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1.
Pharmacol Rev ; 75(2): 263-308, 2023 03.
Article in English | MEDLINE | ID: mdl-36549866

ABSTRACT

Lysine-selective molecular tweezers (MTs) are supramolecular host molecules displaying a remarkably broad spectrum of biologic activities. MTs act as inhibitors of the self-assembly and toxicity of amyloidogenic proteins using a unique mechanism. They destroy viral membranes and inhibit infection by enveloped viruses, such as HIV-1 and SARS-CoV-2, by mechanisms unrelated to their action on protein self-assembly. They also disrupt biofilm of Gram-positive bacteria. The efficacy and safety of MTs have been demonstrated in vitro, in cell culture, and in vivo, suggesting that these versatile compounds are attractive therapeutic candidates for various diseases, infections, and injuries. A lead compound called CLR01 has been shown to inhibit the aggregation of various amyloidogenic proteins, facilitate their clearance in vivo, prevent infection by multiple viruses, display potent anti-biofilm activity, and have a high safety margin in animal models. The inhibitory effect of CLR01 against amyloidogenic proteins is highly specific to abnormal self-assembly of amyloidogenic proteins with no disruption of normal mammalian biologic processes at the doses needed for inhibition. Therapeutic effects of CLR01 have been demonstrated in animal models of proteinopathies, lysosomal-storage diseases, and spinal-cord injury. Here we review the activity and mechanisms of action of these intriguing compounds and discuss future research directions. SIGNIFICANCE STATEMENT: Molecular tweezers are supramolecular host molecules with broad biological applications, including inhibition of abnormal protein aggregation, facilitation of lysosomal clearance of toxic aggregates, disruption of viral membranes, and interference of biofilm formation by Gram-positive bacteria. This review discusses the molecular and cellular mechanisms of action of the molecular tweezers, including the discovery of distinct mechanisms acting in vitro and in vivo, and the application of these compounds in multiple preclinical disease models.


Subject(s)
Biological Products , COVID-19 , Animals , Organophosphates/pharmacology , SARS-CoV-2 , Amyloidogenic Proteins , Mammals
2.
Anal Chem ; 96(23): 9362-9369, 2024 06 11.
Article in English | MEDLINE | ID: mdl-38826107

ABSTRACT

Amyloid precursor protein (APP) plays a pivotal role in the pathology of Alzheimer's disease (AD). Since the fragmentation of the membrane-bound APP that results in the production of amyloid-ß peptides is the starting point for amyloid toxicity in AD, it is important to investigate the structure and dynamics of APP in a near-native lipid-bilayer environment. However, the reconstitution of APP into a stable and suitable membrane-mimicking lipid environment is a challenging task. In this study, the 99-residue C-terminal domain of APP is successfully reconstituted into polymer nanodiscs and characterized using size-exclusion chromatography, mass spectrometry, solution NMR, and magic-angle spinning solid-state NMR. In addition, the feasibility of using lipid-solubilizing polymers for isolating and characterizing APP in the native Escherichia. coli membrane environment is demonstrated.


Subject(s)
Amyloid beta-Protein Precursor , Nanostructures , Amyloid beta-Protein Precursor/chemistry , Amyloid beta-Protein Precursor/metabolism , Nanostructures/chemistry , Escherichia coli , Humans , Lipid Bilayers/chemistry , Lipid Bilayers/metabolism , Nuclear Magnetic Resonance, Biomolecular
3.
Nucleic Acids Res ; 50(15): 8674-8689, 2022 08 26.
Article in English | MEDLINE | ID: mdl-35904811

ABSTRACT

CGG repeat expansions in the FMR1 5'UTR cause the neurodegenerative disease Fragile X-associated tremor/ataxia syndrome (FXTAS). These repeats form stable RNA secondary structures that support aberrant translation in the absence of an AUG start codon (RAN translation), producing aggregate-prone peptides that accumulate within intranuclear neuronal inclusions and contribute to neurotoxicity. Here, we show that the most abundant RAN translation product, FMRpolyG, is markedly less toxic when generated from a construct with a non-repetitive alternating codon sequence in place of the CGG repeat. While exploring the mechanism of this differential toxicity, we observed a +1 translational frameshift within the CGG repeat from the arginine to glycine reading frame. Frameshifts occurred within the first few translated repeats and were triggered predominantly by RNA sequence and structural features. Short chimeric R/G peptides form aggregates distinct from those formed by either pure arginine or glycine, and these chimeras induce toxicity in cultured rodent neurons. Together, this work suggests that CGG repeats support translational frameshifting and that chimeric RAN translated peptides may contribute to CGG repeat-associated toxicity in FXTAS and related disorders.


Subject(s)
Fragile X Mental Retardation Protein , Neurodegenerative Diseases , Protein Aggregation, Pathological , Trinucleotide Repeats , Arginine/genetics , Ataxia , Fragile X Mental Retardation Protein/genetics , Fragile X Mental Retardation Protein/metabolism , Fragile X Syndrome , Glycine/genetics , Humans , Neurodegenerative Diseases/genetics , Peptides/genetics , Peptides/metabolism , Recombinant Fusion Proteins/metabolism
4.
Acta Neuropathol ; 145(5): 541-559, 2023 05.
Article in English | MEDLINE | ID: mdl-36991261

ABSTRACT

Symptoms in the urogenital organs are common in multiple system atrophy (MSA), also in the years preceding the MSA diagnosis. It is unknown how MSA is triggered and these observations in prodromal MSA led us to hypothesize that synucleinopathy could be triggered by infection of the genitourinary tract causing ɑ-synuclein (ɑSyn) to aggregate in peripheral nerves innervating these organs. As a first proof that peripheral infections could act as a trigger in MSA, this study focused on lower urinary tract infections (UTIs), given the relevance and high frequency of UTIs in prodromal MSA, although other types of infection might also be important triggers of MSA. We performed an epidemiological nested-case control study in the Danish population showing that UTIs are associated with future diagnosis of MSA several years after infection and that it impacts risk in both men and women. Bacterial infection of the urinary bladder triggers synucleinopathy in mice and we propose a novel role of ɑSyn in the innate immune system response to bacteria. Urinary tract infection with uropathogenic E. coli results in the de novo aggregation of ɑSyn during neutrophil infiltration. During the infection, ɑSyn is released extracellularly from neutrophils as part of their extracellular traps. Injection of MSA aggregates into the urinary bladder leads to motor deficits and propagation of ɑSyn pathology to the central nervous system in mice overexpressing oligodendroglial ɑSyn. Repeated UTIs lead to progressive development of synucleinopathy with oligodendroglial involvement in vivo. Our results link bacterial infections with synucleinopathy and show that a host response to environmental triggers can result in ɑSyn pathology that bears semblance to MSA.


Subject(s)
Multiple System Atrophy , Synucleinopathies , Urinary Tract Infections , Mice , Female , Animals , Synucleinopathies/pathology , Case-Control Studies , Escherichia coli , Mice, Transgenic , alpha-Synuclein , Multiple System Atrophy/complications , Multiple System Atrophy/pathology , Urinary Tract Infections/complications , Immunity, Innate
5.
J Biol Chem ; 296: 100508, 2021.
Article in English | MEDLINE | ID: mdl-33675750

ABSTRACT

The aggregation of amyloidogenic polypeptides is strongly linked to several neurodegenerative disorders, including Alzheimer's and Parkinson's diseases. Conformational antibodies that selectively recognize protein aggregates are leading therapeutic agents for selectively neutralizing toxic aggregates, diagnostic and imaging agents for detecting disease, and biomedical reagents for elucidating disease mechanisms. Despite their importance, it is challenging to generate high-quality conformational antibodies in a systematic and site-specific manner due to the properties of protein aggregates (hydrophobic, multivalent, and heterogeneous) and limitations of immunization (uncontrolled antigen presentation and immunodominant epitopes). Toward addressing these challenges, we have developed a systematic directed evolution procedure for affinity maturing antibodies against Alzheimer's Aß fibrils and selecting variants with strict conformational and sequence specificity. We first designed a library based on a lead conformational antibody by sampling combinations of amino acids in the antigen-binding site predicted to mediate high antibody specificity. Next, we displayed this library on the surface of yeast, sorted it against Aß42 aggregates, and identified promising clones using deep sequencing. The resulting antibodies displayed similar or higher affinities than clinical-stage Aß antibodies (aducanumab and crenezumab). Moreover, the affinity-matured antibodies retained high conformational specificity for Aß aggregates, as observed for aducanumab and unlike crenezumab. Notably, the affinity-maturated antibodies displayed extremely low levels of nonspecific interactions, as observed for crenezumab and unlike aducanumab. We expect that our systematic methods for generating antibodies with unique combinations of desirable properties will improve the generation of high-quality conformational antibodies specific for diverse types of aggregated conformers.


Subject(s)
Amyloid/metabolism , Antibodies, Monoclonal/immunology , Brain/pathology , Amyloid/antagonists & inhibitors , Amyloid/immunology , Animals , Antibodies, Monoclonal/chemistry , Antibodies, Monoclonal/metabolism , Binding Sites, Antibody , Brain/immunology , Case-Control Studies , Humans , Mice , Models, Molecular , Protein Conformation
6.
Nature ; 525(7570): 486-90, 2015 Sep 24.
Article in English | MEDLINE | ID: mdl-26352473

ABSTRACT

The protein α-synuclein is the main component of Lewy bodies, the neuron-associated aggregates seen in Parkinson disease and other neurodegenerative pathologies. An 11-residue segment, which we term NACore, appears to be responsible for amyloid formation and cytotoxicity of human α-synuclein. Here we describe crystals of NACore that have dimensions smaller than the wavelength of visible light and thus are invisible by optical microscopy. As the crystals are thousands of times too small for structure determination by synchrotron X-ray diffraction, we use micro-electron diffraction to determine the structure at atomic resolution. The 1.4 Å resolution structure demonstrates that this method can determine previously unknown protein structures and here yields, to our knowledge, the highest resolution achieved by any cryo-electron microscopy method to date. The structure exhibits protofibrils built of pairs of face-to-face ß-sheets. X-ray fibre diffraction patterns show the similarity of NACore to toxic fibrils of full-length α-synuclein. The NACore structure, together with that of a second segment, inspires a model for most of the ordered portion of the toxic, full-length α-synuclein fibril, presenting opportunities for the design of inhibitors of α-synuclein fibrils.


Subject(s)
Nanoparticles/chemistry , Nanoparticles/toxicity , alpha-Synuclein/chemistry , alpha-Synuclein/toxicity , Amyloid/chemistry , Cryoelectron Microscopy , Electrons , Humans , Lewy Bodies/chemistry , Models, Molecular , Parkinson Disease , Protein Structure, Tertiary , Scattering, Radiation
7.
Proc Natl Acad Sci U S A ; 115(44): E10495-E10504, 2018 10 30.
Article in English | MEDLINE | ID: mdl-30333186

ABSTRACT

UBQLN2 is one of a family of proteins implicated in ubiquitin-dependent protein quality control and integrally tied to human neurodegenerative disease. Whereas wild-type UBQLN2 accumulates in intraneuronal deposits in several common age-related neurodegenerative diseases, mutations in the gene encoding this protein result in X-linked amyotrophic lateral sclerosis/frontotemporal dementia associated with TDP43 accumulation. Using in vitro protein analysis, longitudinal fluorescence imaging and cellular, neuronal, and transgenic mouse models, we establish that UBQLN2 is intrinsically prone to self-assemble into higher-order complexes, including liquid-like droplets and amyloid aggregates. UBQLN2 self-assembly and solubility are reciprocally modulated by the protein's ubiquitin-like and ubiquitin-associated domains. Moreover, a pathogenic UBQLN2 missense mutation impairs droplet dynamics and favors amyloid-like aggregation associated with neurotoxicity. These data emphasize the critical link between UBQLN2's role in ubiquitin-dependent pathways and its propensity to self-assemble and aggregate in neurodegenerative diseases.


Subject(s)
Adaptor Proteins, Vesicular Transport/metabolism , Protein Aggregation, Pathological , Adaptor Proteins, Signal Transducing , Adaptor Proteins, Vesicular Transport/genetics , Amyotrophic Lateral Sclerosis/genetics , Amyotrophic Lateral Sclerosis/metabolism , Animals , Autophagy-Related Proteins , Frontotemporal Dementia/genetics , Frontotemporal Dementia/metabolism , Gene Expression Regulation , Mice , Mice, Transgenic , Mutation , Neurons , Protein Conformation , Protein Domains , Ubiquitin
8.
Biochemistry ; 59(24): 2249-2258, 2020 06 23.
Article in English | MEDLINE | ID: mdl-32469202

ABSTRACT

Aggregation and the formation of oligomeric intermediates of amyloid-ß (Aß) at the membrane interface of neuronal cells are implicated in the cellular toxicity and pathology of Alzheimer's disease. Small molecule compounds have been shown to suppress amyloid aggregation and cellular toxicity, but often the presence of a lipid membrane negates their activity. A high-throughput screen of 1800 small molecules was performed to search for membrane active inhibitors, and 21 primary hits were discovered. Through the use of fluorescence-based assays, transmission electron microscopy, and dot blot assays, the initial 21 primary hits were narrowed down to five lead compounds. Nuclear magnetic resonance and circular dichroism experiments were used for further confirmation of amyloid inhibition at the membrane interface and to obtain insights into the secondary structure of amyloid-ß, while size exclusion chromatography was used to characterize the size of Aß species. Lastly, dye-leakage assays allowed us to understand how the addition of the five lead compounds affected amyloid-ß's ability to permeate the lipid bilayer. These results provide insights into small molecules that stabilize small amyloid species in the presence of membranes for the development of tool compounds for deeper investigations of these transient species.


Subject(s)
Amyloid beta-Peptides/chemistry , Lipid Bilayers/chemistry , Circular Dichroism , Humans , Nuclear Magnetic Resonance, Biomolecular
9.
J Biol Chem ; 294(49): 18624-18638, 2019 12 06.
Article in English | MEDLINE | ID: mdl-31649034

ABSTRACT

Repeat-associated non-AUG (RAN) translation is a noncanonical translation initiation event that occurs at nucleotide-repeat expansion mutations that are associated with several neurodegenerative diseases, including fragile X-associated tremor ataxia syndrome (FXTAS), ALS, and frontotemporal dementia (FTD). Translation of expanded repeats produces toxic proteins that accumulate in human brains and contribute to disease pathogenesis. Consequently, RAN translation constitutes a potentially important therapeutic target for managing multiple neurodegenerative disorders. Here, we adapted a previously developed RAN translation assay to a high-throughput format to screen 3,253 bioactive compounds for inhibition of RAN translation of expanded CGG repeats associated with FXTAS. We identified five diverse small molecules that dose-dependently inhibited CGG RAN translation, while relatively sparing canonical translation. All five compounds also inhibited RAN translation of expanded GGGGCC repeats associated with ALS and FTD. Using CD and native gel analyses, we found evidence that three of these compounds, BIX01294, CP-31398, and propidium iodide, bind directly to the repeat RNAs. These findings provide proof-of-principle supporting the development of selective small-molecule RAN translation inhibitors that act across multiple disease-causing repeats.


Subject(s)
Amyotrophic Lateral Sclerosis/genetics , Ataxia/genetics , Fragile X Syndrome/genetics , Tremor/genetics , Trinucleotide Repeat Expansion/genetics , Amyotrophic Lateral Sclerosis/drug therapy , Animals , Ataxia/drug therapy , Azepines/pharmacology , Azepines/therapeutic use , Cells, Cultured , Circular Dichroism , DNA Repeat Expansion/drug effects , DNA Repeat Expansion/genetics , Drug Evaluation, Preclinical , Fragile X Syndrome/drug therapy , HEK293 Cells , Humans , Neurodegenerative Diseases/genetics , Propidium/pharmacology , Propidium/therapeutic use , Pyrimidines/pharmacology , Pyrimidines/therapeutic use , Quinazolines/pharmacology , Quinazolines/therapeutic use , Rats , Tremor/drug therapy , Trinucleotide Repeat Expansion/drug effects
10.
Proc Natl Acad Sci U S A ; 114(46): 12184-12189, 2017 11 14.
Article in English | MEDLINE | ID: mdl-29087319

ABSTRACT

During biofilm formation, Escherichia coli and other Enterobacteriaceae produce an extracellular matrix consisting of curli amyloid fibers and cellulose. The precursor of curli fibers is the amyloidogenic protein CsgA. The human systemic amyloid precursor protein transthyretin (TTR) is known to inhibit amyloid-ß (Aß) aggregation in vitro and suppress the Alzheimer's-like phenotypes in a transgenic mouse model of Aß deposition. We hypothesized that TTR might have broad antiamyloid activity because the biophysical properties of amyloids are largely conserved across species and kingdoms. Here, we report that both human WT tetrameric TTR (WT-TTR) and its engineered nontetramer-forming monomer (M-TTR, F87M/L110M) inhibit CsgA amyloid formation in vitro, with M-TTR being the more efficient inhibitor. Preincubation of WT-TTR with small molecules that occupy the T4 binding site eliminated the inhibitory capacity of the tetramer; however, they did not significantly compromise the ability of M-TTR to inhibit CsgA amyloidogenesis. TTR also inhibited amyloid-dependent biofilm formation in two different bacterial species with no apparent bactericidal or bacteriostatic effects. These discoveries suggest that TTR is an effective antibiofilm agent that could potentiate antibiotic efficacy in infections associated with significant biofilm formation.


Subject(s)
Amyloid/chemistry , Amyloidogenic Proteins/chemistry , Biofilms/drug effects , Escherichia coli Proteins/chemistry , Escherichia coli/drug effects , Prealbumin/pharmacology , Amyloid/antagonists & inhibitors , Amyloid/metabolism , Amyloidogenic Proteins/antagonists & inhibitors , Amyloidogenic Proteins/genetics , Amyloidogenic Proteins/metabolism , Binding Sites , Biofilms/growth & development , Escherichia coli/genetics , Escherichia coli/metabolism , Escherichia coli Proteins/antagonists & inhibitors , Escherichia coli Proteins/genetics , Escherichia coli Proteins/metabolism , Gene Expression , Humans , Kinetics , Prealbumin/chemistry , Prealbumin/metabolism , Protein Aggregates/drug effects , Protein Binding , Protein Interaction Domains and Motifs , Protein Multimerization
11.
J Biol Chem ; 292(11): 4638-4650, 2017 03 17.
Article in English | MEDLINE | ID: mdl-28154182

ABSTRACT

The aggregation of amyloid-ß (Aß) on lipid bilayers has been implicated as a mechanism by which Aß exerts its toxicity in Alzheimer's disease (AD). Lipid bilayer thinning has been observed during both oxidative stress and protein aggregation in AD, but whether these pathological modifications of the bilayer correlate with Aß misfolding is unclear. Here, we studied peptide-lipid interactions in synthetic bilayers of the short-chain lipid dilauroyl phosphatidylcholine (DLPC) as a simplified model for diseased bilayers to determine their impact on Aß aggregate, protofibril, and fibril formation. Aß aggregation and fibril formation in membranes composed of dioleoyl phosphatidylcholine (DOPC) or 1- palmitoyl-2-oleoyl phosphatidylcholine mimicking normal bilayers served as controls. Differences in aggregate formation and stability were monitored by a combination of thioflavin-T fluorescence, circular dichroism, atomic force microscopy, transmission electron microscopy, and NMR. Despite the ability of all three lipid bilayers to catalyze aggregation, DLPC accelerates aggregation at much lower concentrations and prevents the fibrillation of Aß at low micromolar concentrations. DLPC stabilized globular, membrane-associated oligomers, which could disrupt the bilayer integrity. DLPC bilayers also remodeled preformed amyloid fibrils into a pseudo-unfolded, molten globule state, which resembled on-pathway, protofibrillar aggregates. Whereas the stabilized, membrane-associated oligomers were found to be nontoxic, the remodeled species displayed toxicity similar to that of conventionally prepared aggregates. These results provide mechanistic insights into the roles that pathologically thin bilayers may play in Aß aggregation on neuronal bilayers, and pathological lipid oxidation may contribute to Aß misfolding.


Subject(s)
Alzheimer Disease/metabolism , Amyloid beta-Peptides/metabolism , Lipid Bilayers/metabolism , Amyloid beta-Peptides/ultrastructure , Humans , Phosphatidylcholines/metabolism , Protein Aggregates , Protein Structure, Secondary
12.
Brain ; 139(11): 2891-2908, 2016 11 01.
Article in English | MEDLINE | ID: mdl-27645800

ABSTRACT

No disease-modifying treatment exists for the fatal neurodegenerative polyglutamine disease known both as Machado-Joseph disease and spinocerebellar ataxia type 3. As a potential route to therapy, we identified small molecules that reduce levels of the mutant disease protein, ATXN3. Screens of a small molecule collection, including 1250 Food and Drug Administration-approved drugs, in a novel cell-based assay, followed by secondary screens in brain slice cultures from transgenic mice expressing the human disease gene, identified the atypical antipsychotic aripiprazole as one of the hits. Aripiprazole increased longevity in a Drosophila model of Machado-Joseph disease and effectively reduced aggregated ATXN3 species in flies and in brains of transgenic mice treated for 10 days. The aripiprazole-mediated decrease in ATXN3 abundance may reflect a complex response culminating in the modulation of specific components of cellular protein homeostasis. Aripiprazole represents a potentially promising therapeutic drug for Machado-Joseph disease and possibly other neurological proteinopathies.


Subject(s)
Antipsychotic Agents/therapeutic use , Aripiprazole/therapeutic use , Ataxin-3/metabolism , Machado-Joseph Disease/drug therapy , Machado-Joseph Disease/metabolism , Mutant Proteins/drug effects , Animals , Animals, Genetically Modified , Ataxin-3/genetics , Brain/drug effects , Brain/metabolism , Brain/ultrastructure , Disease Models, Animal , Drosophila , Drug Evaluation, Preclinical , Gene Expression Regulation/drug effects , Gene Expression Regulation/genetics , HEK293 Cells/drug effects , HEK293 Cells/metabolism , HEK293 Cells/ultrastructure , Humans , Machado-Joseph Disease/genetics , Mice , Mutant Proteins/metabolism , Nerve Tissue Proteins/metabolism , Organ Culture Techniques , Peptides/genetics , Piperidines/pharmacology , Pyrans/pharmacology , Pyrazoles/pharmacology
13.
Proc Natl Acad Sci U S A ; 111(1): 197-201, 2014 Jan 07.
Article in English | MEDLINE | ID: mdl-24344300

ABSTRACT

ALS is a terminal disease of motor neurons that is characterized by accumulation of proteinaceous deposits in affected cells. Pathological deposition of mutated Cu/Zn superoxide dismutase (SOD1) accounts for ∼20% of the familial ALS (fALS) cases. However, understanding the molecular link between mutation and disease has been difficult, given that more than 140 different SOD1 mutants have been observed in fALS patients. In addition, the molecular origin of sporadic ALS (sALS) is unclear. By dissecting the amino acid sequence of SOD1, we identified four short segments with a high propensity for amyloid fibril formation. We find that fALS mutations in these segments do not reduce their propensity to form fibrils. The atomic structures of two fibril-forming segments from the C terminus, (101)DSVISLS(107) and (147)GVIGIAQ(153), reveal tightly packed ß-sheets with steric zipper interfaces characteristic of the amyloid state. Based on these structures, we conclude that both C-terminal segments are likely to form aggregates if available for interaction. Proline substitutions in (101)DSVISLS(107) and (147)GVIGIAQ(153) impaired nucleation and fibril growth of full-length protein, confirming that these segments participate in aggregate formation. Our hypothesis is that improper protein maturation and incompletely folded states that render these aggregation-prone segments available for interaction offer a common molecular pathway for sALS and fALS.


Subject(s)
Amyotrophic Lateral Sclerosis/metabolism , Superoxide Dismutase/metabolism , Algorithms , Amino Acid Sequence , Computer Simulation , Humans , Metals/chemistry , Models, Molecular , Molecular Sequence Data , Mutation , Peptides/chemistry , Protein Binding , Protein Multimerization , Protein Structure, Secondary , Protein Structure, Tertiary , Saccharomyces cerevisiae/metabolism , Superoxide Dismutase-1 , Time Factors
14.
J Biol Chem ; 289(15): 10727-10737, 2014 Apr 11.
Article in English | MEDLINE | ID: mdl-24567327

ABSTRACT

Recent work on α-synuclein has shown that aggregation is controlled kinetically by the rate of reconfiguration of the unstructured chain, such that the faster the reconfiguration, the slower the aggregation. In this work we investigate this relationship by examining α-synuclein in the presence of a small molecular tweezer, CLR01, which binds selectively to Lys side chains. We find strong binding to multiple Lys within the chain as measured by fluorescence and mass-spectrometry and a linear increase in the reconfiguration rate with concentration of the inhibitor. Top-down mass-spectrometric analysis shows that the main binding of CLR01 to α-synuclein occurs at the N-terminal Lys-10/Lys-12. Photo-induced cross-linking of unmodified proteins (PICUP) analysis shows that under the conditions used for the fluorescence analysis, α-synuclein is predominantly monomeric. The results can be successfully modeled using a kinetic scheme in which two aggregation-prone monomers can form an encounter complex that leads to further oligomerization but can also dissociate back to monomers if the reconfiguration rate is sufficiently high. Taken together, the data provide important insights into the preferred binding site of CLR01 on α-synuclein and the mechanism by which the molecular tweezer prevents self-assembly into neurotoxic aggregates by α-synuclein and presumably other amyloidogenic proteins.


Subject(s)
Bridged-Ring Compounds/chemistry , Lysine/chemistry , Organophosphates/chemistry , alpha-Synuclein/chemistry , Amino Acid Sequence , Binding Sites , Diffusion , Humans , Kinetics , Mass Spectrometry , Molecular Sequence Data , Parkinson Disease/metabolism , Probability , Protein Binding , Protein Structure, Tertiary , Spectrometry, Fluorescence , Treatment Outcome
15.
Protein Sci ; 33(8): e5119, 2024 Aug.
Article in English | MEDLINE | ID: mdl-39012029

ABSTRACT

Despite causing over 1 million deaths annually, Type 2 Diabetes (T2D) currently has no curative treatments. Aggregation of the islet amyloid polypeptide (hIAPP) into amyloid plaques plays an important role in the pathophysiology of T2D and thus presents a target for therapeutic intervention. The mechanism by which hIAPP aggregates contribute to the development of T2D is unclear, but it is proposed to involve disruption of cellular membranes. However, nearly all research on hIAPP-lipid interactions has focused on anionic phospholipids, which are primarily present in the cytosolic face of plasma membranes. We seek here to characterize the effects of three gangliosides, the dominant anionic lipids in the outer leaflet of the plasma membrane, on the aggregation, structure, and toxicity of hIAPP. Our results show a dual behavior that depends on the molar ratio between the gangliosides and hIAPP. For each ganglioside, a low-lipid:peptide ratio enhances hIAPP aggregation and alters the morphology of hIAPP fibrils, while a high ratio eliminates aggregation and stabilizes an α-helix-rich hIAPP conformation. A more negative lipid charge more efficiently promotes aggregation, and a larger lipid headgroup improves inhibition of aggregation. hIAPP also alters the phase transitions of the lipids, favoring spherical micelles over larger tubular micelles. We discuss our results in the context of the available lipid surface area for hIAPP binding and speculate on a role for gangliosides in facilitating toxic hIAPP aggregation.


Subject(s)
Gangliosides , Islet Amyloid Polypeptide , Islet Amyloid Polypeptide/chemistry , Islet Amyloid Polypeptide/metabolism , Gangliosides/chemistry , Gangliosides/metabolism , Humans , Protein Aggregates/drug effects , Diabetes Mellitus, Type 2/metabolism , Protein Conformation
16.
bioRxiv ; 2024 Apr 21.
Article in English | MEDLINE | ID: mdl-38659865

ABSTRACT

Amyloid precursor protein (APP) plays a pivotal role in the pathology of Alzheimer's disease. Since the fragmentation of the membrane-bound APP that results in the production of amyloid-beta peptides is the starting point for amyloid toxicity in AD, it is important to investigate the structure and dynamics of APP in a near-native lipid-bilayer environment. However, the reconstitution of APP into a stable/suitable membrane-mimicking lipid environment is a challenging task. In this study, the 99-residue C-terminal domain of APP is successfully reconstituted into polymer nanodiscs and characterized using size-exclusion chromatography, mass spectrometry, solution NMR, and magic-angle spinning solid-state NMR. In addition, the feasibility of using lipid-solubilizing polymers for isolating and characterizing APP in native E. coli membrane environment is demonstrated.

17.
Commun Biol ; 7(1): 776, 2024 Jun 27.
Article in English | MEDLINE | ID: mdl-38937578

ABSTRACT

Aggregation of the human islet amyloid polypeptide (hIAPP) contributes to the development and progression of Type 2 Diabetes (T2D). hIAPP aggregates within a few hours at few micromolar concentration in vitro but exists at millimolar concentrations in vivo. Natively occurring inhibitors of hIAPP aggregation might therefore provide a model for drug design against amyloid formation associated with T2D. Here, we describe the combined ability of low pH, zinc, and insulin to inhibit hIAPP fibrillation. Insulin dose-dependently slows hIAPP aggregation near neutral pH but had less effect on the aggregation kinetics at acidic pH. We determine that insulin alters hIAPP aggregation in two manners. First, insulin diverts the aggregation pathway to large nonfibrillar aggregates with ThT-positive molecular structure, rather than to amyloid fibrils. Second, soluble insulin suppresses hIAPP dimer formation, which is an important early aggregation event. Further, we observe that zinc significantly modulates the inhibition of hIAPP aggregation by insulin. We hypothesize that this effect arose from controlling the oligomeric state of insulin and show that hIAPP interacts more strongly with monomeric than oligomeric insulin.


Subject(s)
Insulin , Islet Amyloid Polypeptide , Protein Aggregates , Zinc , Islet Amyloid Polypeptide/chemistry , Islet Amyloid Polypeptide/metabolism , Hydrogen-Ion Concentration , Humans , Zinc/pharmacology , Zinc/metabolism , Zinc/chemistry , Insulin/metabolism , Protein Aggregates/drug effects , Diabetes Mellitus, Type 2/drug therapy , Diabetes Mellitus, Type 2/metabolism , Kinetics , Amyloid/metabolism , Amyloid/chemistry , Protein Aggregation, Pathological/metabolism
18.
Nature ; 447(7143): 453-7, 2007 May 24.
Article in English | MEDLINE | ID: mdl-17468747

ABSTRACT

Amyloid fibrils formed from different proteins, each associated with a particular disease, contain a common cross-beta spine. The atomic architecture of a spine, from the fibril-forming segment GNNQQNY of the yeast prion protein Sup35, was recently revealed by X-ray microcrystallography. It is a pair of beta-sheets, with the facing side chains of the two sheets interdigitated in a dry 'steric zipper'. Here we report some 30 other segments from fibril-forming proteins that form amyloid-like fibrils, microcrystals, or usually both. These include segments from the Alzheimer's amyloid-beta and tau proteins, the PrP prion protein, insulin, islet amyloid polypeptide (IAPP), lysozyme, myoglobin, alpha-synuclein and beta(2)-microglobulin, suggesting that common structural features are shared by amyloid diseases at the molecular level. Structures of 13 of these microcrystals all reveal steric zippers, but with variations that expand the range of atomic architectures for amyloid-like fibrils and offer an atomic-level hypothesis for the basis of prion strains.


Subject(s)
Amyloid/chemistry , Peptide Fragments/chemistry , Amino Acid Sequence , Crystallization , Models, Molecular , Prions/chemistry , Protein Conformation
19.
Biophys Chem ; 301: 107091, 2023 10.
Article in English | MEDLINE | ID: mdl-37549471

ABSTRACT

Alzheimer's disease is a progressive degenerative condition that mainly affects cognition and memory. Recently, distinct clinical and neuropathological phenotypes have been identified in AD. Studies revealed that structural variation in Aß fibrillar aggregates correlates with distinct disease phenotypes. Moreover, environmental surroundings, including other biomolecules such as proteins and lipids, have been shown to interact and modulate Aß aggregation. Model membranes containing ganglioside (GM1) clusters are specifically known to promote Aß fibrillogenesis. This study unravels the modulatory effect of non-micellar GM1, a glycosphingolipid frequently released from the damaged neuronal membranes, on Aß42 amyloid fibril formation. Using far-UV circular dichroism experiments, we observed a change in the peptide secondary structure from random-coil to ß-turn structures with subsequent generation of predominantly ß-sheet-rich species upon interaction with GM1. Thioflavin-T (ThT) fluorescence assays further indicated that GM1 likely interacts with an amyloidogenic Aß42 intermediate species leading to a possible formation of GM1-modified Aß42 fibril. Statistically, no significant difference in toxicity to RA-differentiated SH-SY5Y cells was observed between Aß42 fibrils and GM1-tweaked Aß42 aggregates. Moreover, GM1-modified Aß42 aggregates exhibited prion-like properties in catalyzing the amyloid fibril formation of both major isomers of Aß, Aß40, and Aß42.


Subject(s)
Alzheimer Disease , Neuroblastoma , Humans , Amyloid beta-Peptides/chemistry , G(M1) Ganglioside/chemistry , Amyloid/chemistry , Peptide Fragments/chemistry , Alzheimer Disease/metabolism
20.
Nat Commun ; 14(1): 3132, 2023 05 30.
Article in English | MEDLINE | ID: mdl-37253728

ABSTRACT

Endoplasmic reticulum (ER)-associated degradation (ERAD) and ER-phagy are two principal degradative mechanisms for ER proteins and aggregates, respectively; however, the crosstalk between these two pathways under physiological settings remains unexplored. Using adipocytes as a model system, here we report that SEL1L-HRD1 protein complex of ERAD degrades misfolded ER proteins and limits ER-phagy and that, only when SEL1L-HRD1 ERAD is impaired, the ER becomes fragmented and cleared by ER-phagy. When both are compromised, ER fragments containing misfolded proteins spatially coalesce into a distinct architecture termed Coalescence of ER Fragments (CERFs), consisted of lipoprotein lipase (LPL, a key lipolytic enzyme and an endogenous SEL1L-HRD1 substrate) and certain ER chaperones. CERFs enlarge and become increasingly insoluble with age. Finally, we reconstitute the CERFs through LPL and BiP phase separation in vitro, a process influenced by both redox environment and C-terminal tryptophan loop of LPL. Hence, our findings demonstrate a sequence of events centered around SEL1L-HRD1 ERAD to dispose of misfolded proteins in the ER of adipocytes, highlighting the profound cellular adaptability to misfolded proteins in the ER in vivo.


Subject(s)
Proteins , Ubiquitin-Protein Ligases , Ubiquitin-Protein Ligases/metabolism , Proteins/metabolism , Endoplasmic Reticulum-Associated Degradation , Endoplasmic Reticulum/metabolism , Adipocytes/metabolism
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