1
|
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. Cell Mol Life Sci 2023; 80:376. [PMID: 38010414 PMCID: PMC11061799 DOI: 10.1007/s00018-023-05026-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/06/2023] [Accepted: 10/30/2023] [Indexed: 11/29/2023]
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.
Collapse
Affiliation(s)
- Emily Lewkowicz
- Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, W302, 700 Albany Street, Boston, MA, 02118, USA
| | - Mari N Nakamura
- Undergraduate program, Department of Chemistry and Biochemistry, Middlebury College, 14 Old Chapel Rd, Middlebury, VT, 05753, USA
| | - Michael J Rynkiewicz
- Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, W302, 700 Albany Street, Boston, MA, 02118, USA
| | - Olga Gursky
- Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, W302, 700 Albany Street, Boston, MA, 02118, USA.
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Chen Y, Strickland MR, Soranno A, Holtzman DM. Apolipoprotein E: Structural Insights and Links to Alzheimer Disease Pathogenesis. Neuron 2020; 109:205-221. [PMID: 33176118 DOI: 10.1016/j.neuron.2020.10.008] [Citation(s) in RCA: 134] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 01/02/2023]
Abstract
Apolipoprotein E (ApoE) is of great interest due to its role as a cholesterol/lipid transporter in the central nervous system (CNS) and as the most influential genetic risk factor for Alzheimer disease (AD). Work over the last four decades has given us important insights into the structure of ApoE and how this might impact the neuropathology and pathogenesis of AD. In this review, we highlight the history and progress in the structural and molecular understanding of ApoE and discuss how these studies on ApoE have illuminated the physiology of ApoE, receptor binding, and interaction with amyloid-β (Aβ). We also identify future areas of study needed to advance our understanding of how ApoE influences neurodegeneration.
Collapse
Affiliation(s)
- Yun Chen
- Department of Neurology, Washington University in St. Louis, St. Louis, MO, USA; Hope Center for Neurological Disorders, Washington University in St. Louis, St. Louis, MO, USA; Knight Alzheimer's Disease Research Center, Washington University in St. Louis, St. Louis, MO, USA; The Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, USA; Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA
| | - Michael R Strickland
- Department of Neurology, Washington University in St. Louis, St. Louis, MO, USA; Hope Center for Neurological Disorders, Washington University in St. Louis, St. Louis, MO, USA; Knight Alzheimer's Disease Research Center, Washington University in St. Louis, St. Louis, MO, USA; The Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, USA
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO, USA; Center for Science & Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO, USA
| | - David M Holtzman
- Department of Neurology, Washington University in St. Louis, St. Louis, MO, USA; Center for Science & Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO, USA; Knight Alzheimer's Disease Research Center, Washington University in St. Louis, St. Louis, MO, USA.
| |
Collapse
|
4
|
Ghosh S, Sil TB, Dolai S, Garai K. High‐affinity multivalent interactions between apolipoprotein E and the oligomers of amyloid‐β. FEBS J 2019; 286:4737-4753. [DOI: 10.1111/febs.14988] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 05/06/2019] [Accepted: 07/06/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Shamasree Ghosh
- Tata Institute of Fundamental Research Hyderabad Hyderabad India
| | - Timir Baran Sil
- Tata Institute of Fundamental Research Hyderabad Hyderabad India
| | | | - Kanchan Garai
- Tata Institute of Fundamental Research Hyderabad Hyderabad India
| |
Collapse
|
5
|
Deroo S, Stengel F, Mohammadi A, Henry N, Hubin E, Krammer EM, Aebersold R, Raussens V. Chemical cross-linking/mass spectrometry maps the amyloid β peptide binding region on both apolipoprotein E domains. ACS Chem Biol 2015; 10:1010-6. [PMID: 25546376 DOI: 10.1021/cb500994j] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Apolipoprotein E (apoE) binds the amyloid β peptide (Aβ), one of the major culprits in Alzheimer's disease development. The formation of apoE:Aβ complexes is implicated in both Aβ clearance and fibrillization. However, the binding interface between apoE and Aβ is poorly defined despite substantial previous research efforts, and the exact role of apoE in the pathology of Alzheimer's disease remains largely elusive. Here, we compared the three main isoforms of apoE (E2, E3, and E4) for their interaction with Aβ1-42 in an early stage of aggregation and at near physiological conditions. Using electron microscopy and Western blots, we showed that all three isoforms are able to prevent Aβ fibrillization and form a noncovalent complex, with one molecule of Aβ bound per apoE. Using chemical cross-linking coupled to mass spectrometry, we further examined the interface of interaction between apoE2/3/4 and Aβ. Multiple high-confidence intermolecular apoE2/3/4:Aβ cross-links confirmed that Lys16 is located in the region of Aβ binding to apoE2/3/4. Further, we demonstrated that both N- and C-terminal domains of apoE2/3/4 are interacting with Aβ. The cross-linked sites were mapped onto and evaluated in light of a recent structure of apoE. Our results support binding of the hydrophobic Aβ at the apoE domain-domain interaction interface, which would explain how apoE is able to stabilize Aβ and thereby prevent its subsequent aggregation.
Collapse
Affiliation(s)
- Stéphanie Deroo
- †Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium
| | - Florian Stengel
- ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Azadeh Mohammadi
- †Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium
| | - Nicolas Henry
- †Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium
| | - Ellen Hubin
- ∥Nanobiophysics Group, MIRA Institute for Biomedical Technology and Technical Medicine, Faculty of Science and Technology, University of Twente, Enschede, The Netherlands
- ⊥Structural Biology Brussels, Department of Biotechnology, and Structural Biology Research Center, VIB, Vrije Universiteit Brussel, Brussels, Belgium
| | - Eva-Maria Krammer
- †Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium
| | - Ruedi Aebersold
- ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- §Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Vincent Raussens
- †Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium
| |
Collapse
|
6
|
Abstract
Although all neurons carry the same genetic information, they vary considerably in morphology and functions and respond differently to environmental conditions. Such variability results mostly from differences in gene expression. Among the processes that regulate gene activity, epigenetic mechanisms play a key role and provide an additional layer of complexity to the genome. They allow the dynamic modulation of gene expression in a locus- and cell-specific manner. These mechanisms primarily involve DNA methylation, posttranslational modifications (PTMs) of histones and noncoding RNAs that together remodel chromatin and facilitate or suppress gene expression. Through these mechanisms, the brain gains high plasticity in response to experience and can integrate and store new information to shape future neuronal and behavioral responses. Dynamic epigenetic footprints underlying the plasticity of brain cells and circuits contribute to the persistent impact of life experiences on an individual's behavior and physiology ranging from the formation of long-term memory to the sequelae of traumatic events or of drug addiction. They also contribute to the way lifestyle, life events, or exposure to environmental toxins can predispose an individual to disease. This chapter describes the most prominent examples of epigenetic marks associated with long-lasting changes in the brain induced by experience. It discusses the role of epigenetic processes in behavioral plasticity triggered by environmental experiences. A particular focus is placed on learning and memory where the importance of epigenetic modifications in brain circuits is best understood. The relevance of epigenetics in memory disorders such as dementia and Alzheimer's disease is also addressed, and promising perspectives for potential epigenetic drug treatment discussed.
Collapse
|
7
|
Gapp K, Woldemichael BT, Bohacek J, Mansuy IM. Epigenetic regulation in neurodevelopment and neurodegenerative diseases. Neuroscience 2012; 264:99-111. [PMID: 23256926 DOI: 10.1016/j.neuroscience.2012.11.040] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 11/08/2012] [Accepted: 11/21/2012] [Indexed: 01/25/2023]
Abstract
From fertilization throughout development and until death, cellular programs in individual cells are dynamically regulated to fulfill multiple functions ranging from cell lineage specification to adaptation to internal and external stimuli. Such regulation is of major importance in brain cells, because the brain continues to develop long after birth and incorporates information from the environment across life. When compromised, these regulatory mechanisms can have detrimental consequences on neurodevelopment and lead to severe brain pathologies and neurodegenerative diseases in the adult individual. Elucidating these processes is essential to better understand their implication in disease etiology. Because they are strongly influenced by environmental factors, they have been postulated to depend on epigenetic mechanisms. This review describes recent studies that have identified epigenetic dysfunctions in the pathophysiology of several neurodevelopmental and neurodegenerative diseases. It discusses currently known pathways and molecular targets implicated in pathologies including imprinting disorders, Rett syndrome, and Alzheimer's, Parkinson's and Hungtinton's disease, and their relevance to these diseases.
Collapse
Affiliation(s)
- K Gapp
- Brain Research Institute, Medical Faculty of the University of Zürich and Swiss Federal Institute of Technology, Neuroscience Center Zürich, Zürich, Switzerland
| | - B T Woldemichael
- Brain Research Institute, Medical Faculty of the University of Zürich and Swiss Federal Institute of Technology, Neuroscience Center Zürich, Zürich, Switzerland
| | - J Bohacek
- Brain Research Institute, Medical Faculty of the University of Zürich and Swiss Federal Institute of Technology, Neuroscience Center Zürich, Zürich, Switzerland
| | - I M Mansuy
- Brain Research Institute, Medical Faculty of the University of Zürich and Swiss Federal Institute of Technology, Neuroscience Center Zürich, Zürich, Switzerland.
| |
Collapse
|
8
|
|
9
|
Yang S, Griffin MDW, Binger KJ, Schuck P, Howlett GJ. An equilibrium model for linear and closed-loop amyloid fibril formation. J Mol Biol 2012; 421:364-77. [PMID: 22370559 DOI: 10.1016/j.jmb.2012.02.026] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 02/08/2012] [Accepted: 02/18/2012] [Indexed: 11/30/2022]
Abstract
Amyloid fibrils and their soluble oligomeric intermediates are implicated in several age-related diseases including Alzheimer's and Parkinson's diseases. The distribution of oligomers and fibrils is related to toxicity and is dependent on the pathways for fibril assembly, generally considered to occur via a slow nucleation step that precedes fibril elongation. Human apolipoprotein (apo) C-II forms amyloid fibrils via a reversible self-assembly process accompanied by closed-loop formation and fibril breaking and joining. Our fluorescence quenching and sedimentation velocity experiments with Alexa488-labeled apoC-II indicated a time-dependent subunit interchange for both linear and closed-loop fibrils, while dilution experiments using mature fibrils indicated a shift to smaller size distributions consistent with a reversible assembly pathway. To account for this behavior, we developed an equilibrium self-association model that describes the final size distributions of apoC-II fibrils formed at different starting concentrations. The model proposes a reversible isomerization of apoC-II monomer to form an active conformer that self-assembles into fibrils via an isodesmic self-association pathway coupled to fibril length-dependent closed-loop formation. The model adequately described fibril size distributions and the proportion of closed loops as a function of total apoC-II concentration over the concentration range 0.1-0.5 mg/ml. Extension of the model to include the rates of isomerization, self-association and fibril breaking and joining provided satisfactory global fits to kinetic data on fibril formation and changes in average fibril size at different apoC-II starting concentrations. The model provides a simple thermodynamic description of the processes governing the size distribution of apoC-II fibrils at equilibrium and the formation of discrete oligomeric intermediates.
Collapse
Affiliation(s)
- Shuo Yang
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
| | | | | | | | | |
Collapse
|
10
|
Georgiadou D, Chroni A, Vezeridis A, Zannis VI, Stratikos E. Biophysical analysis of apolipoprotein E3 variants linked with development of type III hyperlipoproteinemia. PLoS One 2011; 6:e27037. [PMID: 22069485 PMCID: PMC3206067 DOI: 10.1371/journal.pone.0027037] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Accepted: 10/10/2011] [Indexed: 01/20/2023] Open
Abstract
Background Apolipoprotein E (apoE) is a major protein of the lipoprotein transport system that plays important roles in lipid homeostasis and protection from atherosclerosis. ApoE is characterized by structural plasticity and thermodynamic instability and can undergo significant structural rearrangements as part of its biological function. Mutations in the 136–150 region of the N-terminal domain of apoE, reduce its low density lipoprotein (LDL) receptor binding capacity and have been linked with lipoprotein disorders, such as type III hyperlipoproteinemia (HLP) in humans. However, the LDL-receptor binding defects for these apoE variants do not correlate well with the severity of dyslipidemia, indicating that these variants may carry additional properties that contribute to their pathogenic potential. Methodology/Principal Findings In this study we examined whether three type III HLP predisposing apoE3 variants, namely R136S, R145C and K146E affect the biophysical properties of the protein. Circular dichroism (CD) spectroscopy revealed that these mutations do not significantly alter the secondary structure of the protein. Thermal and chemical unfolding analysis revealed small thermodynamic alterations in each variant compared to wild-type apoE3, as well as effects in the reversibility of the unfolding transition. All variants were able to remodel multillamelar 1,2-Dimyristoyl-sn-glycero-3-phosphocholine (DMPC) vesicles, but R136S and R145C had reduced kinetics. Dynamic light scattering analysis indicated that the variant R136S exists in a higher-order oligomerization state in solution. Finally, 1-anilinonaphthalene-8-sulfonic acid (ANS) binding suggested that the variant R145C exposes a larger amount of hydrophobic surface to the solvent. Conclusions/Significance Overall, our findings suggest that single amino acid changes in the functionally important region 136–150 of apoE3 can affect the molecule's stability and conformation in solution and may underlie functional consequences. However, the magnitude and the non-concerted nature of these changes, make it unlikely that they constitute a distinct unifying mechanism leading to type III HLP pathogenesis.
Collapse
Affiliation(s)
- Dimitra Georgiadou
- Protein Chemistry Laboratory, National Centre for Scientific Research Demokritos, Agia Paraskevi, Athens, Greece
| | - Angeliki Chroni
- Institute of Biology, National Centre for Scientific Research Demokritos, Agia Paraskevi, Athens, Greece
| | - Alexander Vezeridis
- Molecular Genetics, Departments of Medicine and Biochemistry, Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Vassilis I. Zannis
- Molecular Genetics, Departments of Medicine and Biochemistry, Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Efstratios Stratikos
- Protein Chemistry Laboratory, National Centre for Scientific Research Demokritos, Agia Paraskevi, Athens, Greece
- * E-mail:
| |
Collapse
|
11
|
Yam AY, Wang X, Gao CM, Connolly MD, Zuckermann RN, Bleu T, Hall J, Fedynyshyn JP, Allauzen S, Peretz D, Salisbury CM. A Universal Method for Detection of Amyloidogenic Misfolded Proteins. Biochemistry 2011; 50:4322-9. [DOI: 10.1021/bi200215j] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Alice Y. Yam
- Novartis Vaccines and Diagnostics, Inc., 4560 Horton St, Emeryville, California 94608, United States
| | - Xuemei Wang
- Novartis Vaccines and Diagnostics, Inc., 4560 Horton St, Emeryville, California 94608, United States
| | - Carol Man Gao
- Novartis Vaccines and Diagnostics, Inc., 4560 Horton St, Emeryville, California 94608, United States
| | - Michael D. Connolly
- Novartis Vaccines and Diagnostics, Inc., 4560 Horton St, Emeryville, California 94608, United States
| | - Ronald N. Zuckermann
- Novartis Vaccines and Diagnostics, Inc., 4560 Horton St, Emeryville, California 94608, United States
| | - Thieu Bleu
- Novartis Vaccines and Diagnostics, Inc., 4560 Horton St, Emeryville, California 94608, United States
| | - John Hall
- Novartis Vaccines and Diagnostics, Inc., 4560 Horton St, Emeryville, California 94608, United States
| | - Joseph P. Fedynyshyn
- Novartis Vaccines and Diagnostics, Inc., 4560 Horton St, Emeryville, California 94608, United States
| | - Sophie Allauzen
- Novartis Vaccines and Diagnostics, Inc., 4560 Horton St, Emeryville, California 94608, United States
| | - David Peretz
- Novartis Vaccines and Diagnostics, Inc., 4560 Horton St, Emeryville, California 94608, United States
| | - Cleo M. Salisbury
- Novartis Vaccines and Diagnostics, Inc., 4560 Horton St, Emeryville, California 94608, United States
| |
Collapse
|
12
|
Haupt C, Bereza M, Kumar ST, Kieninger B, Morgado I, Hortschansky P, Fritz G, Röcken C, Horn U, Fändrich M. Pattern Recognition with a Fibril-Specific Antibody Fragment Reveals the Surface Variability of Natural Amyloid Fibrils. J Mol Biol 2011; 408:529-40. [DOI: 10.1016/j.jmb.2011.02.032] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Revised: 01/24/2011] [Accepted: 02/13/2011] [Indexed: 10/18/2022]
|
13
|
Teoh CL, Bekard IB, Asimakis P, Griffin MDW, Ryan TM, Dunstan DE, Howlett GJ. Shear flow induced changes in apolipoprotein C-II conformation and amyloid fibril formation. Biochemistry 2011; 50:4046-57. [PMID: 21476595 DOI: 10.1021/bi2002482] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The misfolding and self-assembly of proteins into amyloid fibrils that occur in several debilitating diseases are affected by a variety of environmental factors, including mechanical factors associated with shear flow. We examined the effects of shear flow on amyloid fibril formation by human apolipoprotein C-II (apoC-II). Shear fields (150, 300, and 500 s(-1)) accelerated the rate of apoC-II fibril formation (1 mg/mL) approximately 5-10-fold. Fibrils produced at shear rates of 150 and 300 s(-1) were similar to the twisted ribbon fibrils formed in the absence of shear, while at 500 s(-1), tangled ropelike structures were observed. The mechanism of the shear-induced acceleration of amyloid fibril formation was investigated at low apoC-II concentrations (50 μg/mL) where fibril formation does not occur. Circular dichroism and tryptophan fluorescence indicated that shear induced an irreversible change in apoC-II secondary structure. Fluorescence resonance energy transfer experiments using the single tryptophan residue in apoC-II as the donor and covalently attached acceptors showed that shear flow increased the distance between the donor and acceptor molecules. Shear-induced higher-order oligomeric species were identified by sedimentation velocity experiments using fluorescence detection, while fibril seeding experiments showed that species formed during shear flow are on the fibril formation pathway. These studies suggest that physiological shear flow conditions and conditions experienced during protein manufacturing can exert significant effects on protein conformation, leading to protein misfolding, aggregation, and amyloid fibril formation.
Collapse
Affiliation(s)
- Chai Lean Teoh
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | | | | | | | | | | | | |
Collapse
|
14
|
Teoh CL, Griffin MDW, Howlett GJ. Apolipoproteins and amyloid fibril formation in atherosclerosis. Protein Cell 2011; 2:116-27. [PMID: 21400045 DOI: 10.1007/s13238-011-1013-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Accepted: 01/29/2011] [Indexed: 10/18/2022] Open
Abstract
Amyloid fibrils arise from the aggregation of misfolded proteins into highly-ordered structures. The accumulation of these fibrils along with some non-fibrillar constituents within amyloid plaques is associated with the pathogenesis of several human degenerative diseases. A number of plasma apolipoproteins, including apolipoprotein (apo) A-I, apoA-II, apoC-II and apoE are implicated in amyloid formation or influence amyloid formation by other proteins. We review present knowledge of amyloid formation by apolipoproteins in disease, with particular focus on atherosclerosis. Further insights into the molecular mechanisms underlying their amyloidogenic propensity are obtained from in vitro studies which describe factors affecting apolipoprotein amyloid fibril formation and interactions. Additionally, we outline the evidence that amyloid fibril formation by apolipoproteins might play a role in the development and progression of atherosclerosis, and highlight possible molecular mechanisms that could contribute to the pathogenesis of this disease.
Collapse
Affiliation(s)
- Chai Lean Teoh
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | | | | |
Collapse
|
15
|
Perrin RJ, Craig-Schapiro R, Malone JP, Shah AR, Gilmore P, Davis AE, Roe CM, Peskind ER, Li G, Galasko DR, Clark CM, Quinn JF, Kaye JA, Morris JC, Holtzman DM, Townsend RR, Fagan AM. Identification and validation of novel cerebrospinal fluid biomarkers for staging early Alzheimer's disease. PLoS One 2011; 6:e16032. [PMID: 21264269 PMCID: PMC3020224 DOI: 10.1371/journal.pone.0016032] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Accepted: 12/03/2010] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Ideally, disease modifying therapies for Alzheimer disease (AD) will be applied during the 'preclinical' stage (pathology present with cognition intact) before severe neuronal damage occurs, or upon recognizing very mild cognitive impairment. Developing and judiciously administering such therapies will require biomarker panels to identify early AD pathology, classify disease stage, monitor pathological progression, and predict cognitive decline. To discover such biomarkers, we measured AD-associated changes in the cerebrospinal fluid (CSF) proteome. METHODS AND FINDINGS CSF samples from individuals with mild AD (Clinical Dementia Rating [CDR] 1) (n = 24) and cognitively normal controls (CDR 0) (n = 24) were subjected to two-dimensional difference-in-gel electrophoresis. Within 119 differentially-abundant gel features, mass spectrometry (LC-MS/MS) identified 47 proteins. For validation, eleven proteins were re-evaluated by enzyme-linked immunosorbent assays (ELISA). Six of these assays (NrCAM, YKL-40, chromogranin A, carnosinase I, transthyretin, cystatin C) distinguished CDR 1 and CDR 0 groups and were subsequently applied (with tau, p-tau181 and Aβ42 ELISAs) to a larger independent cohort (n = 292) that included individuals with very mild dementia (CDR 0.5). Receiver-operating characteristic curve analyses using stepwise logistic regression yielded optimal biomarker combinations to distinguish CDR 0 from CDR>0 (tau, YKL-40, NrCAM) and CDR 1 from CDR<1 (tau, chromogranin A, carnosinase I) with areas under the curve of 0.90 (0.85-0.94 95% confidence interval [CI]) and 0.88 (0.81-0.94 CI), respectively. CONCLUSIONS Four novel CSF biomarkers for AD (NrCAM, YKL-40, chromogranin A, carnosinase I) can improve the diagnostic accuracy of Aβ42 and tau. Together, these six markers describe six clinicopathological stages from cognitive normalcy to mild dementia, including stages defined by increased risk of cognitive decline. Such a panel might improve clinical trial efficiency by guiding subject enrollment and monitoring disease progression. Further studies will be required to validate this panel and evaluate its potential for distinguishing AD from other dementing conditions.
Collapse
Affiliation(s)
- Richard J Perrin
- Division of Neuropathology, Washington University School of Medicine, St. Louis, Missouri, United States of America.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Haupt C, Morgado I, Kumar ST, Parthier C, Bereza M, Hortschansky P, Stubbs MT, Horn U, Fändrich M. Amyloid Fibril Recognition with the Conformational B10 Antibody Fragment Depends on Electrostatic Interactions. J Mol Biol 2011; 405:341-8. [DOI: 10.1016/j.jmb.2010.10.059] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Revised: 10/29/2010] [Accepted: 10/31/2010] [Indexed: 11/16/2022]
|
17
|
Teoh CL, Pham CLL, Todorova N, Hung A, Lincoln CN, Lees E, Lam YH, Binger KJ, Thomson NH, Radford SE, Smith TA, Müller SA, Engel A, Griffin MDW, Yarovsky I, Gooley PR, Howlett GJ. A structural model for apolipoprotein C-II amyloid fibrils: experimental characterization and molecular dynamics simulations. J Mol Biol 2010; 405:1246-66. [PMID: 21146539 DOI: 10.1016/j.jmb.2010.12.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Revised: 12/02/2010] [Accepted: 12/03/2010] [Indexed: 10/18/2022]
Abstract
The self-assembly of specific proteins to form insoluble amyloid fibrils is a characteristic feature of a number of age-related and debilitating diseases. Lipid-free human apolipoprotein C-II (apoC-II) forms characteristic amyloid fibrils and is one of several apolipoproteins that accumulate in amyloid deposits located within atherosclerotic plaques. X-ray diffraction analysis of aligned apoC-II fibrils indicated a simple cross-β-structure composed of two parallel β-sheets. Examination of apoC-II fibrils using transmission electron microscopy, scanning transmission electron microscopy, and atomic force microscopy indicated that the fibrils are flat ribbons composed of one apoC-II molecule per 4.7-Å rise of the cross-β-structure. Cross-linking results using single-cysteine substitution mutants are consistent with a parallel in-register structural model for apoC-II fibrils. Fluorescence resonance energy transfer analysis of apoC-II fibrils labeled with specific fluorophores provided distance constraints for selected donor-acceptor pairs located within the fibrils. These findings were used to develop a simple 'letter-G-like' β-strand-loop-β-strand model for apoC-II fibrils. Fully solvated all-atom molecular dynamics (MD) simulations showed that the model contained a stable cross-β-core with a flexible connecting loop devoid of persistent secondary structure. The time course of the MD simulations revealed that charge clusters in the fibril rearrange to minimize the effects of same-charge interactions inherent in parallel in-register models. Our structural model for apoC-II fibrils suggests that apoC-II monomers fold and self-assemble to form a stable cross-β-scaffold containing relatively unstructured connecting loops.
Collapse
Affiliation(s)
- Chai Lean Teoh
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Abstract
Neurodegenerative diseases are characterized by progressive dysfunction of specific populations of neurons, determining clinical presentation. Neuronal loss is associated with extra and intracellular accumulation of misfolded proteins, the hallmarks of many neurodegenerative proteinopathies. Major basic processes include abnormal protein dynamics due to deficiency of the ubiquitin-proteosome-autophagy system, oxidative stress and free radical formation, mitochondrial dysfunction, impaired bioenergetics, dysfunction of neurotrophins, 'neuroinflammatory' processes and (secondary) disruptions of neuronal Golgi apparatus and axonal transport. These interrelated mechanisms lead to programmed cell death is a long run over many years. Neurodegenerative disorders are classified according to known genetic mechanisms or to major components of protein deposits, but recent studies showed both overlap and intraindividual diversities between different phenotypes. Synergistic mechanisms between pathological proteins suggest common pathogenic mechanisms. Animal models and other studies have provided insight into the basic neurodegeneration and cell death programs, offering new ways for future prevention/treatment strategies.
Collapse
Affiliation(s)
- Kurt A Jellinger
- Institute of Clinical Neurobiology, Kenyongasse, Vienna, Austria.
| |
Collapse
|
19
|
Luo J, Maréchal JD, Wärmländer S, Gräslund A, Perálvarez-Marín A. In silico analysis of the apolipoprotein E and the amyloid beta peptide interaction: misfolding induced by frustration of the salt bridge network. PLoS Comput Biol 2010; 6:e1000663. [PMID: 20140182 PMCID: PMC2816681 DOI: 10.1371/journal.pcbi.1000663] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2009] [Accepted: 12/30/2009] [Indexed: 11/18/2022] Open
Abstract
The relationship between Apolipoprotein E (ApoE) and the aggregation processes of the amyloid β (Aβ) peptide has been shown to be crucial for Alzheimer's disease (AD). The presence of the ApoE4 isoform is considered to be a contributing risk factor for AD. However, the detailed molecular properties of ApoE4 interacting with the Aβ peptide are unknown, although various mechanisms have been proposed to explain the physiological and pathological role of this relationship. Here, computer simulations have been used to investigate the process of Aβ interaction with the N-terminal domain of the human ApoE isoforms (ApoE2, ApoE3 and ApoE4). Molecular docking combined with molecular dynamics simulations have been undertaken to determine the Aβ peptide binding sites and the relative stability of binding to each of the ApoE isoforms. Our results show that from the several ApoE isoforms investigated, only ApoE4 presents a misfolded intermediate when bound to Aβ. Moreover, the initial α-helix used as the Aβ peptide model structure also becomes unstructured due to the interaction with ApoE4. These structural changes appear to be related to a rearrangement of the salt bridge network in ApoE4, for which we propose a model. It seems plausible that ApoE4 in its partially unfolded state is incapable of performing the clearance of Aβ, thereby promoting amyloid forming processes. Hence, the proposed model can be used to identify potential drug binding sites in the ApoE4-Aβ complex, where the interaction between the two molecules can be inhibited. Unraveling the molecular details of the interaction between apolipoprotein E and the amyloid β peptide will yield insights into the relationship between Alzheimer's disease and lipid transport and metabolism. The isoform E4 of apolipoprotein E has been shown to be closely related to Alzheimer's disease. We have therefore used a computational approach to depict a detailed interaction map for this peptide-lipoprotein interaction. The simulation shows that the specific formation of the lipoprotein isoform E4 and the peptide complex affects the structure of the lipoprotein and the peptide. We suggest that this is related to some of the pathogenic effects in Alzheimer's disease. Our results provide a molecular model to work with for the design of potential therapeutic agents capable of modulating this interaction.
Collapse
Affiliation(s)
- Jinghui Luo
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Jean-Didier Maréchal
- Unitat de Química Física, Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Sebastian Wärmländer
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Astrid Gräslund
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Alex Perálvarez-Marín
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
- Unitat de Biofísica, Departament de Bioquímica i de Biologia Molecular i Centre d'Estudis en Biofísica, Universitat Autònoma de Barcelona, Bellaterra, Spain
- * E-mail:
| |
Collapse
|
20
|
Urdinguio RG, Sanchez-Mut JV, Esteller M. Epigenetic mechanisms in neurological diseases: genes, syndromes, and therapies. Lancet Neurol 2009; 8:1056-72. [PMID: 19833297 DOI: 10.1016/s1474-4422(09)70262-5] [Citation(s) in RCA: 340] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Epigenetic mechanisms such as DNA methylation and modifications to histone proteins regulate high-order DNA structure and gene expression. Aberrant epigenetic mechanisms are involved in the development of many diseases, including cancer. The neurological disorder most intensely studied with regard to epigenetic changes is Rett syndrome; patients with Rett syndrome have neurodevelopmental defects associated with mutations in MeCP2, which encodes the methyl CpG binding protein 2, that binds to methylated DNA. Other mental retardation disorders are also linked to the disruption of genes involved in epigenetic mechanisms; such disorders include alpha thalassaemia/mental retardation X-linked syndrome, Rubinstein-Taybi syndrome, and Coffin-Lowry syndrome. Moreover, aberrant DNA methylation and histone modification profiles of discrete DNA sequences, and those at a genome-wide level, have just begun to be described for neurodegenerative disorders such as Alzheimer's disease, Parkinson's disease, and Huntington's disease, and in other neurological disorders such as multiple sclerosis, epilepsy, and amyotrophic lateral sclerosis. In this Review, we describe epigenetic changes present in neurological diseases and discuss the therapeutic potential of epigenetic drugs, such as histone deacetylase inhibitors.
Collapse
Affiliation(s)
- Rocio G Urdinguio
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, Catalonia, Spain
| | | | | |
Collapse
|
21
|
Salvatore A, Cigliano L, Carlucci A, Bucci EM, Abrescia P. Haptoglobin binds apolipoprotein E and influences cholesterol esterification in the cerebrospinal fluid. J Neurochem 2009; 110:255-63. [PMID: 19457062 DOI: 10.1111/j.1471-4159.2009.06121.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Haptoglobin (Hpt) binds the apolipoprotein (Apo) A-I domain, which is involved in stimulating the enzyme lecithin-cholesterol acyltransferase (LCAT) for cholesterol esterification. This binding was shown to protect ApoA-I against hydroxyl radicals, thus preventing loss of ApoA-I function in enzyme stimulation. In this study, we report that Hpt is also able to bind ApoE. The Hpt binding site on the ApoE structure was mapped by using synthetic peptides, and found homologous to the Hpt binding site of ApoA-I. Hydroxyl radicals promoted in vitro the formation of ApoE-containing adducts which were detected by immunoblotting. Hpt impaired this oxidative modification whereas albumin did not. CSF from patients with multiple sclerosis or subjects without neurodegeneration contains oxidized forms of ApoE and ApoA-I similar to those observed in vitro. CSF was analyzed for its level of ApoA-I, ApoE, Hpt, cholesteryl esters, and unesterified cholesterol. The ratio of esterified with unesterified cholesterol, assumed to reflect the LCAT activity ex vivo, did not correlate with either analyzed protein, but conversely correlated with the ratio [Hpt]/([ApoE]+[ApoA-I]). The results suggest that Hpt might save the function of ApoA-I and ApoE for cholesterol esterification, a process contributing to cholesterol elimination from the brain.
Collapse
Affiliation(s)
- Alfonso Salvatore
- Dipartimento delle Scienze Biologiche Università di Napoli Federico II, Mezzocannone, Napoli, Italia
| | | | | | | | | |
Collapse
|
22
|
Kawasaki K, Ogiwara N, Sugano M, Okumura N, Yamauchi K. Sialic acid moiety of apolipoprotein E and its impact on the formation of lipoprotein particles in human cerebrospinal fluid. Clin Chim Acta 2008; 402:61-6. [PMID: 19138682 DOI: 10.1016/j.cca.2008.12.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2008] [Revised: 12/08/2008] [Accepted: 12/12/2008] [Indexed: 11/19/2022]
Abstract
BACKGROUND Apolipoprotein (apo) E in the cerebrospinal fluid (CSF) is abundant with sialic acid (SA), and sialylation of certain proteins is known to modulate biological function. The aim of the present study was to quantify the SA content in CSF apoE and carry out the more detailed characterization of the CSF apoE-containing lipoproteins. METHODS The method for the determination of the SA in CSF apoE was based on the conversion of SA into p-aminobenzoic acid ethyl ester-derivatized N-acetylmannosamine, followed by HPLC analysis. RESULTS The levels of CSF SA and serum SA were 25.9+/-1.5 and 2209+/-196 micromol/l, respectively; however, when the SA values were corrected by the total protein concentrations, CSF SA values were approximately 3.5-fold of those in the serum. The SA levels in the CSF apoE-containing lipoprotein fractions were 5.3+/-1.3% of total CSF SA, and were correlated with the CSF apoE concentrations. However, the ratios of SA to apoE were inversely proportional to the CSF lipid concentrations. The lipoprotein particle sizes were larger when the ratios of SA to CSF apoE were greater. CONCLUSION The SA moiety of the CSF apoE molecules may affect the formation of the apoE-containing lipoprotein particles and the regulation of lipid delivery in CNS.
Collapse
Affiliation(s)
- Kenji Kawasaki
- Department of Laboratory Medicine, Shinshu University Hospital, Japan
| | | | | | | | | |
Collapse
|
23
|
Sugano M, Yamauchi K, Kawasaki K, Tozuka M, Fujita K, Okumura N, Ota H. Sialic acid moiety of apolipoprotein E3 at Thr(194) affects its interaction with beta-amyloid(1-42) peptides. Clin Chim Acta 2007; 388:123-9. [PMID: 18023277 DOI: 10.1016/j.cca.2007.10.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2007] [Revised: 10/15/2007] [Accepted: 10/18/2007] [Indexed: 10/22/2022]
Abstract
BACKGROUND The interaction between apolipoprotein (apo) E and beta-amyloid (Abeta) is associated with the development of Alzheimer's disease (AD); however, the details remain unknown. ApoE in cerebrospinal fluid is extensively sialylated, and sialylation of certain proteins are known to modulate biological function. We investigated the effects of a sialic acid moiety of apoE on the apoE-Abeta interaction. METHODS We prepared normal apoE3 and its mutant (Thr(194) --> Ala) and analyzed their interactions with Abeta(1-42) by using the surface plasmon resonance (SPR) assay. In addition, we performed the SPR assay by using apoE-containing lipoproteins treated with neuraminidase. We also assessed the effect of the mutation on the interaction of apoE3 with liposomes. RESULTS The binding avidity of the mutant apoE3(#) was approximately 50% that of normal apoE3 (p<0.0001). The binding avidity of the apoE-containing lipoproteins for Abeta(1-42) reduced after neuraminidase treatment. CONCLUSIONS We suggest that AD development is controlled not only by the apoE isoforms but also by the posttranslational modifications in apoE, such as those in the sialic acid moieties, which are abundant in apoE derived from the brain.
Collapse
Affiliation(s)
- Mitsutoshi Sugano
- Department of Laboratory Medicine, Shinshu University Hospital, Matsumoto, Japan
| | | | | | | | | | | | | |
Collapse
|