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Fu Z, Crooks EJ, Irizarry BA, Zhu X, Chowdhury S, Van Nostrand WE, Smith SO. An electrostatic cluster guides Aβ40 fibril formation in sporadic and Dutch-type cerebral amyloid angiopathy. J Struct Biol 2024; 216:108092. [PMID: 38615725 PMCID: PMC11162928 DOI: 10.1016/j.jsb.2024.108092] [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: 02/16/2024] [Revised: 04/08/2024] [Accepted: 04/11/2024] [Indexed: 04/16/2024]
Abstract
Cerebral amyloid angiopathy (CAA) is associated with the accumulation of fibrillar Aβ peptides upon and within the cerebral vasculature, which leads to loss of vascular integrity and contributes to disease progression in Alzheimer's disease (AD). We investigate the structure of human-derived Aβ40 fibrils obtained from patients diagnosed with sporadic or familial Dutch-type (E22Q) CAA. Using cryo-EM, two primary structures are identified containing elements that have not been observed in in vitro Aβ40 fibril structures. One population has an ordered N-terminal fold comprised of two β-strands stabilized by electrostatic interactions involving D1, E22, D23 and K28. This charged cluster is disrupted in the second population, which exhibits a disordered N-terminus and is favored in fibrils derived from the familial Dutch-type CAA patient. These results illustrate differences between human-derived CAA and AD fibrils, and how familial CAA mutations can guide fibril formation.
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Affiliation(s)
- Ziao Fu
- Center for Structural Biology, Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, United States; Laboratory of Molecular Neurobiology and Biophysics, The Rockefeller University, New York, NY 10065, United States
| | - Elliot J Crooks
- Center for Structural Biology, Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, United States
| | - Brandon A Irizarry
- Center for Structural Biology, Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, United States
| | - Xiaoyue Zhu
- George and Anne Ryan Institute for Neuroscience, Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, RI 02881, United States
| | - Saikat Chowdhury
- Center for Structural Biology, Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, United States; CSIR-Centre for Cellular & Molecular Biology, Habsiguda, Uppal Road, Hyderabad 500 007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Kamala Nehru Nagar, Gaziabad 201 002, Uttar Pradesh, India
| | - William E Van Nostrand
- George and Anne Ryan Institute for Neuroscience, Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, RI 02881, United States.
| | - Steven O Smith
- Center for Structural Biology, Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, United States
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2
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Bai Y, Zhang S, Dong H, Liu Y, Liu C, Zhang X. Advanced Techniques for Detecting Protein Misfolding and Aggregation in Cellular Environments. Chem Rev 2023; 123:12254-12311. [PMID: 37874548 DOI: 10.1021/acs.chemrev.3c00494] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Protein misfolding and aggregation, a key contributor to the progression of numerous neurodegenerative diseases, results in functional deficiencies and the creation of harmful intermediates. Detailed visualization of this misfolding process is of paramount importance for improving our understanding of disease mechanisms and for the development of potential therapeutic strategies. While in vitro studies using purified proteins have been instrumental in delivering significant insights into protein misfolding, the behavior of these proteins in the complex milieu of living cells often diverges significantly from such simplified environments. Biomedical imaging performed in cell provides cellular-level information with high physiological and pathological relevance, often surpassing the depth of information attainable through in vitro methods. This review highlights a variety of methodologies used to scrutinize protein misfolding within biological systems. This includes optical-based methods, strategies leaning on mass spectrometry, in-cell nuclear magnetic resonance, and cryo-electron microscopy. Recent advancements in these techniques have notably deepened our understanding of protein misfolding processes and the features of the resulting misfolded species within living cells. The progression in these fields promises to catalyze further breakthroughs in our comprehension of neurodegenerative disease mechanisms and potential therapeutic interventions.
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Affiliation(s)
- Yulong Bai
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Shengnan Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Hui Dong
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- University of the Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Xin Zhang
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
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3
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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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4
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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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5
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Banerjee S, Holcombe B, Ringold S, Foes A, Naik T, Baghel D, Ghosh A. Nanoscale Infrared Spectroscopy Identifies Structural Heterogeneity in Individual Amyloid Fibrils and Prefibrillar Aggregates. J Phys Chem B 2022; 126:5832-5841. [PMID: 35914320 DOI: 10.1021/acs.jpcb.2c04797] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Amyloid plaques are one of the central manifestations of Alzheimer's disease pathology. Aggregation of the amyloid beta (Aβ) protein from amorphous oligomeric species to mature fibrils has been extensively studied. However, structural heterogeneities in prefibrillar species, and how that affects the structure of later-stage aggregates are not yet well understood. The integration of infrared spectroscopy with atomic force microscopy (AFM-IR) allows for identifying the signatures of individual nanoscale aggregates by spatially resolving spectra. We use AFM-IR to demonstrate that amyloid oligomers exhibit significant structural variations as evidenced in their infrared spectra. This heterogeneity is transmitted to and retained in protofibrils and fibrils. We show that amyloid fibrils do not always conform to their putative ordered structure and structurally different domains exist in the same fibril. We further demonstrate that these structural heterogeneities manifest themselves as a lack of β sheet structure in amyloid plaques in Alzheimer's tissue using infrared imaging.
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Affiliation(s)
- Siddhartha Banerjee
- Department of Chemistry and Biochemistry, The University of Alabama, 1007E Shelby Hall, Tuscaloosa, Alabama 35487, United States
| | - Brooke Holcombe
- Department of Chemistry and Biochemistry, The University of Alabama, 1007E Shelby Hall, Tuscaloosa, Alabama 35487, United States
| | - Sydney Ringold
- Department of Chemistry and Biochemistry, The University of Alabama, 1007E Shelby Hall, Tuscaloosa, Alabama 35487, United States
| | - Abigail Foes
- Department of Chemistry and Biochemistry, The University of Alabama, 1007E Shelby Hall, Tuscaloosa, Alabama 35487, United States
| | - Tanmayee Naik
- Department of Chemistry and Biochemistry, The University of Alabama, 1007E Shelby Hall, Tuscaloosa, Alabama 35487, United States
| | - Divya Baghel
- Department of Chemistry and Biochemistry, The University of Alabama, 1007E Shelby Hall, Tuscaloosa, Alabama 35487, United States
| | - Ayanjeet Ghosh
- Department of Chemistry and Biochemistry, The University of Alabama, 1007E Shelby Hall, Tuscaloosa, Alabama 35487, United States
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6
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Bücker R, Seuring C, Cazey C, Veith K, García-Alai M, Grünewald K, Landau M. The Cryo-EM structures of two amphibian antimicrobial cross-β amyloid fibrils. Nat Commun 2022; 13:4356. [PMID: 35896552 PMCID: PMC9329304 DOI: 10.1038/s41467-022-32039-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 07/13/2022] [Indexed: 12/14/2022] Open
Abstract
The amyloid-antimicrobial link hypothesis is based on antimicrobial properties found in human amyloids involved in neurodegenerative and systemic diseases, along with amyloidal structural properties found in antimicrobial peptides (AMPs). Supporting this hypothesis, we here determined the fibril structure of two AMPs from amphibians, uperin 3.5 and aurein 3.3, by cryogenic electron microscopy (cryo-EM), revealing amyloid cross-β fibrils of mated β-sheets at atomic resolution. Uperin 3.5 formed a 3-blade symmetrical propeller of nine peptides per fibril layer including tight β-sheet interfaces. This cross-β cryo-EM structure complements the cross-α fibril conformation previously determined by crystallography, substantiating a secondary structure switch mechanism of uperin 3.5. The aurein 3.3 arrangement consisted of six peptides per fibril layer, all showing kinked β-sheets allowing a rounded compactness of the fibril. The kinked β-sheets are similar to LARKS (Low-complexity, Amyloid-like, Reversible, Kinked Segments) found in human functional amyloids. In this work the authors provide high-resolution structural support for the amyloid-antimicrobial link via functional amyloids displaying propeller-like and kinked cross-β fibrils.
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Affiliation(s)
- Robert Bücker
- Centre for Structural Systems Biology, Hamburg, Germany.,Department of Chemistry, University of Hamburg, Hamburg, Germany.,Rigaku Europe SE, Neu-Isenburg, Germany.,Leibniz Institute of Virology, Hamburg, Germany
| | - Carolin Seuring
- Centre for Structural Systems Biology, Hamburg, Germany.,Department of Chemistry, University of Hamburg, Hamburg, Germany.,Leibniz Institute of Virology, Hamburg, Germany
| | - Cornelia Cazey
- Centre for Structural Systems Biology, Hamburg, Germany.,Department of Chemistry, University of Hamburg, Hamburg, Germany
| | - Katharina Veith
- European Molecular Biology Laboratory, EMBL Hamburg, Hamburg, Germany
| | - Maria García-Alai
- Centre for Structural Systems Biology, Hamburg, Germany.,European Molecular Biology Laboratory, EMBL Hamburg, Hamburg, Germany
| | - Kay Grünewald
- Centre for Structural Systems Biology, Hamburg, Germany. .,Department of Chemistry, University of Hamburg, Hamburg, Germany. .,Leibniz Institute of Virology, Hamburg, Germany. .,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Meytal Landau
- Centre for Structural Systems Biology, Hamburg, Germany. .,European Molecular Biology Laboratory, EMBL Hamburg, Hamburg, Germany. .,Department of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel.
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7
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Golan N, Engelberg Y, Landau M. Structural Mimicry in Microbial and Antimicrobial Amyloids. Annu Rev Biochem 2022; 91:403-422. [PMID: 35729071 DOI: 10.1146/annurev-biochem-032620-105157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The remarkable variety of microbial species of human pathogens and microbiomes generates significant quantities of secreted amyloids, which are structured protein fibrils that serve diverse functions related to virulence and interactions with the host. Human amyloids are associated largely with fatal neurodegenerative and systemic aggregation diseases, and current research has put forward the hypothesis that the interspecies amyloid interactome has physiological and pathological significance. Moreover, functional and molecular-level connections between antimicrobial activity and amyloid structures suggest a neuroimmune role for amyloids that are otherwise known to be pathological. Compared to the extensive structural information that has been accumulated for human amyloids, high-resolution structures of microbial and antimicrobial amyloids are only emerging. These recent structures reveal both similarities and surprising departures from the typical amyloid motif, in accordance with their diverse activities, and advance the discovery of novel antivirulence and antimicrobial agents. In addition, the structural information has led researchers to postulate that amyloidogenic sequences are natural targets for structural mimicry, for instance in host-microbe interactions. Microbial amyloid research could ultimately be used to fight aggressive infections and possibly processes leading to autoimmune and neurodegenerative diseases.
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Affiliation(s)
- Nimrod Golan
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel;
| | - Yizhaq Engelberg
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel;
| | - Meytal Landau
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel; .,European Molecular Biology Laboratory (EMBL) and Center for Structural Systems Biology (CSSB), Hamburg, Germany
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8
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Ghosh U, Yau WM, Collinge J, Tycko R. Structural differences in amyloid-β fibrils from brains of nondemented elderly individuals and Alzheimer's disease patients. Proc Natl Acad Sci U S A 2021; 118:e2111863118. [PMID: 34725161 PMCID: PMC8609303 DOI: 10.1073/pnas.2111863118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 09/20/2021] [Indexed: 02/05/2023] Open
Abstract
Although amyloid plaques composed of fibrillar amyloid-β (Aβ) assemblies are a diagnostic hallmark of Alzheimer's disease (AD), quantities of amyloid similar to those in AD patients are observed in brain tissue of some nondemented elderly individuals. The relationship between amyloid deposition and neurodegeneration in AD has, therefore, been unclear. Here, we use solid-state NMR to investigate whether molecular structures of Aβ fibrils from brain tissue of nondemented elderly individuals with high amyloid loads differ from structures of Aβ fibrils from AD tissue. Two-dimensional solid-state NMR spectra of isotopically labeled Aβ fibrils, prepared by seeded growth from frontal lobe tissue extracts, are similar in the two cases but with statistically significant differences in intensity distributions of cross-peak signals. Differences in solid-state NMR data are greater for 42-residue amyloid-β (Aβ42) fibrils than for 40-residue amyloid-β (Aβ40) fibrils. These data suggest that similar sets of fibril polymorphs develop in nondemented elderly individuals and AD patients but with different relative populations on average.
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Affiliation(s)
- Ujjayini Ghosh
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892-0520
- Department of Chemistry, Michigan State University, East Lansing, MI 48824
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892-0520
| | - John Collinge
- Medical Research Council Prion Unit, University College London, London W1W 7FF, United Kingdom
- Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892-0520;
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9
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Hu ZW, Cruceta L, Zhang S, Sun Y, Qiang W. Cross-Seeded Fibrillation Induced by Pyroglutamate-3 and Truncated Aβ 40 Variants Leads to Aβ 40 Structural Polymorphism Modulation and Elevated Toxicity. ACS Chem Neurosci 2021; 12:3625-3637. [PMID: 34524791 DOI: 10.1021/acschemneuro.1c00341] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The pathological amyloid plaques in Alzheimer's disease (AD) patients contain not only the wild-type β-amyloid (wt-Aβ) peptide sequences but also a variety of post-translationally modified variants. The pyroglutamate-3 Aβ (pyroE3-Aβ), which is generated from its truncated precursors ΔE3-Aβ, shows the highest abundance among all modified Aβ variants. Previous works have shown that pyroE3-Aβ and/or ΔE3-Aβ, compared with the wild-type sequences, led to a more rapid fibrillation process and final fibrils with higher neuronal cytotoxicity levels. However, much less is known about how the formation of pyroE3/ΔE3-Aβ fibrils would affect the amyloid deposition of wt-Aβ peptides, which are the main pathological events in AD. We show in the present work that the pyroE3/ΔE3-Aβ40 fibrils differ significantly from the wt-Aβ40 fibrils in terms of their molecular structures. When added into monomeric wt-Aβ40 peptides, these variant fibrils can cross-seed the formation of wt-Aβ40 fibrils with fibrillation kinetics that are greater than the self-seeded fibrillation of wt-Aβ40. Furthermore, the cross-seeding process modulates the molecular structures of the yielded wt-Aβ40 fibrils, which show similar features as their variant seeds. The cross-seeded fibrillation process also induces higher cytotoxicity levels compared with the self-seeded fibrillation of wt-Aβ40. Overall, our results support the hypothesis that pyroE3 and ΔE3-Aβ40 variants may serve as triggering factors of the pathological amyloid aggregation of wt-Aβ40 and may underlie the pathological significance of pyroE3/ΔE3-Aβ40 variants on the structural polymorphism of Aβ deposits.
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Affiliation(s)
- Zhi-Wen Hu
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, P. R. China
| | - Letticia Cruceta
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
| | - Shiyue Zhang
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
| | - Yan Sun
- Small Scale Systems Integration and Package (S3IP) Center, Binghamton University, Binghamton, New York 13902, United States
| | - Wei Qiang
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
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10
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Irizarry BA, Davis J, Zhu X, Boon BDC, Rozemuller AJM, Van Nostrand WE, Smith SO. Human cerebral vascular amyloid contains both antiparallel and parallel in-register Aβ40 fibrils. J Biol Chem 2021; 297:101259. [PMID: 34599967 PMCID: PMC8528725 DOI: 10.1016/j.jbc.2021.101259] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 09/19/2021] [Accepted: 09/27/2021] [Indexed: 01/02/2023] Open
Abstract
The accumulation of fibrillar amyloid-β (Aβ) peptides alongside or within the cerebral vasculature is the hallmark of cerebral amyloid angiopathy (CAA). This condition commonly co-occurs with Alzheimer's disease (AD) and leads to cerebral microbleeds, intracranial hemorrhages, and stroke. CAA also occurs sporadically in an age-dependent fashion and can be accelerated by the presence of familial Aβ mutant peptides. Recent studies using Fourier transform infrared (FTIR) spectroscopy of vascular Aβ fibrils derived from rodents containing the double E22Q/D23N mutations indicated the presence of a novel antiparallel β-sheet structure. To address whether this structure is associated solely with the familial mutations or is a common feature of CAA, we propagated Aβ fibrils from human brain vascular tissue of patients diagnosed with nonfamilial CAA. Aβ fibrils were isolated from cerebral blood vessels using laser capture microdissection in which specific amyloid deposits were removed from thin slices of the brain tissue. Transmission electron microscopy revealed that these deposits were organized into a tight meshwork of fibrils, which FTIR measurements showed could serve as seeds to propagate the growth of Aβ40 fibrils for structural studies. Solid-state NMR measurements of the fibrils propagated from vascular amyloid showed they contained a mixture of parallel, in-register, and antiparallel β-sheet structures. The presence of fibrils with antiparallel structure derived from vascular amyloid is distinct from the typical parallel, in-register β-sheet structure that appears in fibrils derived from parenchymal amyloid in AD. These observations reveal that different microenvironments influence the structures of Aβ fibrils in the human brain.
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Affiliation(s)
- Brandon A Irizarry
- Center for Structural Biology, Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA
| | - Judianne Davis
- George and Anne Ryan Institute for Neuroscience, Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Xiaoyue Zhu
- George and Anne Ryan Institute for Neuroscience, Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Baayla D C Boon
- Department of Neurology, Alzheimer Center Amsterdam, Amsterdam Neuroscience, Amsterdam UMC - VUmc, Amsterdam, the Netherlands; Department of Pathology, Alzheimer Center Amsterdam, Amsterdam Neuroscience, Amsterdam UMC - VUmc, Amsterdam, the Netherlands
| | - Annemieke J M Rozemuller
- Department of Pathology, Alzheimer Center Amsterdam, Amsterdam Neuroscience, Amsterdam UMC - VUmc, Amsterdam, the Netherlands
| | - William E Van Nostrand
- George and Anne Ryan Institute for Neuroscience, Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Steven O Smith
- Center for Structural Biology, Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA.
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11
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Wickramasinghe A, Xiao Y, Kobayashi N, Wang S, Scherpelz KP, Yamazaki T, Meredith SC, Ishii Y. Sensitivity-Enhanced Solid-State NMR Detection of Structural Differences and Unique Polymorphs in Pico- to Nanomolar Amounts of Brain-Derived and Synthetic 42-Residue Amyloid-β Fibrils. J Am Chem Soc 2021; 143:11462-11472. [PMID: 34308630 PMCID: PMC10279877 DOI: 10.1021/jacs.1c03346] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amyloid-β (Aβ) fibrils in neuritic plaques are a hallmark of Alzheimer's disease (AD). Since the 42-residue Aβ (Aβ42) fibril is the most pathogenic among different Aβ species, its structural characterization is crucial to our understanding of AD. While several polymorphs have been reported for Aβ40, previous studies of Aβ42 fibrils prepared at neutral pH detected essentially only one structure, with an S-shaped β-sheet arrangement (e.g., Xiao et al. Nat. Struct. Mol. Biol. 2015, 22, 499). Herein, we demonstrate the feasibility of characterizing the structure of trace amounts of brain-derived and synthetic amyloid fibrils by sensitivity-enhanced 1H-detected solid-state NMR (SSNMR) under ultrafast magic angle spinning. By taking advantage of the high sensitivity of this technique, we first demonstrate its applicability for the high-throughput screening of trace amounts of selectively 13C- and 15N-labeled Aβ42 fibril prepared with ∼0.01% patient-derived amyloid (ca. 4 pmol) as a seed. The comparison of 2D 13C/1H SSNMR data revealed marked structural differences between AD-derived Aβ42 (∼40 nmol or ∼200 μg) and synthetic fibrils in less than 10 min, confirming the feasibility of assessing the fibril structure from ∼1 pmol of brain amyloid seed in ∼2.5 h. We also present the first structural characterization of synthetic fully protonated Aβ42 fibril by 1H-detected 3D and 4D SSNMR. With procedures assisted by automated assignments, main-chain resonance assignments were completed for trace amounts (∼42 nmol) of a fully protonated amyloid fibril in the 1H-detection approach. The results suggest that this Aβ42 fibril exhibits a novel fold or polymorph structure.
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Affiliation(s)
- Ayesha Wickramasinghe
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
- NMR Division, RIKEN SPring-8 Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yiling Xiao
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - Naohiro Kobayashi
- NMR Division, RIKEN SPring-8 Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Songlin Wang
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - Kathryn P. Scherpelz
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA
| | - Toshio Yamazaki
- NMR Division, RIKEN SPring-8 Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Stephen C. Meredith
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA
- Department of Pathology, The University of Chicago, Chicago, Illinois 60637, USA
| | - Yoshitaka Ishii
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
- NMR Division, RIKEN SPring-8 Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, USA
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12
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Masrati G, Landau M, Ben-Tal N, Lupas A, Kosloff M, Kosinski J. Integrative Structural Biology in the Era of Accurate Structure Prediction. J Mol Biol 2021; 433:167127. [PMID: 34224746 DOI: 10.1016/j.jmb.2021.167127] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/28/2021] [Accepted: 06/28/2021] [Indexed: 11/16/2022]
Abstract
Characterizing the three-dimensional structure of macromolecules is central to understanding their function. Traditionally, structures of proteins and their complexes have been determined using experimental techniques such as X-ray crystallography, NMR, or cryo-electron microscopy-applied individually or in an integrative manner. Meanwhile, however, computational methods for protein structure prediction have been improving their accuracy, gradually, then suddenly, with the breakthrough advance by AlphaFold2, whose models of monomeric proteins are often as accurate as experimental structures. This breakthrough foreshadows a new era of computational methods that can build accurate models for most monomeric proteins. Here, we envision how such accurate modeling methods can combine with experimental structural biology techniques, enhancing integrative structural biology. We highlight the challenges that arise when considering multiple structural conformations, protein complexes, and polymorphic assemblies. These challenges will motivate further developments, both in modeling programs and in methods to solve experimental structures, towards better and quicker investigation of structure-function relationships.
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Affiliation(s)
- Gal Masrati
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Meytal Landau
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel; European Molecular Biology Laboratory (EMBL), Hamburg 22607, Germany
| | - Nir Ben-Tal
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Andrei Lupas
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
| | - Mickey Kosloff
- Department of Human Biology, Faculty of Natural Sciences, University of Haifa, 199 Aba Khoushy Ave., Mt. Carmel, 3498838 Haifa, Israel.
| | - Jan Kosinski
- European Molecular Biology Laboratory (EMBL), Hamburg 22607, Germany; Centre for Structural Systems Biology (CSSB), Hamburg 22607, Germany; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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13
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Molecular structure of a prevalent amyloid-β fibril polymorph from Alzheimer's disease brain tissue. Proc Natl Acad Sci U S A 2021; 118:2023089118. [PMID: 33431654 DOI: 10.1073/pnas.2023089118] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Amyloid-β (Aβ) fibrils exhibit self-propagating, molecular-level polymorphisms that may contribute to variations in clinical and pathological characteristics of Alzheimer's disease (AD). We report the molecular structure of a specific fibril polymorph, formed by 40-residue Aβ peptides (Aβ40), that is derived from cortical tissue of an AD patient by seeded fibril growth. The structure is determined from cryogenic electron microscopy (cryoEM) images, supplemented by mass-per-length (MPL) measurements and solid-state NMR (ssNMR) data. Previous ssNMR studies with multiple AD patients had identified this polymorph as the most prevalent brain-derived Aβ40 fibril polymorph from typical AD patients. The structure, which has 2.8-Å resolution according to standard criteria, differs qualitatively from all previously described Aβ fibril structures, both in its molecular conformations and its organization of cross-β subunits. Unique features include twofold screw symmetry about the fibril growth axis, despite an MPL value that indicates three Aβ40 molecules per 4.8-Å β-sheet spacing, a four-layered architecture, and fully extended conformations for molecules in the central two cross-β layers. The cryoEM density, ssNMR data, and MPL data are consistent with β-hairpin conformations for molecules in the outer cross-β layers. Knowledge of this brain-derived fibril structure may contribute to the development of structure-specific amyloid imaging agents and aggregation inhibitors with greater diagnostic and therapeutic utility.
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14
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The amphibian antimicrobial peptide uperin 3.5 is a cross-α/cross-β chameleon functional amyloid. Proc Natl Acad Sci U S A 2021; 118:2014442118. [PMID: 33431675 DOI: 10.1073/pnas.2014442118] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Antimicrobial activity is being increasingly linked to amyloid fibril formation, suggesting physiological roles for some human amyloids, which have historically been viewed as strictly pathological agents. This work reports on formation of functional cross-α amyloid fibrils of the amphibian antimicrobial peptide uperin 3.5 at atomic resolution, an architecture initially discovered in the bacterial PSMα3 cytotoxin. The fibrils of uperin 3.5 and PSMα3 comprised antiparallel and parallel helical sheets, respectively, recapitulating properties of β-sheets. Uperin 3.5 demonstrated chameleon properties of a secondary structure switch, forming mostly cross-β fibrils in the absence of lipids. Uperin 3.5 helical fibril formation was largely induced by, and formed on, bacterial cells or membrane mimetics, and led to membrane damage and cell death. These findings suggest a regulation mechanism, which includes storage of inactive peptides as well as environmentally induced activation of uperin 3.5, via chameleon cross-α/β amyloid fibrils.
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15
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Thurber KR, Yin Y, Tycko R. Automated picking of amyloid fibrils from cryo-EM images for helical reconstruction with RELION. J Struct Biol 2021; 213:107736. [PMID: 33831509 DOI: 10.1016/j.jsb.2021.107736] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 11/16/2022]
Abstract
Cryogenic electron microscopy (cryo-EM) is an important tool for determining the molecular structure of proteins and protein assemblies, including helical assemblies such as amyloid fibrils. In reconstruction of amyloid fibril structures from cryo-EM images, an important early step is the selection of fibril locations. This fibril picking step is typically done by hand, a tedious process when thousands of images need to be analyzed. Here we present a computer program called FibrilFinder that identifies the locations and directions of fibril segments in cryo-EM images, by using the properties that the fibrils should be linear objects and have widths within a specified range. The program outputs the fibril locations in text files compatible with the RELION density reconstruction program. After RELION is used to extract the particle image boxes contained in the fibril segments identified by FibrilFinder, a second program called FibrilFixer removes boxes that contain more than one fibril, for instance because two fibrils cross each other. As concrete and realistic examples, we describe the application of the two programs to cryo-EM images of two different amyloid fibrils, namely 40-residue amyloid-β fibrils derived from human brain tissue by seeded growth and fibrils formed by the C-terminal half of the low-complexity domain of the RNA-binding protein FUS. Both examples of amyloid fibrils can be picked from cryo-EM images using the same set of FibrilFinder and FibrilFixer parameters, showing that this software does not require re-optimization for each sample. A set of 1337 cryo-EM images was analyzed in 17 min with one multi-core computer. The new fibril picking software should enable the rapid analysis and comparison of more helical structures using cryo-EM, and perhaps serve as part of the greater automation of the entire structure determination process.
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Affiliation(s)
- Kent R Thurber
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA.
| | - Yi Yin
- Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford OX3 9DU, UK
| | - 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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16
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Khatua P, Jana AK, Hansmann UHE. Effect of Lauric Acid on the Stability of Aβ 42 Oligomers. ACS OMEGA 2021; 6:5795-5804. [PMID: 33681618 PMCID: PMC7931375 DOI: 10.1021/acsomega.0c06211] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 01/25/2021] [Indexed: 06/12/2023]
Abstract
While Alzheimer's disease is correlated with the presence of Aβ fibrils in patient brains, the more likely agents are their precursors, soluble oligomers that may form pores or otherwise distort cell membranes. Using all-atom molecular dynamics simulation, we study how the presence of fatty acids such as lauric acid changes the stability of pore-forming oligomers built from three-stranded Aβ42 chains. Such a change would alter the distribution of amyloids in the fatty acid-rich brain environment and therefore could explain the lower polymorphism observed in Aβ fibrils derived from brains of patients with Alzheimer's disease. We find that lauric acid stabilizes both ring-like and barrel-shaped models, with the effect being stronger for barrel-like models than for ring-like oligomers.
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17
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Hu ZW, Au DF, Cruceta L, Vugmeyster L, Qiang W. N-Terminal Modified Aβ Variants Enable Modulations to the Structures and Cytotoxicity Levels of Wild-Type Aβ Fibrils through Cross-Seeding. ACS Chem Neurosci 2020; 11:2058-2065. [PMID: 32603584 DOI: 10.1021/acschemneuro.0c00316] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Post-translational modifications (PTMs) of β-amyloid (Aβ) peptides are considered as triggering factors in sporadic Alzheimer's disease. However, studies to show the influence of pre-existing PTM-Aβ fibrils on wild-type Aβ peptides, which directly mimic the triggering scenarios, are rare. Here we show that three types of pathologically relevant PTM-Aβ variants with modifications in a particular segment (from D7 to V12) of the primary sequence lead to distinct impacts on the fibrillization of wild-type Aβ peptides. In general, the triggering effects are observed through cross-seeding between the PTM-Aβ seeds and wild-type peptides, which consequently induce modulations in the resultant wild-type fibril structures and elevations in the fibrillar cytotoxicity levels. Modifications with a similar chemical nature, such as the S8-phosphorylation and Y10-nitration, both of which introduce additional side-chain negative charges, show comparable structural-modulation and cytotoxicity-elevation effects. The results imply the biological influences of PTM-Aβ variants on the formation of amyloid deposits through cross-seeded fibrillization.
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Affiliation(s)
- Zhi-Wen Hu
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
| | - Dan Fai Au
- Department of Chemistry, University of Colorado at Denver, Denver, Colorado 80204, United States
| | - Letticia Cruceta
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
| | - Liliya Vugmeyster
- Department of Chemistry, University of Colorado at Denver, Denver, Colorado 80204, United States
| | - Wei Qiang
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
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18
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Fibrillization of 40-Residue β-Amyloid Peptides in Membrane-Like Environments Leads to Different Fibril Structures and Reduced Molecular Polymorphisms. Biomolecules 2020; 10:biom10060881. [PMID: 32521743 PMCID: PMC7356566 DOI: 10.3390/biom10060881] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 05/28/2020] [Accepted: 06/04/2020] [Indexed: 12/31/2022] Open
Abstract
The molecular-level polymorphism in β-Amyloid (Aβ) fibrils have recently been considered as a pathologically relevant factor in Alzheimer’s disease (AD). Studies showed that the structural deviations in human-brain-seeded Aβ fibrils potentially correlated with the clinical histories of AD patients. For the 40-residue Aβ (Aβ40) fibrils derived from human brain tissues, a predominant molecular structure was proposed based on solid-state nuclear magnetic resonance (ssNMR) spectroscopy. However, previous studies have shown that the molecular structures of Aβ40 fibrils were sensitive to their growth conditions in aqueous environments. We show in this work that biological membranes and their phospholipid bilayer mimics serve as environmental factors to reduce the structural heterogeneity in Aβ40 fibrils. Fibrillization in the presence of membranes leads to fibril structures that are significantly different to the Aβ40 fibrils grown in aqueous solutions. Fibrils grown from multiple types of membranes, including the biological membranes extracted from the rats’ synaptosomes, shared similar ssNMR spectral features. Our studies emphasize the biological relevance of membranes in Aβ40 fibril structures and fibrillization processes.
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19
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Burakova E, Vasa SK, Klein A, Linser R. Non-uniform sampling in quantitative assessment of heterogeneous solid-state NMR line shapes. JOURNAL OF BIOMOLECULAR NMR 2020; 74:71-82. [PMID: 31834579 DOI: 10.1007/s10858-019-00291-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 11/26/2019] [Indexed: 06/10/2023]
Abstract
Non-uniform sampling has been successfully used for solution and solid-state NMR of homogeneous samples. In the solid state, protein samples are often dominated by inhomogeneous contributions to the homogeneous line widths. In spite of different technical strategies for peak reconstruction by different methods, we validate that NUS can generally be used also for such situations where spectra are made up of complex peak shapes rather than Lorentian lines. Using the RMSD between subsampled and reconstructed data and those spectra obtained with uniform sampling for a sample comprising a wide conformational distribution, we quantitatively evaluate the identity of inhomogeneous peak patterns. The evaluation comprises Iterative Soft Thresholding (hmsIST implementation) as a method explicitly not assuming Lorentian lineshapes, as well as Sparse Multidimensional Iterative Lineshape Enhanced (SMILE) algorithm and Signal Separation Algorithm (SSA) reconstruction, which do work on the basis of Lorentian lineshape models, with different sampling densities. Even though individual peculiarities are apparent, all methods turn out principally viable to reconstruct the heterogeneously broadened peak shapes.
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Affiliation(s)
- Ekaterina Burakova
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 4a, 44227, Dortmund, Germany
| | - Suresh K Vasa
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 4a, 44227, Dortmund, Germany
| | - Alexander Klein
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 4a, 44227, Dortmund, Germany
| | - Rasmus Linser
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany.
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 4a, 44227, Dortmund, Germany.
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20
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Xi W, Vanderford EK, Liao Q, Hansmann UHE. Stability of Aβ-fibril fragments in the presence of fatty acids. Protein Sci 2019; 28:1973-1981. [PMID: 31461191 DOI: 10.1002/pro.3719] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 07/10/2019] [Accepted: 08/22/2019] [Indexed: 11/07/2022]
Abstract
We consider the effect of lauric acid on the stability of various fibril-like assemblies of Aβ peptides. For this purpose, we have performed molecular dynamics simulations of these assemblies either in complex with lauric acid or without presence of the ligand. While we do not observe a stabilizing effect on Aβ40 -fibrils, we find that addition of lauric acid strengthens the stability of fibrils built from the triple-stranded S-shaped Aβ42 -peptides considered to be more toxic. Or results may help to understand how the specifics of the brain-environment modulate amyloid formation and propagation.
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Affiliation(s)
- Wenhui Xi
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma
| | - Elliott K Vanderford
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma
| | - Qinxin Liao
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Ulrich H E Hansmann
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma
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21
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Chen M, Schafer NP, Wolynes PG. Surveying the Energy Landscapes of Aβ Fibril Polymorphism. J Phys Chem B 2018; 122:11414-11430. [PMID: 30215519 DOI: 10.1021/acs.jpcb.8b07364] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Many unrelated proteins and peptides have been found spontaneously to form amyloid fibers above a critical concentration. Even for a single sequence, however, the amyloid fold is not a single well-defined structure. Although the cross-β hydrogen bonding pattern is common to all amyloids, all other aspects of amyloid fiber structures are sensitive to both the sequence of the aggregating peptides and the solvent conditions under which the aggregation occurs. Amyloid fibers are easy to identify and grossly characterize using microscopy, but their insolubility and aperiodicity along the dimensions transverse to the fiber axis have complicated detailed experimental structural characterization. In this paper, we explore the landscape of possibilities for amyloid protofilament structures that are made up of a single stack of peptides associated in a parallel in-register manner. We view this landscape as a two-dimensional version of the usual three-dimensional protein folding problem: the survey of the two-dimensional folds of protein ribbons. Adopting this view leads to a practical method of predicting stable protofilament structures of arbitrary sequences. We apply this scheme to variants of Aβ, the amyloid forming peptide that is characteristically associated with Alzheimer's disease. Consistent with what is known from experiment, we find that Aβ protofibrils are polymorphic. To our surprise, however, the ribbon-folding landscape of Aβ turned out to be strikingly simple. We confirm that, at the level of the monomeric protofilament, the landscape for the Aβ sequence is reasonably well funneled toward structures that are similar to those that have been determined by experiment. The landscape has more distinct minima than does a typical globular protein landscape but fewer and deeper minima than the landscape of a randomly shuffled sequence having the same overall composition. It is tempting to consider the possibility that the significant degree of funneling of Aβ's ribbon-folding landscape has arisen as a result of natural selection. More likely, however, the intermediate complexity of Aβ's ribbon-folding landscape has come from the post facto selection of the Aβ sequence as an object of study by researchers because only by having a landscape with some degree of funneling can ordered aggregation of such a peptide occur at in vivo concentrations. In addition to predicting polymorph structures, we show that predicted solubilities of polymorphs correlate with experiment and with their elongation free energies computed by coarse-grained molecular dynamics.
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Affiliation(s)
- Mingchen Chen
- Center for Theoretical Biological Physics , Rice University , Houston , Texas 77005 , United States.,Department of Bioengineering , Rice University , Houston , Texas 77005 , United States
| | - Nicholas P Schafer
- Center for Theoretical Biological Physics , Rice University , Houston , Texas 77005 , United States.,Department of Chemistry , Rice University , Houston , Texas 77005 , United States
| | - Peter G Wolynes
- Center for Theoretical Biological Physics , Rice University , Houston , Texas 77005 , United States.,Department of Chemistry , Rice University , Houston , Texas 77005 , United States
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