101
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Guo J, Rich-New ST, Liu C, Huang Y, Tan W, He H, Yi M, Zhang X, Egelman EH, Wang F, Xu B. Hierarchical Assembly of Intrinsically Disordered Short Peptides. Chem 2023; 9:2530-2546. [PMID: 38094164 PMCID: PMC10715794 DOI: 10.1016/j.chempr.2023.04.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
The understanding on how short peptide assemblies transit from disorder to order remains limited due to the lack of atomistic structures. Here we report cryo-EM structure of the nanofibers short intrinsically disordered peptides (IDPs). Upon lowering pH or adding calcium ions, the IDP transitions from individual nanoparticles to nanofibers containing an aromatic core and a disordered periphery comprised of 2 to 5 amino acids. Protonating the phosphate or adding more metal ions further assembles the nanofibers into filament bundles. The assemblies of the IDP analogs with controlled chemistry, such as phosphorylation site, hydrophobic interactions, and sequences indicate that metal ions interact with the flexible periphery of the nanoparticles of the IDPs to form fibrils and enhance the interfibrillar interactions to form filament bundles. Illustrating that an IDP self-assembles from disorder to order, this work offers atomistic molecular insights to understand assemblies of short peptides driven by noncovalent interactions.
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Affiliation(s)
- Jiaqi Guo
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Shane T. Rich-New
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Chen Liu
- Physical Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Yimeng Huang
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Weiyi Tan
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Hongjian He
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Meihui Yi
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Xixiang Zhang
- Physical Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Edward H. Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
- O’Neal Comprehensive Cancer Center University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
- Lead contact
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102
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Scheres SHW, Ryskeldi-Falcon B, Goedert M. Molecular pathology of neurodegenerative diseases by cryo-EM of amyloids. Nature 2023; 621:701-710. [PMID: 37758888 DOI: 10.1038/s41586-023-06437-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 07/14/2023] [Indexed: 09/29/2023]
Abstract
Abnormal assembly of tau, α-synuclein, TDP-43 and amyloid-β proteins into amyloid filaments defines most human neurodegenerative diseases. Genetics provides a direct link between filament formation and the causes of disease. Developments in cryo-electron microscopy (cryo-EM) have made it possible to determine the atomic structures of amyloids from postmortem human brains. Here we review the structures of brain-derived amyloid filaments that have been determined so far and discuss their impact on research into neurodegeneration. Whereas a given protein can adopt many different filament structures, specific amyloid folds define distinct diseases. Amyloid structures thus provide a description of neuropathology at the atomic level and a basis for studying disease. Future research should focus on model systems that replicate the structures observed in disease to better understand the molecular mechanisms of disease and develop improved diagnostics and therapies.
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Affiliation(s)
- Sjors H W Scheres
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
| | | | - Michel Goedert
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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103
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Khaled M, Rönnbäck I, Ilag LL, Gräslund A, Strodel B, Österlund N. A Hairpin Motif in the Amyloid-β Peptide Is Important for Formation of Disease-Related Oligomers. J Am Chem Soc 2023; 145:18340-18354. [PMID: 37555670 PMCID: PMC10450692 DOI: 10.1021/jacs.3c03980] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Indexed: 08/10/2023]
Abstract
The amyloid-β (Aβ) peptide is associated with the development of Alzheimer's disease and is known to form highly neurotoxic prefibrillar oligomeric aggregates, which are difficult to study due to their transient, low-abundance, and heterogeneous nature. To obtain high-resolution information about oligomer structure and dynamics as well as relative populations of assembly states, we here employ a combination of native ion mobility mass spectrometry and molecular dynamics simulations. We find that the formation of Aβ oligomers is dependent on the presence of a specific β-hairpin motif in the peptide sequence. Oligomers initially grow spherically but start to form extended linear aggregates at oligomeric states larger than those of the tetramer. The population of the extended oligomers could be notably increased by introducing an intramolecular disulfide bond, which prearranges the peptide in the hairpin conformation, thereby promoting oligomeric structures but preventing conversion into mature fibrils. Conversely, truncating one of the β-strand-forming segments of Aβ decreased the hairpin propensity of the peptide and thus decreased the oligomer population, removed the formation of extended oligomers entirely, and decreased the aggregation propensity of the peptide. We thus propose that the observed extended oligomer state is related to the formation of an antiparallel sheet state, which then nucleates into the amyloid state. These studies provide increased mechanistic understanding of the earliest steps in Aβ aggregation and suggest that inhibition of Aβ folding into the hairpin conformation could be a viable strategy for reducing the amount of toxic oligomers.
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Affiliation(s)
- Mohammed Khaled
- Institute
of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Isabel Rönnbäck
- Department
of Biochemistry and Biophysics, Stockholm
University, 106 91 Stockholm, Sweden
| | - Leopold L. Ilag
- Department
of Materials and Environmental Chemistry, Stockholm University, 106 91 Stockholm, Sweden
| | - Astrid Gräslund
- Department
of Biochemistry and Biophysics, Stockholm
University, 106 91 Stockholm, Sweden
| | - Birgit Strodel
- Institute
of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52428 Jülich, Germany
- Institute
of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Nicklas Österlund
- Department
of Biochemistry and Biophysics, Stockholm
University, 106 91 Stockholm, Sweden
- Department
of Materials and Environmental Chemistry, Stockholm University, 106 91 Stockholm, Sweden
- Department
of Microbiology, Tumor and Cell Biology, Karolinska Institutet − Biomedicum, 171 65 Solna, Sweden
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104
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Bridges LR. Replicating RNA as a component of scrapie fibrils. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.17.553578. [PMID: 37645951 PMCID: PMC10462133 DOI: 10.1101/2023.08.17.553578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Recently, electron cryo-microscopy (cryo-EM) maps of fibrils from the brains of mice and hamsters with five infectious scrapie strains have been published1-5 and deposited in the electron microscopy data bank (EMDB)6. This represents long-awaited near-atomic level structural evidence, widely expected to confirm the protein-only prion hypothesis7,8. Instead, the maps reveal a second component, other than protein. The aim of the present study was to identify the nature of this second component, in the published maps1-5, using an in silico approach. Extra densities (EDs) containing this component were continuous, straight, axial, at right angles to protein rungs and within hydrogen-bonding distance of protein, consistent with a role as guide and support in fibril construction. EDs co-located with strips of basic residues, notably lysines, and formed a conspicuous cladding over parts of the N-terminal lobe of the protein. In one ED, there was evidence of a Y-shaped polymer forming two antiparallel chains, consistent with replicating RNA. Although the protein-only prion hypothesis7 is still popular, convincing counter-evidence for an essential role of RNA as a cofactor has amassed in the last 20 years8. The present findings go beyond this in providing evidence for RNA as the genetic element of scrapie. To reflect the monotonous nature of the protein interface, it is suggested that the RNA may be a tandem repeat. This is against the protein-only prion hypothesis and in favour of a more orthodox agent, more akin to a virus. Fibrils from brains of patients with Alzheimer's disease (AD), Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS) and other neurodegenerations also contain EDs9 and may be of a similar aetiology.
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Affiliation(s)
- Leslie R Bridges
- Neuropathology, Cellular Pathology, South West London Pathology, St George's Hospital, St George's University Hospitals NHS Foundation Trust, London, UK and Molecular and Clinical Sciences Research Institute, St George's University of London, London, UK
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105
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Lewkowicz E, Nakamura MN, Rynkiewicz MJ, Gursky O. Molecular modeling of apoE in complexes with Alzheimer's amyloid-β fibrils from human brain suggests a structural basis for apolipoprotein co-deposition with amyloids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.04.551703. [PMID: 37577501 PMCID: PMC10418262 DOI: 10.1101/2023.08.04.551703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Apolipoproteins co-deposit with amyloids, yet apolipoprotein-amyloid interactions are enigmatic. To understand how apoE interacts with Alzheimer's amyloid-β (Aβ) peptide in fibrillary deposits, the NMR structure of full-length human apoE was docked to four structures of patient-derived Aβ1-40 and Aβ1-42 fibrils determined previously using cryo-electron microscopy or solid-state NMR. Similar docking was done using the NMR structure of human apoC-III. In all complexes, conformational changes in apolipoproteins were required to expose large hydrophobic faces of their amphipathic α-helices for sub-stoichiometric binding to hydrophobic surfaces on sides or ends of fibrils. Basic residues flanking the hydrophobic helical faces in apolipoproteins interacted favorably with acidic residue ladders in some amyloid polymorphs. Molecular dynamics simulations of selected apoE-fibril complexes confirmed their stability. Amyloid binding via cryptic sites, which became available upon opening of flexibly linked apolipoprotein α-helices, resembled apolipoprotein-lipid binding. This mechanism probably extends to other apolipoprotein-amyloid interactions. Apolipoprotein binding alongside fibrils could interfere with fibril fragmentation and secondary nucleation, while binding at the fibril ends could halt amyloid elongation and dissolution in a polymorph-specific manner. The proposed mechanism is supported by extensive prior experimental evidence and helps reconcile disparate reports on apoE's role in Aβ aggregation. Furthermore, apoE domain opening and direct interaction of Arg/Cys158 with amyloid potentially contributes to isoform-specific effects in Alzheimer's disease. In summary, current modeling supported by prior experimental studies suggests similar mechanisms for apolipoprotein-amyloid and apolipoprotein-lipid interactions; explains why apolipoproteins co-deposit with amyloids; and helps reconcile conflicting reports on the chaperone-like apoE action in Aβ aggregation.
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Affiliation(s)
- Emily Lewkowicz
- Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, W302, 700 Albany Street, Boston, MA, 02118, United States
| | - Mari N. Nakamura
- Undergraduate program, Department of Chemistry, Middlebury College, 14 Old Chapel Rd, Middlebury, VT 05753VT United States
| | - Michael J. Rynkiewicz
- Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, W302, 700 Albany Street, Boston, MA, 02118, United States
| | - Olga Gursky
- Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, W302, 700 Albany Street, Boston, MA, 02118, United States
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106
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Johansson B, Oasa S, Muntsant Soria A, Tiiman A, Söderberg L, Amandius E, Möller C, Lannfelt L, Terenius L, Giménez-Llort L, Vukojević V. The interwoven fibril-like structure of amyloid-beta plaques in mouse brain tissue visualized using super-resolution STED microscopy. Cell Biosci 2023; 13:142. [PMID: 37542303 PMCID: PMC10403925 DOI: 10.1186/s13578-023-01086-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 07/14/2023] [Indexed: 08/06/2023] Open
Abstract
BACKGROUND Standard neuropathologic analysis of Alzheimer's brain relies on traditional fluorescence microscopy, which suffers from limited spatial resolution due to light diffraction. As a result, it fails to reveal intricate details of amyloid plaques. While electron microscopy (EM) offers higher resolution, its extensive sample preparation, involving fixation, dehydration, embedding, and sectioning, can introduce artifacts and distortions in the complex brain tissue. Moreover, EM lacks molecular specificity and has limited field of view and imaging depth. RESULTS In our study, we employed super-resolution Stimulated Emission Depletion (STED) microscopy in conjunction with the anti-human APP recombinant antibody 1C3 fluorescently labelled with DyLightTM633 (1C3-DyLight633). This combination allowed us to visualize amyloidogenic aggregates in vitro and in brain sections from a 17-month-old 3×Tg-AD mouse with sub-diffraction limited spatial resolution. Remarkably, we achieved a spatial resolution of 29 nm in vitro and 62 nm in brain tissue sections, surpassing the capabilities of conventional confocal microscopy by 5-10 times. Consequently, we could discern individual fibrils within plaques, an achievement previously only possible with EM. CONCLUSIONS The utilization of STED microscopy represents a groundbreaking advancement in the field, enabling researchers to delve into the characterization of local mechanisms that underlie Amyloid (Aβ) deposition into plaques and their subsequent clearance. This unprecedented level of detail is especially crucial for comprehending the etiology of Alzheimer's disease and developing the next generation of anti-amyloid treatments. By facilitating the evaluation of drug candidates and non-pharmacological interventions aiming to reduce amyloid burden, STED microscopy emerges as an indispensable tool for driving scientific progress in Alzheimer's research.
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Affiliation(s)
- Björn Johansson
- Department of Clinical Neuroscience, Karolinska Institutet, SE-17176, Stockholm, Sweden
- Theme Aging, Karolinska University Hospital, Karolinska Institutet, SE-17176, Stockholm, Sweden
| | - Sho Oasa
- Department of Clinical Neuroscience, Karolinska Institutet, SE-17176, Stockholm, Sweden
| | - Aida Muntsant Soria
- Institut de Neurociències, Universitat Autònoma de Barcelona, 08193, Barcelona, Spain
- Department of Psychiatry and Forensic Medicine, School of Medicine, Universitat Autònoma de Barcelona, 08193, Barcelona, Spain
| | - Ann Tiiman
- Department of Clinical Neuroscience, Karolinska Institutet, SE-17176, Stockholm, Sweden
| | | | | | | | | | - Lars Terenius
- Department of Clinical Neuroscience, Karolinska Institutet, SE-17176, Stockholm, Sweden
| | - Lydia Giménez-Llort
- Institut de Neurociències, Universitat Autònoma de Barcelona, 08193, Barcelona, Spain
- Department of Psychiatry and Forensic Medicine, School of Medicine, Universitat Autònoma de Barcelona, 08193, Barcelona, Spain
| | - Vladana Vukojević
- Department of Clinical Neuroscience, Karolinska Institutet, SE-17176, Stockholm, Sweden.
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107
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Quan M, Cao S, Wang Q, Wang S, Jia J. Genetic Phenotypes of Alzheimer's Disease: Mechanisms and Potential Therapy. PHENOMICS (CHAM, SWITZERLAND) 2023; 3:333-349. [PMID: 37589021 PMCID: PMC10425323 DOI: 10.1007/s43657-023-00098-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/28/2023] [Accepted: 02/02/2023] [Indexed: 08/18/2023]
Abstract
Years of intensive research has brought us extensive knowledge on the genetic and molecular factors involved in Alzheimer's disease (AD). In addition to the mutations in the three main causative genes of familial AD (FAD) including presenilins and amyloid precursor protein genes, studies have identified several genes as the most plausible genes for the onset and progression of FAD, such as triggering receptor expressed on myeloid cells 2, sortilin-related receptor 1, and adenosine triphosphate-binding cassette transporter subfamily A member 7. The apolipoprotein E ε4 allele is reported to be the strongest genetic risk factor for sporadic AD (SAD), and it also plays an important role in FAD. Here, we reviewed recent developments in genetic and molecular studies that contributed to the understanding of the genetic phenotypes of FAD and compared them with SAD. We further reviewed the advancements in AD gene therapy and discussed the future perspectives based on the genetic phenotypes.
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Affiliation(s)
- Meina Quan
- Innovation Center for Neurological Disorders and Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, 100053 China
- National Medical Center for Neurological Disorders and National Clinical Research Center for Geriatric Diseases, Beijing, 100053 China
| | - Shuman Cao
- Innovation Center for Neurological Disorders and Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, 100053 China
| | - Qi Wang
- Innovation Center for Neurological Disorders and Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, 100053 China
- National Medical Center for Neurological Disorders and National Clinical Research Center for Geriatric Diseases, Beijing, 100053 China
| | - Shiyuan Wang
- Innovation Center for Neurological Disorders and Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, 100053 China
| | - Jianping Jia
- Innovation Center for Neurological Disorders and Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, 100053 China
- National Medical Center for Neurological Disorders and National Clinical Research Center for Geriatric Diseases, Beijing, 100053 China
- Beijing Key Laboratory of Geriatric Cognitive Disorders, Beijing, 100053 China
- Clinical Center for Neurodegenerative Disease and Memory Impairment, Capital Medical University, Beijing, 100053 China
- Center of Alzheimer’s Disease, Collaborative Innovation Center for Brain Disorders, Beijing Institute of Brain Disorders, Capital Medical University, Beijing, 100053 China
- Key Laboratory of Neurodegenerative Diseases, Ministry of Education, Beijing, 100053 China
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108
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Stephens DC, Crabtree A, Beasley HK, Garza-Lopez E, Mungai M, Vang L, Neikirk K, Vue Z, Vue N, Marshall AG, Turner K, Shao JQ, Sarker B, Murray S, Gaddy JA, Hinton AO, Damo S, Davis J. In the Age of Machine Learning Cryo-EM Research is Still Necessary: A Path toward Precision Medicine. Adv Biol (Weinh) 2023; 7:e2300122. [PMID: 37246245 DOI: 10.1002/adbi.202300122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/29/2023] [Indexed: 05/30/2023]
Abstract
Machine learning has proven useful in analyzing complex biological data and has greatly influenced the course of research in structural biology and precision medicine. Deep neural network models oftentimes fail to predict the structure of complex proteins and are heavily dependent on experimentally determined structures for their training and validation. Single-particle cryogenic electron microscopy (cryoEM) is also advancing the understanding of biology and will be needed to complement these models by continuously supplying high-quality experimentally validated structures for improvements in prediction quality. In this perspective, the significance of structure prediction methods is highlighted, but the authors also ask, what if these programs cannot accurately predict a protein structure important for preventing disease? The role of cryoEM is discussed to help fill the gaps left by artificial intelligence predictive models in resolving targetable proteins and protein complexes that will pave the way for personalized therapeutics.
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Affiliation(s)
- Dominique C Stephens
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
- Department of Life and Physical Sciences, Fisk University, Nashville, TN, 37232, USA
| | - Amber Crabtree
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Heather K Beasley
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Edgar Garza-Lopez
- Department of Internal Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Margaret Mungai
- Department of Internal Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Larry Vang
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Kit Neikirk
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Zer Vue
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Neng Vue
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Andrea G Marshall
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Kyrin Turner
- Department of Life and Physical Sciences, Fisk University, Nashville, TN, 37232, USA
| | - Jian-Qiang Shao
- Central Microscopy Research Facility, University of Iowa, Iowa City, IA, 52242, USA
| | - Bishnu Sarker
- School of Applied Computational Sciences, Meharry Medical College, Nashville, TN, 37208, USA
| | - Sandra Murray
- Department of Cell Biology, College of Medicine, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Jennifer A Gaddy
- Division of Infectious Diseases, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
- U.S. Department of Veterans Affairs, Tennessee Valley Healthcare Systems, Nashville, TN, 37212, USA
| | - Antentor O Hinton
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Steven Damo
- Department of Life and Physical Sciences, Fisk University, Nashville, TN, 37232, USA
| | - Jamaine Davis
- Department of Biochemistry and Cancer Biology, Meharry Medical College, Nashville, TN, 37208, USA
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109
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Yu L, Wang R, Li S, Kara UI, Boerner EC, Chen B, Zhang F, Jian Z, Li S, Liu M, Wang Y, Liu S, Yang Y, Wang C, Zhang W, Yao Y, Wang X, Wang C. Experimental Insights into Conformational Ensembles of Assembled β-Sheet Peptides. ACS CENTRAL SCIENCE 2023; 9:1480-1487. [PMID: 37521785 PMCID: PMC10375872 DOI: 10.1021/acscentsci.3c00230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Indexed: 08/01/2023]
Abstract
Deciphering the conformations and interactions of peptides in their assemblies offers a basis for guiding the rational design of peptide-assembled materials. Here we report the use of scanning tunneling microscopy (STM), a single-molecule imaging method with a submolecular resolution, to distinguish 18 types of coexisting conformational substates of the β-strand of the 8-37 segment of human islet amyloid polypeptide (hIAPP 8-37). We analyzed the pairwise peptide-peptide interactions in the hIAPP 8-37 assembly and found 82 interconformation interactions within a free energy difference of 3.40 kBT. Besides hIAPP 8-37, this STM method validates the existence of multiple conformations of other β-sheet peptide assemblies, including mutated hIAPP 8-37 and amyloid-β 42. Overall, the results reported in this work provide single-molecule experimental insights into the conformational ensemble and interpeptide interactions in the β-sheet peptide assembly.
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Affiliation(s)
- Lanlan Yu
- State
Key Laboratory of Common Mechanism Research for Major Diseases, Haihe
Laboratory of Cell Ecosystem, Department of Biophysics and Structural
Biology, Institute of Basic Medical Sciences,
Chinese Academy of Medical Sciences, School of Basic Medicine Peking
Union Medical College, Beijing 100005, People’s
Republic of China
| | - Ruonan Wang
- State
Key Laboratory of Common Mechanism Research for Major Diseases, Haihe
Laboratory of Cell Ecosystem, Department of Biophysics and Structural
Biology, Institute of Basic Medical Sciences,
Chinese Academy of Medical Sciences, School of Basic Medicine Peking
Union Medical College, Beijing 100005, People’s
Republic of China
| | - Shucong Li
- Department
of Chemistry and Chemical Biology, Harvard
University, Cambridge, Massachusetts, 02138, United States
| | - Ufuoma I. Kara
- William
G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, United States
| | - Eric C. Boerner
- William
G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, United States
| | - Boyuan Chen
- William
G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, United States
| | - Feiyi Zhang
- State
Key Laboratory of Common Mechanism Research for Major Diseases, Haihe
Laboratory of Cell Ecosystem, Department of Biophysics and Structural
Biology, Institute of Basic Medical Sciences,
Chinese Academy of Medical Sciences, School of Basic Medicine Peking
Union Medical College, Beijing 100005, People’s
Republic of China
- Institute
for Advanced Materials, Jiangsu University, Zhenjiang, Jiangsu 212013, People’s
Republic of China
| | - Zhongyi Jian
- State
Key Laboratory of Common Mechanism Research for Major Diseases, Haihe
Laboratory of Cell Ecosystem, Department of Biophysics and Structural
Biology, Institute of Basic Medical Sciences,
Chinese Academy of Medical Sciences, School of Basic Medicine Peking
Union Medical College, Beijing 100005, People’s
Republic of China
| | - Shuyuan Li
- State
Key Laboratory of Common Mechanism Research for Major Diseases, Haihe
Laboratory of Cell Ecosystem, Department of Biophysics and Structural
Biology, Institute of Basic Medical Sciences,
Chinese Academy of Medical Sciences, School of Basic Medicine Peking
Union Medical College, Beijing 100005, People’s
Republic of China
| | - Mingwei Liu
- State
Key Laboratory of Common Mechanism Research for Major Diseases, Haihe
Laboratory of Cell Ecosystem, Department of Biophysics and Structural
Biology, Institute of Basic Medical Sciences,
Chinese Academy of Medical Sciences, School of Basic Medicine Peking
Union Medical College, Beijing 100005, People’s
Republic of China
| | - Yang Wang
- State
Key Laboratory of Common Mechanism Research for Major Diseases, Haihe
Laboratory of Cell Ecosystem, Department of Biophysics and Structural
Biology, Institute of Basic Medical Sciences,
Chinese Academy of Medical Sciences, School of Basic Medicine Peking
Union Medical College, Beijing 100005, People’s
Republic of China
| | - Shuli Liu
- Department
of Clinical Laboratory, Peking University
Civil Aviation School of Clinical Medicine, Beijing 100123, People’s Republic of China
| | - Yanlian Yang
- CAS Key Laboratory
of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory
of Standardization and Measurement for Nanotechnology, Laboratory of Theoretical and Computational Nanoscience,
CAS Center for Excellence in Nanoscience, National Center for Nanoscience
and Technology, Beijing 100190, People’s Republic
of China
| | - Chen Wang
- CAS Key Laboratory
of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory
of Standardization and Measurement for Nanotechnology, Laboratory of Theoretical and Computational Nanoscience,
CAS Center for Excellence in Nanoscience, National Center for Nanoscience
and Technology, Beijing 100190, People’s Republic
of China
| | - Wenbo Zhang
- State
Key Laboratory of Common Mechanism Research for Major Diseases, Haihe
Laboratory of Cell Ecosystem, Department of Biophysics and Structural
Biology, Institute of Basic Medical Sciences,
Chinese Academy of Medical Sciences, School of Basic Medicine Peking
Union Medical College, Beijing 100005, People’s
Republic of China
| | - Yuxing Yao
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Xiaoguang Wang
- William
G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, United States
- Sustainability
Institute, The Ohio State University, Columbus, Ohio, 43210, United
States
| | - Chenxuan Wang
- State
Key Laboratory of Common Mechanism Research for Major Diseases, Haihe
Laboratory of Cell Ecosystem, Department of Biophysics and Structural
Biology, Institute of Basic Medical Sciences,
Chinese Academy of Medical Sciences, School of Basic Medicine Peking
Union Medical College, Beijing 100005, People’s
Republic of China
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110
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Ha JH, Xu Y, Sekhon H, Wilkens S, Ren D, Loh SN. Mimicking Kidney Flow Shear Efficiently Induces Aggregation of LECT2, a Protein Involved in Renal Amyloidosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.13.548788. [PMID: 37503176 PMCID: PMC10369975 DOI: 10.1101/2023.07.13.548788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Aggregation of leukocyte cell-derived chemotaxin 2 (LECT2) causes ALECT2, a systemic amyloidosis that affects the kidney and liver. Homozygosity of the I40V LECT2 mutation is believed to be necessary but not sufficient for the disease. Previous studies established that LECT2 fibrillogenesis is greatly accelerated by loss of its single bound zinc ion and stirring or shaking. These forms of agitation are often used to facilitate protein aggregation, but they create heterogeneous shear conditions, including air-liquid interfaces that denature proteins, that are not present in the body. Here, we determined the extent to which a more physiological form of mechanical stress-shear generated by fluid flow through a network of artery and capillary-sized channels-drives LECT2 fibrillogenesis. To mimic blood flow through the human kidney, where LECT2 and other proteins form amyloid deposits, we developed a microfluidic device consisting of progressively branched channels narrowing from 5 mm to 20 μm in width. Flow shear was particularly pronounced at the branch points and in the smallest capillaries, and this induced LECT2 aggregation much more efficiently than conventional shaking methods. EM images suggested the resulting fibril structures were different in the two conditions. Importantly, results from the microfluidic device showed the first evidence that the I40V mutation accelerated fibril formation and increased both size and density of the aggregates. These findings suggest that kidney-like flow shear, in combination with zinc loss, acts in combination with the I40V mutation to trigger LECT2 amyloidogenesis. These microfluidic devices may be of general use for uncovering the mechanisms by which blood flow induces misfolding and amyloidosis of circulating proteins.
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Affiliation(s)
- Jeung-Hoi Ha
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
| | - Yikang Xu
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY 13244
| | - Harsimranjit Sekhon
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
| | - Stephan Wilkens
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
| | - Dacheng Ren
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY 13244
- Department of Civil and Environmental Engineering, Syracuse University, Syracuse, NY 13244
- Department of Biology, Syracuse University, Syracuse, NY 13244
| | - Stewart N. Loh
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
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111
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Zhang W, Wang R, Liu M, Li S, Vokoun AE, Deng W, Dupont RL, Zhang F, Li S, Wang Y, Liu Z, Zheng Y, Liu S, Yang Y, Wang C, Yu L, Yao Y, Wang X, Wang C. Single-molecule visualization determines conformational substate ensembles in β-sheet-rich peptide fibrils. SCIENCE ADVANCES 2023; 9:eadg7943. [PMID: 37406110 DOI: 10.1126/sciadv.adg7943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 06/01/2023] [Indexed: 07/07/2023]
Abstract
An understanding of protein conformational ensembles is essential for revealing the underlying mechanisms of interpeptide recognition and association. However, experimentally resolving multiple simultaneously existing conformational substates remains challenging. Here, we report the use of scanning tunneling microscopy (STM) to analyze the conformational substate ensembles of β sheet peptides with a submolecular resolution (in-plane <2.6 Å). We observed ensembles of more than 10 conformational substates (with free energy fluctuations between several kBTs) in peptide homoassemblies of keratin (KRT) and amyloidal peptides (-5Aβ42 and TDP-43 341-357). Furthermore, STM reveals a change in the conformational ensemble of peptide mutants, which is correlated with the macroscopic properties of peptide assemblies. Our results demonstrate that the STM-based single-molecule imaging can capture a thorough picture of the conformational substates with which to build an energetic landscape of interconformational interactions and can rapidly screen conformational ensembles, which can complement conventional characterization techniques.
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Affiliation(s)
- Wenbo Zhang
- State Key Laboratory of Medical Molecular Biology, Haihe Laboratory of Cell Ecosystem, Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, P. R. China
| | - Ruonan Wang
- State Key Laboratory of Medical Molecular Biology, Haihe Laboratory of Cell Ecosystem, Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, P. R. China
| | - Mingwei Liu
- State Key Laboratory of Medical Molecular Biology, Haihe Laboratory of Cell Ecosystem, Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, P. R. China
| | - Shucong Li
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Asher E Vokoun
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Weichen Deng
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Robert L Dupont
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Feiyi Zhang
- State Key Laboratory of Medical Molecular Biology, Haihe Laboratory of Cell Ecosystem, Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, P. R. China
- Institute for Advanced Materials, Jiangsu University, Zhenjiang, Jiangsu 212013, P. R. China
| | - Shuyuan Li
- State Key Laboratory of Medical Molecular Biology, Haihe Laboratory of Cell Ecosystem, Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, P. R. China
| | - Yang Wang
- State Key Laboratory of Medical Molecular Biology, Haihe Laboratory of Cell Ecosystem, Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, P. R. China
| | - Zhenyu Liu
- Center for Applied Physics and Technology, HEDPS and State Key Laboratory of Nuclear Physics and Technology, School of Physics, Peking University, Beijing 100871, P. R. China
| | - Yongfang Zheng
- Engineering Research Center of Industrial Biocatalysis, Fujian Province Universities, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Provincial Key Laboratory of Polymer Materials, College of Chemistry and Materials Science, Fujian Normal University, Fuzhou 350007, P.R. China
| | - Shuli Liu
- Department of Clinical Laboratory, Peking University Civil Aviation School of Clinical Medicine, Beijing 100123, P. R. China
| | - Yanlian Yang
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, Laboratory of Theoretical and Computational Nanoscience, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P. R. China
| | - Chen Wang
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, Laboratory of Theoretical and Computational Nanoscience, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P. R. China
| | - Lanlan Yu
- State Key Laboratory of Medical Molecular Biology, Haihe Laboratory of Cell Ecosystem, Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, P. R. China
| | - Yuxing Yao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Xiaoguang Wang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA
- Sustainability Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Chenxuan Wang
- State Key Laboratory of Medical Molecular Biology, Haihe Laboratory of Cell Ecosystem, Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, P. R. China
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112
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Stern AM, Yang Y, Jin S, Yamashita K, Meunier AL, Liu W, Cai Y, Ericsson M, Liu L, Goedert M, Scheres SHW, Selkoe DJ. Abundant Aβ fibrils in ultracentrifugal supernatants of aqueous extracts from Alzheimer's disease brains. Neuron 2023; 111:2012-2020.e4. [PMID: 37167969 PMCID: PMC10330525 DOI: 10.1016/j.neuron.2023.04.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 03/21/2023] [Accepted: 04/07/2023] [Indexed: 05/13/2023]
Abstract
Soluble oligomers of amyloid β-protein (Aβ) have been defined as aggregates in supernatants following ultracentrifugation of aqueous extracts from Alzheimer's disease (AD) brains and are believed to be upstream initiators of synaptic dysfunction, but little is known about their structures. We now report the unexpected presence of Aβ fibrils in synaptotoxic high-speed supernatants from AD brains extracted by soaking in an aqueous buffer. The fibrils did not appear to form during preparation, and their counts by EM correlated with Aβ ELISA quantification. Cryo-EM structures of aqueous Aβ fibrils were identical to those from sarkosyl-insoluble homogenates. The fibrils in aqueous extracts were labeled by lecanemab, an Aβ aggregate-directed antibody reported to improve AD cognitive outcomes. Lecanemab provided protection against aqueous fibril synaptotoxicity. We conclude that fibrils are abundant in aqueous extracts from AD brains and have the same structures as those from plaques. These findings have implications for AD pathogenesis and drug design.
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Affiliation(s)
- Andrew M Stern
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Yang Yang
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Shanxue Jin
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Keitaro Yamashita
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Angela L Meunier
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Wen Liu
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Yuqi Cai
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Maria Ericsson
- Harvard Medical School Electron Microscopy Facility, Boston, MA 02115, USA
| | - Lei Liu
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Michel Goedert
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Sjors H W Scheres
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Dennis J Selkoe
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA.
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113
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Silva JL, Foguel D, Ferreira VF, Vieira TCRG, Marques MA, Ferretti GDS, Outeiro TF, Cordeiro Y, de Oliveira GAP. Targeting Biomolecular Condensation and Protein Aggregation against Cancer. Chem Rev 2023. [PMID: 37379327 DOI: 10.1021/acs.chemrev.3c00131] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
Biomolecular condensates, membrane-less entities arising from liquid-liquid phase separation, hold dichotomous roles in health and disease. Alongside their physiological functions, these condensates can transition to a solid phase, producing amyloid-like structures implicated in degenerative diseases and cancer. This review thoroughly examines the dual nature of biomolecular condensates, spotlighting their role in cancer, particularly concerning the p53 tumor suppressor. Given that over half of the malignant tumors possess mutations in the TP53 gene, this topic carries profound implications for future cancer treatment strategies. Notably, p53 not only misfolds but also forms biomolecular condensates and aggregates analogous to other protein-based amyloids, thus significantly influencing cancer progression through loss-of-function, negative dominance, and gain-of-function pathways. The exact molecular mechanisms underpinning the gain-of-function in mutant p53 remain elusive. However, cofactors like nucleic acids and glycosaminoglycans are known to be critical players in this intersection between diseases. Importantly, we reveal that molecules capable of inhibiting mutant p53 aggregation can curtail tumor proliferation and migration. Hence, targeting phase transitions to solid-like amorphous and amyloid-like states of mutant p53 offers a promising direction for innovative cancer diagnostics and therapeutics.
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Affiliation(s)
- Jerson L Silva
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Debora Foguel
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Vitor F Ferreira
- Faculty of Pharmacy, Fluminense Federal University (UFF), Rio de Janeiro, RJ 21941-902, Brazil
| | - Tuane C R G Vieira
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Mayra A Marques
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Giulia D S Ferretti
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Tiago F Outeiro
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center, 37075 Göttingen, Germany
- Max Planck Institute for Multidisciplinary Sciences, 37075 Göttingen, Germany
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne NE2 4HH, U.K
- Scientific employee with an honorary contract at Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 37075 Göttingen, Germany
| | - Yraima Cordeiro
- Faculty of Pharmacy, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Guilherme A P de Oliveira
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
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114
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Xia Z, Wu Y, Lam JYL, Zhang Z, Burke M, Fertan E, Ranasinghe RT, Hidari E, Danial JS, Klenerman D. A computational suite for the structural and functional characterization of amyloid aggregates. CELL REPORTS METHODS 2023; 3:100499. [PMID: 37426747 PMCID: PMC10326375 DOI: 10.1016/j.crmeth.2023.100499] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 04/11/2023] [Accepted: 05/17/2023] [Indexed: 07/11/2023]
Abstract
We developed the aggregate characterization toolkit (ACT), a fully automated computational suite based on existing and widely used core algorithms to measure the number, size, and permeabilizing activity of recombinant and human-derived aggregates imaged with diffraction-limited and super-resolution microscopy methods at high throughput. We have validated ACT on simulated ground-truth images of aggregates mimicking those from diffraction-limited and super-resolution microscopies and showcased its use in characterizing protein aggregates from Alzheimer's disease. ACT is developed for high-throughput batch processing of images collected from multiple samples and is available as an open-source code. Given its accuracy, speed, and accessibility, ACT is expected to be a fundamental tool in studying human and non-human amyloid intermediates, developing early disease stage diagnostics, and screening for antibodies that bind toxic and heterogeneous human amyloid aggregates.
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Affiliation(s)
- Zengjie Xia
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge CB2 0AH, UK
| | - Yunzhao Wu
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge CB2 0AH, UK
| | - Jeff Yui Long Lam
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge CB2 0AH, UK
| | - Ziwei Zhang
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge CB2 0AH, UK
| | - Melanie Burke
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge CB2 0AH, UK
| | - Emre Fertan
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge CB2 0AH, UK
| | - Rohan T. Ranasinghe
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge CB2 0AH, UK
| | - Eric Hidari
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge CB2 0AH, UK
| | - John S.H. Danial
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge CB2 0AH, UK
| | - David Klenerman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge CB2 0AH, UK
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115
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Ma B, Ju A, Zhang S, An Q, Xu S, Liu J, Yu L, Fu Y, Luo Y. Albumosomes formed by cytoplasmic pre-folding albumin maintain mitochondrial homeostasis and inhibit nonalcoholic fatty liver disease. Signal Transduct Target Ther 2023; 8:229. [PMID: 37321990 PMCID: PMC10272166 DOI: 10.1038/s41392-023-01437-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 03/01/2023] [Accepted: 04/06/2023] [Indexed: 06/17/2023] Open
Abstract
Hepatic mitochondrial dysfunction contributes to the progression of nonalcoholic fatty liver disease (NAFLD). However, the factors that maintain mitochondrial homeostasis, especially in hepatocytes, are largely unknown. Hepatocytes synthesize various high-level plasma proteins, among which albumin is most abundant. In this study, we found that pre-folding albumin in the cytoplasm is completely different from folded albumin in the serum. Mechanistically, endogenous pre-folding albumin undergoes phase transition in the cytoplasm to form a shell-like spherical structure, which we call the "albumosome". Albumosomes interact with and trap pre-folding carnitine palmitoyltransferase 2 (CPT2) in the cytoplasm. Albumosomes control the excessive sorting of CPT2 to the mitochondria under high-fat-diet-induced stress conditions; in this way, albumosomes maintain mitochondrial homeostasis from exhaustion. Physiologically, albumosomes accumulate in hepatocytes during murine aging and protect the livers of aged mice from mitochondrial damage and fat deposition. Morphologically, mature albumosomes have a mean diameter of 4μm and are surrounded by heat shock protein Hsp90 and Hsp70 family proteins, forming a larger shell. The Hsp90 inhibitor 17-AAG promotes hepatic albumosomal accumulation in vitro and in vivo, through which suppressing the progression of NAFLD in mice.
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Affiliation(s)
- Boyuan Ma
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
- The National Engineering Research Center for Protein Technology, Tsinghua University, 100084, Beijing, China
- Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, 100084, Beijing, China
| | - Anji Ju
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
- The National Engineering Research Center for Protein Technology, Tsinghua University, 100084, Beijing, China
- Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, 100084, Beijing, China
| | - Shaosen Zhang
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
- The National Engineering Research Center for Protein Technology, Tsinghua University, 100084, Beijing, China
- Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, 100084, Beijing, China
- Department of Etiology and Carcinogenesis, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Qi An
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
- The National Engineering Research Center for Protein Technology, Tsinghua University, 100084, Beijing, China
- Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, 100084, Beijing, China
| | - Siran Xu
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
- The National Engineering Research Center for Protein Technology, Tsinghua University, 100084, Beijing, China
- Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, 100084, Beijing, China
| | - Jie Liu
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
- The National Engineering Research Center for Protein Technology, Tsinghua University, 100084, Beijing, China
- Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, 100084, Beijing, China
- Immunogenetics Laboratory, Shenzhen Blood Center, 518025, Shenzhen, Guangdong, China
| | - Li Yu
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Centre for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Yan Fu
- School of Life Sciences, Tsinghua University, 100084, Beijing, China.
- The National Engineering Research Center for Protein Technology, Tsinghua University, 100084, Beijing, China.
- Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, 100084, Beijing, China.
| | - Yongzhang Luo
- School of Life Sciences, Tsinghua University, 100084, Beijing, China.
- The National Engineering Research Center for Protein Technology, Tsinghua University, 100084, Beijing, China.
- Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, 100084, Beijing, China.
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116
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Wang Y, Xu J, Huang F, Yan J, Fan X, Zou Y, Wang C, Ding F, Sun Y. SEVI Inhibits Aβ Amyloid Aggregation by Capping the β-Sheet Elongation Edges. J Chem Inf Model 2023; 63:3567-3578. [PMID: 37246935 PMCID: PMC10363411 DOI: 10.1021/acs.jcim.3c00414] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Inhibiting the aggregation of amyloid peptides with endogenous peptides has broad interest due to their intrinsically high biocompatibility and low immunogenicity. Here, we investigated the inhibition mechanism of the prostatic acidic phosphatase fragment SEVI (semen-derived enhancer of viral infection) against Aβ42 fibrillization using atomistic discrete molecular dynamic simulations. Our result revealed that SEVI was intrinsically disordered with dynamic formation of residual helices. With a high positive net charge, the self-aggregation tendency of SEVI was weak. Aβ42 had a strong aggregation propensity by readily self-assembling into β-sheet-rich aggregates. SEVI preferred to interact with Aβ42, rather than SEVI themselves. In the heteroaggregates, Aβ42 mainly adopted β-sheets buried inside and capped by SEVI in the outer layer. SEVI could bind to various Aβ aggregation species─including monomers, dimers, and proto-fibrils─by capping the exposed β-sheet elongation edges. The aggregation processes Aβ42 from the formation of oligomers to conformational nucleation into fibrils and fibril growth should be inhibited as their β-sheet elongation edges are being occupied by the highly charged SEVI. Overall, our computational study uncovered the molecular mechanism of experimentally observed inhibition of SEVI against Aβ42 aggregation, providing novel insights into the development of therapeutic strategies against Alzheimer's disease.
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Affiliation(s)
- Ying Wang
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
- Ningbo Institute of Innovation for Combined Medicine and Engineering (NIIME), Ningbo Medical Center Lihuili Hospital, Ningbo 315211, China
| | - Jia Xu
- School of Medicine, Ningbo University, Ningbo 315211, China
| | - Fengjuan Huang
- Ningbo Institute of Innovation for Combined Medicine and Engineering (NIIME), Ningbo Medical Center Lihuili Hospital, Ningbo 315211, China
| | - Jiajia Yan
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Xinjie Fan
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Yu Zou
- Department of Sport and Exercise Science, Zhejiang University, Hangzhou 310058, China
| | - Chuang Wang
- School of Medicine, Ningbo University, Ningbo 315211, China
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Yunxiang Sun
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
- Ningbo Institute of Innovation for Combined Medicine and Engineering (NIIME), Ningbo Medical Center Lihuili Hospital, Ningbo 315211, China
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
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117
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Vendruscolo M. Thermodynamic and kinetic approaches for drug discovery to target protein misfolding and aggregation. Expert Opin Drug Discov 2023:1-11. [PMID: 37276120 DOI: 10.1080/17460441.2023.2221024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 05/30/2023] [Indexed: 06/07/2023]
Abstract
INTRODUCTION Protein misfolding diseases, including Alzheimer's and Parkinson's diseases, are characterized by the aberrant aggregation of proteins. These conditions are still largely untreatable, despite having a major impact on our healthcare systems and societies. AREAS COVERED We describe drug discovery strategies to target protein misfolding and aggregation. We compare thermodynamic approaches, which are based on the stabilization of the native states of proteins, with kinetic approaches, which are based on the slowing down of the aggregation process. This comparison is carried out in terms of the current knowledge of the process of protein misfolding and aggregation, the mechanisms of disease and the therapeutic targets. EXPERT OPINION There is an unmet need for disease-modifying treatments that target protein misfolding and aggregation for the over 50 human disorders known to be associated with this phenomenon. With the approval of the first drugs that can prevent misfolding or inhibit aggregation, future efforts will be focused on the discovery of effective compounds with these mechanisms of action for a wide range of conditions.
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Affiliation(s)
- Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
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118
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Pinzi L, Bisi N, Sorbi C, Franchini S, Tonali N, Rastelli G. Insights into the Structural Conformations of the Tau Protein in Different Aggregation Status. Molecules 2023; 28:molecules28114544. [PMID: 37299020 DOI: 10.3390/molecules28114544] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/23/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
Tau is a protein characterized by large structural portions displaying extended conformational changes. Unfortunately, the accumulation of this protein into toxic aggregates in neuronal cells leads to a number of severe pathologies, collectively named tauopathies. In the last decade, significant research advancements were achieved, including a better understanding of Tau structures and their implication in different tauopathies. Interestingly, Tau is characterized by a high structural variability depending on the type of disease, the crystallization conditions, and the formation of pathologic aggregates obtained from in vitro versus ex vivo samples. In this review, we reported an up-to-date and comprehensive overview of Tau structures reported in the Protein Data Bank, with a special focus on discussing the connections between structural features, different tauopathies, different crystallization conditions, and the use of in vitro or ex vivo samples. The information reported in this article highlights very interesting links between all these aspects, which we believe may be of particular relevance for a more informed structure-based design of compounds able to modulate Tau aggregation.
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Affiliation(s)
- Luca Pinzi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125 Modena, Italy
| | - Nicolò Bisi
- Centre National de la Recherche Scientifique (CNRS), Université de Paris-Saclay, BioCIS, Bat. Henri Moissan, 17 Av. des Sciences, 91400 Orsay, France
| | - Claudia Sorbi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125 Modena, Italy
| | - Silvia Franchini
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125 Modena, Italy
| | - Nicolò Tonali
- Centre National de la Recherche Scientifique (CNRS), Université de Paris-Saclay, BioCIS, Bat. Henri Moissan, 17 Av. des Sciences, 91400 Orsay, France
| | - Giulio Rastelli
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125 Modena, Italy
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119
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Biyani R, Hirata K, Oqmhula K, Yurtsever A, Hongo K, Maezono R, Takagi M, Fukuma T, Biyani M. Biophysical Properties of the Fibril Structure of the Toxic Conformer of Amyloid-β42: Characterization by Atomic Force Microscopy in Liquid and Molecular Docking. ACS APPLIED MATERIALS & INTERFACES 2023. [PMID: 37261999 DOI: 10.1021/acsami.3c06460] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Alzheimer's disease is associated with the aggregation of the misfolded neuronal peptide, amyloid-β42 (Aβ42). Evidence has suggested that several reasons are responsible for the toxicity caused by the aggregation of Aβ42, including the conformational restriction of Aβ42. In this study, one of the toxic conformers of Aβ42, which contains a Glu-to-Pro substitution (E22P-Aβ42), was explored using atomic force microscopy and molecular docking to study the aggregation dynamics. We proposed a systematic model of fibril formation to better understand the molecular basis of conformational transitions in the Aβ42 species. Our results demonstrated the formation of amorphous aggregates in E22P-Aβ42 that are stem-based, network-like structures, while the formation of mature fibrils occurred in the less toxic conformer of Aβ42, E22-Aβ42, that are sphere-like flexible structures. A comparison was made between the biophysical properties of E22P-Aβ42 and E22-Aβ42 that revealed that E22P-Aβ42 had greater stiffness, dihedral angle, number of β sheets involved, and elasticity, compared with E22-Aβ42. These findings will have considerable implications toward our understanding of the structural basis of the toxicity caused by conformational diversity in Aβ42 species.
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Affiliation(s)
- Radhika Biyani
- Department of Bioscience, Biotechnology, and Biomedical Engineering, School of Material Science, Japan Advanced Institute of Science and Technology, Asahidai 1-1, Nomi, Ishikawa 923-1292, Japan
| | - Kaito Hirata
- Institute for Frontier Science and Initiative, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Kenji Oqmhula
- School of Information Science, JAIST, Asahidai 1-1, Nomi, Ishikawa 923-1292, Japan
| | - Ayhan Yurtsever
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Kenta Hongo
- Research Center for Advanced Computing Infrastructure, JAIST, Asahidai 1-1, Nomi, Ishikawa 923-1292, Japan
| | - Ryo Maezono
- School of Information Science, JAIST, Asahidai 1-1, Nomi, Ishikawa 923-1292, Japan
| | - Masahiro Takagi
- Department of Bioscience, Biotechnology, and Biomedical Engineering, School of Material Science, Japan Advanced Institute of Science and Technology, Asahidai 1-1, Nomi, Ishikawa 923-1292, Japan
| | - Takeshi Fukuma
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Manish Biyani
- Department of Bioscience, Biotechnology, and Biomedical Engineering, School of Material Science, Japan Advanced Institute of Science and Technology, Asahidai 1-1, Nomi, Ishikawa 923-1292, Japan
- BioSeeds Corporation, JAIST Venture Business Laboratory, Asahidai 2-13, Nomi, Ishikawa 923-1211, Japan
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120
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McGregor L, Soler-López M. Structural basis of bioenergetic protein complexes in Alzheimer's disease pathogenesis. Curr Opin Struct Biol 2023; 80:102573. [DOI: 10.1016/j.sbi.2023.102573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/15/2023] [Accepted: 02/20/2023] [Indexed: 04/03/2023]
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121
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Björk L, Klingstedt T, Nilsson KPR. Thiophene-Based Ligands: Design, Synthesis and Their Utilization for Optical Assignment of Polymorphic-Disease-Associated Protein Aggregates. Chembiochem 2023; 24:e202300044. [PMID: 36891883 PMCID: PMC10404026 DOI: 10.1002/cbic.202300044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/03/2023] [Accepted: 03/08/2023] [Indexed: 03/10/2023]
Abstract
The development of ligands for detecting protein aggregates is of great interest, as these aggregated proteinaceous species are the pathological hallmarks of several devastating diseases, including Alzheimer's disease. In this regard, thiophene-based ligands have emerged as powerful tools for fluorescent assessment of these pathological entities. The intrinsic conformationally sensitive photophysical properties of poly- and oligothiophenes have allowed optical assignment of disease-associated protein aggregates in tissue sections, as well as real-time in vivo imaging of protein deposits. Herein, we recount the chemical evolution of different generations of thiophene-based ligands, and exemplify their use for the optical distinction of polymorphic protein aggregates. Furthermore, the chemical determinants for achieving a superior fluorescent thiophene-based ligand, as well as the next generation of thiophene-based ligands targeting distinct aggregated species are described. Finally, the directions for future research into the chemical design of thiophene-based ligands that can aid in resolving the scientific challenges around protein aggregation diseases are discussed.
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Affiliation(s)
- Linnea Björk
- Department of Physics, Chemistry and Biology, Linköping University, 581 83, Linköping, Sweden
| | - Therése Klingstedt
- Department of Physics, Chemistry and Biology, Linköping University, 581 83, Linköping, Sweden
| | - K Peter R Nilsson
- Department of Physics, Chemistry and Biology, Linköping University, 581 83, Linköping, Sweden
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122
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Sud K, Narula N, Aikawa E, Arbustini E, Pibarot P, Merlini G, Rosenson RS, Seshan SV, Argulian E, Ahmadi A, Zhou F, Moreira AL, Côté N, Tsimikas S, Fuster V, Gandy S, Bonow RO, Gursky O, Narula J. The contribution of amyloid deposition in the aortic valve to calcification and aortic stenosis. Nat Rev Cardiol 2023; 20:418-428. [PMID: 36624274 PMCID: PMC10199673 DOI: 10.1038/s41569-022-00818-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/17/2022] [Indexed: 01/11/2023]
Abstract
Calcific aortic valve disease (CAVD) and stenosis have a complex pathogenesis, and no therapies are available that can halt or slow their progression. Several studies have shown the presence of apolipoprotein-related amyloid deposits in close proximity to calcified areas in diseased aortic valves. In this Perspective, we explore a possible relationship between amyloid deposits, calcification and the development of aortic valve stenosis. These amyloid deposits might contribute to the amplification of the inflammatory cycle in the aortic valve, including extracellular matrix remodelling and myofibroblast and osteoblast-like cell proliferation. Further investigation in this area is needed to characterize the amyloid deposits associated with CAVD, which could allow the use of antisense oligonucleotides and/or isotype gene therapies for the prevention and/or treatment of CAVD.
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Affiliation(s)
- Karan Sud
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Navneet Narula
- New York University Grossman School of Medicine, New York, NY, USA.
| | - Elena Aikawa
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Philippe Pibarot
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, Canada
| | | | | | | | - Edgar Argulian
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Amir Ahmadi
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fang Zhou
- New York University Grossman School of Medicine, New York, NY, USA
| | - Andre L Moreira
- New York University Grossman School of Medicine, New York, NY, USA
| | - Nancy Côté
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, Canada
| | | | | | - Sam Gandy
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert O Bonow
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Olga Gursky
- Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Jagat Narula
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
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123
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Grover S, Pham T, Jones A, Sinobas-Pereira C, Villoch Diaz Maurino M, Garrad EC, Makoni NJ, Parks A, Domalewski RJ, Riggio G, An H, Chen K, Nichols MR. A new class of monoclonal Aβ antibodies selectively targets and triggers deposition of Aβ protofibrils. J Neurochem 2023; 165:860-873. [PMID: 37002186 DOI: 10.1111/jnc.15817] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 03/10/2023] [Accepted: 03/23/2023] [Indexed: 04/03/2023]
Abstract
Aggregation and accumulation of amyloid-β peptide (Aβ) are a critical trigger for the onset of Alzheimer's disease (AD). While the plaques are the most outstanding Aβ pathological feature, much of the recent research emphasis has been on soluble Aβ species because of their diffusible, proinflammatory, and toxic properties. The focus on soluble aggregated Aβ species has also increased the interest in antibodies that are selective for different Aβ conformations. In the current study, we developed and characterized a new class of monoclonal antibodies (referred to as mAbSL) that are selective for Aβ protofibrils. Cloning and sequencing of the heavy and light chain variable regions for multiple antibodies identified sequence characteristics that may impart the conformational selectivity by the antibodies. Transfection of FreeStyle 293F cells with the plasmids permitted in-house expression and purification of mAbSL antibodies along with non-conformation-selective Aβ monoclonal antibodies (Aβ mAbs). Several of the purified mAbSL antibodies demonstrated significant affinity and selectivity for Aβ42 protofibrils compared with Aβ42 monomers and Aβ42 fibrils. Competition ELISA assays assessing the best overall antibody, mAbSL 113, yielded affinity constants of 7 nM for the antibody-Aβ42 protofibril interaction, while the affinity for either Aβ42 monomers or Aβ42 fibrils was roughly 80 times higher. mAbSL 113 significantly inhibited Aβ42 monomer aggregation by a unique mechanism compared with the inhibition displayed by Aβ mAb 513. Aβ42 protofibril dynamics were also markedly altered in the presence of mAbSL 113, whereby insoluble complex formation and protofibril deposition were stimulated by the antibody at low substoichiometric molar ratios. As the field contemplates the therapeutic effectiveness of Aβ conformation-selective antibodies, the findings presented here demonstrate new information on a monoclonal antibody that selectively targets Aβ protofibrils and impacts Aβ dynamics.
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Affiliation(s)
- Shikha Grover
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, Missouri, USA
| | - Thao Pham
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, Missouri, USA
| | - Anna Jones
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, Missouri, USA
| | - Cristina Sinobas-Pereira
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, Missouri, USA
| | | | - Evan C Garrad
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, Missouri, USA
| | - Nyasha J Makoni
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, Missouri, USA
| | - Antanisha Parks
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, Missouri, USA
| | - Ryan J Domalewski
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, Missouri, USA
| | - Gabriel Riggio
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, Missouri, USA
| | - Hannah An
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, Missouri, USA
| | | | - Michael R Nichols
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, Missouri, USA
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124
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Schilling S, Pradhan A, Heesch A, Helbig A, Blennow K, Koch C, Bertgen L, Koo EH, Brinkmalm G, Zetterberg H, Kins S, Eggert S. Differential effects of familial Alzheimer's disease-causing mutations on amyloid precursor protein (APP) trafficking, proteolytic conversion, and synaptogenic activity. Acta Neuropathol Commun 2023; 11:87. [PMID: 37259128 DOI: 10.1186/s40478-023-01577-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/04/2023] [Indexed: 06/02/2023] Open
Abstract
The amyloid precursor protein (APP) is a key player in Alzheimer`s disease (AD) and the precursor of the Aβ peptide, which is generated by consecutive cleavages of β- and γ-secretases. Familial Alzheimer's disease (FAD) describes a hereditary subgroup of AD that represents a low percentage of AD cases with an early onset of the disease. Different APP FAD mutations are thought to have qualitatively different effects on its proteolytic conversion. However, few studies have explored the pathogenic and putative physiological differences in more detail. Here, we compared different FAD mutations, located at the β- (Swedish), α- (Flemish, Arctic, Iowa) or γ-secretase (Iberian) cleavage sites. We examined heterologous expression of APP WT and FAD mutants in non-neuronal cells and their impact on presynaptic differentiation in contacting axons of co-cultured neurons. To decipher the underlying molecular mechanism, we tested the subcellular localization, the endocytosis rate and the proteolytic processing in detail by immunoprecipitation-mass spectrometry. Interestingly, we found that only the Iberian mutation showed altered synaptogenic function. Furthermore, the APP Iowa mutant shows significantly decreased α-secretase processing which is in line with our results that APP carrying the Iowa mutation was significantly increased in early endosomes. However, most interestingly, immunoprecipitation-mass spectrometry analysis revealed that the amino acid substitutions of APP FAD mutants have a decisive impact on their processing reflected in altered Aβ profiles. Importantly, N-terminally truncated Aβ peptides starting at position 5 were detected preferentially for APP Flemish, Arctic, and Iowa mutants containing amino acid substitutions around the α-secretase cleavage site. The strongest change in the ratio of Aβ40/Aβ42 was observed for the Iberian mutation while APP Swedish showed a substantial increase in Aβ1-17 peptides. Together, our data indicate that familial AD mutations located at the α-, β-, and γ-secretase cleavage sites show considerable differences in the underlying pathogenic mechanisms.
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Affiliation(s)
- Sandra Schilling
- Department of Human Biology and Human Genetics, University of Kaiserslautern, 67663, Kaiserslautern, Germany
| | - Ajay Pradhan
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Amelie Heesch
- Department of Human Biology and Human Genetics, University of Kaiserslautern, 67663, Kaiserslautern, Germany
| | - Andrea Helbig
- Department of Human Biology and Human Genetics, University of Kaiserslautern, 67663, Kaiserslautern, Germany
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Christian Koch
- Department of Human Biology and Human Genetics, University of Kaiserslautern, 67663, Kaiserslautern, Germany
| | - Lea Bertgen
- Department of Human Biology and Human Genetics, University of Kaiserslautern, 67663, Kaiserslautern, Germany
| | - Edward H Koo
- San Diego (UCSD), Department of Neuroscience, University of California, La Jolla, CA, 92093-0662, USA
| | - Gunnar Brinkmalm
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, UK
- UK Dementia Research Institute at UCL, London, UK
- Hong Kong Center for Neurodegenerative Diseases, Clear Water Bay, Hong Kong, China
| | - Stefan Kins
- Department of Human Biology and Human Genetics, University of Kaiserslautern, 67663, Kaiserslautern, Germany
| | - Simone Eggert
- Department of Human Biology and Human Genetics, University of Kaiserslautern, 67663, Kaiserslautern, Germany.
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, City-Campus, Hermann-Rein-Str. 3, 37075, Göttingen, Germany.
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125
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Kreutzer AG, Guaglianone G, Yoo S, Parrocha CMT, Ruttenberg SM, Malonis RJ, Tong K, Lin YF, Nguyen JT, Howitz WJ, Diab MN, Hamza IL, Lai JR, Wysocki VH, Nowick JS. Probing differences among Aβ oligomers with two triangular trimers derived from Aβ. Proc Natl Acad Sci U S A 2023; 120:e2219216120. [PMID: 37216514 PMCID: PMC10235986 DOI: 10.1073/pnas.2219216120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 04/17/2023] [Indexed: 05/24/2023] Open
Abstract
The assembly of the β-amyloid peptide (Aβ) to form oligomers and fibrils is closely associated with the pathogenesis and progression of Alzheimer's disease. Aβ is a shape-shifting peptide capable of adopting many conformations and folds within the multitude of oligomers and fibrils the peptide forms. These properties have precluded detailed structural elucidation and biological characterization of homogeneous, well-defined Aβ oligomers. In this paper, we compare the structural, biophysical, and biological characteristics of two different covalently stabilized isomorphic trimers derived from the central and C-terminal regions Aβ. X-ray crystallography reveals the structures of the trimers and shows that each trimer forms a ball-shaped dodecamer. Solution-phase and cell-based studies demonstrate that the two trimers exhibit markedly different assembly and biological properties. One trimer forms small soluble oligomers that enter cells through endocytosis and activate capase-3/7-mediated apoptosis, while the other trimer forms large insoluble aggregates that accumulate on the outer plasma membrane and elicit cellular toxicity through an apoptosis-independent mechanism. The two trimers also exhibit different effects on the aggregation, toxicity, and cellular interaction of full-length Aβ, with one trimer showing a greater propensity to interact with Aβ than the other. The studies described in this paper indicate that the two trimers share structural, biophysical, and biological characteristics with oligomers of full-length Aβ. The varying structural, assembly, and biological characteristics of the two trimers provide a working model for how different Aβ trimers can assemble and lead to different biological effects, which may help shed light on the differences among Aβ oligomers.
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Affiliation(s)
- Adam G. Kreutzer
- Department of Chemistry, University of California Irvine, Irvine, CA92697
| | | | - Stan Yoo
- Department of Chemistry, University of California Irvine, Irvine, CA92697
| | | | | | - Ryan J. Malonis
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY10461
| | - Karen Tong
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY10461
| | - Yu-Fu Lin
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH43210
| | - Jennifer T. Nguyen
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA92697
| | - William J. Howitz
- Department of Chemistry, University of California Irvine, Irvine, CA92697
| | - Michelle N. Diab
- Department of Chemistry, University of California Irvine, Irvine, CA92697
| | - Imane L. Hamza
- Department of Chemistry, University of California Irvine, Irvine, CA92697
| | - Jonathan R. Lai
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY10461
| | - Vicki H. Wysocki
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH43210
| | - James S. Nowick
- Department of Chemistry, University of California Irvine, Irvine, CA92697
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA92697
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126
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Jeon J, Yau WM, Tycko R. Early events in amyloid-β self-assembly probed by time-resolved solid state NMR and light scattering. Nat Commun 2023; 14:2964. [PMID: 37221174 DOI: 10.1038/s41467-023-38494-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/04/2023] [Indexed: 05/25/2023] Open
Abstract
Self-assembly of amyloid-β peptides leads to oligomers, protofibrils, and fibrils that are likely instigators of neurodegeneration in Alzheimer's disease. We report results of time-resolved solid state nuclear magnetic resonance (ssNMR) and light scattering experiments on 40-residue amyloid-β (Aβ40) that provide structural information for oligomers that form on time scales from 0.7 ms to 1.0 h after initiation of self-assembly by a rapid pH drop. Low-temperature ssNMR spectra of freeze-trapped intermediates indicate that β-strand conformations within and contacts between the two main hydrophobic segments of Aβ40 develop within 1 ms, while light scattering data imply a primarily monomeric state up to 5 ms. Intermolecular contacts involving residues 18 and 33 develop within 0.5 s, at which time Aβ40 is approximately octameric. These contacts argue against β-sheet organizations resembling those found previously in protofibrils and fibrils. Only minor changes in the Aβ40 conformational distribution are detected as larger assemblies develop.
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Affiliation(s)
- Jaekyun Jeon
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
- Institute for Bioscience and Biotechnology Research, University of Maryland/National Institute of Standards and Technology, Rockville, MD, 20850, USA
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA.
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127
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Leistner C, Wilkinson M, Burgess A, Lovatt M, Goodbody S, Xu Y, Deuchars S, Radford SE, Ranson NA, Frank RAW. The in-tissue molecular architecture of β-amyloid pathology in the mammalian brain. Nat Commun 2023; 14:2833. [PMID: 37198197 PMCID: PMC10192217 DOI: 10.1038/s41467-023-38495-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 05/04/2023] [Indexed: 05/19/2023] Open
Abstract
Amyloid plaques composed of Aβ fibrils are a hallmark of Alzheimer's disease (AD). However, the molecular architecture of amyloid plaques in the context of fresh mammalian brain tissue is unknown. Here, using cryogenic correlated light and electron tomography we report the in situ molecular architecture of Aβ fibrils in the AppNL-G-F familial AD mouse model containing the Arctic mutation and an atomic model of ex vivo purified Arctic Aβ fibrils. We show that in-tissue Aβ fibrils are arranged in a lattice or parallel bundles, and are interdigitated by subcellular compartments, extracellular vesicles, extracellular droplets and extracellular multilamellar bodies. The Arctic Aβ fibril differs significantly from an earlier AppNL-F fibril structure, indicating a striking effect of the Arctic mutation. These structural data also revealed an ensemble of additional fibrillar species, including thin protofilament-like rods and branched fibrils. Together, these results provide a structural model for the dense network architecture that characterises β-amyloid plaque pathology.
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Affiliation(s)
- Conny Leistner
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Martin Wilkinson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Ailidh Burgess
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Megan Lovatt
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Stanley Goodbody
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Yong Xu
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0AA, UK
| | - Susan Deuchars
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
| | - René A W Frank
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
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128
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Zhang A, Portugal Barron D, Chen EW, Guo Z. A protein aggregation platform that distinguishes oligomers from amyloid fibrils. Analyst 2023; 148:2283-2294. [PMID: 37129054 PMCID: PMC10266934 DOI: 10.1039/d3an00487b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Deposition of aggregated proteins is a pathological feature in many neurodegenerative disorders such as Alzheimer's and Parkinson's. In addition to insoluble amyloid fibrils, protein aggregation leads to the formation of soluble oligomers, which are more toxic and pathogenic than fibrils. However, it is challenging to screen for inhibitors targeting oligomers due to the overlapping processes of oligomerization and fibrillization. Here we report a protein aggregation platform that uses intact and split TEM-1 β-lactamase proteins as reporters of protein aggregation. The intact β-lactamase fused with an amyloid protein can report the overall protein aggregation, which leads to loss of lactamase activity. On the other hand, reconstitution of active β-lactamase from the split lactamase construct requires the formation of amyloid oligomers, making the split lactamase system sensitive to oligomerization. Using Aβ, a protein that forms amyloid plaques in Alzheimer's disease, we show that the growth curves of bacterial cells expressing either intact or split lactamase-Aβ fusion proteins can report changes in the Aβ aggregation. The cell lysate lactamase activity assays show that the oligomer fraction accounts for 20% of total activity for the split lactamase-Aβ construct, but only 3% of total activity for the intact lactamase-Aβ construct, confirming the sensitivity of the split lactamase to oligomerization. The combination of the intact and split lactamase constructs allows the distinction of aggregation modulators targeting oligomerization from those targeting overall aggregation. These low-cost bacterial cell-based and biochemical assays are suitable for high-throughput screening of aggregation inhibitors targeting oligomers of various amyloid proteins.
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Affiliation(s)
- Amy Zhang
- Department of Neurology, Brain Research Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Diana Portugal Barron
- Department of Neurology, Brain Research Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Erica W Chen
- Department of Neurology, Brain Research Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Zhefeng Guo
- Department of Neurology, Brain Research Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
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129
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Qi C, Verheijen BM, Kokubo Y, Shi Y, Tetter S, Murzin AG, Nakahara A, Morimoto S, Vermulst M, Sasaki R, Aronica E, Hirokawa Y, Oyanagi K, Kakita A, Ryskeldi-Falcon B, Yoshida M, Hasegawa M, Scheres SH, Goedert M. Tau Filaments from Amyotrophic Lateral Sclerosis/Parkinsonism-Dementia Complex (ALS/PDC) adopt the CTE Fold. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.26.538417. [PMID: 37162924 PMCID: PMC10168338 DOI: 10.1101/2023.04.26.538417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The amyotrophic lateral sclerosis/parkinsonism-dementia complex (ALS/PDC) of the island of Guam and the Kii peninsula of Japan is a fatal neurodegenerative disease of unknown cause that is characterised by the presence of abundant filamentous tau inclusions in brains and spinal cords. Here we used electron cryo-microscopy (cryo-EM) to determine the structures of tau filaments from the cerebral cortex of three cases of ALS/PDC from Guam and eight cases from Kii, as well as from the spinal cord of two of the Guam cases. Tau filaments had the chronic traumatic encephalopathy (CTE) fold, with variable amounts of Type I and Type II filaments. Paired helical tau filaments were also found in two Kii cases. We also identified a novel Type III CTE tau filament, where protofilaments pack against each other in an anti-parallel fashion. ALS/PDC is the third known tauopathy with CTE-type filaments and abundant tau inclusions in cortical layers II/III, the others being CTE and subacute sclerosing panencephalitis. Because these tauopathies are believed to have environmental causes, our findings support the hypothesis that ALS/PDC is caused by exogenous factors.
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Affiliation(s)
- Chao Qi
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Bert M. Verheijen
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, USA
| | - Yasumasa Kokubo
- Graduate School of Regional Innovation Studies, Mie University, Tsu, Japan
| | - Yang Shi
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Current address: MOE Frontier Science Center for Brain Science and Brain-machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, China
| | | | | | - Asa Nakahara
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Satoru Morimoto
- Department of Oncologic Pathology, Graduate School of Medicine, Mie University, Tsu, Japan
| | - Marc Vermulst
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, USA
| | - Ryogen Sasaki
- Department of Nursing, Suzuka University of Medical Science, Suzuka, Japan
| | - Eleonora Aronica
- Department of Neuropathology, University of Amsterdam, Amsterdam, The Netherlands
| | - Yoshifumi Hirokawa
- Department of Oncologic Pathology, Graduate School of Medicine, Mie University, Tsu, Japan
| | - Kiyomitsu Oyanagi
- Department of Brain Disease Research, Shinshu University School of Medicine, Matsumoto, Japan
| | - Akiyoshi Kakita
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
| | | | - Mari Yoshida
- Department of Neuropathology, Institute for Medical Science of Aging, Aichi Medical University, Nagakute, Japan
| | - Masato Hasegawa
- Department of Brain and Neuroscience, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
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130
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Holcombe B, Foes A, Banerjee S, Yeh K, Wang SHJ, Bhargava R, Ghosh A. Intermediate antiparallel beta structure in amyloid plaques revealed by infrared spectroscopic imaging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.18.537414. [PMID: 37131832 PMCID: PMC10153194 DOI: 10.1101/2023.04.18.537414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Aggregation of amyloid beta (Aβ) peptides into extracellular plaques is a hallmark of the molecular pathology of Alzheimer's disease (AD). Amyloid aggregates have been extensively studied in-vitro, and it is well known that mature amyloid fibrils contain an ordered parallel β structure. The structural evolution from unaggregated peptide to fibrils can be mediated through intermediate structures that deviate significantly from mature fibrils, such as antiparallel β-sheets. However, it is currently unknown if these intermediate structures exist in plaques, which limits the translation of findings from in-vitro structural characterizations of amyloid aggregates to AD. This arises from the inability to extend common structural biology techniques to ex-vivo tissue measurements. Here we report the use of infrared (IR) imaging, wherein we can spatially localize plaques and probe their protein structural distributions with the molecular sensitivity of IR spectroscopy. Analyzing individual plaques in AD tissues, we demonstrate that fibrillar amyloid plaques exhibit antiparallel β-sheet signatures, thus providing a direct connection between in-vitro structures and amyloid aggregates in AD brain. We further validate results with IR imaging of in-vitro aggregates and show that antiparallel β-sheet structure is a distinct structural facet of amyloid fibrils.
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Affiliation(s)
- Brooke Holcombe
- Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, AL 35401, USA
| | - Abigail Foes
- Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, AL 35401, USA
| | - Siddhartha Banerjee
- Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, AL 35401, USA
| | - Kevin Yeh
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shih-Hsiu J. Wang
- Departments of Pathology and Neurology, Duke University, Durham, NC 27710, USA
| | - Rohit Bhargava
- Departments of Bioengineering, Electrical and Computer Engineering, Mechanical Science and Engineering, Chemical and Biomolecular Engineering, and Chemistry, Beckman Institute for Advanced Science and Technology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ayanjeet Ghosh
- Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, AL 35401, USA
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131
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Sun Y, Jack K, Ercolani T, Sangar D, Hosszu L, Collinge J, Bieschke J. Direct Observation of Competing Prion Protein Fibril Populations with Distinct Structures and Kinetics. ACS NANO 2023; 17:6575-6588. [PMID: 36802500 PMCID: PMC10100569 DOI: 10.1021/acsnano.2c12009] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
In prion diseases, fibrillar assemblies of misfolded prion protein (PrP) self-propagate by incorporating PrP monomers. These assemblies can evolve to adapt to changing environments and hosts, but the mechanism of prion evolution is poorly understood. We show that PrP fibrils exist as a population of competing conformers, which are selectively amplified under different conditions and can "mutate" during elongation. Prion replication therefore possesses the steps necessary for molecular evolution analogous to the quasispecies concept of genetic organisms. We monitored structure and growth of single PrP fibrils by total internal reflection and transient amyloid binding super-resolution microscopy and detected at least two main fibril populations, which emerged from seemingly homogeneous PrP seeds. All PrP fibrils elongated in a preferred direction by an intermittent "stop-and-go" mechanism, but each population possessed distinct elongation mechanisms that incorporated either unfolded or partially folded monomers. Elongation of RML and ME7 prion rods likewise exhibited distinct kinetic features. The discovery of polymorphic fibril populations growing in competition, which were previously hidden in ensemble measurements, suggests that prions and other amyloid replicating by prion-like mechanisms may represent quasispecies of structural isomorphs that can evolve to adapt to new hosts and conceivably could evade therapeutic intervention.
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Affiliation(s)
- Yuanzi Sun
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
| | - Kezia Jack
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
| | - Tiziana Ercolani
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
| | - Daljit Sangar
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
| | - Laszlo Hosszu
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
| | - John Collinge
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
| | - Jan Bieschke
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
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132
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Kumar R, Arroyo-García LE, Manchanda S, Adam L, Pizzirusso G, Biverstål H, Nilsson P, Fisahn A, Johansson J, Abelein A. Molecular Mechanisms of Amyloid-β Self-Assembly Seeded by In Vivo-Derived Fibrils and Inhibitory Effects of the BRICHOS Chaperone. ACS Chem Neurosci 2023. [PMID: 37023330 PMCID: PMC10119923 DOI: 10.1021/acschemneuro.3c00044] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023] Open
Abstract
Self-replication of amyloid-β-peptide (Aβ) fibril formation is a hallmark in Alzheimer's disease (AD). Detailed insights have been obtained in Aβ self-assembly in vitro, yet whether similar mechanisms are relevant in vivo has remained elusive. Here, we investigated the ability of in vivo-derived Aβ fibrils from two different amyloid precursor protein knock-in AD mouse models to seed Aβ42 aggregation, where we quantified the microscopic rate constants. We found that the nucleation mechanism of in vivo-derived fibril-seeded Aβ42 aggregation can be described with the same kinetic model as that in vitro. Further, we identified the inhibitory mechanism of the anti-amyloid BRICHOS chaperone on seeded Aβ42 fibrillization, revealing a suppression of secondary nucleation and fibril elongation, which is strikingly similar as observed in vitro. These findings hence provide a molecular understanding of the Aβ42 nucleation process triggered by in vivo-derived Aβ42 propagons, providing a framework for the search for new AD therapeutics.
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Affiliation(s)
- Rakesh Kumar
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 52 Huddinge, Sweden
| | - Luis Enrique Arroyo-García
- Division of Neurogeriatrics; Center for Alzheimer Research; Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, 171 64 Solna, Sweden
- Department of Women's and Children's Health, Karolinska Institutet, 171 64 Solna, Sweden
| | - Shaffi Manchanda
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 52 Huddinge, Sweden
| | - Laurène Adam
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 52 Huddinge, Sweden
| | - Giusy Pizzirusso
- Division of Neurogeriatrics; Center for Alzheimer Research; Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, 171 64 Solna, Sweden
- Department of Women's and Children's Health, Karolinska Institutet, 171 64 Solna, Sweden
| | - Henrik Biverstål
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 52 Huddinge, Sweden
| | - Per Nilsson
- Division of Neurogeriatrics; Center for Alzheimer Research; Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, 171 64 Solna, Sweden
| | - André Fisahn
- Division of Neurogeriatrics; Center for Alzheimer Research; Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, 171 64 Solna, Sweden
| | - Jan Johansson
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 52 Huddinge, Sweden
| | - Axel Abelein
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 52 Huddinge, Sweden
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133
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Sun X, Dyson HJ, Wright PE. Role of conformational dynamics in pathogenic protein aggregation. Curr Opin Chem Biol 2023; 73:102280. [PMID: 36878172 PMCID: PMC10033434 DOI: 10.1016/j.cbpa.2023.102280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/13/2023] [Accepted: 02/02/2023] [Indexed: 03/06/2023]
Abstract
The accumulation of pathogenic protein oligomers and aggregates is associated with several devastating amyloid diseases. As protein aggregation is a multi-step nucleation-dependent process beginning with unfolding or misfolding of the native state, it is important to understand how innate protein dynamics influence aggregation propensity. Kinetic intermediates composed of heterogeneous ensembles of oligomers are frequently formed on the aggregation pathway. Characterization of the structure and dynamics of these intermediates is critical to the understanding of amyloid diseases since oligomers appear to be the main cytotoxic agents. In this review, we highlight recent biophysical studies of the roles of protein dynamics in driving pathogenic protein aggregation, yielding new mechanistic insights that can be leveraged for design of aggregation inhibitors.
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Affiliation(s)
- Xun Sun
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - H Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Peter E Wright
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.
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134
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Chakraborty D, Straub JE, Thirumalai D. Energy landscapes of Aβ monomers are sculpted in accordance with Ostwald's rule of stages. SCIENCE ADVANCES 2023; 9:eadd6921. [PMID: 36947617 PMCID: PMC10032606 DOI: 10.1126/sciadv.add6921] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
The transition from a disordered to an assembly-competent monomeric state (N*) in amyloidogenic sequences is a crucial event in the aggregation cascade. Using a well-calibrated model for intrinsically disordered proteins (IDPs), we show that the N* states, which bear considerable resemblance to the polymorphic fibril structures found in experiments, not only appear as excitations in the free energy landscapes of Aβ40 and Aβ42, but also initiate the aggregation cascade. For Aβ42, the transitions to the different N* states are in accord with Ostwald's rule of stages, with the least stable structures forming ahead of thermodynamically favored ones. The Aβ40 and Aβ42 monomer landscapes exhibit different extents of local frustration, which we show have profound implications in dictating subsequent self-assembly. Using kinetic transition networks, we illustrate that the most favored dimerization routes proceed via N* states. We argue that Ostwald's rule also holds for the aggregation of fused in sarcoma and polyglutamine proteins.
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Affiliation(s)
- Debayan Chakraborty
- Department of Chemistry, The University of Texas at Austin, 105 E 24th Street, Stop A5300, Austin TX 78712, USA
| | - John E. Straub
- Department of Chemistry, Boston University, MA 022155, USA
| | - D. Thirumalai
- Department of Chemistry, The University of Texas at Austin, 105 E 24th Street, Stop A5300, Austin TX 78712, USA
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135
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Lee M, Yau WM, Louis JM, Tycko R. Structures of brain-derived 42-residue amyloid-β fibril polymorphs with unusual molecular conformations and intermolecular interactions. Proc Natl Acad Sci U S A 2023; 120:e2218831120. [PMID: 36893281 PMCID: PMC10089215 DOI: 10.1073/pnas.2218831120] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/04/2023] [Indexed: 03/11/2023] Open
Abstract
Fibrils formed by the 42-residue amyloid-β peptide (Aβ42), a main component of amyloid deposits in Alzheimer's disease (AD), are known to be polymorphic, i.e., to contain multiple possible molecular structures. Previous studies of Aβ42 fibrils, including fibrils prepared entirely in vitro or extracted from brain tissue and using solid-state NMR (ssNMR) or cryogenic electron microscopy (cryo-EM) methods, have found polymorphs with differences in amino acid sidechain orientations, lengths of structurally ordered segments, and contacts between cross-β subunit pairs within a single filament. Despite these differences, Aβ42 molecules adopt a common S-shaped conformation in all previously described high-resolution Aβ42 fibril structures. Here we report two cryo-EM-based structures of Aβ42 fibrils that are qualitatively different, in samples derived from AD brain tissue by seeded growth. In type A fibrils, residues 12 to 42 adopt a ν-shaped conformation, with both intra-subunit and intersubunit hydrophobic contacts to form a compact core. In type B fibrils, residues 2 to 42 adopt an υ-shaped conformation, with only intersubunit contacts and internal pores. Type A and type B fibrils have opposite helical handedness. Cryo-EM density maps and molecular dynamics simulations indicate intersubunit K16-A42 salt bridges in type B fibrils and partially occupied K28-A42 salt bridges in type A fibrils. The coexistence of two predominant polymorphs, with differences in N-terminal dynamics, is supported by ssNMR data, as is faithful propagation of structures from first-generation to second-generation brain-seeded Aβ42 fibril samples. These results demonstrate that Aβ42 fibrils can exhibit a greater range of structural variations than seen in previous studies.
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Affiliation(s)
- Myungwoon Lee
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD20892-0520
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD20892-0520
| | - John M. Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD20892-0520
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD20892-0520
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136
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Zangiabadi M, Ghosh A, Zhao Y. Nanoparticle Scanners for the Identification of Key Sequences Involved in the Assembly and Disassembly of β-Amyloid Peptides. ACS NANO 2023; 17:4764-4774. [PMID: 36857741 DOI: 10.1021/acsnano.2c11186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The aggregation of β-amyloid peptides (Aβ), implied in the development and progression of Alzheimer's disease, is driven by a complex set of intramolecular and intermolecular interactions involving both hydrophobic and polar residues. The key residues responsible for the forward assembling process may be different from those that should be targeted to disassemble already formed aggregates. Molecularly imprinted nanoparticle (MINP) receptors are reported in this work to strongly and selectively bind specific segments of Aβ40. Combined fluorescence spectroscopy, atomic force microscopy (AFM) imaging, and circular dichroism (CD) spectroscopy indicate that binding residues 21-30 near the loop region is most effective at inhibiting the aggregation of monomeric Aβ40, but residues 11-20 that include the internal β strand closer to the N-terminal represent the best target for disaggregating already formed aggregates in the polymerization phase. Once the aggregation proceeds to the saturation phase, binding residues 1-10 has the largest effect on the disaggregation, likely because of the accessibility of these amino acids relative to others to the MINP receptors.
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Affiliation(s)
- Milad Zangiabadi
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, United States
| | - Avijit Ghosh
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, United States
| | - Yan Zhao
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, United States
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137
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Penke B, Szűcs M, Bogár F. New Pathways Identify Novel Drug Targets for the Prevention and Treatment of Alzheimer’s Disease. Int J Mol Sci 2023; 24:ijms24065383. [PMID: 36982456 PMCID: PMC10049476 DOI: 10.3390/ijms24065383] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/06/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023] Open
Abstract
Alzheimer’s disease (AD) is an incurable, progressive neurodegenerative disorder. AD is a complex and multifactorial disease that is responsible for 60–80% of dementia cases. Aging, genetic factors, and epigenetic changes are the main risk factors for AD. Two aggregation-prone proteins play a decisive role in AD pathogenesis: β-amyloid (Aβ) and hyperphosphorylated tau (pTau). Both of them form deposits and diffusible toxic aggregates in the brain. These proteins are the biomarkers of AD. Different hypotheses have tried to explain AD pathogenesis and served as platforms for AD drug research. Experiments demonstrated that both Aβ and pTau might start neurodegenerative processes and are necessary for cognitive decline. The two pathologies act in synergy. Inhibition of the formation of toxic Aβ and pTau aggregates has been an old drug target. Recently, successful Aβ clearance by monoclonal antibodies has raised new hopes for AD treatments if the disease is detected at early stages. More recently, novel targets, e.g., improvements in amyloid clearance from the brain, application of small heat shock proteins (Hsps), modulation of chronic neuroinflammation by different receptor ligands, modulation of microglial phagocytosis, and increase in myelination have been revealed in AD research.
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Affiliation(s)
- Botond Penke
- Department of Medical Chemistry, University of Szeged, Dóm Square 8, H-6720 Szeged, Hungary
- Correspondence:
| | - Mária Szűcs
- Department of Medical Chemistry, University of Szeged, Dóm Square 8, H-6720 Szeged, Hungary
| | - Ferenc Bogár
- ELKH-SZTE Biomimetic Systems Research Group, Eötvös Loránd Research Network (ELKH), Dóm Square 8, H-6720 Szeged, Hungary
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138
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Wilkinson M, Gallardo RU, Martinez RM, Guthertz N, So M, Aubrey LD, Radford SE, Ranson NA. Disease-relevant β 2-microglobulin variants share a common amyloid fold. Nat Commun 2023; 14:1190. [PMID: 36864041 PMCID: PMC9981686 DOI: 10.1038/s41467-023-36791-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 02/16/2023] [Indexed: 03/04/2023] Open
Abstract
β2-microglobulin (β2m) and its truncated variant ΔΝ6 are co-deposited in amyloid fibrils in the joints, causing the disorder dialysis-related amyloidosis (DRA). Point mutations of β2m result in diseases with distinct pathologies. β2m-D76N causes a rare systemic amyloidosis with protein deposited in the viscera in the absence of renal failure, whilst β2m-V27M is associated with renal failure, with amyloid deposits forming predominantly in the tongue. Here we use cryoEM to determine the structures of fibrils formed from these variants under identical conditions in vitro. We show that each fibril sample is polymorphic, with diversity arising from a 'lego-like' assembly of a common amyloid building block. These results suggest a 'many sequences, one amyloid fold' paradigm in contrast with the recently reported 'one sequence, many amyloid folds' behaviour of intrinsically disordered proteins such as tau and Aβ.
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Affiliation(s)
- Martin Wilkinson
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Rodrigo U Gallardo
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Aelin Therapeutics, Bio-Incubator Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Roberto Maya Martinez
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Peak Proteins, Birchwood House, Larkwood Way, Macclesfield, Cheshire, SK10 2XR, UK
| | - Nicolas Guthertz
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Bicycle Therapeutics, Blocks A & B, Portway Building, Grant Park, Abingdon, Cambridge, CB21 6GS, UK
| | - Masatomo So
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan
| | - Liam D Aubrey
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
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139
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Liu J, Wu XL, Zeng YT, Hu ZH, Lu JX. Solid-state NMR studies of amyloids. Structure 2023; 31:230-243. [PMID: 36750098 DOI: 10.1016/j.str.2023.01.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/10/2022] [Accepted: 01/09/2023] [Indexed: 02/08/2023]
Abstract
Amyloids have special structural properties and are involved in many aspects of biological function. In particular, amyloids are the cause or hallmarks of a group of notorious and incurable neurodegenerative diseases. The extraordinary high molecular weight and aggregation states of amyloids have posed a challenge for researchers studying them. Solid-state NMR (SSNMR) has been extensively applied to study the structures and dynamics of amyloids for the past 20 or more years and brought us tremendous progress in understanding their structure and related diseases. These studies, at the same time, helped to push SSNMR technical developments in sensitivity and resolution. In this review, some interesting research studies and important technical developments are highlighted to give the reader an overview of the current state of this field.
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Affiliation(s)
- Jing Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xia-Lian Wu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yu-Teng Zeng
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Zhi-Heng Hu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jun-Xia Lu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
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140
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Yang Y, Zhang W, Murzin AG, Schweighauser M, Huang M, Lövestam S, Peak-Chew SY, Saito T, Saido TC, Macdonald J, Lavenir I, Ghetti B, Graff C, Kumar A, Nordberg A, Goedert M, Scheres SHW. Cryo-EM structures of amyloid-β filaments with the Arctic mutation (E22G) from human and mouse brains. Acta Neuropathol 2023; 145:325-333. [PMID: 36611124 PMCID: PMC9925504 DOI: 10.1007/s00401-022-02533-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/15/2022] [Accepted: 12/15/2022] [Indexed: 01/09/2023]
Abstract
The Arctic mutation, encoding E693G in the amyloid precursor protein (APP) gene [E22G in amyloid-β (Aβ)], causes dominantly inherited Alzheimer's disease. Here, we report the high-resolution cryo-EM structures of Aβ filaments from the frontal cortex of a previously described case (AβPParc1) with the Arctic mutation. Most filaments consist of two pairs of non-identical protofilaments that comprise residues V12-V40 (human Arctic fold A) and E11-G37 (human Arctic fold B). They have a substructure (residues F20-G37) in common with the folds of type I and type II Aβ42. When compared to the structures of wild-type Aβ42 filaments, there are subtle conformational changes in the human Arctic folds, because of the lack of a side chain at G22, which may strengthen hydrogen bonding between mutant Aβ molecules and promote filament formation. A minority of Aβ42 filaments of type II was also present, as were tau paired helical filaments. In addition, we report the cryo-EM structures of Aβ filaments with the Arctic mutation from mouse knock-in line AppNL-G-F. Most filaments are made of two identical mutant protofilaments that extend from D1 to G37 (AppNL-G-F murine Arctic fold). In a minority of filaments, two dimeric folds pack against each other in an anti-parallel fashion. The AppNL-G-F murine Arctic fold differs from the human Arctic folds, but shares some substructure.
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Affiliation(s)
- Yang Yang
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Wenjuan Zhang
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Medical Research Council Prion Unit and Institute of Prion Diseases, University College London, London, UK
| | - Alexey G Murzin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | | | - Melissa Huang
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Dementia Research Institute, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Sofia Lövestam
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Sew Y Peak-Chew
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Takashi Saito
- RIKEN Brain Science Institute, Saitama, Japan
- Department of Neurocognitive Science, Nagoya City University, Nagoya, Japan
| | | | | | - Isabelle Lavenir
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Bernardino Ghetti
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Caroline Graff
- Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
- Theme Inflammation and Aging, Karolinska University Hospital, Stockholm, Sweden
| | - Amit Kumar
- Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Agneta Nordberg
- Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
- Theme Inflammation and Aging, Karolinska University Hospital, Stockholm, Sweden
| | - Michel Goedert
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
| | - Sjors H W Scheres
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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141
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I F. The unique neuropathological vulnerability of the human brain to aging. Ageing Res Rev 2023; 87:101916. [PMID: 36990284 DOI: 10.1016/j.arr.2023.101916] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/19/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023]
Abstract
Alzheimer's disease (AD)-related neurofibrillary tangles (NFT), argyrophilic grain disease (AGD), aging-related tau astrogliopathy (ARTAG), limbic predominant TDP-43 proteinopathy (LATE), and amygdala-predominant Lewy body disease (LBD) are proteinopathies that, together with hippocampal sclerosis, progressively appear in the elderly affecting from 50% to 99% of individuals aged 80 years, depending on the disease. These disorders usually converge on the same subject and associate with additive cognitive impairment. Abnormal Tau, TDP-43, and α-synuclein pathologies progress following a pattern consistent with an active cell-to-cell transmission and abnormal protein processing in the host cell. However, cell vulnerability and transmission pathways are specific for each disorder, albeit abnormal proteins may co-localize in particular neurons. All these alterations are unique or highly prevalent in humans. They all affect, at first, the archicortex and paleocortex to extend at later stages to the neocortex and other regions of the telencephalon. These observations show that the phylogenetically oldest areas of the human cerebral cortex and amygdala are not designed to cope with the lifespan of actual humans. New strategies aimed at reducing the functional overload of the human telencephalon, including optimization of dream repair mechanisms and implementation of artificial circuit devices to surrogate specific brain functions, appear promising.
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Affiliation(s)
- Ferrer I
- Department of Pathology and Experimental Therapeutics, University of Barcelona, Barcelona, Spain; Emeritus Researcher of the Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain; Biomedical Research Network of Neurodegenerative Diseases (CIBERNED), Barcelona, Spain; Institute of Neurosciences, University of Barcelona, Barcelona, Spain; Hospitalet de Llobregat, Barcelona, Spain.
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142
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The interactions of amyloid β aggregates with phospholipid membranes and the implications for neurodegeneration. Biochem Soc Trans 2023; 51:147-159. [PMID: 36629697 DOI: 10.1042/bst20220434] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 01/12/2023]
Abstract
Misfolding, aggregation and accumulation of Amyloid-β peptides (Aβ) in neuronal tissue and extracellular matrix are hallmark features of Alzheimer's disease (AD) pathology. Soluble Aβ oligomers are involved in neuronal toxicity by interacting with the lipid membrane, compromising its integrity, and affecting the function of receptors. These facts indicate that the interaction between Aβ oligomers and cell membranes may be one of the central molecular level factors responsible for the onset of neurodegeneration. The present review provides a structural understanding of Aβ neurotoxicity via membrane interactions and contributes to understanding early events in Alzheimer's disease.
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143
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Plascencia-Villa G, Perry G. Lessons from antiamyloid-β immunotherapies in Alzheimer's disease. HANDBOOK OF CLINICAL NEUROLOGY 2023; 193:267-292. [PMID: 36803816 DOI: 10.1016/b978-0-323-85555-6.00019-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
The amyloid hypothesis, that established amyloid-β (Aβ) peptide as the primary cause of Alzheimer's disease (AD) and related dementia, has driven the development of treatments for neurodegeneration for 30 years. During the last decades, more than 200 clinical trials testing more than 30 anti-Aβ immunotherapies have been assessed as potential treatments for AD. A vaccine against Aβ was the first immunotherapy intended to avoid aggregation of Aβ into fibrils and senile plaques, but it dramatically failed. Several other vaccines have been proposed as potential AD treatments, targeting different domains or structural motifs of Aβ aggregates, but without clear clinical benefits or effectiveness. In contrast, anti-Aβ therapeutic antibodies have focused on recognizing and removing Aβ aggregates (oligomers, fibrils, or plaques) by eliciting immune clearance. In 2021, the first anti-Aβ antibody, aducanumab (branded as Aduhelm), received FDA approval under an accelerated approval process. The effectiveness and the overall processes regarding the approval of Aduhelm have been under major criticism and scrutiny, prompting a vote of no confidence by public and private health providers, limiting the coverage only to patients enrolled in clinical trials and not for the general elderly patients. Additionally, another three therapeutic anti-Aβ antibodies are following the same path for potential FDA approval. Here, we present the current status of anti-Aβ immunotherapies under evaluation in preclinical and clinical trials for the treatment of AD and related dementia, with a discussion of the main findings and critical lessons learned from the observations from Phase III, II, and I clinical trials of anti-Aβ vaccines and antibodies.
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Affiliation(s)
- Germán Plascencia-Villa
- Department of Neurosciences, Developmental and Regenerative Biology, The University of Texas at San Antonio (UTSA), San Antonio, TX, United States
| | - George Perry
- Department of Neurosciences, Developmental and Regenerative Biology, The University of Texas at San Antonio (UTSA), San Antonio, TX, United States.
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144
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Mullapudi V, Vaquer-Alicea J, Bommareddy V, Vega AR, Ryder BD, White CL, Diamond MI, Joachimiak LA. Network of hotspot interactions cluster tau amyloid folds. Nat Commun 2023; 14:895. [PMID: 36797278 PMCID: PMC9935906 DOI: 10.1038/s41467-023-36572-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 02/06/2023] [Indexed: 02/18/2023] Open
Abstract
Cryogenic electron microscopy has revealed unprecedented molecular insight into the conformations of β-sheet-rich protein amyloids linked to neurodegenerative diseases. It remains unknown how a protein can adopt a diversity of folds and form multiple distinct fibrillar structures. Here we develop an in silico alanine scan method to estimate the relative energetic contribution of each amino acid in an amyloid assembly. We apply our method to twenty-seven ex vivo and in vitro fibril structural polymorphs of the microtubule-associated protein tau. We uncover networks of energetically important interactions involving amyloid-forming motifs that stabilize the different fibril folds. We evaluate our predictions in cellular and in vitro aggregation assays. Using a machine learning approach, we classify the structures based on residue energetics to identify distinguishing and unifying features. Our energetic profiling suggests that minimal sequence elements control the stability of tau fibrils, allowing future design of protein sequences that fold into unique structures.
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Affiliation(s)
- Vishruth Mullapudi
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jaime Vaquer-Alicea
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Vaibhav Bommareddy
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Anthony R Vega
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Bryan D Ryder
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Molecular Biophysics Graduate Program, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Charles L White
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Marc I Diamond
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Lukasz A Joachimiak
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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145
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Galzitskaya OV, Grishin SY, Glyakina AV, Dovidchenko NV, Konstantinova AV, Kravchenko SV, Surin AK. The Strategies of Development of New Non-Toxic Inhibitors of Amyloid Formation. Int J Mol Sci 2023; 24:ijms24043781. [PMID: 36835194 PMCID: PMC9964835 DOI: 10.3390/ijms24043781] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 02/16/2023] Open
Abstract
In recent years, due to the aging of the population and the development of diagnostic medicine, the number of identified diseases associated with the accumulation of amyloid proteins has increased. Some of these proteins are known to cause a number of degenerative diseases in humans, such as amyloid-beta (Aβ) in Alzheimer's disease (AD), α-synuclein in Parkinson's disease (PD), and insulin and its analogues in insulin-derived amyloidosis. In this regard, it is important to develop strategies for the search and development of effective inhibitors of amyloid formation. Many studies have been carried out aimed at elucidating the mechanisms of amyloid aggregation of proteins and peptides. This review focuses on three amyloidogenic peptides and proteins-Aβ, α-synuclein, and insulin-for which we will consider amyloid fibril formation mechanisms and analyze existing and prospective strategies for the development of effective and non-toxic inhibitors of amyloid formation. The development of non-toxic inhibitors of amyloid will allow them to be used more effectively for the treatment of diseases associated with amyloid.
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Affiliation(s)
- Oxana V. Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia
- Correspondence:
| | - Sergei Y. Grishin
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia
| | - Anna V. Glyakina
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
- Institute of Mathematical Problems of Biology RAS, The Branch of Keldysh Institute of Applied Mathematics, Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Nikita V. Dovidchenko
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Anastasiia V. Konstantinova
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
- Faculty of Biotechnology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Sergey V. Kravchenko
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia
| | - Alexey K. Surin
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
- The Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Russia
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146
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Yi Y, Lim MH. Current understanding of metal-dependent amyloid-β aggregation and toxicity. RSC Chem Biol 2023; 4:121-131. [PMID: 36794021 PMCID: PMC9906324 DOI: 10.1039/d2cb00208f] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/22/2022] [Indexed: 11/23/2022] Open
Abstract
The discovery of effective therapeutics targeting amyloid-β (Aβ) aggregates for Alzheimer's disease (AD) has been very challenging, which suggests its complicated etiology associated with multiple pathogenic elements. In AD-affected brains, highly concentrated metals, such as copper and zinc, are found in senile plaques mainly composed of Aβ aggregates. These metal ions are coordinated to Aβ and affect its aggregation and toxicity profiles. In this review, we illustrate the current view on molecular insights into the assembly of Aβ peptides in the absence and presence of metal ions as well as the effect of metal ions on their toxicity.
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Affiliation(s)
- Yelim Yi
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
| | - Mi Hee Lim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
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147
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Roldán-Martín L, Sodupe M, Maréchal JD. Computational assessment of the impact of Cu(II) and Al(III) on β-amyloid 42 fibrils: Binding sites, structural stability, and possible physiological implications. Front Neurosci 2023; 17:1110311. [PMID: 36814794 PMCID: PMC9940836 DOI: 10.3389/fnins.2023.1110311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/10/2023] [Indexed: 02/09/2023] Open
Abstract
One of Alzheimer's disease major hallmarks is the aggregation of β-amyloid peptide, a process in which metal ions play an important role. In the present work, an integrative computational study has been performed to identify the metal-binding regions and determine the conformational impact of Cu(II) and Al(III) ion binding to the β-amyloid (Aβ42) fibrillary structure. Through classical and Gaussian accelerated molecular dynamics, it has been observed that the metal-free fiber shows a hinge fan-like motion of the S-shaped structure, maintaining the general conformation. Upon metal coordination, distinctive patterns are observed depending on the metal. Cu(II) binds to the flexible N-terminal region and induces structural changes that could ultimately disrupt the fibrillary structure. In contrast, Al(III) binding takes place with the residues Glu22 and Asp23, and its binding reinforces the core stability of the system. These results give clues on the molecular impact of the interaction of metal ions with the aggregates and sustain their non-innocent roles in the evolution of the illness.
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148
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Yang H, Yuan P, Wu Y, Shi M, Caro CD, Tengeiji A, Yamanoi S, Inoue M, DeGrado WF, Condello C. EMBER multi-dimensional spectral microscopy enables quantitative determination of disease- and cell-specific amyloid strains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.01.526692. [PMID: 36778268 PMCID: PMC9915571 DOI: 10.1101/2023.02.01.526692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
In neurodegenerative diseases proteins fold into amyloid structures with distinct conformations (strains) that are characteristic of different diseases. However, there is a need to rapidly identify amyloid conformations in situ . Here we use machine learning on the full information available in fluorescent excitation/emission spectra of amyloid binding dyes to identify six distinct different conformational strains in vitro , as well as Aβ deposits in different transgenic mouse models. Our EMBER (excitation multiplexed bright emission recording) imaging method rapidly identifies conformational differences in Aβ and tau deposits from Down syndrome, sporadic and familial Alzheimer's disease human brain slices. EMBER has in situ identified distinct conformational strains of tau inclusions in astrocytes, oligodendrocytes, and neurons from Pick's disease. In future studies, EMBER should enable high-throughput measurements of the fidelity of strain transmission in cellular and animal neurodegenerative diseases models, time course of amyloid strain propagation, and identification of pathogenic versus benign strains. Significance In neurodegenerative diseases proteins fold into amyloid structures with distinct conformations (strains) that are characteristic of different diseases. There is a need to rapidly identify these amyloid conformations in situ . Here we use machine learning on the full information available in fluorescent excitation/emission spectra of amyloid binding dyes to identify six distinct different conformational strains in vitro , as well as Aβ deposits in different transgenic mouse models. Our imaging method rapidly identifies conformational differences in Aβ and tau deposits from Down syndrome, sporadic and familial Alzheimer's disease human brain slices. We also identified distinct conformational strains of tau inclusions in astrocytes, oligodendrocytes, and neurons from Pick's disease. These findings will facilitate the identification of pathogenic protein aggregates to guide research and treatment of protein misfolding diseases.
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Affiliation(s)
- Hyunjun Yang
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94143
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, CA 94158
| | - Peng Yuan
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94143
| | - Yibing Wu
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, CA 94158
| | - Marie Shi
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94143
| | - Christoffer D Caro
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94143
| | | | | | | | - William F DeGrado
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94143
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, CA 94158
| | - Carlo Condello
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94143
- Department of Neurology, University of California, San Francisco, CA 94143
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149
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Chen P, Guo Z, Zhou B. Insight into the role of adult hippocampal neurogenesis in aging and Alzheimer's disease. Ageing Res Rev 2023; 84:101828. [PMID: 36549424 DOI: 10.1016/j.arr.2022.101828] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 12/09/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
Alzheimer's disease (AD) is the most common form of dementia and seriously affects the quality of life of the elderly. Neurodegeneration is closely related to hippocampal dysfunction in AD patients. The hippocampus is key to creating new memories and is also one of the first areas of the brain to deteriorate with age. Mammalian neurogenesis occurs mainly in the hippocampus. Recent studies have confirmed that neurogenesis in the hippocampus is sustainable but decreases with age, which seriously affects the learning and memory function of AD patients. At present, our understanding of neurogenesis is still relatively shallow, especially pertaining to the influence and role of neurogenesis during aging and cognitive deficits in AD patients. Interestingly, many recent studies have described the characteristics of neurogenesis in animal models. This article reviews the progress of neurogenesis research in the context of aging and AD to provide new insights into neurogenesis.
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Affiliation(s)
- Peng Chen
- Department of Pharmacy, Renmin Hospital of Wuhan University, Wuhan, Hubei, China.
| | - ZhiLei Guo
- Department of Pharmacy, Wuhan Fourth Hospital, Wuhan, Hubei, China.
| | - Benhong Zhou
- Department of Pharmacy, Renmin Hospital of Wuhan University, Wuhan, Hubei, China.
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150
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Mukherjee S, Dubois C, Perez K, Varghese S, Birchall IE, Leckey M, Davydova N, McLean C, Nisbet RM, Roberts BR, Li QX, Masters CL, Streltsov VA. Quantitative proteomics of tau and Aβ in detergent fractions from Alzheimer's disease brains. J Neurochem 2023; 164:529-552. [PMID: 36271678 DOI: 10.1111/jnc.15713] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/16/2022] [Accepted: 10/17/2022] [Indexed: 11/27/2022]
Abstract
The two hallmarks of Alzheimer's disease (AD) are amyloid-β (Aβ) plaques and neurofibrillary tangles marked by phosphorylated tau. Increasing evidence suggests that aggregating Aβ drives tau accumulation, a process that involves synaptic degeneration leading to cognitive impairment. Conversely, there is a realization that non-fibrillar (oligomeric) forms of Aβ mediate toxicity in AD. Fibrillar (filamentous) aggregates of proteins across the spectrum of the primary and secondary tauopathies were the focus of recent structural studies with a filament structure-based nosologic classification, but less emphasis was given to non-filamentous co-aggregates of insoluble proteins in the fractions derived from post-mortem human brains. Here, we revisited sarkosyl-soluble and -insoluble extracts to characterize tau and Aβ species by quantitative targeted mass spectrometric proteomics, biochemical assays, and electron microscopy. AD brain sarkosyl-insoluble pellets were greatly enriched with Aβ42 at almost equimolar levels to N-terminal truncated microtubule-binding region (MTBR) isoforms of tau with multiple site-specific post-translational modifications (PTMs). MTBR R3 and R4 tau peptides were most abundant in the sarkosyl-insoluble materials with a 10-fold higher concentration than N-terminal tau peptides. This indicates that the major proportion of the enriched tau was the aggregation-prone N-terminal and proline-rich region (PRR) of truncated mixed 4R and 3R tau with more 4R than 3R isoforms. High concentration and occupancies of site-specific phosphorylation pT181 (~22%) and pT217 (~16%) (key biomarkers of AD) along with other PTMs in the PRR and MTBR indicated a regional susceptibility of PTMs in aggregated tau. Immunogold labelling revealed that tau may exist in globular non-filamentous form (N-terminal intact tau) co-localized with Aβ in the sarkosyl-insoluble pellets along with tau filaments (N-truncated MTBR tau). Our results suggest a model that Aβ and tau interact forming globular aggregates, from which filamentous tau and Aβ emerge. These characterizations contribute towards unravelling the sequence of events which lead to end-stage AD changes.
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Affiliation(s)
- Soumya Mukherjee
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Celine Dubois
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Keyla Perez
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Shiji Varghese
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Ian E Birchall
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Miranda Leckey
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Natalia Davydova
- National Deuteration Facility, Australian Nuclear Science and Technology Organization, Lucas Heights, New South Wales, Australia
| | - Catriona McLean
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia.,Department of Anatomical Pathology, Alfred Hospital, Prahran, Victoria, Australia
| | - Rebecca M Nisbet
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Blaine R Roberts
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Qiao-Xin Li
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Colin L Masters
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Victor A Streltsov
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia
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