide (Aß) in the brain tissues of Alzheimer's disease (AD) patients leads to Aß accumulation and the formation of noxious Aß oligomers/plaques. A promising approach to AD prevention is the reduction of free Aß levels by directed enhancement of Aß binding to its natural depot, human serum albumin (HSA). We previously demonstrated the ability of specific low-molecular-weight ligands (LMWLs) in HSA to improve its affinity for Aß. Here we develop this approach through a bioinformatic search for the clinically approved AD-related LMWLs in HSA, followed by classification of the candidates according to the predicted location of their binding sites on the HSA surface, ranking of the candidates, and selective experimental validation of their impact on HSA affinity for Aß. The top 100 candidate LMWLs were classified into five clusters. The specific representatives of the different clusters exhibit dramatically different behavior, with 3- to 13-fold changes in equilibrium dissociation constants for the HSA-Aß40 interaction: prednisone favors HSA-Aß interaction, mefenamic acid shows the opposite effect, and levothyroxine exhibits bidirectional effects. Overall, the LMWLs in HSA chosen here provide a basis for drug repurposing for AD prevention, and for the search of medications promoting AD progression.


Subject(s)
Alzheimer Disease , Amyloid beta-Peptides , Protein Binding , Serum Albumin, Human , Humans , Amyloid beta-Peptides/metabolism , Amyloid beta-Peptides/chemistry , Ligands , Serum Albumin, Human/metabolism , Serum Albumin, Human/chemistry , Alzheimer Disease/metabolism , Molecular Weight , Binding Sites , Peptide Fragments/metabolism , Peptide Fragments/chemistry
5.
J Phys Chem B ; 128(19): 4655-4669, 2024 May 16.
Article in English | MEDLINE | ID: mdl-38700150

ABSTRACT

Protein misfolding, aggregation, and fibril formation play a central role in the development of severe neurological disorders, including Alzheimer's and Parkinson's diseases. The structural stability of mature fibrils in these diseases is of great importance, as organisms struggle to effectively eliminate amyloid plaques. To address this issue, it is crucial to investigate the early stages of fibril formation when monomers aggregate into small, toxic, and soluble oligomers. However, these structures are inherently disordered, making them challenging to study through experimental approaches. Recently, it has been shown experimentally that amyloid-ß 42 (Aß42) and α-synuclein (α-Syn) can coassemble. This has motivated us to investigate the interaction between their monomers as a first step toward exploring the possibility of forming heterodimeric complexes. In particular, our study involves the utilization of various Amber and CHARMM force-fields, employing both implicit and explicit solvent models in replica exchange and conventional simulation modes. This comprehensive approach allowed us to assess the strengths and weaknesses of these solvent models and force fields in comparison to experimental and theoretical findings, ensuring the highest level of robustness. Our investigations revealed that Aß42 and α-Syn monomers can indeed form stable heterodimers, and the resulting heterodimeric model exhibits stronger interactions compared to the Aß42 dimer. The binding of α-Syn to Aß42 reduces the propensity of Aß42 to adopt fibril-prone conformations and induces significant changes in its conformational properties. Notably, in AMBER-FB15 and CHARMM36m force fields with the use of explicit solvent, the presence of Aß42 significantly increases the ß-content of α-Syn, consistent with the experiments showing that Aß42 triggers α-Syn aggregation. Our analysis clearly shows that although the use of implicit solvent resulted in too large compactness of monomeric α-Syn, structural properties of monomeric Aß42 and the heterodimer were preserved in explicit-solvent simulations. We anticipate that our study sheds light on the interaction between α-Syn and Aß42 proteins, thus providing the atom-level model required to assess the initial stage of aggregation mechanisms related to Alzheimer's and Parkinson's diseases.


Subject(s)
Amyloid beta-Peptides , Molecular Dynamics Simulation , Peptide Fragments , Solvents , alpha-Synuclein , Amyloid beta-Peptides/chemistry , Amyloid beta-Peptides/metabolism , alpha-Synuclein/chemistry , alpha-Synuclein/metabolism , Solvents/chemistry , Peptide Fragments/chemistry , Peptide Fragments/metabolism , Protein Multimerization , Humans
6.
Inorg Chem ; 63(21): 10001-10010, 2024 May 27.
Article in English | MEDLINE | ID: mdl-38742626

ABSTRACT

There is a growing interest in the search for metal-based therapeutics for protein misfolding disorders such as Alzheimer's disease (AD). A novel and largely unexplored class of metallodrugs is constituted by paddlewheel diruthenium complexes, which exhibit unusual water solubility and stability and unique coordination modes to proteins. Here, we investigate the ability of the complexes [Ru2Cl(DPhF)(O2CCH3)3]·H2O (1), [Ru2Cl(DPhF)2(O2CCH3)2]·H2O (2), and K2[Ru2(DPhF)(CO3)3]·3H2O (3) (DPhF- = N,N'-diphenylformamidinate) to interfere with the amyloid aggregation of the Aß1-42 peptide. These compounds differ in charge and steric hindrance due to the coordination of a different number of bulky ligands. The mechanisms of action of the three complexes were studied by employing a plethora of physicochemical and biophysical techniques as well as cellular assays. All these studies converge on different mechanisms of inhibition of amyloid fibrillation: complexes 1 and 2 show a clear inhibitory effect due to an exchange ligand process in the Ru2 unit aided by aromatic interactions. Complex 3 shows no inhibition of aggregation, probably due to its negative charge in solution. This study demonstrates that slight variations in the ligands surrounding the bimetallic core can modulate the amyloid aggregation inhibition and supports the use of paddlewheel diruthenium complexes as promising therapeutics for Alzheimer's disease.


Subject(s)
Amyloid beta-Peptides , Coordination Complexes , Peptide Fragments , Ruthenium , Amyloid beta-Peptides/antagonists & inhibitors , Amyloid beta-Peptides/metabolism , Amyloid beta-Peptides/chemistry , Ruthenium/chemistry , Ruthenium/pharmacology , Coordination Complexes/chemistry , Coordination Complexes/pharmacology , Coordination Complexes/chemical synthesis , Peptide Fragments/chemistry , Peptide Fragments/antagonists & inhibitors , Peptide Fragments/metabolism , Humans , Protein Aggregates/drug effects , Molecular Structure , Alzheimer Disease/drug therapy , Alzheimer Disease/metabolism
7.
Biosens Bioelectron ; 259: 116405, 2024 Sep 01.
Article in English | MEDLINE | ID: mdl-38776801

ABSTRACT

Alzheimer's disease (AD) is affecting more and more people worldwide without the effective treatment, while the existed pathological mechanism has been confirmed barely useful in the treatment. Amyloid-ß peptide (Aß), a main component of senile plaque, is regarded as the most promising target in AD treatment. Aß clearance from AD brain seems to be a reliably therapeutic strategy, as the two exited drugs, GV-971 and aducanumab, are both developed based on it. However, doubt still exists. To exhaustive expound on the pathological mechanism of Aß, rigorous analyses on the concentrations and aggregation forms are essential. Thus, it is attracting broad attention these years. However, most of the sensors have not been used in pathological studies, as the lack of the bridge between analytical chemist and pathologists. In this review, we made a brief introduce on Aß-related pathological mechanism included in ß-amyloid hypothesis to elucidate the detection conditions of sensor methods. Furthermore, a summary of the sensor methods was made, which were based on Aß concentrations and form detections that have been developed in the past 10 years. As the greatest number of the sensors were built on fluorescent spectroscopy, electrochemistry, and Roman spectroscopy, detailed elucidation on them was made. Notably, the aggregation process is another important factor in revealing the progress of AD and developing the treatment methods, so the sensors on monitoring Aß aggregation processes were also summarized.


Subject(s)
Alzheimer Disease , Amyloid beta-Peptides , Biosensing Techniques , Amyloid beta-Peptides/analysis , Amyloid beta-Peptides/metabolism , Amyloid beta-Peptides/chemistry , Humans , Biosensing Techniques/methods , Alzheimer Disease/metabolism , Alzheimer Disease/pathology , Animals , Spectrometry, Fluorescence/methods , Electrochemical Techniques/methods , Antibodies, Monoclonal, Humanized
8.
ACS Appl Mater Interfaces ; 16(21): 27127-27138, 2024 May 29.
Article in English | MEDLINE | ID: mdl-38747495

ABSTRACT

The excessive depositions of ß-amyloid (Aß) and abnormal level of reactive oxygen species (ROS) are considered as the important pathogenic factors of Alzheimer's disease (AD). Strategies targeting only one of them have no obvious effects in clinic. In this study, a multifunctional nanocarrier CICe@M-K that crosses the blood-brain barrier (BBB) efficiently was developed for inhibiting Aß aggregation and scavenging ROS synchronously. Antioxidant curcumin (Cur) and photosensitizer IR780 were loaded in mesoporous silica nanomaterials (MSNs). Their surfaces were grafted with cerium oxide nanoparticles (CeO2 NPs) and a short peptide K (CKLVFFAED). Living imaging showed that CICe@M-K was mainly distributed in the brain, liver, and kidneys, indicating CICe@M-K crossed BBB efficiently and accumulated in brain. After the irradiation of 808 nm laser, Cur was continuously released. Both of Cur and the peptide K can recognize and bind to Aß through multiple interaction including π-π stacking interaction, hydrophobic interaction, and hydrogen bond, inhibiting Aß aggregation. On the other hand, Cur and CeO2 NPs cooperate to relieve the oxidative stress in the brains by scavenging ROS. In vivo assays showed that the CICe@M-K could diminish Aß depositions, alleviate oxidative stress, and improve cognitive ability of the APP/PS1 AD mouse model, which demonstrated that CICe@M-K is a potential agent for AD treatment.


Subject(s)
Alzheimer Disease , Amyloid beta-Peptides , Curcumin , Reactive Oxygen Species , Alzheimer Disease/drug therapy , Alzheimer Disease/metabolism , Alzheimer Disease/pathology , Amyloid beta-Peptides/metabolism , Amyloid beta-Peptides/chemistry , Reactive Oxygen Species/metabolism , Animals , Mice , Curcumin/chemistry , Curcumin/pharmacology , Drug Carriers/chemistry , Blood-Brain Barrier/metabolism , Blood-Brain Barrier/drug effects , Cerium/chemistry , Cerium/pharmacology , Humans , Antioxidants/chemistry , Antioxidants/pharmacology , Nanoparticles/chemistry , Multifunctional Nanoparticles/chemistry , Silicon Dioxide/chemistry , Photosensitizing Agents/chemistry , Photosensitizing Agents/pharmacology , Photosensitizing Agents/therapeutic use
9.
Dalton Trans ; 53(21): 9001-9010, 2024 May 28.
Article in English | MEDLINE | ID: mdl-38726661

ABSTRACT

Cyclometallated Pt(II) complexes possessing hydrophobic 2-phenylpyridine (ppy) ligands and hydrophilic acetonylacetone (acac) ligands have been investigated for their ability to detect amyloid fibrils via luminescence response. Using hen egg-white lysozyme (HEWL) as a model amyloid protein, Pt(II) complexes featuring benzanilide-substituted ppy ligands and ethylene glycol-functionalized acac ligands demonstrated enhanced luminescence in the presence of HEWL fibrils, whereas Pt(II) complexes lacking complementary hydrophobic/hydrophilic ligand sets displayed little to no emission enhancement. An amphiphilic Pt(II) complex incorporating a bis(ethylene glycol)-derivatized acac ligand was additionally found to trigger restructuring of HEWL fibrils into smaller spherical aggregates. Amphiphilic Pt(II) complexes were generally non-toxic to SH-SY5Y neuroblastoma cells, and several complexes also exhibited enhanced luminescence in the presence of Aß42 fibrils associated with Alzheimer's disease. This study demonstrates that easily prepared and robust (ppy)PtII(acac) complexes show promising reactivity toward amyloid fibrils and represent attractive molecular scaffolds for design of small-molecule probes targeting amyloid assemblies.


Subject(s)
Amyloid , Muramidase , Humans , Amyloid/chemistry , Amyloid/metabolism , Muramidase/chemistry , Muramidase/metabolism , Cell Line, Tumor , Coordination Complexes/chemistry , Coordination Complexes/chemical synthesis , Luminescence , Amyloid beta-Peptides/metabolism , Amyloid beta-Peptides/chemistry , Animals , Hydrophobic and Hydrophilic Interactions , Protein Aggregates/drug effects , Platinum/chemistry , Organoplatinum Compounds/chemistry , Organoplatinum Compounds/pharmacology , Organoplatinum Compounds/chemical synthesis , Ligands , Surface-Active Agents/chemistry , Surface-Active Agents/chemical synthesis
10.
Phys Chem Chem Phys ; 26(20): 14664-14674, 2024 May 22.
Article in English | MEDLINE | ID: mdl-38715538

ABSTRACT

Amyloid fibrils have been implicated in the pathogenesis of several neurodegenerative diseases, the most prevalent example being Alzheimer's disease (AD). Despite the prevalence of AD, relatively little is known about the structure of the associated amyloid fibrils. This has motivated our studies of fibril structures, extended here to the familial Arctic mutant of Aß1-42, E22G-Aß1-42. We found E22G-AßM0,1-42 is toxic to Escherichia coli, thus we expressed E22G-Aß1-42 fused to the self-cleavable tag NPro in the form of its EDDIE mutant. Since the high surface activity of E22G-Aß1-42 makes it difficult to obtain more than sparse quantities of fibrils, we employed 1H detected magic angle spinning (MAS) nuclear magnetic resonance (NMR) experiments to characterize the protein. The 1H detected 13C-13C methods were first validated by application to fully protonated amyloidogenic nanocrystals of GNNQQNY, and then applied to fibrils of the Arctic mutant of Aß, E22G-Aß1-42. The MAS NMR spectra indicate that the biosynthetic samples of E22G-Aß1-42 fibrils comprise a single conformation with 13C chemical shifts extracted from hCH, hNH, and hCCH spectra that are very similar to those of wild type Aß1-42 fibrils. These results suggest that E22G-Aß1-42 fibrils have a structure similar to that of wild type Aß1-42.


Subject(s)
Amyloid beta-Peptides , Peptide Fragments , Amyloid beta-Peptides/chemistry , Amyloid beta-Peptides/genetics , Amyloid beta-Peptides/metabolism , Peptide Fragments/chemistry , Peptide Fragments/genetics , Peptide Fragments/metabolism , Amyloid/chemistry , Amyloid/metabolism , Nuclear Magnetic Resonance, Biomolecular , Escherichia coli/genetics , Escherichia coli/metabolism , Mutation , Humans
11.
J Am Soc Mass Spectrom ; 35(6): 1310-1319, 2024 Jun 05.
Article in English | MEDLINE | ID: mdl-38780475

ABSTRACT

The accumulation of amyloid beta (Aß1-42) results in neurotoxicity and is strongly related to neurodegenerative disorders, especially Alzheimer's disease (AD), but the underlying molecular mechanism is still poorly understood. Therefore, there is an urgent need for researchers to discover the proteins that interact with Aß1-42 to determine the molecular basis. Previously, we developed peptide-ligand-induced changes in the abundance of proTeinS (PACTS)-assisted thermal proteome profiling (TPP) to identify proteins that interact with peptide ligands. In the present study, we applied this technique to analyze clinical samples to identify Aß1-42-interacting proteins. We detected 115 proteins that interact with Aß1-42 in human frontal lobe tissue. Pathway enrichment analysis revealed that the differentially expressed proteins were involved mainly in neurodegenerative diseases. Further orthogonal validation revealed that Aß1-42 interacted with the AD-associated protein mitogen-activated protein kinase 3 (MAPK3), and knockdown of the Aß1-42 amyloid precursor protein (APP) inhibited the MAPK signaling pathway, suggesting potential functional roles for Aß1-42 in interacting with MAPK3. Overall, this study demonstrated the application of the PACTS-TPP in clinical samples and provided a valuable data source for research on neurodegenerative diseases.


Subject(s)
Alzheimer Disease , Amyloid beta-Peptides , Peptide Fragments , Proteomics , Humans , Amyloid beta-Peptides/metabolism , Amyloid beta-Peptides/chemistry , Peptide Fragments/chemistry , Peptide Fragments/metabolism , Peptide Fragments/analysis , Proteomics/methods , Alzheimer Disease/metabolism , Proteome/analysis , Proteome/metabolism , Frontal Lobe/metabolism , Frontal Lobe/chemistry , Amyloid beta-Protein Precursor/metabolism , Amyloid beta-Protein Precursor/chemistry , Protein Binding
12.
ACS Chem Neurosci ; 15(11): 2296-2307, 2024 Jun 05.
Article in English | MEDLINE | ID: mdl-38785363

ABSTRACT

Oligomeric assemblies consisting of only a few protein subunits are key species in the cytotoxicity of neurodegenerative disorders, such as Alzheimer's and Parkinson's diseases. Their lifetime in solution and abundance, governed by the balance of their sources and sinks, are thus important determinants of disease. While significant advances have been made in elucidating the processes that govern oligomer production, the mechanisms behind their dissociation are still poorly understood. Here, we use chemical kinetic modeling to determine the fate of oligomers formed in vitro and discuss the implications for their abundance in vivo. We discover that oligomeric species formed predominantly on fibril surfaces, a broad class which includes the bulk of oligomers formed by the key Alzheimer's disease-associated Aß peptides, also dissociate overwhelmingly on fibril surfaces, not in solution as had previously been assumed. We monitor this "secondary nucleation in reverse" by measuring the dissociation of Aß42 oligomers in the presence and absence of fibrils via two distinct experimental methods. Our findings imply that drugs that bind fibril surfaces to inhibit oligomer formation may also inhibit their dissociation, with important implications for rational design of therapeutic strategies for Alzheimer's and other amyloid diseases.


Subject(s)
Amyloid beta-Peptides , Peptide Fragments , Amyloid beta-Peptides/metabolism , Amyloid beta-Peptides/chemistry , Humans , Peptide Fragments/chemistry , Peptide Fragments/metabolism , Amyloid/metabolism , Amyloid/chemistry , Alzheimer Disease/metabolism , Kinetics
13.
ACS Chem Neurosci ; 15(11): 2322-2333, 2024 Jun 05.
Article in English | MEDLINE | ID: mdl-38804618

ABSTRACT

Nicotinic acetylcholine receptors (nAChRs) are a family of ligand-gated ion channel receptors that contribute to cognition, memory, and motor control in many organisms. The pharmacological targeting of these receptors, using small molecules or peptides, presents an important strategy for the development of drugs that can treat important human diseases, including neurodegenerative disorders. The Aplysia californica acetylcholine binding protein (Ac-AChBP) is a structural surrogate of the nAChR with high homology to the extracellular ligand binding domain of homopentameric nAChRs. In this study, we optimized protein-painting-based mass spectrometry to identify regions of interaction between the Ac-AChBP and several nAChR ligands. Using molecular dyes that adhere to the surface of a solubilized Ac-AChBP complex, we identified amino acid residues that constitute a contact site within the Ac-AChBP for α-bungarotoxin, choline, nicotine, and amyloid-ß 1-42. By integrating innovation in protein painting mass spectrometry with computational structural modeling, we present a new experimental tool for analyzing protein interactions of the nAChR.


Subject(s)
Aplysia , Mass Spectrometry , Receptors, Nicotinic , Animals , Receptors, Nicotinic/metabolism , Receptors, Nicotinic/chemistry , Mass Spectrometry/methods , Binding Sites , Protein Binding/physiology , Carrier Proteins/metabolism , Bungarotoxins/pharmacology , Bungarotoxins/metabolism , Bungarotoxins/chemistry , Acetylcholine/metabolism , Amyloid beta-Peptides/metabolism , Amyloid beta-Peptides/chemistry , Models, Molecular
14.
Nat Commun ; 15(1): 4479, 2024 May 27.
Article in English | MEDLINE | ID: mdl-38802343

ABSTRACT

Deposition of amyloid-ß (Aß) peptides in the brain is a hallmark of Alzheimer's disease. Aßs are generated through sequential proteolysis of the amyloid precursor protein by the γ-secretase complexes (GSECs). Aß peptide length, modulated by the Presenilin (PSEN) and APH-1 subunits of GSEC, is critical for Alzheimer's pathogenesis. Despite high relevance, mechanistic understanding of the proteolysis of Aß, and its modulation by APH-1, remain incomplete. Here, we report cryo-EM structures of human GSEC (PSEN1/APH-1B) reconstituted into lipid nanodiscs in apo form and in complex with the intermediate Aß46 substrate without cross-linking. We find that three non-conserved and structurally divergent APH-1 regions establish contacts with PSEN1, and that substrate-binding induces concerted rearrangements in one of the identified PSEN1/APH-1 interfaces, providing structural basis for APH-1 allosteric-like effects. In addition, the GSEC-Aß46 structure reveals an interaction between Aß46 and loop 1PSEN1, and identifies three other H-bonding interactions that, according to functional validation, are required for substrate recognition and efficient sequential catalysis.


Subject(s)
Amyloid Precursor Protein Secretases , Amyloid beta-Peptides , Cryoelectron Microscopy , Membrane Proteins , Presenilin-1 , Humans , Amyloid Precursor Protein Secretases/metabolism , Amyloid Precursor Protein Secretases/chemistry , Presenilin-1/metabolism , Presenilin-1/chemistry , Presenilin-1/genetics , Amyloid beta-Peptides/metabolism , Amyloid beta-Peptides/chemistry , Membrane Proteins/metabolism , Membrane Proteins/chemistry , Endopeptidases/metabolism , Endopeptidases/chemistry , Amyloid beta-Protein Precursor/metabolism , Amyloid beta-Protein Precursor/chemistry , Protein Binding , Protein Isoforms/metabolism , Protein Isoforms/chemistry , Alzheimer Disease/metabolism , Peptide Fragments/metabolism , Peptide Fragments/chemistry , Peptide Hydrolases/metabolism , Peptide Hydrolases/chemistry , Models, Molecular , Proteolysis
15.
Methods Enzymol ; 697: 113-150, 2024.
Article in English | MEDLINE | ID: mdl-38816120

ABSTRACT

The self-assembly of proteins and peptides into ordered structures called amyloid fibrils is a hallmark of numerous diseases, impacting the brain, heart, and other organs. The structure of amyloid aggregates is central to their function and thus has been extensively studied. However, the structural heterogeneities between aggregates as they evolve throughout the aggregation pathway are still not well understood. Conventional biophysical spectroscopic methods are bulk techniques and only report on the average structural parameters. Understanding the structure of individual aggregate species in a heterogeneous ensemble necessitates spatial resolution on the length scale of the aggregates. Recent technological advances have led to augmentation of infrared (IR) spectroscopy with imaging modalities, wherein the photothermal response of the sample upon vibrational excitation is leveraged to provide spatial resolution beyond the diffraction limit. These combined approaches are ideally suited to map out the structural heterogeneity of amyloid ensembles. AFM-IR, which integrates IR spectroscopy with atomic force microscopy enables identification of the structural facets the oligomers and fibrils at individual aggregate level with nanoscale resolution. These capabilities can be extended to chemical mapping in diseased tissue specimens with submicron resolution using optical photothermal microscopy, which combines IR spectroscopy with optical imaging. This book chapter provides the basic premise of these novel techniques and provides the typical methodology for using these approaches for amyloid structure determination. Detailed procedures pertaining to sample preparation and data acquisition and analysis are discussed and the aggregation of the amyloid ß peptide is provided as a case study to provide the reader the experimental parameters necessary to use these techniques to complement their research efforts.


Subject(s)
Amyloid , Microscopy, Atomic Force , Spectrophotometry, Infrared , Humans , Spectrophotometry, Infrared/methods , Microscopy, Atomic Force/methods , Amyloid/chemistry , Protein Aggregates , Amyloid beta-Peptides/chemistry , Amyloid beta-Peptides/metabolism , Spectroscopy, Fourier Transform Infrared/methods , Animals
16.
Nanoscale ; 16(16): 8074-8089, 2024 Apr 25.
Article in English | MEDLINE | ID: mdl-38563405

ABSTRACT

Amyloid aggregation is implicated in the pathogenesis of various neurodegenerative disorders, such as Alzheimer's disease (AD) and Parkinson's disease (PD). It is critical to develop high-performance drugs to combat amyloid-related diseases. Most identified nanomaterials exhibit limited biocompatibility and therapeutic efficacy. In this work, we used a solvent-free carbonization process to prepare new photo-responsive carbon nanodots (CNDs). The surface of the CNDs is densely packed with chemical groups. CNDs with large, conjugated domains can interact with proteins through π-π stacking and hydrophobic interactions. Furthermore, CNDs possess the ability to generate singlet oxygen species (1O2) and can be used to oxidize amyloid. The hydrophobic interaction and photo-oxidation can both influence amyloid aggregation and disaggregation. Thioflavin T (ThT) fluorescence analysis and circular dichroism (CD) spectroscopy indicate that CNDs can block the transition of amyloid from an α-helix structure to a ß-sheet structure. CNDs demonstrate efficacy in alleviating cytotoxicity induced by Aß42 and exhibit promising blood-brain barrier (BBB) permeability. CNDs have small size, low biotoxicity, good fluorescence and photocatalytic properties, and provide new ideas for the diagnosis and treatment of amyloid-related diseases.


Subject(s)
Amyloid beta-Peptides , Carbon , Carbon/chemistry , Amyloid beta-Peptides/metabolism , Amyloid beta-Peptides/chemistry , Humans , Catalysis , Singlet Oxygen/metabolism , Singlet Oxygen/chemistry , Blood-Brain Barrier/metabolism , Animals , Protein Aggregates/drug effects , Quantum Dots/chemistry , Amyloid/chemistry , Amyloid/metabolism , Cell Survival/drug effects , Peptide Fragments/chemistry , Peptide Fragments/metabolism , Hydrophobic and Hydrophilic Interactions
17.
ACS Appl Mater Interfaces ; 16(15): 18268-18284, 2024 Apr 17.
Article in English | MEDLINE | ID: mdl-38564419

ABSTRACT

The essential amino acid histidine plays a central role in the manifestation of several metabolic processes, including protein synthesis, enzyme-catalysis, and key biomolecular interactions. However, excess accumulation of histidine causes histidinemia, which shows brain-related medical complications, and the molecular mechanism of such histidine-linked complications is largely unknown. Here, we show that histidine undergoes a self-assembly process, leading to the formation of amyloid-like cytotoxic and catalytically active nanofibers. The kinetics of histidine self-assembly was favored in the presence of Mg(II) and Co(II) ions. Molecular dynamics data showed that preferential noncovalent interactions dominated by H-bonds between histidine molecules facilitate the formation of histidine nanofibers. The histidine nanofibers induced amyloid cross-seeding reactions in several proteins and peptides including pathogenic Aß1-42 and brain extract components. Further, the histidine nanofibers exhibited oxidase activity and enhanced the oxidation of neurotransmitters. Cell-based studies confirmed the cellular internalization of histidine nanofibers in SH-SY5Y cells and subsequent cytotoxic effects through necrosis and apoptosis-mediated cell death. Since several complications including behavioral abnormality, developmental delay, and neurological disabilities are directly linked to abnormal accumulation of histidine, our findings provide a foundational understanding of the mechanism of histidine-related complications. Further, the ability of histidine nanofibers to catalyze amyloid seeding and oxidation reactions is equally important for both biological and materials science research.


Subject(s)
Nanofibers , Nanostructures , Neuroblastoma , Humans , Histidine , Peptides/chemistry , Nanofibers/chemistry , Amyloid/chemistry , Amyloid beta-Peptides/chemistry
18.
Phys Chem Chem Phys ; 26(15): 11880-11892, 2024 Apr 17.
Article in English | MEDLINE | ID: mdl-38568008

ABSTRACT

Recent experiments have revealed that adenosine triphosphate (ATP) suppresses the fibrillation of amyloid peptides - a process closely linked to neurodegenerative diseases such as Alzheimer's and Parkinson's. Apart from the adsorption of ATP onto amyloid peptides, the molecular understanding is still limited, leaving the underlying mechanism for the fibrillation suppression by ATP largely unclear, especially in regards to the molecular energetics. Here we provide an explanation at the molecular scale by quantifying the free energies using all-atom molecular dynamics simulations. We found that the changes of the free energies due to the addition of ATP lead to a significant equilibrium shift towards monomeric peptides in agreement with experiments. Despite ATP being a highly charged species, the decomposition of the free energies reveals that the van der Waals interactions with the peptide are decisive in determining the relative stabilization of the monomeric state. While the phosphate moiety exhibits strong electrostatic interactions, the compensation by the water solvent results in a minor, overall Coulomb contribution. Our quantitative analysis of the free energies identifies which intermolecular interactions are responsible for the suppression of the amyloid fibril formation by ATP and offers a promising method to analyze the roles of similarly complex cosolvents in aggregation processes.


Subject(s)
Amyloid , Peptides , Amyloid/chemistry , Peptides/chemistry , Water/chemistry , Entropy , Solvents/chemistry , Molecular Dynamics Simulation , Amyloidogenic Proteins , Amyloid beta-Peptides/chemistry , Peptide Fragments/chemistry
19.
Colloids Surf B Biointerfaces ; 238: 113907, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38608464

ABSTRACT

Multifunctional agents with therapeutic and diagnostic capabilities are imperative to the prevention of Alzheimer's disease (AD), which is considered due to abnormal aggregation and deposition of ß-amyloid protein (Aß) as well as oxidative stress. Herein, quercetin (Que)- and p-phenylenediamine (p-PD)-derived red emission carbon dots (CDs) synthesized via a one-step hydrothermal method were designed as a novel theranostic nano-agent for the multi-target treatment of AD. R-CD-75 with an optimized composition exhibited significant inhibition of Aß aggregation and rapid depolymerization of mature Aß fibrils (<4 h) at micromolar concentrations (2 and 5 µg/mL, respectively). Moreover, R-CD-75 potently scavenged reactive oxygen species and showed turned-on red fluorescence imaging of Aß plaques both in vitro and in vivo. In vitro assays proved that R-CD-75 significantly mitigated the Aß-induced cytotoxicity and enhanced the cultured cell viability from 74.9 % to 98.0 %, while in vivo studies demonstrated that R-CD-75 prolonged the lifespan of AD nematodes by over 50 % (from 13 to 20 d). Compared to the precursors Que and p-PD, R-CD-75 inherited some of their structures and functional groups, such as aromatic structures, phenolic hydroxyl and amino groups, which were considered to interact with Aß species through hydrogen bonding, electrostatic interactions, hydrophobic interactions, and π-π stacking, thus contributing to its effectiveness in its theranostic functions. This research has opened a new avenue to the development of potent theranostic agents by designing novel carbon dots.


Subject(s)
Alzheimer Disease , Amyloid beta-Peptides , Carbon , Quantum Dots , Quercetin , Theranostic Nanomedicine , Quercetin/chemistry , Quercetin/pharmacology , Amyloid beta-Peptides/metabolism , Amyloid beta-Peptides/antagonists & inhibitors , Amyloid beta-Peptides/chemistry , Alzheimer Disease/drug therapy , Alzheimer Disease/pathology , Alzheimer Disease/metabolism , Carbon/chemistry , Carbon/pharmacology , Quantum Dots/chemistry , Animals , Humans , Cell Survival/drug effects , Reactive Oxygen Species/metabolism , Caenorhabditis elegans/drug effects , Caenorhabditis elegans/metabolism , Particle Size
20.
Bioorg Med Chem ; 105: 117715, 2024 May 01.
Article in English | MEDLINE | ID: mdl-38615460

ABSTRACT

Amyloid-ß (Aß) oligomers are a cause of neurodegeneration in Alzheimer's disease (AD). These soluble aggregates of the Aß peptide have proven difficult to study due to their inherent metastability and heterogeneity. Strategies to isolate and stabilize homogenous Aß oligomer populations have emerged such as mutations, covalent cross-linking, and protein fusions. These strategies along with molecular dynamics simulations have provided a variety of proposed structures of Aß oligomers, many of which consist of molecules of Aß in ß-hairpin conformations. ß-Hairpins are intramolecular antiparallel ß-sheets composed of two ß-strands connected by a loop or turn. Three decades of research suggests that Aß peptides form several different ß-hairpin conformations, some of which are building blocks of toxic Aß oligomers. The insights from these studies are currently being used to design anti-Aß antibodies and vaccines to treat AD. Research suggests that antibody therapies designed to target oligomeric Aß may be more successful at treating AD than antibodies designed to target linear epitopes of Aß or fibrillar Aß. Aß ß-hairpins are good epitopes to use in antibody development to selectively target oligomeric Aß. This review summarizes the research on ß-hairpins in Aß peptides and discusses the relevance of this conformation in AD pathogenesis and drug development.


Subject(s)
Alzheimer Disease , Amyloid beta-Peptides , Alzheimer Disease/metabolism , Alzheimer Disease/drug therapy , Alzheimer Disease/pathology , Amyloid beta-Peptides/metabolism , Amyloid beta-Peptides/antagonists & inhibitors , Amyloid beta-Peptides/chemistry , Humans
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