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Dey A, Verma A, Bhaskar U, Sarkar B, Kallianpur M, Vishvakarma V, Das AK, Garai K, Mukherjee O, Ishii K, Tahara T, Maiti S. A Toxicogenic Interaction between Intracellular Amyloid-β and Apolipoprotein-E. ACS Chem Neurosci 2024; 15:1265-1275. [PMID: 38421952 DOI: 10.1021/acschemneuro.4c00048] [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: 03/02/2024] Open
Abstract
Alzheimer's disease (AD) is associated with the aggregation of amyloid β (Aβ) and tau proteins. Why ApoE variants are significant genetic risk factors remains a major unsolved puzzle in understanding AD, although intracellular interactions with ApoE are suspected to play a role. Here, we show that specific changes in the fluorescence lifetime of fluorescently tagged small Aβ oligomers in rat brain cells correlate with the cellular ApoE content. An inhibitor of the Aβ-ApoE interaction suppresses these changes and concomitantly reduces Aβ toxicity in a dose-dependent manner. Single-molecule techniques show changes both in the conformation and in the stoichiometry of the oligomers. Neural stem cells derived from hiPSCs of Alzheimer's patients also exhibit these fluorescence lifetime changes. We infer that intracellular interaction with ApoE modifies the N-terminus of the Aβ oligomers, inducing changes in their stoichiometry, membrane affinity, and toxicity. These changes can be directly imaged in live cells and can potentially be used as a rapid and quantitative cellular assay for AD drug discovery.
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Affiliation(s)
- Arpan Dey
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Aditi Verma
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Uchit Bhaskar
- Institute of Stem Cell Science and Regenerative Medicine, Bangalore 560065, India
| | - Bidyut Sarkar
- Molecular Spectroscopy Laboratory, RIKEN, Wako, Saitama 3510198, Japan
| | - Mamata Kallianpur
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Vicky Vishvakarma
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Anand Kant Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Kanchan Garai
- Tata Institute of Fundamental Research, Hyderabad 500107, India
| | - Odity Mukherjee
- Institute of Stem Cell Science and Regenerative Medicine, Bangalore 560065, India
| | - Kunihiko Ishii
- Molecular Spectroscopy Laboratory, RIKEN, Wako, Saitama 3510198, Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, RIKEN, Wako, Saitama 3510198, Japan
| | - Sudipta Maiti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
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2
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Das A, Korn A, Carroll A, Carver JA, Maiti S. Application of the Double-Mutant Cycle Strategy to Protein Aggregation Reveals Transient Interactions in Amyloid-β Oligomers. J Phys Chem B 2021; 125:12426-12435. [PMID: 34748334 DOI: 10.1021/acs.jpcb.1c05829] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Transient oligomeric intermediates in the peptide or protein aggregation pathway are suspected to be the key toxic species in many amyloid diseases, but deciphering their molecular nature has remained a challenge. Here we show that the strategy of "double-mutant cycles", used effectively in probing protein-folding intermediates, can reveal transient interactions during protein aggregation. It does so by comparing the changes in thermodynamic parameters between the wild type, and single and double mutants. We demonstrate the strategy by probing the possible transient salt bridge partner of lysine 28 (K28) in the oligomeric states of amyloid β-40 (Aβ40), the putative toxic species in Alzheimer's disease. In mature fibrils, the binding partner is aspartate 23. This interaction differentiates Aβ40 from the more toxic Aβ42, where K28's binding partner is the C-terminal carboxylate. We selectively acetylated K28 and amidated the C-terminus of Aβ40, creating four distinct variants. Spectroscopic measurements of the kinetics and thermodynamics of aggregation show that K28 and the C-terminus interact transiently in the early phases of the Aβ40 aggregation pathway. Hydrogen-deuterium exchange mass spectrometry (using a simple analysis method that we introduce here that takes into account the isotopic mass distribution) supports this interpretation. It is also supported by cellular toxicity measurements, suggesting possible similarities in the mechanisms of toxicity of Aβ40 oligomers (which are more toxic than Aβ40 fibrils) and Aβ42. Our results show that double-mutant cycles can be a powerful tool for probing transient interactions during protein aggregation.
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Affiliation(s)
- Anirban Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Alexander Korn
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. 16-18, D-04107 Leipzig, Germany
| | - Adam Carroll
- Research School of Chemistry, The Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - John A Carver
- Research School of Chemistry, The Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - Sudipta Maiti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
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3
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Li Y, Tang H, Andrikopoulos N, Javed I, Cecchetto L, Nandakumar A, Kakinen A, Davis TP, Ding F, Ke PC. The membrane axis of Alzheimer's nanomedicine. ADVANCED NANOBIOMED RESEARCH 2021; 1:2000040. [PMID: 33748816 PMCID: PMC7971452 DOI: 10.1002/anbr.202000040] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Alzheimer's disease (AD) is a major neurological disorder impairing its carrier's cognitive function, memory and lifespan. While the development of AD nanomedicine is still nascent, the field is evolving into a new scientific frontier driven by the diverse physicochemical properties and theranostic potential of nanomaterials and nanocomposites. Characteristic to the AD pathology is the deposition of amyloid plaques and tangles of amyloid beta (Aβ) and tau, whose aggregation kinetics may be curbed by nanoparticle inhibitors via sequence-specific targeting or nonspecific interactions with the amyloidogenic proteins. As literature implicates cell membrane as a culprit in AD pathogenesis, here we summarize the membrane axis of AD nanomedicine and present a new rationale that the field development may greatly benefit from harnessing our existing knowledge of Aβ-membrane interaction, nanoparticle-membrane interaction and Aβ-nanoparticle interaction.
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Affiliation(s)
- Yuhuan Li
- Zhongshan Hospital, Fudan University, 111 Yixueyuan Rd, Xuhui District, Shanghai, 200032, China
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Huayuan Tang
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Nicholas Andrikopoulos
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Ibrahim Javed
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Luca Cecchetto
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Department of Chemical and Pharmaceutical Science, University of Trieste, Via Licio Giorgieri 1, 34127 Trieste, Italy
| | - Aparna Nandakumar
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Aleksandr Kakinen
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Thomas P. Davis
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Pu Chun Ke
- Zhongshan Hospital, Fudan University, 111 Yixueyuan Rd, Xuhui District, Shanghai, 200032, China
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
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4
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Dey S, Das A, Dey A, Maiti S. Membrane affinity of individual toxic protein oligomers determined at the single-molecule level. Phys Chem Chem Phys 2020; 22:14613-14620. [PMID: 32483579 DOI: 10.1039/d0cp00450b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Oligomers are the key suspects in protein aggregation-linked diseases, such as Alzheimer's and Type II diabetes, and most likely exert their toxicity by interacting with lipid membranes. However, the "which oligomer" question remains an obstacle in understanding the disease mechanism, as the exact identity of the toxic oligomer(s) is not yet known. Oligomers exist as a mixture of species of different sizes (i.e. as different 'n-mers') in a physiological solution, making it difficult to determine the properties of individual species. Here we demonstrate a method based on single-molecule photo-bleaching (smPB) which can provide an answer to the "which oligomer" question, at least as far as membrane affinity is concerned. We calculate the ratio of the oligomer size distribution of human Islet Amyloid Polypeptide (IAPP) in the aqueous phase and that on a coexisting artificial lipid bilayer, and this measures the relative membrane affinity of individual oligomeric species. A problem with smPB measurements is that they can be very sensitive to pre-measurement bleaching. Here we correct for pre-bleaching using a covalently linked multimeric peptide as a bleaching standard. We find that the order of membrane affinity for IAPP n-mers is trimer > dimer > tetramer ≫ monomer. Our results agree well with the average membrane affinity values of oligomeric and monomeric solutions previously measured with Fluorescence Correlation Spectroscopy. The "which oligomer" question, in the context of membrane affinity, can therefore, be solved quantitatively for any membrane-active toxic protein aggregate.
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Affiliation(s)
- Simli Dey
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India.
| | - Anirban Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India.
| | - Arpan Dey
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India.
| | - Sudipta Maiti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India.
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5
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Farrugia MY, Caruana M, Ghio S, Camilleri A, Farrugia C, Cauchi RJ, Cappelli S, Chiti F, Vassallo N. Toxic oligomers of the amyloidogenic HypF-N protein form pores in mitochondrial membranes. Sci Rep 2020; 10:17733. [PMID: 33082392 PMCID: PMC7575562 DOI: 10.1038/s41598-020-74841-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 10/06/2020] [Indexed: 12/30/2022] Open
Abstract
Studies on the amyloidogenic N-terminal domain of the E. coli HypF protein (HypF-N) have contributed significantly to a detailed understanding of the pathogenic mechanisms in neurodegenerative diseases characterised by the formation of misfolded oligomers, by proteins such as amyloid-β, α-synuclein and tau. Given that both cell membranes and mitochondria are increasingly recognised as key targets of oligomer toxicity, we investigated the damaging effects of aggregates of HypF-N on mitochondrial membranes. Essentially, we found that HypF-N oligomers characterised by high surface hydrophobicity (type A) were able to trigger a robust permeabilisation of mito-mimetic liposomes possessing cardiolipin-rich membranes and dysfunction of isolated mitochondria, as demonstrated by a combination of mitochondrial shrinking, lowering of mitochondrial membrane potential and cytochrome c release. Furthermore, using single-channel electrophysiology recordings we obtained evidence that the type A aggregates induced currents reflecting formation of ion-conducting pores in mito-mimetic planar phospholipid bilayers, with multi-level conductances ranging in the hundreds of pS at negative membrane voltages. Conversely, HypF-N oligomers with low surface hydrophobicity (type B) could not permeabilise or porate mitochondrial membranes. These results suggest an inherent toxicity of membrane-active aggregates of amyloid-forming proteins to mitochondria, and that targeting of oligomer-mitochondrial membrane interactions might therefore afford protection against such damage.
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Affiliation(s)
- Maria Ylenia Farrugia
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
- Centre for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Mario Caruana
- Centre for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Stephanie Ghio
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
- Centre for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Angelique Camilleri
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
- Centre for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | | | - Ruben J Cauchi
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
- Centre for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Sara Cappelli
- Section of Biochemistry, Department of Experimental and Clinical Biomedical Sciences, University of Florence, 50134, Florence, Italy
| | - Fabrizio Chiti
- Section of Biochemistry, Department of Experimental and Clinical Biomedical Sciences, University of Florence, 50134, Florence, Italy
| | - Neville Vassallo
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta.
- Centre for Molecular Medicine and Biobanking, University of Malta, Msida, Malta.
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6
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Rudajev V, Novotny J. The Role of Lipid Environment in Ganglioside GM1-Induced Amyloid β Aggregation. MEMBRANES 2020; 10:membranes10090226. [PMID: 32916822 PMCID: PMC7558528 DOI: 10.3390/membranes10090226] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/04/2020] [Accepted: 09/07/2020] [Indexed: 01/14/2023]
Abstract
Ganglioside GM1 is the most common brain ganglioside enriched in plasma membrane regions known as lipid rafts or membrane microdomains. GM1 participates in many modulatory and communication functions associated with the development, differentiation, and protection of neuronal tissue. It has, however, been demonstrated that GM1 plays a negative role in the pathophysiology of Alzheimer's disease (AD). The two features of AD are the formation of intracellular neurofibrillary bodies and the accumulation of extracellular amyloid β (Aβ). Aβ is a peptide characterized by intrinsic conformational flexibility. Depending on its partners, Aβ can adopt different spatial arrangements. GM1 has been shown to induce specific changes in the spatial organization of Aβ, which lead to enhanced peptide accumulation and deleterious effect especially on neuronal membranes containing clusters of this ganglioside. Changes in GM1 levels and distribution during the development of AD may contribute to the aggravation of the disease.
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7
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Das A, Gupta A, Hong Y, Carver JA, Maiti S. A Spectroscopic Marker for Structural Transitions Associated with Amyloid-β Aggregation. Biochemistry 2020; 59:1813-1822. [PMID: 32329604 DOI: 10.1021/acs.biochem.0c00113] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
An amyloid aggregate evolves through a series of intermediates that have different secondary structures and intra- and intermolecular contacts. The structural parameters of these intermediates are important determinants of their toxicity. For example, the early oligomeric species of the amyloid-β (Aβ) peptide have been implicated as the most cytotoxic species in Alzheimer's disease but are difficult to identify because of their dynamic and transitory nature. Conventional aggregation monitors such as the fluorescent dye thioflavin T report on only the overall transition of the soluble species to the final amyloid fibrillar aggregated state. Here, we show that the fluorescent dye bis(triphenylphosphonium) tetraphenylethene (TPE-TPP) identifies at least three distinct aggregation intermediates of Aβ. Some atomic-level features of these intermediates are known from solid state nuclear magnetic resonance spectroscopy. Hence, the TPE-TPP fluorescence data may be interpreted in terms of these Aβ structural transitions. Steady state fluorescence and lifetime characteristics of TPE-TPP distinguish between the small oligomeric species (emission wavelength maximum, λmax = 465 nm; average fluorescence lifetime, τFl measured at 420 nm = 3.58 ± 0.04 ns), the intermediate species (λmax = 452 nm; τFl = 3.00 ± 0.03 ns), and the fibrils (λmax = 406 nm; τFl = 5.19 ± 0.08 ns). Thus, TPE-TPP provides a ready diagnostic for differentiating between the various, including the toxic, Aβ aggregates and potentially can be utilized to screen for amyloid aggregation inhibitors.
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Affiliation(s)
- Anirban Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Ankur Gupta
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Yuning Hong
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - John A Carver
- Research School of Chemistry, The Australian National University, Acton, ACT 2601, Australia
| | - Sudipta Maiti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
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8
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Nuebling GS, Plesch E, Ruf VC, Högen T, Lorenzl S, Kamp F, Giese A, Levin J. Binding of Metal-Ion-Induced Tau Oligomers to Lipid Surfaces Is Enhanced by GSK-3β-Mediated Phosphorylation. ACS Chem Neurosci 2020; 11:880-887. [PMID: 32069020 DOI: 10.1021/acschemneuro.9b00459] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
While fibrillar deposits of hyperphosphorylated protein tau are a key hallmark of several neurodegenerative diseases such as Alzheimer's disease, small oligomers have been speculated to be the key toxic aggregate species. Trivalent metal ions were shown to promote tau oligomer formation in vitro. However, little is known about potential intercellular spreading mechanisms or toxic modes of action of such oligomers. We investigated interactions of tau monomers and Fe3+/Al3+-induced oligomers with small unilamellar vesicles derived from 1-palmitoyl-2-oleoyl-phosphatidylcholine (neutral, liquid-crystalline phase) and dipalmitoyl-phosphatidylcholine (neutral, gel-phase). We further evaluated the influence of glycogen synthase kinase 3β (GSK-3β)-mediated tau phosphorylation applying the single-particle fluorescence spectroscopy techniques fluorescence correlation spectroscopy, fluorescence intensity distribution analysis, and scanning for intensely fluorescent targets. In these experiments, no binding to neutral lipid surfaces was observed for tau monomers. In contrast, metal-ion-induced tau oligomers showed a gain of function in binding to neutral lipid surfaces. Of note, tau phosphorylation by GSK-3β increased both oligomer formation and membrane affinity of the resulting oligomers. In conclusion, our data imply a pathological gain of function of metal-ion-induced oligomers of hyperphosphorylated tau, enabling membrane binding irrespective of surface charge even at nanomolar protein concentrations.
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Affiliation(s)
- Georg S. Nuebling
- Department of Neurology, Klinikum der Universität München, Ludwig-Maximilians-University, 81377 Munich, Germany
- Center of Neuropathology and Prion Research, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
- Department for Palliative Medicine, Klinikum der Universität München, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Eva Plesch
- Center of Neuropathology and Prion Research, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Viktoria C. Ruf
- Center of Neuropathology and Prion Research, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Tobias Högen
- Department of Neurology, Klinikum der Universität München, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Stefan Lorenzl
- Department of Neurology, Klinikum der Universität München, Ludwig-Maximilians-University, 81377 Munich, Germany
- Department for Palliative Medicine, Klinikum der Universität München, Ludwig-Maximilians-University, 81377 Munich, Germany
- Endowed Professorship for Interdisciplinary Research in Palliative Care, Institute of Nursing Science and Practice, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Frits Kamp
- Center of Neuropathology and Prion Research, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
- Biomedical Research Center, Metabolic Chemistry, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Armin Giese
- Center of Neuropathology and Prion Research, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Johannes Levin
- Department of Neurology, Klinikum der Universität München, Ludwig-Maximilians-University, 81377 Munich, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen DZNE, 81377 Munich, Germany
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9
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Ingargiola A, Weiss S, Lerner E. Monte Carlo Diffusion-Enhanced Photon Inference: Distance Distributions and Conformational Dynamics in Single-Molecule FRET. J Phys Chem B 2018; 122:11598-11615. [PMID: 30252475 DOI: 10.1021/acs.jpcb.8b07608] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Single-molecule Förster resonance energy transfer (smFRET) is utilized to study the structure and dynamics of many biomolecules, such as proteins, DNA, and their various complexes. The structural assessment is based on the well-known Förster relationship between the measured efficiency of energy transfer between a donor (D) and an acceptor (A) dye and the distance between them. Classical smFRET analysis methods called photon distribution analysis (PDA) take into account photon shot-noise, D-A distance distribution, and, more recently, interconversion between states in order to extract accurate distance information. It is known that rapid D-A distance fluctuations on the order of the D lifetime (or shorter) can increase the measured mean FRET efficiency and thus decrease the estimated D-A distance. Nonetheless, this effect has been so far neglected in smFRET experiments, potentially leading to biases in estimated distances. Here we introduce a PDA approach dubbed Monte Carlo diffusion-enhanced photon inference (MC-DEPI). MC-DEPI recolor detected photons of smFRET experiments taking into account dynamics of D-A distance fluctuations, multiple interconverting states, and photoblinking. Using this approach, we show how different underlying conditions may yield identical FRET histograms and how the additional information from fluorescence decays helps in distinguishing between the different conditions. We also introduce a machine learning fitting approach for retrieving the D-A distance distribution, decoupled from the above-mentioned effects. We show that distance interpretation of smFRET experiments of even the simplest dsDNA is nontrivial and requires decoupling the effects of rapid D-A distance fluctuations on FRET in order to avoid systematic biases in the estimation of the D-A distance distribution.
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Affiliation(s)
- Antonino Ingargiola
- Department of Chemistry and Biochemistry , University of California Los Angeles , Los Angeles , California , United States
| | - Shimon Weiss
- Department of Chemistry and Biochemistry , University of California Los Angeles , Los Angeles , California , United States
| | - Eitan Lerner
- Department of Chemistry and Biochemistry , University of California Los Angeles , Los Angeles , California , United States.,Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences , The Hebrew University , Jerusalem , Israel
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10
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Rawat A, Maity BK, Chandra B, Maiti S. Aggregation-induced conformation changes dictate islet amyloid polypeptide (IAPP) membrane affinity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1734-1740. [DOI: 10.1016/j.bbamem.2018.03.027] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/20/2018] [Accepted: 03/21/2018] [Indexed: 11/30/2022]
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11
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Ultrafast dynamics-driven biomolecular recognition where fast activities dictate slow events. J Biosci 2018. [DOI: 10.1007/s12038-018-9776-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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12
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13
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Dey S, Gupta A, Bhowmik D, Das A, Rawat A, Maiti S. Lipid Membrane Interaction of Amyloidogenic Peptides. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.lb178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Simli Dey
- Chemical ScienceTata Institute of Fundamental ResearchMumbaiIndia
| | - Ankur Gupta
- Chemical ScienceTata Institute of Fundamental ResearchMumbaiIndia
| | - Debanjan Bhowmik
- Chemical ScienceTata Institute of Fundamental ResearchMumbaiIndia
| | - Anirban Das
- Chemical ScienceTata Institute of Fundamental ResearchMumbaiIndia
| | - Anoop Rawat
- Chemical ScienceTata Institute of Fundamental ResearchMumbaiIndia
| | - Sudipta Maiti
- Chemical ScienceTata Institute of Fundamental ResearchMumbaiIndia
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14
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Xiang N, Lyu Y, Zhu X, Narsimhan G. Investigation of the interaction of amyloid β peptide (11–42) oligomers with a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) membrane using molecular dynamics simulation. Phys Chem Chem Phys 2018; 20:6817-6829. [PMID: 29299557 DOI: 10.1039/c7cp07148e] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The mechanism of pore formation in model neural cell membranes by β amyloid (Aβ) peptides was investigated using molecular dynamics simulation which indicated that Aβ oligomers of size equal or greater than 3 has a higher tendency for pore formation than monomers and that cholesterol tends to retard Aβ binding and insertion into the membrane.
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Affiliation(s)
- Ning Xiang
- Department of Agricultural and Biological Engineering
- Purdue University
- West Lafayette
- USA
| | - Yuan Lyu
- Department of Agricultural and Biological Engineering
- Purdue University
- West Lafayette
- USA
| | - Xiao Zhu
- ItaP
- Research Computing
- Rosen Center for Advanced Computing
- Purdue University
- West Lafayette
| | - Ganesan Narsimhan
- Department of Agricultural and Biological Engineering
- Purdue University
- West Lafayette
- USA
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15
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Chandra B, Maity BK, Das A, Maiti S. Fluorescence quenching by lipid encased nanoparticles shows that amyloid-β has a preferred orientation in the membrane. Chem Commun (Camb) 2018; 54:7750-7753. [DOI: 10.1039/c8cc02108b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Short range plasmonic fields around a nanoparticle can modulate fluorescence or Raman processes.
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Affiliation(s)
| | | | - Anirban Das
- Tata Institute of Fundamental Research
- Homi Bhabha Road
- Mumbai
- India
| | - Sudipta Maiti
- Tata Institute of Fundamental Research
- Homi Bhabha Road
- Mumbai
- India
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16
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Major Reaction Coordinates Linking Transient Amyloid-β Oligomers to Fibrils Measured at Atomic Level. Biophys J 2017; 113:805-816. [PMID: 28834717 DOI: 10.1016/j.bpj.2017.06.068] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 06/22/2017] [Accepted: 06/22/2017] [Indexed: 11/22/2022] Open
Abstract
The structural underpinnings for the higher toxicity of the oligomeric intermediates of amyloidogenic peptides, compared to the mature fibrils, remain unknown at present. The transient nature and heterogeneity of the oligomers make it difficult to follow their structure. Here, using vibrational and solid-state nuclear magnetic resonance spectroscopy, and molecular dynamics simulations, we show that freely aggregating Aβ40 oligomers in physiological solutions have an intramolecular antiparallel configuration that is distinct from the intermolecular parallel β-sheet structure observed in mature fibrils. The intramolecular hydrogen-bonding network flips nearly 90°, and the two β-strands of each monomeric unit move apart, to give rise to the well-known intermolecular in-register parallel β-sheet structure in the mature fibrils. Solid-state nuclear magnetic resonance distance measurements capture the interstrand separation within monomer units during the transition from the oligomer to the fibril form. We further find that the D23-K28 salt-bridge, a major feature of the Aβ40 fibrils and a focal point of mutations linked to early onset Alzheimer's disease, is not detectable in the small oligomers. Molecular dynamics simulations capture the correlation between changes in the D23-K28 distance and the flipping of the monomer secondary structure between antiparallel and parallel β-sheet architectures. Overall, we propose interstrand separation and salt-bridge formation as key reaction coordinates describing the structural transition of the small Aβ40 oligomers to fibrils.
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17
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Kedia N, Almisry M, Bieschke J. Glucose directs amyloid-beta into membrane-active oligomers. Phys Chem Chem Phys 2017; 19:18036-18046. [PMID: 28671211 PMCID: PMC5654640 DOI: 10.1039/c7cp02849k] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Oligomeric amyloid-β 1-42 (Aβ-42) peptides are considered to be the most toxic species connected to the occurrence of Alzheimer's disease. However, not all aggregation conditions promote oligomer formation in vitro, raising the question whether oligomer formation in vivo also requires a specific suitable cellular environment. We recently found that interaction with neuronal membranes initiates aggregation of Aβ-42 and neuronal uptake. Our data suggest that small molecules in the extracellular space can facilitate the formation of membrane-active Aβ-42 oligomers. We analyzed the early stage of Aβ-42 aggregation in the presence of glucose and sucrose and found that these sugars strongly favor Aβ-42 oligomer formation. We characterized oligomers by dynamic light scattering, atomic force microscopy, immuno-transmission electron microscopy and fluorescence cross correlation spectroscopy. We found that Aβ-42 spontaneously and rapidly forms low molecular weight oligomers in the presence of sugars. Slightly acidic pH (6.7-7) greatly favors oligomer formation when compared to the extracellular physiological pH (7.4). Circular dichroism demonstrated that these Aβ-42 oligomers did not adopt a β-sheet structure. Unstructured oligomeric Aβ-42 interacted with membrane bilayers of giant unilamellar vesicles (GUV) and neuronal model cells, facilitated cellular uptake of Aβ-42, and inhibition of mitochondrial activity. Our data therefore suggest that elevated concentrations of glucose within the range observed in diabetic individuals (10 mM) facilitate the formation of membrane-active Aβ-42 oligomers.
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Affiliation(s)
- Niraja Kedia
- Department of Biomedical Engineering, Washington University, 63130 St. Louis, MO, USA.
| | - Michael Almisry
- Department of Biomedical Engineering, Washington University, 63130 St. Louis, MO, USA.
| | - Jan Bieschke
- Department of Biomedical Engineering, Washington University, 63130 St. Louis, MO, USA.
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18
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Chandra B, Korn A, Maity BK, Adler J, Rawat A, Krueger M, Huster D, Maiti S. Stereoisomers Probe Steric Zippers in Amyloid-β. J Phys Chem B 2017; 121:1835-1842. [PMID: 28140589 DOI: 10.1021/acs.jpcb.6b12332] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Shape complementarity between close-packed residues plays a critical role in the amyloid aggregation process. Here, we probe such "steric zipper" interactions in amyloid-β (Aβ40), whose aggregation is linked to Alzheimer's disease, by replacing natural residues by their stereoisomers. Such mutations are expected to specifically destabilize the shape sensitive "packing" interactions, which may potentially increase their solubility and change other properties. We study the stereomutants DF19 and DL34 and also the DA2/DF4/DH6/DS8 mutant of Aβ40. F19-L34 is a critical contact in a tightly packed region of Aβ, while residues 1-9 are known to be disordered. While both DF19 and DL34 slow down the kinetics of aggregation and form amyloid fibrils efficiently, only DL34 increases the final solubility. DF19 gives rise to additional off-pathway aggregation which results in large, kinetically stable aggregates, and has lower net solubility. DA2/DF4/DH6/DS8 does not have an effect on the kinetics or the solubility. Notably, both DF19 and DL34 oligomers have a significantly lower level of interactions with lipid vesicles and live cells. We conclude that stereoisomers can cause complex site dependent changes in amyloid properties, and provide an effective tool to determine the role of individual residues in shaping the packed interiors of amyloid aggregates.
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Affiliation(s)
- Bappaditya Chandra
- Department of Chemical Science, Tata Institute of Fundamental Research , Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Alexander Korn
- Institut für Medizinische Physik und Biophysik, Universität Leipzig , Härtelstrasse 16-18, D-04107 Leipzig, Germany
| | - Barun Kumar Maity
- Department of Chemical Science, Tata Institute of Fundamental Research , Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Juliane Adler
- Institut für Medizinische Physik und Biophysik, Universität Leipzig , Härtelstrasse 16-18, D-04107 Leipzig, Germany
| | - Anoop Rawat
- Department of Chemical Science, Tata Institute of Fundamental Research , Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Martin Krueger
- Institut für Medizinische Physik und Biophysik, Universität Leipzig , Härtelstrasse 16-18, D-04107 Leipzig, Germany.,Institut für Anatomie, Universität Leipzig , Liebigstr. 13, D-04103 Leipzig, Germany
| | - Daniel Huster
- Institut für Medizinische Physik und Biophysik, Universität Leipzig , Härtelstrasse 16-18, D-04107 Leipzig, Germany
| | - Sudipta Maiti
- Department of Chemical Science, Tata Institute of Fundamental Research , Homi Bhabha Road, Colaba, Mumbai 400005, India
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19
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Abstract
Dozens of proteins are known to convert to the aggregated amyloid state. These include fibrils associated with systemic and neurodegenerative diseases and cancer, functional amyloid fibrils in microorganisms and animals, and many denatured proteins. Amyloid fibrils can be much more stable than other protein assemblies. In contrast to globular proteins, a single protein sequence can aggregate into several distinctly different amyloid structures, termed polymorphs, and a given polymorph can reproduce itself by seeding. Amyloid polymorphs may be the molecular basis of prion strains. Whereas the Protein Data Bank contains some 100,000 globular protein and 3,000 membrane protein structures, only a few dozen amyloid protein structures have been determined, and most of these are short segments of full amyloid-forming proteins. Regardless, these amyloid structures illuminate the architecture of the amyloid state, including its stability and its capacity for formation of polymorphs.
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Affiliation(s)
- David S Eisenberg
- Howard Hughes Medical Institute and Molecular Biology Institute, University of California, Los Angeles, California 90095-1570; ,
| | - Michael R Sawaya
- Howard Hughes Medical Institute and Molecular Biology Institute, University of California, Los Angeles, California 90095-1570; ,
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20
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Singh P, Choudhury S, Chandra GK, Lemmens P, Pal SK. Molecular recognition of genomic DNA in a condensate with a model surfactant for potential gene-delivery applications. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 157:105-12. [DOI: 10.1016/j.jphotobiol.2016.02.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 02/10/2016] [Accepted: 02/11/2016] [Indexed: 01/25/2023]
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21
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Choudhury S, Naiya G, Singh P, Lemmens P, Roy S, Pal SK. Modulation of Ultrafast Conformational Dynamics in Allosteric Interaction of Gal Repressor Protein with Different Operator DNA Sequences. Chembiochem 2016; 17:605-13. [DOI: 10.1002/cbic.201500657] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Indexed: 01/15/2023]
Affiliation(s)
- Susobhan Choudhury
- Department of Chemical, Biological & Macromolecular Sciences; S. N. Bose National Centre for Basic Sciences; Block JD Sector III Salt Lake Kolkata 700 098 India
| | - Gitashri Naiya
- Division of Structural Biology and Bioinformatics; Indian Institute of Chemical Biology; 4, Raja S.C. Mullick Road Kolkata 700 032 India
| | - Priya Singh
- Department of Chemical, Biological & Macromolecular Sciences; S. N. Bose National Centre for Basic Sciences; Block JD Sector III Salt Lake Kolkata 700 098 India
| | - Peter Lemmens
- Institute for Condensed Matter Physics and Laboratory for Emerging Nanometrology; TU Braunschweig; Mendelssohnstrasse 3 38106 Braunschweig Germany
| | - Siddhartha Roy
- Division of Structural Biology and Bioinformatics; Indian Institute of Chemical Biology; 4, Raja S.C. Mullick Road Kolkata 700 032 India
| | - Samir Kumar Pal
- Department of Chemical, Biological & Macromolecular Sciences; S. N. Bose National Centre for Basic Sciences; Block JD Sector III Salt Lake Kolkata 700 098 India
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22
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Das AK, Pandit R, Maiti S. Effect of amyloids on the vesicular machinery: implications for somatic neurotransmission. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0187. [PMID: 26009766 DOI: 10.1098/rstb.2014.0187] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Certain neurodegenerative diseases are thought to be initiated by the aggregation of amyloidogenic proteins. However, the mechanism underlying toxicity remains obscure. Most of the suggested mechanisms are generic in nature and do not directly explain the neuron-type specific lesions observed in many of these diseases. Some recent reports suggest that the toxic aggregates impair the synaptic vesicular machinery. This may lead to an understanding of the neuron-type specificity observed in these diseases. A disruption of the vesicular machinery can also be deleterious for extra-synaptic, especially somatic, neurotransmission (common in serotonergic and dopaminergic systems which are specifically affected in Alzheimer's disease (AD) and Parkinson's disease (PD), respectively), though this relationship has remained unexplored. In this review, we discuss amyloid-induced damage to the neurotransmitter vesicular machinery, with an eye on the possible implications for somatic exocytosis. We argue that the larger size of the system, and the availability of multi-photon microscopy techniques for directly visualizing monoamines, make the somatic exocytosis machinery a more tractable model for understanding the effect of amyloids on all types of vesicular neurotransmission. Indeed, exploring this neglected connection may not just be important, it may be a more fruitful route for understanding AD and PD.
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Affiliation(s)
- Anand Kant Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, Maharashtra 400005, India
| | - Rucha Pandit
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, Maharashtra 400005, India
| | - Sudipta Maiti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, Maharashtra 400005, India
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23
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Maximally asymmetric transbilayer distribution of anionic lipids alters the structure and interaction with lipids of an amyloidogenic protein dimer bound to the membrane surface. Chem Phys Lipids 2016; 196:33-51. [PMID: 26827904 DOI: 10.1016/j.chemphyslip.2016.01.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 01/13/2016] [Accepted: 01/14/2016] [Indexed: 12/23/2022]
Abstract
We used molecular dynamics simulations to explore the effects of asymmetric transbilayer distribution of anionic phosphatidylserine (PS) lipids on the structure of a protein on the membrane surface and subsequent protein-lipid interactions. Our simulation systems consisted of an amyloidogenic, beta-sheet rich dimeric protein (D42) absorbed to the phosphatidylcholine (PC) leaflet, or protein-contact PC leaflet, of two membrane systems: a single-component PC bilayer and double PC/PS bilayers. The latter comprised of a stable but asymmetric transbilayer distribution of PS in the presence of counterions, with a 1-component PC leaflet coupled to a 1-component PS leaflet in each bilayer. The maximally asymmetric PC/PS bilayer had a non-zero transmembrane potential (TMP) difference and higher lipid order packing, whereas the symmetric PC bilayer had a zero TMP difference and lower lipid order packing under physiologically relevant conditions. Analysis of the adsorbed protein structures revealed weaker protein binding, more folding in the N-terminal domain, more aggregation of the N- and C-terminal domains and larger tilt angle of D42 on the PC leaflet surface of the PC/PS bilayer versus the PC bilayer. Also, analysis of protein-induced membrane structural disruption revealed more localized bilayer thinning in the PC/PS versus PC bilayer. Although the electric field profile in the non-protein-contact PS leaflet of the PC/PS bilayer differed significantly from that in the non-protein-contact PC leaflet of the PC bilayer, no significant difference in the electric field profile in the protein-contact PC leaflet of either bilayer was evident. We speculate that lipid packing has a larger effect on the surface adsorbed protein structure than the electric field for a maximally asymmetric PC/PS bilayer. Our results support the mechanism that the higher lipid packing in a lipid leaflet promotes stronger protein-protein but weaker protein-lipid interactions for a dimeric protein on membrane surfaces.
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24
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Single Molecule Tools for Probing Protein Aggregation. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES INDIA SECTION A-PHYSICAL SCIENCES 2015. [DOI: 10.1007/s40010-015-0248-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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25
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Chandrakesan M, Bhowmik D, Sarkar B, Abhyankar R, Singh H, Kallianpur M, Dandekar SP, Madhu PK, Maiti S, Mithu VS. Steric Crowding of the Turn Region Alters the Tertiary Fold of Amyloid-β18-35 and Makes It Soluble. J Biol Chem 2015; 290:30099-107. [PMID: 26487720 DOI: 10.1074/jbc.m115.674135] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Indexed: 11/06/2022] Open
Abstract
Aβ self-assembles into parallel cross-β fibrillar aggregates, which is associated with Alzheimer's disease pathology. A central hairpin turn around residues 23-29 is a defining characteristic of Aβ in its aggregated state. Major biophysical properties of Aβ, including this turn, remain unaltered in the central fragment Aβ18-35. Here, we synthesize a single deletion mutant, ΔG25, with the aim of sterically hindering the hairpin turn in Aβ18-35. We find that the solubility of the peptide goes up by more than 20-fold. Although some oligomeric structures do form, solution state NMR spectroscopy shows that they have mostly random coil conformations. Fibrils ultimately form at a much higher concentration but have widths approximately twice that of Aβ18-35, suggesting an opening of the hairpin bend. Surprisingly, two-dimensional solid state NMR shows that the contact between Phe(19) and Leu(34) residues, observed in full-length Aβ and Aβ18-35, is still intact in these fibrils. This is possible if the monomers in the fibril are arranged in an antiparallel β-sheet conformation. Indeed, IR measurements, supported by tyrosine cross-linking experiments, provide a characteristic signature of the antiparallel β-sheet. We conclude that the self-assembly of Aβ is critically dependent on the hairpin turn and on the contact between the Phe(19) and Leu(34) regions, making them potentially sensitive targets for Alzheimer's therapeutics. Our results show the importance of specific conformations in an aggregation process thought to be primarily driven by nonspecific hydrophobic interactions.
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Affiliation(s)
- Muralidharan Chandrakesan
- From the Department of Biochemistry, Seth G. S. Medical College and King Edward Memorial Hospital, Parel, Mumbai 400012, India
| | - Debanjan Bhowmik
- the Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai 400005, India
| | - Bidyut Sarkar
- the Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai 400005, India
| | - Rajiv Abhyankar
- the Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai 400005, India
| | - Harwinder Singh
- the Department of Chemistry, Guru Nanak Dev University, Amritsar 143005, India, and
| | - Mamata Kallianpur
- the Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai 400005, India
| | - Sucheta P Dandekar
- From the Department of Biochemistry, Seth G. S. Medical College and King Edward Memorial Hospital, Parel, Mumbai 400012, India
| | - Perunthiruthy K Madhu
- the Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai 400005, India, the Tata Institute of Fundamental Research Centre for Interdisciplinary Sciences, Narsinghi, Hyderabad 500 075, India
| | - Sudipta Maiti
- the Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai 400005, India,
| | - Venus Singh Mithu
- the Department of Chemistry, Guru Nanak Dev University, Amritsar 143005, India, and
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26
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Bhowmik D, Mote KR, MacLaughlin CM, Biswas N, Chandra B, Basu JK, Walker GC, Madhu PK, Maiti S. Cell-Membrane-Mimicking Lipid-Coated Nanoparticles Confer Raman Enhancement to Membrane Proteins and Reveal Membrane-Attached Amyloid-β Conformation. ACS NANO 2015; 9:9070-7. [PMID: 26391443 DOI: 10.1021/acsnano.5b03175] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Identifying the structures of membrane bound proteins is critical to understanding their function in healthy and diseased states. We introduce a surface enhanced Raman spectroscopy technique which can determine the conformation of membrane-bound proteins, at low micromolar concentrations, and also in the presence of a substantial membrane-free fraction. Unlike conventional surface enhanced Raman spectroscopy, our approach does not require immobilization of molecules, as it uses spontaneous binding of proteins to lipid bilayer-encapsulated Ag nanoparticles. We apply this technique to probe membrane-attached oligomers of Amyloid-β40 (Aβ40), whose conformation is keenly sought in the context of Alzheimer's disease. Isotope-shifts in the Raman spectra help us obtain secondary structure information at the level of individual residues. Our results show the presence of a β-turn, flanked by two β-sheet regions. We use solid-state NMR data to confirm the presence of the β-sheets in these regions. In the membrane-attached oligomer, we find a strongly contrasting and near-orthogonal orientation of the backbone H-bonds compared to what is found in the mature, less-toxic Aβ fibrils. Significantly, this allows a "porin" like β-barrel structure, providing a structural basis for proposed mechanisms of Aβ oligomer toxicity.
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Affiliation(s)
- Debanjan Bhowmik
- Department of Chemical Sciences, Tata Institute of Fundamental Research , Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Kaustubh R Mote
- TIFR Centre for Interdisciplinary Sciences , 21 Brundavan Colony, Narsinghi, Hyderabad 500075, India
| | - Christina M MacLaughlin
- Department of Chemistry, Lash Miller Laboratories, University of Toronto , Toronto, ON M5S 3H6, Canada
| | - Nupur Biswas
- Department of Physics, Indian Institute of Science , Bengaluru 560012, India
| | - Bappaditya Chandra
- Department of Chemical Sciences, Tata Institute of Fundamental Research , Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Jaydeep K Basu
- Department of Physics, Indian Institute of Science , Bengaluru 560012, India
| | - Gilbert C Walker
- Department of Chemistry, Lash Miller Laboratories, University of Toronto , Toronto, ON M5S 3H6, Canada
| | - Perunthiruthy K Madhu
- Department of Chemical Sciences, Tata Institute of Fundamental Research , Homi Bhabha Road, Colaba, Mumbai 400005, India
- TIFR Centre for Interdisciplinary Sciences , 21 Brundavan Colony, Narsinghi, Hyderabad 500075, India
| | - Sudipta Maiti
- Department of Chemical Sciences, Tata Institute of Fundamental Research , Homi Bhabha Road, Colaba, Mumbai 400005, India
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27
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Das AK, Rawat A, Bhowmik D, Pandit R, Huster D, Maiti S. An early folding contact between Phe19 and Leu34 is critical for amyloid-β oligomer toxicity. ACS Chem Neurosci 2015; 6:1290-5. [PMID: 25951510 DOI: 10.1021/acschemneuro.5b00074] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Small hydrophobic oligomers of aggregation-prone proteins are thought to be generically toxic. Here we examine this view by perturbing an early folding contact between Phe19 and Leu34 formed during the aggregation of Alzheimer's amyloid-β (Aβ40) peptide. We find that even conservative single mutations altering this interaction can abolish Aβ40 toxicity. Significantly, the mutants are not distinguishable either by the oligomers size or by the end-state fibrillar structure from the wild type Aβ40. We trace the change in their toxicity to a drastic lowering of membrane affinity. Therefore, nonlocal folding contacts play a key role in steering the oligomeric intermediates through specific conformations with very different properties and toxicity levels. Our results suggest that engineering the folding energy landscape may provide an alternative route to Alzheimer therapeutics.
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Affiliation(s)
- Anand K. Das
- Department
of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Anoop Rawat
- Department
of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Debanjan Bhowmik
- Department
of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Rucha Pandit
- Department
of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Daniel Huster
- Institute
of Medical Physics and Biophysics, University of Leipzig, Härtelstr.
16-18, D-04107 Leipzig, Germany
| | - Sudipta Maiti
- Department
of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
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28
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Choudhury S, Mondal PK, Sharma VK, Mitra S, Sakai VG, Mukhopadhyay R, Pal SK. Direct Observation of Coupling between Structural Fluctuation and Ultrafast Hydration Dynamics of Fluorescent Probes in Anionic Micelles. J Phys Chem B 2015; 119:10849-57. [PMID: 25874585 DOI: 10.1021/jp511899q] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The coupling of structural fluctuation and the dynamics of associated water molecules of biological macromolecules is vital for various biological activities. Although a number of molecular dynamics (MD) studies on proteins/DNA predicted the importance of such coupling, experimental evidence of variation of hydration dynamics with controlled structural fluctuation even in model macromolecule is sparse and raised controversies in the contemporary literature. Here, we have investigated dynamics of hydration at the surfaces of two similar anionic micelles sodium dodecyl sulfate (SDS) and sodium dodecylbenzenesulfonate (SDBS) as model macromolecules using coumarin 500 (C500) as spectroscopic probe with femtosecond to picosecond time resolution up to 20 ns time window. The constituting surfactants SDS and SDBS are structurally similar except one benzene moiety in the SDBS may offer additional rigidity to the SDBS micelles through π-stacking and added bulkiness. The structural integrity of the micelles in the aqueous medium is confirmed in dynamic light scattering (DLS) studies. A variety of studies including polarization gated fluorescence spectroscopy and quasielastic neutron scattering (QENS) have been used to confirm differential structural fluctuation of SDS and SDBS micelles. We have also employed femtosecond-resolved Förster resonance energy transfer (FRET) in order to study binding of a cationic organic ligand ethidium bromide (EtBr) salt at the micellar surfaces. The distance distribution of the donor (C500)-acceptor (EtBr) in the micellar media reveals the manifestation of the structural flexibility of the micelles. Our studies on dynamical coupling of the structural flexibility with surface hydration in the nanoscopic micellar media may find the relevance in the "master-slave" type water dynamics in biologically relevant macromolecules.
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Affiliation(s)
- Susobhan Choudhury
- Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences , Block JD, Sector III, Salt Lake, Kolkata 700 098, India
| | - Prasanna Kumar Mondal
- Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences , Block JD, Sector III, Salt Lake, Kolkata 700 098, India
| | - V K Sharma
- Solid State Physics Division, Bhabha Atomic Research Centre , Mumbai 400085, India
| | - S Mitra
- Solid State Physics Division, Bhabha Atomic Research Centre , Mumbai 400085, India
| | - V Garcia Sakai
- Science and Technology Facilities Council, Rutherford Appleton Laboratory , Didcot, OX11 0QX, U.K
| | - R Mukhopadhyay
- Solid State Physics Division, Bhabha Atomic Research Centre , Mumbai 400085, India
| | - Samir Kumar Pal
- Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences , Block JD, Sector III, Salt Lake, Kolkata 700 098, India
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29
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Nasica-Labouze J, Nguyen PH, Sterpone F, Berthoumieu O, Buchete NV, Coté S, De Simone A, Doig AJ, Faller P, Garcia A, Laio A, Li MS, Melchionna S, Mousseau N, Mu Y, Paravastu A, Pasquali S, Rosenman DJ, Strodel B, Tarus B, Viles JH, Zhang T, Wang C, Derreumaux P. Amyloid β Protein and Alzheimer's Disease: When Computer Simulations Complement Experimental Studies. Chem Rev 2015; 115:3518-63. [PMID: 25789869 DOI: 10.1021/cr500638n] [Citation(s) in RCA: 475] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Jessica Nasica-Labouze
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Phuong H Nguyen
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Fabio Sterpone
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Olivia Berthoumieu
- ‡LCC (Laboratoire de Chimie de Coordination), CNRS, Université de Toulouse, Université Paul Sabatier (UPS), Institut National Polytechnique de Toulouse (INPT), 205 route de Narbonne, BP 44099, Toulouse F-31077 Cedex 4, France
| | | | - Sébastien Coté
- ∥Département de Physique and Groupe de recherche sur les protéines membranaires (GEPROM), Université de Montréal, C.P. 6128, succursale Centre-ville, Montréal, Québec H3C 3T5, Canada
| | - Alfonso De Simone
- ⊥Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Andrew J Doig
- #Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Peter Faller
- ‡LCC (Laboratoire de Chimie de Coordination), CNRS, Université de Toulouse, Université Paul Sabatier (UPS), Institut National Polytechnique de Toulouse (INPT), 205 route de Narbonne, BP 44099, Toulouse F-31077 Cedex 4, France
| | | | - Alessandro Laio
- ○The International School for Advanced Studies (SISSA), Via Bonomea 265, 34136 Trieste, Italy
| | - Mai Suan Li
- ◆Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland.,¶Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
| | - Simone Melchionna
- ⬠Instituto Processi Chimico-Fisici, CNR-IPCF, Consiglio Nazionale delle Ricerche, 00185 Roma, Italy
| | | | - Yuguang Mu
- ▲School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Anant Paravastu
- ⊕National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States
| | - Samuela Pasquali
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | | | - Birgit Strodel
- △Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Bogdan Tarus
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - John H Viles
- ▼School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Tong Zhang
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France.,▲School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | | | - Philippe Derreumaux
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France.,□Institut Universitaire de France, 75005 Paris, France
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Chaudhuri S, Batabyal S, Polley N, Pal SK. Vitamin B2 in Nanoscopic Environments under Visible Light: Photosensitized Antioxidant or Phototoxic Drug? J Phys Chem A 2014; 118:3934-43. [DOI: 10.1021/jp502904r] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Siddhi Chaudhuri
- Department
of Chemical, Biological
and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India
| | - Subrata Batabyal
- Department
of Chemical, Biological
and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India
| | - Nabarun Polley
- Department
of Chemical, Biological
and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India
| | - Samir Kumar Pal
- Department
of Chemical, Biological
and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India
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Sarkar B, Mithu VS, Chandra B, Mandal A, Chandrakesan M, Bhowmik D, Madhu PK, Maiti S. Significant Structural Differences between Transient Amyloid-β Oligomers and Less-Toxic Fibrils in Regions Known To Harbor Familial Alzheimer′s Mutations. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402636] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Sarkar B, Mithu VS, Chandra B, Mandal A, Chandrakesan M, Bhowmik D, Madhu PK, Maiti S. Significant structural differences between transient amyloid-β oligomers and less-toxic fibrils in regions known to harbor familial Alzheimer's mutations. Angew Chem Int Ed Engl 2014; 53:6888-92. [PMID: 24756858 DOI: 10.1002/anie.201402636] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Indexed: 11/11/2022]
Abstract
Small oligomers of the amyloid β (Aβ) peptide, rather than the monomers or the fibrils, are suspected to initiate Alzheimer's disease (AD). However, their low concentration and transient nature under physiological conditions have made structural investigations difficult. A method for addressing such problems has been developed by combining rapid fluorescence techniques with slower two-dimensional solid-state NMR methods. The smallest Aβ40 oligomers that demonstrate a potential sign of toxicity, namely, an enhanced affinity for cell membranes, were thus probed. The two hydrophobic regions (residues 10-21 and 30-40) have already attained the conformation that is observed in the fibrils. However, the turn region (residues 22-29) and the N-terminal tail (residues 1-9) are strikingly different. Notably, ten of eleven known Aβ mutants that are linked to familial AD map to these two regions. Our results provide potential structural cues for AD therapeutics and also suggest a general method for determining transient protein structures.
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Affiliation(s)
- Bidyut Sarkar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005 (India)
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Bhowmik D, MacLaughlin CM, Chandrakesan M, Ramesh P, Venkatramani R, Walker GC, Maiti S. pH changes the aggregation propensity of amyloid-β without altering the monomer conformation. Phys Chem Chem Phys 2013; 16:885-9. [PMID: 24292856 DOI: 10.1039/c3cp54151g] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Decoupling conformational changes from aggregation will help us understand amyloids better. Here we attach Alzheimer's amyloid-β(1-40) monomers to silver nanoparticles, preventing their aggregation, and study their conformation under aggregation-favoring conditions using SERS. Surprisingly, the α-helical character of the peptide remains unchanged between pH 10.5 and 5.5, while the solubility changes >100×. Amyloid aggregation can therefore start without significant conformational changes.
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Affiliation(s)
- Debanjan Bhowmik
- Department of Chemistry, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India.
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