1
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Gelenter MD, Yau WM, Anfinrud PA, Bax A. From Milliseconds to Minutes: Melittin Self-Assembly from Concerted Non-Equilibrium Pressure-Jump and Equilibrium Relaxation Nuclear Magnetic Resonance. J Phys Chem Lett 2024; 15:1930-1935. [PMID: 38346015 PMCID: PMC10896212 DOI: 10.1021/acs.jpclett.3c03563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/25/2024] [Accepted: 01/29/2024] [Indexed: 02/23/2024]
Abstract
Non-equilibrium kinetics techniques like pressure-jump nuclear magnetic resonance (NMR) are powerful in tracking changes in oligomeric populations and are not limited by relaxation rates for the time scales of exchange that can be probed. However, these techniques are less sensitive to minor, transient populations than are Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiments. We integrated non-equilibrium pressure-jump and equilibrium CPMG relaxation dispersion data to fully map the kinetic landscape of melittin tetramerization. While monomeric peptides weakly form dimers (Kd,D/M ≈ 26 mM) whose population never exceeds 1.6% at 288 K, dimers associate tightly to form stable tetrameric species (Kd,T/D ≈ 740 nM). Exchange between the monomer and dimer, along with exchange between the dimer and tetramer, occurs on the millisecond time scale. The NMR approach developed herein can be readily applied to studying the folding and misfolding of a wide range of oligomeric assemblies.
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Affiliation(s)
- Martin D Gelenter
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 5 Memorial Drive, Bethesda, Maryland 20892, United States
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 5 Memorial Drive, Bethesda, Maryland 20892, United States
| | - Philip A Anfinrud
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 5 Memorial Drive, Bethesda, Maryland 20892, United States
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 5 Memorial Drive, Bethesda, Maryland 20892, United States
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2
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Kaur A, Goyal B. Identification of new pentapeptides as potential inhibitors of amyloid-β 42 aggregation using virtual screening and molecular dynamics simulations. J Mol Graph Model 2023; 124:108558. [PMID: 37390790 DOI: 10.1016/j.jmgm.2023.108558] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/02/2023]
Abstract
Alzheimer's disease (AD) is a multifactorial neurodegenerative disease mainly characterized by extracellular accumulation of amyloid-β (Aβ) peptide. Previous studies reported pentapeptide RIIGL as an effective inhibitor of Aβ aggregation and neurotoxicity induced by Aβ aggregates. In this work, a library of 912 pentapeptides based on RIIGL has been designed and assessed for their efficacy to inhibit Aβ42 aggregation using computational techniques. The top hit pentapeptides revealed by molecular docking were further assessed for their binding affinity with Aβ42 monomer using MM-PBSA (molecular mechanics Poisson-Boltzmann surface area) method. The MM-PBSA analysis identified RLAPV, RVVPI, and RIAPA, which bind to Aβ42 monomer with a higher binding affinity -55.80, -46.32, and -44.26 kcal/mol, respectively, as compared to RIIGL (ΔGbinding = -41.29 kcal/mol). The residue-wise binding free energy predicted hydrophobic contacts between Aβ42 monomer and pentapeptides. The secondary structure analysis of the conformational ensembles generated by molecular dynamics (MD) depicted remarkably enhanced sampling of helical and no β-sheet conformations in Aβ42 monomer on the incorporation of RVVPI and RIAPA. Notably, RVVPI and RIAPA destabilized the D23-K28 salt bridge in Aβ42 monomer, which plays a crucial role in Aβ42 oligomer stability and fibril formation. The MD simulations highlighted that the incorporation of proline and arginine in pentapeptides contributed to their strong binding with Aβ42 monomer. Furthermore, RVVPI and RIAPA prevented conformational conversion of Aβ42 monomer to aggregation-prone structures, which, in turn, resulted in a lower aggregation tendency of Aβ42 monomer.
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Affiliation(s)
- Apneet Kaur
- School of Chemistry & Biochemistry, Thapar Institute of Engineering & Technology, Patiala, 147004, Punjab, India
| | - Bhupesh Goyal
- School of Chemistry & Biochemistry, Thapar Institute of Engineering & Technology, Patiala, 147004, Punjab, India.
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3
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Pradhan T, Sarkar R, Meighen-Berger KM, Feige MJ, Zacharias M, Reif B. Mechanistic insights into the aggregation pathway of the patient-derived immunoglobulin light chain variable domain protein FOR005. Nat Commun 2023; 14:3755. [PMID: 37353525 PMCID: PMC10290123 DOI: 10.1038/s41467-023-39280-0] [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: 07/03/2022] [Accepted: 06/05/2023] [Indexed: 06/25/2023] Open
Abstract
Systemic antibody light chain (AL) amyloidosis is characterized by deposition of amyloid fibrils. Prior to fibril formation, soluble oligomeric AL protein has a direct cytotoxic effect on cardiomyocytes. We focus on the patient derived λ-III AL variable domain FOR005 which is mutated at five positions with respect to the closest germline protein. Using solution-state NMR spectroscopy, we follow the individual steps involved in protein misfolding from the native to the amyloid fibril state. Unfavorable mutations in the complementary determining regions introduce a strain in the native protein structure which yields partial unfolding. Driven by electrostatic interactions, the protein converts into a high molecular weight, oligomeric, molten globule. The high local concentration of aggregation prone regions in the oligomer finally catalyzes the conversion into fibrils. The topology is determined by balanced electrostatic interactions in the fibril core implying a 180° rotational switch of the beta-sheets around the conserved disulfide bond.
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Affiliation(s)
- Tejaswini Pradhan
- Bavarian NMR Center (BNMRZ), Department of Bioscience, TUM School of Natural Sciences, Technical University Munich, Lichtenbergstr. 4, 85747, Garching, Germany
- Institute of Structural Biology (STB), Helmholtz-Zentrum München (HMGU), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Riddhiman Sarkar
- Bavarian NMR Center (BNMRZ), Department of Bioscience, TUM School of Natural Sciences, Technical University Munich, Lichtenbergstr. 4, 85747, Garching, Germany
- Institute of Structural Biology (STB), Helmholtz-Zentrum München (HMGU), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Kevin M Meighen-Berger
- Center for Functional Protein Assemblies (CPA), Department of Bioscience, TUM School of Natural Sciences, Technical University Munich, Ernst-Otto-Fischer-Straße 8, 85748, Garching, Germany
| | - Matthias J Feige
- Center for Functional Protein Assemblies (CPA), Department of Bioscience, TUM School of Natural Sciences, Technical University Munich, Ernst-Otto-Fischer-Straße 8, 85748, Garching, Germany
| | - Martin Zacharias
- Center for Functional Protein Assemblies (CPA), Department of Bioscience, TUM School of Natural Sciences, Technical University Munich, Ernst-Otto-Fischer-Straße 8, 85748, Garching, Germany
| | - Bernd Reif
- Bavarian NMR Center (BNMRZ), Department of Bioscience, TUM School of Natural Sciences, Technical University Munich, Lichtenbergstr. 4, 85747, Garching, Germany.
- Institute of Structural Biology (STB), Helmholtz-Zentrum München (HMGU), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
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4
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Morel B, Conejero-Lara F. Preparation and Investigation of Crucial Oligomers in the Early Stages of Aβ40 and Aβ42 Aggregation. Methods Mol Biol 2023; 2551:15-28. [PMID: 36310193 DOI: 10.1007/978-1-0716-2597-2_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Amyloid aggregation is a hallmark in many neuropathologies and other diseases of tremendous impact. It is increasingly evident that neuronal death associated with Alzheimer's disease (AD) is mainly produced by oligomers of the amyloid-β (Aβ) peptide. Yet little is known about the detailed structural and biophysical mechanisms of their formation. This lack of complete understanding comes from the labile nature and handling complexity of the oligomers. Consequently, providing reproducible and robust protocols for oligomer preparation is of particular importance.In this study, we describe detailed methods for the preparation and isolation of micellar oligomers of Aβ that evolve towards larger and more stable oligomers enriched in beta-sheet structure and able to acquire a higher capacity to fibrillate. We also describe briefly some biophysical experiments allowing oligomer characterization.
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Affiliation(s)
- Bertrand Morel
- Departamento de Química Física, Instituto de Biotecnología y Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, Granada, Spain.
| | - Francisco Conejero-Lara
- Departamento de Química Física, Instituto de Biotecnología y Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, Granada, Spain.
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5
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Connor JP, Quinn SD, Schaefer C. Sticker-and-spacer model for amyloid beta condensation and fibrillation. Front Mol Neurosci 2022; 15:962526. [PMID: 36311031 PMCID: PMC9611774 DOI: 10.3389/fnmol.2022.962526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022] Open
Abstract
A major pathogenic hallmark of Alzheimer's disease is the presence of neurotoxic plaques composed of amyloid beta (Aβ) peptides in patients' brains. The pathway of plaque formation remains elusive, though some clues appear to lie in the dominant presence of Aβ1 − 42 in these plaques despite Aβ1−40 making up approximately 90% of the Aβ pool. We hypothesize that this asymmetry is driven by the hydrophobicity of the two extra amino acids that are incorporated in Aβ1−42. To investigate this hypothesis at the level of single molecules, we have developed a molecular “sticker-and-spacer lattice model” of unfolded Aβ. The model protein has a single sticker that may reversibly dimerise and elongate into semi-flexible linear chains. The growth is hampered by excluded-volume interactions that are encoded by the hydrophilic spacers but are rendered cooperative by the attractive interactions of hydrophobic spacers. For sufficiently strong hydrophobicity, the chains undergo liquid-liquid phase-separation (LLPS) into condensates that facilitate the nucleation of fibers. We find that a small fraction of Aβ1−40 in a mixture of Aβ1−40 and Aβ1−42 shifts the critical concentration for LLPS to lower values. This study provides theoretical support for the hypothesis that LLPS condensates act as a precursor for aggregation and provides an explanation for the Aβ1−42-enrichment of aggregates in terms of hydrophobic interactions.
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Affiliation(s)
- Jack P. Connor
- Department of Biology, University of York, York, United Kingdom
- School of Physics, Engineering and Technology, University of York, York, United Kingdom
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- *Correspondence: Jack P. Connor
| | - Steven D. Quinn
- School of Physics, Engineering and Technology, University of York, York, United Kingdom
- York Biomedical Research Institute, University of York, York, United Kingdom
| | - Charley Schaefer
- School of Physics, Engineering and Technology, University of York, York, United Kingdom
- Charley Schaefer
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6
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Mamone S, Glöggler S, Becker S, Rezaei-Ghaleh N. Early Divergence in Misfolding Pathways of Amyloid-Beta Peptides. Chemphyschem 2021; 22:2158-2163. [PMID: 34355840 PMCID: PMC8596873 DOI: 10.1002/cphc.202100542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/05/2021] [Indexed: 01/01/2023]
Abstract
The amyloid cascade hypothesis proposes that amyloid‐beta (Aβ) aggregation is the initial triggering event in Alzheimer's disease. Here, we utilize NMR spectroscopy and monitor the structural dynamics of two variants of Aβ, Aβ40 and Aβ42, as a function of temperature. Despite having identical amino acid sequence except for the two additional C‐terminal residues, Aβ42 has higher aggregation propensity than Aβ40. As revealed by the NMR data on dynamics, including backbone chemical shifts, intra‐methyl cross‐correlated relaxation rates and glycine‐based singlet‐states, the C‐terminal region of Aβ, especially the G33‐L34‐M35 segment, plays a particular role in the early steps of temperature‐induced Aβ aggregation. In Aβ42, the distinct dynamical behaviour of C‐terminal residues at higher temperatures is accompanied with marked changes in the backbone dynamics of residues V24‐K28. The distinctive role of the C‐terminal region of Aβ42 in the initiation of aggregation defines a target for the rational design of Aβ42 aggregation inhibitors.
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Affiliation(s)
- Salvatore Mamone
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany.,Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Von-Siebold-Str. 3A, 37075, Göttingen, Germany
| | - Stefan Glöggler
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany.,Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Von-Siebold-Str. 3A, 37075, Göttingen, Germany
| | - Stefan Becker
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany
| | - Nasrollah Rezaei-Ghaleh
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany.,Department of Neurology, University Medical Center Göttingen, Waldweg 33, 37073, Göttingen, Germany.,Institute of Physical Biology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
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7
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Mahmoudinobar F, Nilsson BL, Dias CL. Effects of Ions and Small Compounds on the Structure of Aβ 42 Monomers. J Phys Chem B 2021; 125:1085-1097. [PMID: 33481611 DOI: 10.1021/acs.jpcb.0c09617] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Aggregation of amyloid-β (Aβ) proteins in the brain is a hallmark of Alzheimer's disease. This phenomenon can be promoted or inhibited by adding small molecules to the solution where Aβ is embedded. These molecules affect the ensemble of conformations sampled by Aβ monomers even before aggregation starts. Here, we perform extensive all-atom replica exchange molecular dynamics (REMD) simulations to provide a comparative study of the ensemble of conformations sampled by Aβ42 monomers in solutions that promote (i.e., aqueous solution containing NaCl) and inhibit (i.e., aqueous solutions containing scyllo-inositol or 4-aminophenol) aggregation. Simulations performed in pure water are used as our reference. We find that secondary-structure content is only affected in an antagonistic manner by promoters and inhibitors at the C-terminus and the central hydrophilic core. Moreover, the end of the C-terminus binds more favorably to the central hydrophobic core region of Aβ42 in NaCl adopting a type of strand-loop-strand structure that is disfavored by inhibitors. Nonpolar residues that form the dry core of larger aggregates of Aβ42 (e.g., PDB ID 2BEG) are found at close proximity in these strand-loop-strand structures, suggesting that their formation could play an important role in initiating nucleation. In the presence of inhibitors, the C-terminus binds the central hydrophilic core with a higher probability than in our reference simulation. This sensitivity of the C-terminus, which is affected in an antagonistic manner by inhibitors and promoters, provides evidence for its critical role in accounting for aggregation.
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Affiliation(s)
- Farbod Mahmoudinobar
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
| | - Bradley L Nilsson
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Cristiano L Dias
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
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8
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McCoy MD, Hamre J, Klimov DK, Jafri MS. Predicting Genetic Variation Severity Using Machine Learning to Interpret Molecular Simulations. Biophys J 2020; 120:189-204. [PMID: 33333034 DOI: 10.1016/j.bpj.2020.12.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 11/20/2020] [Accepted: 12/08/2020] [Indexed: 02/08/2023] Open
Abstract
Distinct missense mutations in a specific gene have been associated with different diseases as well as differing severity of a disease. Current computational methods predict the potential pathogenicity of a missense variant but fail to differentiate between separate disease or severity phenotypes. We have developed a method to overcome this limitation by applying machine learning to features extracted from molecular dynamics simulations, creating a way to predict the effect of novel genetic variants in causing a disease, drug resistance, or another specific trait. As an example, we have applied this novel approach to variants in calmodulin associated with two distinct arrhythmias as well as two different neurodegenerative diseases caused by variants in amyloid-β peptide. The new method successfully predicts the specific disease caused by a gene variant and ranks its severity with more accuracy than existing methods. We call this method molecular dynamics phenotype prediction model.
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Affiliation(s)
- Matthew D McCoy
- Innovation Center for Biomedical Informatics, Department of Oncology, Georgetown University Medical Center, Georgetown University, Washington DC; School of Systems Biology, George Mason University, Manassas, Virginia.
| | - John Hamre
- School of Systems Biology, George Mason University, Manassas, Virginia
| | - Dmitri K Klimov
- School of Systems Biology, George Mason University, Manassas, Virginia
| | - M Saleet Jafri
- School of Systems Biology, George Mason University, Manassas, Virginia; Krasnow Institute for Advanced Study, Interdisciplinary Program in Neuroscience, School of Systems Biology, George Mason University, Fairfax, Virginia.
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9
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Abstract
The spontaneous assembly of proteins into amyloid fibrils is a phenomenon central to many increasingly common and currently incurable human disorders, including Alzheimer's and Parkinson's diseases. Oligomeric species form transiently during this process and not only act as essential intermediates in the assembly of new filaments but also represent major pathogenic agents in these diseases. While amyloid fibrils possess a common, defining set of physicochemical features, oligomers, by contrast, appear much more diverse, and their commonalities and differences have hitherto remained largely unexplored. Here, we use the framework of chemical kinetics to investigate their dynamical properties. By fitting experimental data for several unrelated amyloidogenic systems to newly derived mechanistic models, we find that oligomers present with a remarkably wide range of kinetic and thermodynamic stabilities but that they possess two properties that are generic: they are overwhelmingly nonfibrillar, and they predominantly dissociate back to monomers rather than maturing into fibrillar species. These discoveries change our understanding of the relationship between amyloid oligomers and amyloid fibrils and have important implications for the nature of their cellular toxicity.
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10
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Liu H, Song D, Zhang Y, Yang S, Luo R, Chen HF. Extensive tests and evaluation of the CHARMM36IDPSFF force field for intrinsically disordered proteins and folded proteins. Phys Chem Chem Phys 2019; 21:21918-21931. [PMID: 31552948 DOI: 10.1039/c9cp03434j] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Intrinsically disordered proteins (IDPs) have received increasing attention in recent studies due to their structural heterogeneity and critical biological functions. To fully understand the structural properties and determine accurate ensembles of IDPs, molecular dynamics (MD) simulation was widely used to sample diverse conformations and reveal the structural dynamics. However, the classical state-of-the-art force fields perform well for folded proteins while being unsatisfactory for the simulations of disordered proteins reported in many previous studies. Thus, improved force fields were developed to precisely describe both folded proteins and disordered proteins. Preliminary tests show that our newly developed CHARMM36IDPSFF (C36IDPSFF) force field can well reproduce the experimental observables of several disordered proteins, but more tests on different types of proteins are needed to further evaluate the performance of C36IDPSFF. Here, we extensively simulate short peptides, disordered proteins, and fast-folding proteins as well as folded proteins, and compare the simulated results with the experimental observables. The simulation results show that C36IDPSFF could substantially reproduce the experimental observables for most of the tested proteins but some limitations are also found in the radius of gyration of large disordered proteins and the stability of fast-folding proteins. This force field will facilitate large scale studies of protein structural dynamics and functions using MD simulations.
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Affiliation(s)
- Hao Liu
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
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11
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Yang S, Liu H, Zhang Y, Lu H, Chen H. Residue-Specific Force Field Improving the Sample of Intrinsically Disordered Proteins and Folded Proteins. J Chem Inf Model 2019; 59:4793-4805. [DOI: 10.1021/acs.jcim.9b00647] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sheng Yang
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU−Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Hao Liu
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU−Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Yangpeng Zhang
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU−Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Hui Lu
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU−Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
- SJTU-Yale Joint Center for Biostatistics and Data Science, 800 Dongchuan Road, Shanghai, 200240, China
| | - Haifeng Chen
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU−Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
- Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Shanghai, 200235, China
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12
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Morel B, Conejero-Lara F. Early mechanisms of amyloid fibril nucleation in model and disease-related proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:140264. [PMID: 31437584 DOI: 10.1016/j.bbapap.2019.140264] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/18/2019] [Accepted: 08/12/2019] [Indexed: 02/06/2023]
Abstract
Protein amyloid aggregation is a hallmark in neuropathologies and other diseases of tremendous impact such as Alzheimer's or Parkinson's diseases. During the last decade, it has become increasingly evident that neuronal death is mainly induced by proteinaceous oligomers rather than the mature amyloid fibrils. Therefore, the earliest molecular events occurring during the amyloid aggregation cascade represent a growing interest of study. Important breakthroughs have been achieved using experimental data from different proteins, used as models, as well as systems related to diseases. Here, we summarize the structural properties of amyloid oligomeric and fibrillar aggregates and review the recent advances on how biophysical techniques can be combined with quantitative kinetic analysis and theoretical models to study the detailed mechanism of oligomer formation and nucleation of fibrils. These insights into the mechanism of early oligomerization and amyloid nucleation are of relevant interest in drug discovery and in the design of preventive strategies against neurodegenerative diseases.
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Affiliation(s)
- Bertrand Morel
- Departamento de Química Física e Instituto de Biotecnología, Universidad de Granada, 18071 Granada, Spain.
| | - Francisco Conejero-Lara
- Departamento de Química Física e Instituto de Biotecnología, Universidad de Granada, 18071 Granada, Spain
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13
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Cieplak AS. Tau Inclusions in Alzheimer's, Chronic Traumatic Encephalopathy and Pick's Disease. A Speculation on How Differences in Backbone Polarization Underlie Divergent Pathways of Tau Aggregation. Front Neurosci 2019; 13:488. [PMID: 31156372 PMCID: PMC6530265 DOI: 10.3389/fnins.2019.00488] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/29/2019] [Indexed: 12/13/2022] Open
Abstract
Tau-related dementias appear to involve specific to each disease aggregation pathways and morphologies of filamentous tau assemblies. To understand etiology of these differences, here we elucidate molecular mechanism of formation of tau PHFs based on the PMO theory of misfolding and aggregation of pleiomorphic proteins associated with neurodegenerative diseases. In this model, fibrillization of tau is initiated by the coupled binding and folding of the MTB domains that yields antiparallel homodimers, in analogy to folding of split inteins. The free energy of binding is minimized when the antiparallel alignment brings about backbone-backbone H-bonding between the MTBD segments of similar “strand” propensities. To assess these propensities, a function of the NMR shielding tensors of the Cα atoms is introduced as the folding potential function FPi; the Cα tensors are obtained by the quantum mechanical modeling of protein secondary structure (GIAO//B3LYP/D95**). The calculated FPi plots show that the “strand” propensities of the MBTD segments, and hence the homodimer's register, can be affected by the relatively small changes in the environment's pH, as a result of protonation of MBTD's conserved histidines. The assembly of the antiparallel tau dimers into granular aggregates and their subsequent conversion into the parallel cross-β structure of paired helical filaments is expected to follow the same path as the previously described fibrillization of Aβ. Consequently, the core structure of the nascent tau fibril is determined by the register of the tau homodimer. This model accounts for the reported differences in (i) fibril-core structure of in vivo and in vitro filaments, (ii) cross-seeding of isoforms, (iii) effects of reducing/non-reducing conditions, (iv) effects of PHF6 mutations, and (v) homologs' aggregation properties. The proposed model also suggests that in contrast to Alzheimer's and chronic traumatic encephalopathy disease, the assembly of tau prions in Pick's disease would be facilitated by a moderate drop in pH that accompanies e.g., transit in the endosomal system, inflammation response or an ischemic injury.
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Affiliation(s)
- Andrzej Stanisław Cieplak
- Department of Chemistry, Bilkent University, Ankara, Turkey.,Department of Chemistry, Yale University, New Haven, CT, United States.,Department of Chemistry, Brandeis University, Waltham, MA, United States
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14
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Orts J, Aulikki Wälti M, Ghosh D, Campioni S, Saupe SJ, Riek R. Rational Structure-Based Design of Fluorescent Probes for Amyloid Folds. Chembiochem 2019; 20:1161-1166. [PMID: 30548150 DOI: 10.1002/cbic.201800664] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Indexed: 11/09/2022]
Abstract
Amyloid fibrils are pathological hallmarks of various human diseases, including Parkinson's, Alzheimer's, amyotrophic lateral sclerosis (ALS or motor neurone disease), and prion diseases. Treatment of the amyloid diseases are hindered, among other factors, by timely detection and therefore, early detection of the amyloid fibrils would be beneficial for treatment against these disorders. Here, a small molecular fluorescent probe is reported that selectively recognize the fibrillar form of amyloid beta(1-42), α-synuclein, and HET-s(218-289) protein over their monomeric conformation. The rational design of the reporters relies on the well-known cross-β-sheet repetition motif, the key structural feature of amyloids.
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Affiliation(s)
- Julien Orts
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Hönggerberg, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Marielle Aulikki Wälti
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Hönggerberg, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Dhiman Ghosh
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Hönggerberg, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Silvia Campioni
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Hönggerberg, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland.,Present address: Cellulose & Wood Materials, Empa-Swiss Federal Laboratories for Materials Science and Technology, Überlandstrasse 129, 8600, Dübendorf, Switzerland
| | - Sven J Saupe
- Institut de Biochimie et Génétique Cellulaires, UMR 5095, Université de Bordeaux, 1, rue Camille Saint Saëns, 33077, Bordeaux, France
| | - Roland Riek
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Hönggerberg, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
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15
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Probing the mechanism of inhibition of amyloid-β(1-42)-induced neurotoxicity by the chaperonin GroEL. Proc Natl Acad Sci U S A 2018; 115:E11924-E11932. [PMID: 30509980 DOI: 10.1073/pnas.1817477115] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The human chaperonin Hsp60 is thought to play a role in the progression of Alzheimer's disease by mitigating against intracellular β-amyloid stress. Here, we show that the bacterial homolog GroEL (51% sequence identity) reduces the neurotoxic effects of amyloid-β(1-42) (Aβ42) on human neural stem cell-derived neuronal cultures. To understand the mechanism of GroEL-mediated abrogation of neurotoxicity, we studied the interaction of Aβ42 with GroEL using a variety of biophysical techniques. Aβ42 binds to GroEL as a monomer with a lifetime of ∼1 ms, as determined from global analysis of multiple relaxation-based NMR experiments. Dynamic light scattering demonstrates that GroEL dissolves small amounts of high-molecular-weight polydisperse aggregates present in fresh soluble Aβ42 preparations. The residue-specific transverse relaxation rate profile for GroEL-bound Aβ42 reveals the presence of three anchor-binding regions (residues 16-21, 31-34, and 40-41) located within the hydrophobic GroEL-consensus binding sequences. Single-molecule FRET analysis of Aβ42 binding to GroEL results in no significant change in the FRET efficiency of a doubly labeled Aβ42 construct, indicating that Aβ42 samples a random coil ensemble when bound to GroEL. Finally, GroEL substantially slows down the disappearance of NMR visible Aβ42 species and the appearance of Aβ42 protofibrils and fibrils as monitored by electron and atomic force microscopies. The latter observations correlate with the effect of GroEL on the time course of Aβ42-induced neurotoxicity. These data provide a physical basis for understanding how Hsp60 may serve to slow down the progression of Alzheimer's disease.
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16
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Shigemitsu Y, Hiroaki H. Common molecular pathogenesis of disease-related intrinsically disordered proteins revealed by NMR analysis. J Biochem 2018; 163:11-18. [PMID: 28992347 DOI: 10.1093/jb/mvx056] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 06/17/2017] [Indexed: 01/23/2023] Open
Abstract
Intrinsically disordered proteins (IDPs) are either completely unstructured or contain large disordered regions in their native state; they have drawn much attention in the field of molecular pathology. Some of them substantially tend to form protein self-assemblies, such as toxic or non-toxic aggregates and fibrils, and have been postulated to relate to diseases. These disease-related IDPs include Aβ(1-42) [Alzheimer's disease (AD)], Tau (AD and tauopathy), α-synuclein (Parkinson's disease) and p53 (cancer). Several studies suggest that these aggregation and/or fibril formation processes are often initiated by transient conformational changes of the IDPs prior to protein self-assembly. Interestingly, the pathological molecular processes of these IDPs share multiple common features with those of protein misfolding diseases, such as transmissible spongiform encephalopathy (PrPsc) and AL-amyloidosis (VL-domain of γ-immunoglobulin). This review provides an overview of solution NMR techniques that can help analyse the early and transient events of conformational equilibrium of IDPs and folded proteins.
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Affiliation(s)
- Yoshiki Shigemitsu
- Laboratory of Structural and Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Aichi 464-8601, Japan
| | - Hidekazu Hiroaki
- Laboratory of Structural and Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Aichi 464-8601, Japan
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17
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Brahmkhatri VP, Sharma N, Sunanda P, D’Souza A, Raghothama S, Atreya HS. Curcumin nanoconjugate inhibits aggregation of N-terminal region (Aβ-16) of an amyloid beta peptide. NEW J CHEM 2018. [DOI: 10.1039/c8nj03541e] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A highly stable system of a polymeric nanoparticle-encapsulated curcumin with gold nanoparticles decorated on the surface for inhibition of Aβ1–16 aggregation.
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Affiliation(s)
- Varsha P. Brahmkhatri
- NMR Research Centre
- Indian Institute of Science
- Bangalore 560012
- India
- Centre for Nano and Material Sciences
| | - Naveen Sharma
- Division of Pharmaceutical Science
- Shri Guru Raam Rai Institute of Technology and Science
- Dehradun
- India
| | | | - Aviva D’Souza
- Centre for Nano and Material Sciences
- Jain University
- Jain Global Campus
- Bengaluru 562 112
- India
| | | | - Hanudatta S. Atreya
- NMR Research Centre
- Indian Institute of Science
- Bangalore 560012
- India
- Solid State Structural Chemistry Unit
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18
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Hoffmann ARF, Caillon L, Salazar Vazquez LS, Spath PA, Carlier L, Khemtémourian L, Lequin O. Time dependence of NMR observables reveals salient differences in the accumulation of early aggregated species between human islet amyloid polypeptide and amyloid-β. Phys Chem Chem Phys 2018; 20:9561-9573. [DOI: 10.1039/c7cp07516b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Proton NMR shows that IAPP fibril formation does not involve the accumulation of early aggregated species, in contrast with Aβ.
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Affiliation(s)
- Anaïs R. F. Hoffmann
- Sorbonne Université
- Ecole Normale Supérieure
- PSL University
- CNRS
- Laboratoire des Biomolécules (LBM)
| | - Lucie Caillon
- Sorbonne Université
- Ecole Normale Supérieure
- PSL University
- CNRS
- Laboratoire des Biomolécules (LBM)
| | | | - Pierre-Alexandre Spath
- Sorbonne Université
- Ecole Normale Supérieure
- PSL University
- CNRS
- Laboratoire des Biomolécules (LBM)
| | - Ludovic Carlier
- Sorbonne Université
- Ecole Normale Supérieure
- PSL University
- CNRS
- Laboratoire des Biomolécules (LBM)
| | - Lucie Khemtémourian
- Sorbonne Université
- Ecole Normale Supérieure
- PSL University
- CNRS
- Laboratoire des Biomolécules (LBM)
| | - Olivier Lequin
- Sorbonne Université
- Ecole Normale Supérieure
- PSL University
- CNRS
- Laboratoire des Biomolécules (LBM)
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19
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Morel B, Carrasco MP, Jurado S, Marco C, Conejero-Lara F. Dynamic micellar oligomers of amyloid beta peptides play a crucial role in their aggregation mechanisms. Phys Chem Chem Phys 2018; 20:20597-20614. [DOI: 10.1039/c8cp02685h] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Aβ40 and Aβ42 peptides form micellar precursors of amyloid nuclei contributing to important differences in their aggregation pathways.
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Affiliation(s)
- Bertrand Morel
- Departamento de Química Física e Instituto de Biotecnología
- Facultad de Ciencias
- Universidad de Granada
- 18071 Granada
- Spain
| | - Maria Paz Carrasco
- Departamento de Bioquímica y Biología Molecular I
- Facultad de Ciencias
- Universidad de Granada
- 18071 Granada
- Spain
| | - Samuel Jurado
- Departamento de Química Física e Instituto de Biotecnología
- Facultad de Ciencias
- Universidad de Granada
- 18071 Granada
- Spain
| | - Carmen Marco
- Departamento de Bioquímica y Biología Molecular I
- Facultad de Ciencias
- Universidad de Granada
- 18071 Granada
- Spain
| | - Francisco Conejero-Lara
- Departamento de Química Física e Instituto de Biotecnología
- Facultad de Ciencias
- Universidad de Granada
- 18071 Granada
- Spain
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20
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Cao Y, Jiang X, Han W. Self-Assembly Pathways of β-Sheet-Rich Amyloid-β(1-40) Dimers: Markov State Model Analysis on Millisecond Hybrid-Resolution Simulations. J Chem Theory Comput 2017; 13:5731-5744. [PMID: 29019683 DOI: 10.1021/acs.jctc.7b00803] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Early oligomerization during amyloid-β (Aβ) aggregation is essential for Aβ neurotoxicity. Understanding how unstructured Aβs assemble into oligomers, especially those rich in β-sheets, is essential but remains challenging as the assembly process is too transient for experimental characterization and too slow for molecular dynamics simulations. So far, atomic simulations are limited only to studies of either oligomer structures or assembly pathways for short Aβ segments. To overcome the computational challenge, we combine in this study a hybrid-resolution model and adaptive sampling techniques to perform over 2.7 ms of simulations of formation of full-length Aβ40 dimers that are the earliest toxic oligomeric species. The Markov state model is further employed to characterize the transition pathways and associated kinetics. Our results show that for two major forms of β-sheet-rich structures reported experimentally, the corresponding assembly mechanisms are markedly different. Hairpin-containing structures are formed by direct binding of soluble Aβ in β-hairpin-like conformations. Formation of parallel, in-register structures resembling fibrils occurs ∼100-fold more slowly and involves a rapid encounter of Aβ in arbitrary conformations followed by a slow structural conversion. The structural conversion proceeds via diverse pathways but always requires transient unfolding of encounter complexes. We find that the transition kinetics could be affected differently by intra-/intermolecular interactions involving individual residues in a conformation-dependent manner. In particular, the interactions involving Aβ's N-terminal part promote the assembly into hairpin-containing structures but delay the formation of fibril-like structures, thus explaining puzzling observations reported previously regarding the roles of this region in the early assembly process.
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Affiliation(s)
- Yang Cao
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School , Shenzhen, 518055, China
| | - Xuehan Jiang
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School , Shenzhen, 518055, China
| | - Wei Han
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School , Shenzhen, 518055, China
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21
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Biophysical Aspects of Alzheimer's Disease: Implications for Pharmaceutical Sciences : Theme: Drug Discovery, Development and Delivery in Alzheimer's Disease Guest Editor: Davide Brambilla. Pharm Res 2017; 34:2628-2636. [PMID: 28963701 DOI: 10.1007/s11095-017-2266-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/15/2017] [Indexed: 10/18/2022]
Abstract
An increasing amount of findings suggests that the aggregation of soluble peptides and proteins into amyloid fibrils is a relevant upstream process in the complex cascade of events leading to the pathology of Alzheimer's disease and several other neurodegenerative disorders. Nevertheless, several aspects of the correlation between the aggregation process and the onset and development of the pathology remain largely elusive. In this context, biophysical and biochemical studies in test tubes have proven extremely powerful in providing quantitative information about the structure and the reactivity of amyloids at the molecular level. In this review we use selected recent examples to illustrate the importance of such biophysical research to complement phenomenological studies based on cellular and molecular biology, and we discuss the implications for pharmaceutical applications associated with Alzheimer's disease and other neurodegenerative disorders in both academic and industrial contexts.
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22
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Cieplak AS. Protein folding, misfolding and aggregation: The importance of two-electron stabilizing interactions. PLoS One 2017; 12:e0180905. [PMID: 28922400 PMCID: PMC5603215 DOI: 10.1371/journal.pone.0180905] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 06/22/2017] [Indexed: 12/17/2022] Open
Abstract
Proteins associated with neurodegenerative diseases are highly pleiomorphic and may adopt an all-α-helical fold in one environment, assemble into all-β-sheet or collapse into a coil in another, and rapidly polymerize in yet another one via divergent aggregation pathways that yield broad diversity of aggregates’ morphology. A thorough understanding of this behaviour may be necessary to develop a treatment for Alzheimer’s and related disorders. Unfortunately, our present comprehension of folding and misfolding is limited for want of a physicochemical theory of protein secondary and tertiary structure. Here we demonstrate that electronic configuration and hyperconjugation of the peptide amide bonds ought to be taken into account to advance such a theory. To capture the effect of polarization of peptide linkages on conformational and H-bonding propensity of the polypeptide backbone, we introduce a function of shielding tensors of the Cα atoms. Carrying no information about side chain-side chain interactions, this function nonetheless identifies basic features of the secondary and tertiary structure, establishes sequence correlates of the metamorphic and pH-driven equilibria, relates binding affinities and folding rate constants to secondary structure preferences, and manifests common patterns of backbone density distribution in amyloidogenic regions of Alzheimer’s amyloid β and tau, Parkinson’s α-synuclein and prions. Based on those findings, a split-intein like mechanism of molecular recognition is proposed to underlie dimerization of Aβ, tau, αS and PrPC, and divergent pathways for subsequent association of dimers are outlined; a related mechanism is proposed to underlie formation of PrPSc fibrils. The model does account for: (i) structural features of paranuclei, off-pathway oligomers, non-fibrillar aggregates and fibrils; (ii) effects of incubation conditions, point mutations, isoform lengths, small-molecule assembly modulators and chirality of solid-liquid interface on the rate and morphology of aggregation; (iii) fibril-surface catalysis of secondary nucleation; and (iv) self-propagation of infectious strains of mammalian prions.
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Affiliation(s)
- Andrzej Stanisław Cieplak
- Department of Chemistry, Bilkent University, Ankara, Turkey
- Department of Chemistry, Yale University, New Haven, Connecticut, United States of America
- Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States of America
- * E-mail:
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23
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Kamgar-Parsi K, Hong L, Naito A, Brooks CL, Ramamoorthy A. Growth-incompetent monomers of human calcitonin lead to a noncanonical direct relationship between peptide concentration and aggregation lag time. J Biol Chem 2017; 292:14963-14976. [PMID: 28739873 PMCID: PMC5592673 DOI: 10.1074/jbc.m117.791236] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 07/19/2017] [Indexed: 11/06/2022] Open
Abstract
The role of the peptide hormone calcitonin in skeletal protection has led to its use as a therapeutic for osteoporosis. However, calcitonin aggregation into amyloid fibrils limits its therapeutic efficacy, necessitating a modification of calcitonin's aggregation kinetics. Here, we report a direct relationship between human calcitonin (hCT) concentration and aggregation lag time. This kinetic trend was contrary to the conventional understanding of amyloid aggregation and persisted over a range of aggregation conditions, as confirmed by thioflavin-T kinetics assays, CD spectroscopy, and transmission EM. Dynamic light scattering, 1H NMR experiments, and seeded thioflavin-T assay results indicated that differences in initial peptide species contribute to this trend more than variations in the primary nucleus formation rate. On the basis of kinetics modeling results, we propose a mechanism whereby a structural conversion of hCT monomers is needed before incorporation into the fibril. Our kinetic mechanism recapitulates the experimentally observed relationship between peptide concentration and lag time and represents a novel mechanism in amyloid aggregation. Interestingly, hCT at low pH and salmon calcitonin (sCT) exhibited the canonical inverse relationship between concentration and lag time. Comparative studies of hCT and sCT with molecular dynamics simulations and CD indicated an increased α-helical structure in sCT and low-pH hCT monomers compared with neutral-pH hCT, suggesting that α-helical monomers represent a growth-competent species, whereas unstructured random coil monomers represent a growth-incompetent species. Our finding that initial monomer concentration is positively correlated with lag time in hCT aggregation could help inform future efforts for improving therapeutic applications of CT.
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Affiliation(s)
- Kian Kamgar-Parsi
- From the Applied Physics Program, University of Michigan, Ann Arbor, Michigan 48109
| | - Liu Hong
- Zhou Pei-Yuan Center for Applied Mathematics, Tsinghua University, Beijing 100084, China
| | - Akira Naito
- Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan, and
| | - Charles L Brooks
- Department of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109-1055
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109-1055
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24
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Aleksis R, Oleskovs F, Jaudzems K, Pahnke J, Biverstål H. Structural studies of amyloid-β peptides: Unlocking the mechanism of aggregation and the associated toxicity. Biochimie 2017; 140:176-192. [PMID: 28751216 DOI: 10.1016/j.biochi.2017.07.011] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 07/21/2017] [Indexed: 12/31/2022]
Abstract
Alzheimer's disease (AD) is one of the most prevalent neurodegenerative diseases worldwide. Formation of amyloid plaques consisting of amyloid-β peptides (Aβ) is one of the hallmarks of AD. Several lines of evidence have shown a correlation between the Aβ aggregation and the disease development. Extensive research has been conducted with the aim to reveal the structures of the neurotoxic Aβ aggregates. However, the exact structure of pathological aggregates and mechanism of the disease still remains elusive due to complexity of the occurring processes and instability of various disease-relevant Aβ species. In this article we review up-to-date structural knowledge about amyloid-β peptides, focusing on data acquired using solution and solid state NMR techniques. Furthermore, we discuss implications from these structural studies on the mechanisms of aggregation and neurotoxicity.
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Affiliation(s)
- Rihards Aleksis
- Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, Latvia.
| | - Filips Oleskovs
- Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, Latvia
| | - Kristaps Jaudzems
- Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, Latvia
| | - Jens Pahnke
- Department of Neuro-/Pathology, Translational Neurodegeneration Research and Neuropathology Lab, University of Oslo (UiO) & Oslo University Hospital (OUS), Norway; LIED, University of Lübeck Uzl, Germany; Leibniz-Institute of Plant Biochemistry (IPB), Halle, Germany
| | - Henrik Biverstål
- Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, Latvia; Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Stockholm, Sweden
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25
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Chen YC. Impact of a discordant helix on β-amyloid structure, aggregation ability and toxicity. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2017; 46:681-687. [DOI: 10.1007/s00249-017-1235-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 05/26/2017] [Accepted: 06/26/2017] [Indexed: 11/24/2022]
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26
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Vahdati L, Kaffy J, Brinet D, Bernadat G, Correia I, Panzeri S, Fanelli R, Lequin O, Taverna M, Ongeri S, Piarulli U. Synthesis and Characterization of Hairpin Mimics that Modulate the Early Oligomerization and Fibrillization of Amyloid β-Peptide. European J Org Chem 2017. [DOI: 10.1002/ejoc.201700010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Leila Vahdati
- Università degli Studi dell'Insubria; Dipartimento di Scienza e Alta Tecnologia; Via Valleggio 11 22100 Como Italy
- BioCIS; Univ. Paris-Sud; CNRS; Université Paris-Saclay; 92290 Châtenay-Malabry France
| | - Julia Kaffy
- BioCIS; Univ. Paris-Sud; CNRS; Université Paris-Saclay; 92290 Châtenay-Malabry France
| | - Dimitri Brinet
- BioCIS; Univ. Paris-Sud; CNRS; Université Paris-Saclay; 92290 Châtenay-Malabry France
- Protéins and Nanotechnology in analytical science; Institut Galien de Paris Sud; Univ. Paris-Sud; CNRS; Université Paris-Saclay; 92290 Châtenay-Malabry France
| | - Guillaume Bernadat
- BioCIS; Univ. Paris-Sud; CNRS; Université Paris-Saclay; 92290 Châtenay-Malabry France
| | - Isabelle Correia
- Sorbonne Universités; UPMC Univ Paris 06; Ecole Normale Supérieure; PSL Research University; CNRS; Laboratoire des Biomolécules; 4 place Jussieu 75252 Paris Cedex 05 France
| | - Silvia Panzeri
- Università degli Studi dell'Insubria; Dipartimento di Scienza e Alta Tecnologia; Via Valleggio 11 22100 Como Italy
| | - Roberto Fanelli
- Università degli Studi dell'Insubria; Dipartimento di Scienza e Alta Tecnologia; Via Valleggio 11 22100 Como Italy
| | - Olivier Lequin
- Sorbonne Universités; UPMC Univ Paris 06; Ecole Normale Supérieure; PSL Research University; CNRS; Laboratoire des Biomolécules; 4 place Jussieu 75252 Paris Cedex 05 France
| | - Myriam Taverna
- Protéins and Nanotechnology in analytical science; Institut Galien de Paris Sud; Univ. Paris-Sud; CNRS; Université Paris-Saclay; 92290 Châtenay-Malabry France
| | - Sandrine Ongeri
- BioCIS; Univ. Paris-Sud; CNRS; Université Paris-Saclay; 92290 Châtenay-Malabry France
| | - Umberto Piarulli
- Università degli Studi dell'Insubria; Dipartimento di Scienza e Alta Tecnologia; Via Valleggio 11 22100 Como Italy
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Tomaselli S, Pagano K, D’Arrigo C, Molinari H, Ragona L. Evidence of Molecular Interactions of Aβ1-42 with N-Terminal Truncated Beta Amyloids by NMR. ACS Chem Neurosci 2017; 8:759-765. [PMID: 28135060 DOI: 10.1021/acschemneuro.6b00456] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Aβ peptides, the main protein components of Alzheimer's disease (AD) plaques, derive from a proteolytic cleavage of the amyloid precursor protein. Due to heterogeneous cleavage sites, a series of Aβ peptides, including the major and widely studied species Aβ1-40 (Aβ40) and Aβ1-42 (Aβ42), are produced. In addition to the C-terminal heterogeneity of Aβ peptides, significant amounts of N-terminal truncated (Aβ3-42) and pyroglutamate-modified amyloid-β peptides (AβpE3-42) have been identified in AD affected brains and shown to be more cytotoxic than unmodified Aβ peptides. Little is known about the properties of their mixtures with Aβ42. Nuclear Magnetic Resonance spectroscopy is here employed to investigate the interaction of N-truncated peptides with Aβ42 at different molar ratios. We highlight the critical concentration of N-truncated forms influencing the aggregation kinetics of Aβ42. We provide evidence, at residue level, that the C-terminal region of Aβ42 is the locus of transient specific interactions with highly aggregation prone N-truncated alloforms.
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Affiliation(s)
- Simona Tomaselli
- Istituto per lo Studio delle Macromolecole, CNR, Via Corti 12, 20133 Milan, Italy
| | - Katiuscia Pagano
- Istituto per lo Studio delle Macromolecole, CNR, Via Corti 12, 20133 Milan, Italy
| | - Cristina D’Arrigo
- Istituto per lo Studio delle Macromolecole, CNR, Via De Marini 6, 16149 Genoa, Italy
| | - Henriette Molinari
- Istituto per lo Studio delle Macromolecole, CNR, Via Corti 12, 20133 Milan, Italy
| | - Laura Ragona
- Istituto per lo Studio delle Macromolecole, CNR, Via Corti 12, 20133 Milan, Italy
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28
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Lin TW, Chang CF, Chang YJ, Liao YH, Yu HM, Chen YR. Alzheimer's amyloid-β A2T variant and its N-terminal peptides inhibit amyloid-β fibrillization and rescue the induced cytotoxicity. PLoS One 2017; 12:e0174561. [PMID: 28362827 PMCID: PMC5376091 DOI: 10.1371/journal.pone.0174561] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 03/11/2017] [Indexed: 01/21/2023] Open
Abstract
Alzheimer’s disease (AD) is the most common dementia affecting tens of million people worldwide. The primary neuropathological hallmark in AD is amyloid plaques composed of amyloid-β peptide (Aβ). Several familial mutations found in Aβ sequence result in early onset of AD. Previous studies showed that the mutations located at N-terminus of Aβ, such as the English (H6R) and Tottori (D7N) mutations, promote fibril formation and increase cytotoxicity. However, A2T mutant located at the very N-terminus of Aβ shows low-prevalence incidence of AD, whereas, another mutant A2V causes early onset of AD. To understand the molecular mechanism of the distinct effect and develop new potential therapeutic strategy, here, we examined the effect of full-length and N-terminal A2V/T variants to wild type (WT) Aβ40 by fibrillization assays and NMR studies. We found that full-length and N-terminal A2V accelerated WT fibrillization and induced large chemical shifts on the N-terminus of WT Aβ, whereas, full-length and N-terminal A2T retarded the fibrillization. We further examined the inhibition effect of various N-terminal fragments (NTFs) of A2T to WT Aβ. The A2T NTFs ranging from residue 1 to residue 7 to 10, but not 1 to 6 or shorter, are capable to retard WT Aβ fibrillization and rescue cytotoxicity. The results suggest that in the presence of full-length or specific N-terminal A2T can retard Aβ aggregation and the A2T NTFs can mitigate its toxicity. Our results provide a novel targeting site for future therapeutic development of AD.
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Affiliation(s)
- Tien-Wei Lin
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Yu-Jen Chang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Yi-Hung Liao
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Hui-Ming Yu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Yun-Ru Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- * E-mail:
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Wälti MA, Orts J, Riek R. Quenched hydrogen-deuterium exchange NMR of a disease-relevant Aβ(1-42) amyloid polymorph. PLoS One 2017; 12:e0172862. [PMID: 28319116 PMCID: PMC5358797 DOI: 10.1371/journal.pone.0172862] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 02/12/2017] [Indexed: 11/21/2022] Open
Abstract
Alzheimer’s disease is associated with the aggregation into amyloid fibrils of Aβ(1–42) and Aβ(1–40) peptides. Interestingly, these fibrils often do not obtain one single structure but rather show different morphologies, so-called polymorphs. Here, we compare quenched hydrogen-deuterium (H/D) exchange of a disease-relevant Aβ(1–42) fibril for which the 3D structure has been determined by solid-state NMR with H/D exchange previously determined on another structural polymorph. This comparison reveals secondary structural differences between the two polymorphs suggesting that the two polymorphisms can be classified as segmental polymorphs.
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Affiliation(s)
| | - Julien Orts
- Laboratorium für Physikalische Chemie, ETH Zürich, Zürich, Switzerland
| | - Roland Riek
- Laboratorium für Physikalische Chemie, ETH Zürich, Zürich, Switzerland
- * E-mail:
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30
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Ravotti F, Wälti MA, Güntert P, Riek R, Böckmann A, Meier BH. Solid-state NMR sequential assignment of an Amyloid-β(1-42) fibril polymorph. BIOMOLECULAR NMR ASSIGNMENTS 2016; 10:269-76. [PMID: 27165577 DOI: 10.1007/s12104-016-9682-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 04/30/2016] [Indexed: 05/10/2023]
Abstract
The formation of fibrils of the amyloid-β (Aβ) peptide is considered to be a key event in the pathology of Alzheimer's disease (AD). The determination of a high-resolution structure of these fibrils is relevant for the understanding of the molecular basis of AD. In this work, we present the sequential resonance assignment of one of the polymorphs of Aβ(1-42) fibrils. We show that most of the protein is rigid, while a stretch of 4 residues (11-14) is not visible by solid-state NMR spectroscopy due to dynamics.
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Affiliation(s)
- Francesco Ravotti
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | | | - Peter Güntert
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany.
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami-Ohsawa, Hachioji, Tokyo, 192-0397, Japan.
| | - Roland Riek
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland.
| | - Anja Böckmann
- Institut de Biologie et Chemie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69007, Lyon, France.
| | - Beat H Meier
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland.
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31
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Atomic-resolution structure of a disease-relevant Aβ(1-42) amyloid fibril. Proc Natl Acad Sci U S A 2016; 113:E4976-84. [PMID: 27469165 DOI: 10.1073/pnas.1600749113] [Citation(s) in RCA: 621] [Impact Index Per Article: 77.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Amyloid-β (Aβ) is present in humans as a 39- to 42-amino acid residue metabolic product of the amyloid precursor protein. Although the two predominant forms, Aβ(1-40) and Aβ(1-42), differ in only two residues, they display different biophysical, biological, and clinical behavior. Aβ(1-42) is the more neurotoxic species, aggregates much faster, and dominates in senile plaque of Alzheimer's disease (AD) patients. Although small Aβ oligomers are believed to be the neurotoxic species, Aβ amyloid fibrils are, because of their presence in plaques, a pathological hallmark of AD and appear to play an important role in disease progression through cell-to-cell transmissibility. Here, we solved the 3D structure of a disease-relevant Aβ(1-42) fibril polymorph, combining data from solid-state NMR spectroscopy and mass-per-length measurements from EM. The 3D structure is composed of two molecules per fibril layer, with residues 15-42 forming a double-horseshoe-like cross-β-sheet entity with maximally buried hydrophobic side chains. Residues 1-14 are partially ordered and in a β-strand conformation, but do not display unambiguous distance restraints to the remainder of the core structure.
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32
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Istrate AN, Kozin SA, Zhokhov SS, Mantsyzov AB, Kechko OI, Pastore A, Makarov AA, Polshakov VI. Interplay of histidine residues of the Alzheimer's disease Aβ peptide governs its Zn-induced oligomerization. Sci Rep 2016; 6:21734. [PMID: 26898943 PMCID: PMC4761979 DOI: 10.1038/srep21734] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 01/29/2016] [Indexed: 12/18/2022] Open
Abstract
Conformational changes of Aβ peptide result in its transformation from native monomeric state to the toxic soluble dimers, oligomers and insoluble aggregates that are hallmarks of Alzheimer's disease (AD). Interactions of zinc ions with Aβ are mediated by the N-terminal Aβ(1-16) domain and appear to play a key role in AD progression. There is a range of results indicating that these interactions trigger the Aβ plaque formation. We have determined structure and functional characteristics of the metal binding domains derived from several Aβ variants and found that their zinc-induced oligomerization is governed by conformational changes in the minimal zinc binding site 6HDSGYEVHH14. The residue H6 and segment 11EVHH14, which are part of this site are crucial for formation of the two zinc-mediated interaction interfaces in Aβ. These structural determinants can be considered as promising targets for rational design of the AD-modifying drugs aimed at blocking pathological Aβ aggregation.
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Affiliation(s)
- Andrey N Istrate
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991, Moscow, Russia
| | - Sergey A Kozin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991, Moscow, Russia
| | - Sergey S Zhokhov
- Faculty of Fundamental Medicine, M.V. Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Alexey B Mantsyzov
- Faculty of Fundamental Medicine, M.V. Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Olga I Kechko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991, Moscow, Russia
| | | | - Alexander A Makarov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991, Moscow, Russia
| | - Vladimir I Polshakov
- Faculty of Fundamental Medicine, M.V. Lomonosov Moscow State University, 119991, Moscow, Russia
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33
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Tran L, Basdevant N, Prévost C, Ha-Duong T. Structure of ring-shaped Aβ₄₂ oligomers determined by conformational selection. Sci Rep 2016; 6:21429. [PMID: 26868929 PMCID: PMC4751476 DOI: 10.1038/srep21429] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 01/22/2016] [Indexed: 11/28/2022] Open
Abstract
The oligomerization of amyloid beta (Aβ) peptides into soluble non-fibrillar species plays a critical role in the pathogenesis of Alzheimer’s disease. However, it has been challenging to characterize the tertiary and quaternary structures of Aβ peptides due to their disordered nature and high aggregation propensity. In this work, replica exchange molecular dynamics simulations were used to explore the conformational space of Aβ42 monomer. Among the most populated transient states, we identified a particular conformation which was able to generate ring-shaped pentamers and hexamers, when docked onto itself. The structures of these aggregates were stable during microsecond all-atom MD simulations in explicit solvent. In addition to high resolution models of these oligomers, this study provides support for the conformational selection mechanism of Aβ peptide self-assembly.
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Affiliation(s)
- Linh Tran
- BIOCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay, Châtenay-Malabry, 92290, France
| | | | - Chantal Prévost
- LBT, Univ. Paris-Diderot, CNRS, Sorbonne Paris-Cité, Paris, 75005 France
| | - Tâp Ha-Duong
- BIOCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay, Châtenay-Malabry, 92290, France
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34
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Kaffy J, Brinet D, Soulier JL, Correia I, Tonali N, Fera KF, Iacone Y, Hoffmann ARF, Khemtémourian L, Crousse B, Taylor M, Allsop D, Taverna M, Lequin O, Ongeri S. Designed Glycopeptidomimetics Disrupt Protein-Protein Interactions Mediating Amyloid β-Peptide Aggregation and Restore Neuroblastoma Cell Viability. J Med Chem 2016; 59:2025-40. [PMID: 26789783 DOI: 10.1021/acs.jmedchem.5b01629] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
How anti-Alzheimer's drug candidates that reduce amyloid 1-42 peptide fibrillization interact with the most neurotoxic species is far from being understood. We report herein the capacity of sugar-based peptidomimetics to inhibit both Aβ1-42 early oligomerization and fibrillization. A wide range of bio- and physicochemical techniques, such as a new capillary electrophoresis method, nuclear magnetic resonance, and surface plasmon resonance, were used to identify how these new molecules can delay the aggregation of Aβ1-42. We demonstrate that these molecules interact with soluble oligomers in order to maintain the presence of nontoxic monomers and to prevent fibrillization. These compounds totally suppress the toxicity of Aβ1-42 toward SH-SY5Y neuroblastoma cells, even at substoichiometric concentrations. Furthermore, demonstration that the best molecule combines hydrophobic moieties, hydrogen bond donors and acceptors, ammonium groups, and a hydrophilic β-sheet breaker element provides valuable insight for the future structure-based design of inhibitors of Aβ1-42 aggregation.
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Affiliation(s)
- Julia Kaffy
- Molécules Fluorées et Chimie Médicinale, BioCIS, Univ. Paris-Sud, CNRS, Université Paris Saclay , 5 rue Jean-Baptiste Clément, 92296 Châtenay-Malabry Cedex, France
| | - Dimitri Brinet
- Molécules Fluorées et Chimie Médicinale, BioCIS, Univ. Paris-Sud, CNRS, Université Paris Saclay , 5 rue Jean-Baptiste Clément, 92296 Châtenay-Malabry Cedex, France.,Protéines et Nanotechnologies en Sciences Séparatives, Institut Galien Paris-Sud, Univ. Paris-Sud, CNRS, Université Paris Saclay , 5 rue Jean-Baptiste Clément, 92296 Châtenay-Malabry Cedex, France
| | - Jean-Louis Soulier
- Molécules Fluorées et Chimie Médicinale, BioCIS, Univ. Paris-Sud, CNRS, Université Paris Saclay , 5 rue Jean-Baptiste Clément, 92296 Châtenay-Malabry Cedex, France
| | - Isabelle Correia
- Sorbonne Universités - UPMC Univ Paris 06, Ecole Normale Supérieure - PSL Research University, CNRS UMR 7203 LBM, 4 place Jussieu, 75252 Paris, Cedex 05, France
| | - Nicolo Tonali
- Molécules Fluorées et Chimie Médicinale, BioCIS, Univ. Paris-Sud, CNRS, Université Paris Saclay , 5 rue Jean-Baptiste Clément, 92296 Châtenay-Malabry Cedex, France
| | - Katia Fabiana Fera
- Molécules Fluorées et Chimie Médicinale, BioCIS, Univ. Paris-Sud, CNRS, Université Paris Saclay , 5 rue Jean-Baptiste Clément, 92296 Châtenay-Malabry Cedex, France
| | - Yasmine Iacone
- Molécules Fluorées et Chimie Médicinale, BioCIS, Univ. Paris-Sud, CNRS, Université Paris Saclay , 5 rue Jean-Baptiste Clément, 92296 Châtenay-Malabry Cedex, France.,Protéines et Nanotechnologies en Sciences Séparatives, Institut Galien Paris-Sud, Univ. Paris-Sud, CNRS, Université Paris Saclay , 5 rue Jean-Baptiste Clément, 92296 Châtenay-Malabry Cedex, France
| | - Anaïs R F Hoffmann
- Sorbonne Universités - UPMC Univ Paris 06, Ecole Normale Supérieure - PSL Research University, CNRS UMR 7203 LBM, 4 place Jussieu, 75252 Paris, Cedex 05, France
| | - Lucie Khemtémourian
- Sorbonne Universités - UPMC Univ Paris 06, Ecole Normale Supérieure - PSL Research University, CNRS UMR 7203 LBM, 4 place Jussieu, 75252 Paris, Cedex 05, France
| | - Benoit Crousse
- Molécules Fluorées et Chimie Médicinale, BioCIS, Univ. Paris-Sud, CNRS, Université Paris Saclay , 5 rue Jean-Baptiste Clément, 92296 Châtenay-Malabry Cedex, France
| | - Mark Taylor
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University , Lancaster LA1 4YQ, U.K
| | - David Allsop
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University , Lancaster LA1 4YQ, U.K
| | - Myriam Taverna
- Protéines et Nanotechnologies en Sciences Séparatives, Institut Galien Paris-Sud, Univ. Paris-Sud, CNRS, Université Paris Saclay , 5 rue Jean-Baptiste Clément, 92296 Châtenay-Malabry Cedex, France
| | - Olivier Lequin
- Sorbonne Universités - UPMC Univ Paris 06, Ecole Normale Supérieure - PSL Research University, CNRS UMR 7203 LBM, 4 place Jussieu, 75252 Paris, Cedex 05, France
| | - Sandrine Ongeri
- Molécules Fluorées et Chimie Médicinale, BioCIS, Univ. Paris-Sud, CNRS, Université Paris Saclay , 5 rue Jean-Baptiste Clément, 92296 Châtenay-Malabry Cedex, France
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35
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Roche J, Shen Y, Lee JH, Ying J, Bax A. Monomeric Aβ(1-40) and Aβ(1-42) Peptides in Solution Adopt Very Similar Ramachandran Map Distributions That Closely Resemble Random Coil. Biochemistry 2016; 55:762-75. [PMID: 26780756 PMCID: PMC4750080 DOI: 10.1021/acs.biochem.5b01259] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
The
pathogenesis of Alzheimer’s disease is characterized
by the aggregation and fibrillation of amyloid peptides Aβ1–40 and Aβ1–42 into amyloid
plaques. Despite strong potential therapeutic interest, the structural
pathways associated with the conversion of monomeric Aβ peptides
into oligomeric species remain largely unknown. In particular, the
higher aggregation propensity and associated toxicity of Aβ1–42 compared to that of Aβ1–40 are poorly understood. To explore in detail the structural propensity
of the monomeric Aβ1–40 and Aβ1–42 peptides in solution, we recorded a large set of nuclear magnetic
resonance (NMR) parameters, including chemical shifts, nuclear Overhauser
effects (NOEs), and J couplings. Systematic comparisons
show that at neutral pH the Aβ1–40 and Aβ1–42 peptides populate almost indistinguishable coil-like
conformations. Nuclear Overhauser effect spectra collected at very
high resolution remove assignment ambiguities and show no long-range
NOE contacts. Six sets of backbone J couplings (3JHNHα, 3JC′C′, 3JC′Hα, 1JHαCα, 2JNCα, and 1JNCα) recorded
for Aβ1–40 were used as input for the recently
developed MERA Ramachandran map analysis, yielding residue-specific
backbone ϕ/ψ torsion angle distributions that closely
resemble random coil distributions, the absence of a significantly
elevated propensity for β-conformations in the C-terminal region
of the peptide, and a small but distinct propensity for αL at K28. Our results suggest that the self-association of
Aβ peptides into toxic oligomers is not driven by elevated propensities
of the monomeric species to adopt β-strand-like conformations.
Instead, the accelerated disappearance of Aβ NMR signals in
D2O over H2O, particularly pronounced for Aβ1–42, suggests that intermolecular interactions between
the hydrophobic regions of the peptide dominate the aggregation process.
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Affiliation(s)
- Julien Roche
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0510, United States
| | - Yang Shen
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0510, United States
| | - Jung Ho Lee
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0510, United States
| | - Jinfa Ying
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0510, United States
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0510, United States
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36
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Roche J, Ying J, Bax A. Accurate measurement of (3)J(HNHα) couplings in small or disordered proteins from WATERGATE-optimized TROSY spectra. JOURNAL OF BIOMOLECULAR NMR 2016; 64:1-7. [PMID: 26660434 PMCID: PMC4744140 DOI: 10.1007/s10858-015-0004-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Accepted: 11/30/2015] [Indexed: 06/05/2023]
Abstract
Provided that care is taken in adjusting the WATERGATE element of a (1)H-(15)N TROSY-HSQC experiment, such that neither the water magnetization nor the (1)H(α) protons are inverted by its final 180° pulse, (3)JHNHα couplings can be measured directly from splittings in the (1)H dimension of the spectrum. With band-selective (1)H decoupling, very high (15)N resolution can be achieved. A complete set of (3)JHNHα values, ranging from 3.4 to 10.1 Hz was measured for the 56-residue third domain of IgG-binding protein G (GB3). Using the H-N-C(α)-H(α) dihedral angles extracted from a RDC-refined structure of GB3, (3)JHNHα values predicted by a previously parameterized Karplus equation agree to within a root-mean-square deviation (rmsd) of 0.37 Hz with the experimental data. Values measured for the Alzheimer's implicated Aβ(1-40) peptide fit to within an rmsd of 0.45 Hz to random coil (3)JHNHα values.
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Affiliation(s)
- Julien Roche
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jinfa Ying
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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38
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Potapov A, Yau WM, Ghirlando R, Thurber KR, Tycko R. Successive Stages of Amyloid-β Self-Assembly Characterized by Solid-State Nuclear Magnetic Resonance with Dynamic Nuclear Polarization. J Am Chem Soc 2015; 137:8294-307. [PMID: 26068174 PMCID: PMC5559291 DOI: 10.1021/jacs.5b04843] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Self-assembly of amyloid-β (Aβ) peptides in human brain tissue leads to neurodegeneration in Alzheimer's disease (AD). Amyloid fibrils, whose structures have been extensively characterized by solid state nuclear magnetic resonance (ssNMR) and other methods, are the thermodynamic end point of Aβ self-assembly. Oligomeric and protofibrillar assemblies, whose structures are less well-understood, are also observed as intermediates in the assembly process in vitro and have been implicated as important neurotoxic species in AD. We report experiments in which the structural evolution of 40-residue Aβ (Aβ40) is monitored by ssNMR measurements on frozen solutions prepared at four successive stages of the self-assembly process. Measurements on transient intermediates are enabled by ssNMR signal enhancements from dynamic nuclear polarization (DNP) at temperatures below 30 K. DNP-enhanced ssNMR data reveal a monotonic increase in conformational order from an initial state comprised primarily of monomers and small oligomers in solution at high pH, to larger oligomers near neutral pH, to metastable protofibrils, and finally to fibrils. Surprisingly, the predominant molecular conformation, indicated by (13)C NMR chemical shifts and by side chain contacts between F19 and L34 residues, is qualitatively similar at all stages. However, the in-register parallel β-sheet supramolecular structure, indicated by intermolecular (13)C spin polarization transfers, does not develop before the fibril stage. This work represents the first application of DNP-enhanced ssNMR to the characterization of peptide or protein self-assembly intermediates.
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Affiliation(s)
- Alexey Potapov
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
| | - Kent R. Thurber
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
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