1
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Abstract
Somatostatin (SST14) is strongly related to Alzheimer's disease (AD), as its levels decline during aging, it regulates the proteolytic degradation of the amyloid beta peptide (Aβ), and it binds to Aβ oligomers in vivo. Recently, the 3D structure of a membrane-associated β-sheet pore-forming tetramer (βPFOAβ(1-42) tetramer) has been reported. Here, we show that SST14 binds selectively to the βPFOAβ(1-42) tetramer with a KD value of ∼40 μM without binding to monomeric Aβ(1-42). Specific NMR chemical shift perturbations, observed during titration of SST14, define a binding site in the βPFOAβ(1-42) tetramer and are in agreement with a 2:1 stoichiometry determined by both native mass spectroscopy and isothermal titration calorimetry. These results enabled us to perform driven docking and model the binding mode for the interaction. The present study provides additional evidence on the relation between SST14 and the amyloid cascade and positions the βPFOAβ(1-42) tetramer as a relevant aggregation form of Aβ and as a potential target for AD.
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Affiliation(s)
- Eduard Puig
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, Barcelona 08028, Spain
- CBMN (UMR 5248), University of Bordeaux−CNRS−IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, Pessac 33600, France
| | - James Tolchard
- CBMN (UMR 5248), University of Bordeaux−CNRS−IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, Pessac 33600, France
| | - Antoni Riera
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, Barcelona 08028, Spain
- Departament de Química Inorgànica i Orgànica, Universitat de Barcelona, Martí i Franqués 1, Barcelona 08028, Spain
| | - Natàlia Carulla
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, Barcelona 08028, Spain
- CBMN (UMR 5248), University of Bordeaux−CNRS−IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, Pessac 33600, France
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2
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Ciudad S, Puig E, Botzanowski T, Meigooni M, Arango AS, Do J, Mayzel M, Bayoumi M, Chaignepain S, Maglia G, Cianferani S, Orekhov V, Tajkhorshid E, Bardiaux B, Carulla N. Aβ(1-42) tetramer and octamer structures reveal edge conductivity pores as a mechanism for membrane damage. Nat Commun 2020; 11:3014. [PMID: 32541820 PMCID: PMC7296003 DOI: 10.1038/s41467-020-16566-1] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 05/01/2020] [Indexed: 12/20/2022] Open
Abstract
Formation of amyloid-beta (Aβ) oligomer pores in the membrane of neurons has been proposed to explain neurotoxicity in Alzheimer's disease (AD). Here, we present the three-dimensional structure of an Aβ oligomer formed in a membrane mimicking environment, namely an Aβ(1-42) tetramer, which comprises a six stranded β-sheet core. The two faces of the β-sheet core are hydrophobic and surrounded by the membrane-mimicking environment while the edges are hydrophilic and solvent-exposed. By increasing the concentration of Aβ(1-42) in the sample, Aβ(1-42) octamers are also formed, made by two Aβ(1-42) tetramers facing each other forming a β-sandwich structure. Notably, Aβ(1-42) tetramers and octamers inserted into lipid bilayers as well-defined pores. To establish oligomer structure-membrane activity relationships, molecular dynamics simulations were carried out. These studies revealed a mechanism of membrane disruption in which water permeation occurred through lipid-stabilized pores mediated by the hydrophilic residues located on the core β-sheets edges of the oligomers.
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Affiliation(s)
- Sonia Ciudad
- University of Bordeaux, CBMN (UMR 5248)-CNRS-IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600, Pessac, France
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Eduard Puig
- University of Bordeaux, CBMN (UMR 5248)-CNRS-IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600, Pessac, France
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028, Barcelona, Spain
- Departament de Química Inorgànica i Orgànica, Universitat de Barcelona, Martí i Franqués 1, 08028, Barcelona, Spain
| | - Thomas Botzanowski
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS UMR7178, IPHC, Strasbourg, France
| | - Moeen Meigooni
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology and Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Andres S Arango
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology and Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jimmy Do
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology and Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Maxim Mayzel
- Swedish NMR Centre, University of Gothenburg, Box 465, 405 30, Gothenburg, Sweden
| | - Mariam Bayoumi
- Biochemistry, Molecular and Structural Biology Section, University of Leuven, Celestijnenlaan 200G, 3001, Leuven, Belgium
| | - Stéphane Chaignepain
- University of Bordeaux, CBMN (UMR 5248)-CNRS-IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600, Pessac, France
| | - Giovanni Maglia
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Sarah Cianferani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS UMR7178, IPHC, Strasbourg, France
| | - Vladislav Orekhov
- Swedish NMR Centre, University of Gothenburg, Box 465, 405 30, Gothenburg, Sweden
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 465, 405 30, Gothenburg, Sweden
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology and Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Benjamin Bardiaux
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, C3BI, Institut Pasteur; CNRS UMR3528; CNRS USR3756, Paris, France
| | - Natàlia Carulla
- University of Bordeaux, CBMN (UMR 5248)-CNRS-IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600, Pessac, France.
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028, Barcelona, Spain.
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3
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Serra-Batiste M, Ninot-Pedrosa M, Puig E, Ciudad S, Gairí M, Carulla N. Preparation of a Well-Defined and Stable β-Barrel Pore-Forming Aβ42 Oligomer. Methods Mol Biol 2019; 1779:13-22. [PMID: 29886524 DOI: 10.1007/978-1-4939-7816-8_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The formation of amyloid-β peptide (Aβ) oligomers at the cellular membrane is considered a crucial process that underlies neurotoxicity in Alzheimer's disease (AD). To obtain structural information on this type of oligomers, we were inspired by membrane protein approaches used to stabilize, characterize, and analyze the function of such proteins. Using these approaches, we developed conditions under which Aβ42, the Aβ variant most strongly linked to the aetiology of AD, assembles into an oligomer that inserts into lipid bilayers as a well-defined pore and adopts a specific structure with characteristics of a β-barrel arrangement. We named this oligomer β-barrel Pore-Forming Aβ42 Oligomer (βPFOAβ42). Here, we describe detailed protocols for its preparation and characterization. We expect βPFOAβ42 to be useful in establishing the involvement of membrane-associated Aβ oligomers in AD.
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Affiliation(s)
- Montserrat Serra-Batiste
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute Science and Technology, Barcelona, Spain
| | - Martí Ninot-Pedrosa
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute Science and Technology, Barcelona, Spain.,CBMN (UMR 5248), University of Bordeaux-CNRS-IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Eduard Puig
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute Science and Technology, Barcelona, Spain.,CBMN (UMR 5248), University of Bordeaux-CNRS-IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Sonia Ciudad
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute Science and Technology, Barcelona, Spain.,CBMN (UMR 5248), University of Bordeaux-CNRS-IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Margarida Gairí
- NMR Facility, Scientific and Technological Centers, University of Barcelona (CCiTUB), Barcelona, Spain
| | - Natàlia Carulla
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute Science and Technology, Barcelona, Spain. .,CBMN (UMR 5248), University of Bordeaux-CNRS-IPB, Institut Européen de Chimie et Biologie, Pessac, France.
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4
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Serra-Batiste M, Tolchard J, Giusti F, Zoonens M, Carulla N. Stabilization of a Membrane-Associated Amyloid-β Oligomer for Its Validation in Alzheimer's Disease. Front Mol Biosci 2018; 5:38. [PMID: 29725595 PMCID: PMC5917194 DOI: 10.3389/fmolb.2018.00038] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 03/28/2018] [Indexed: 11/13/2022] Open
Abstract
We have recently reported on the preparation of a membrane-associated β-barrel Pore-Forming Aβ42 Oligomer (βPFOAβ42). It corresponds to a stable and homogeneous Aβ42 oligomer that inserts into lipid bilayers as a well-defined pore and adopts a specific structure with characteristics of a β-barrel arrangement. As a follow-up of this work, we aim to establish βPFOAβ42's relevance in Alzheimer's disease (AD). However, βPFOAβ42 is formed under dodecyl phosphocholine (DPC) micelle conditions-intended to mimic the hydrophobic environment of membranes-which are dynamic. Consequently, dilution of the βPFOAβ42/DPC complex in a detergent-free buffer leads to dispersion of the DPC molecules from the oligomer surface, leaving the oligomer without the hydrophobic micelle belt that stabilizes it. Since dilution is required for any biological test, transfer of βPFOAβ42 from DPC micelles into another hydrophobic biomimetic membrane environment, that remains associated with βPFOAβ42 even under high dilution conditions, is a requisite for the validation of βPFOAβ42 in AD. Here we describe conditions for exchanging DPC micelles with amphipols (APols), which are amphipathic polymers designed to stabilize membrane proteins in aqueous solutions. APols bind in an irreversible but non-covalent manner to the hydrophobic surface of membrane proteins preserving their structure even under extreme dilution conditions. We tested three types of APols with distinct physical-chemical properties and found that the βPFOAβ42/DPC complex can only be trapped in non-ionic APols (NAPols). The characterization of the resulting βPFOAβ42/NAPol complex by biochemical tools and structural biology techniques allowed us to establish that the oligomer structure is maintained even under high dilution. Based on these findings, this work constitutes a first step towards the in vivo validation of βPFOAβ42 in AD.
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Affiliation(s)
- Montserrat Serra-Batiste
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute Science and Technology (BIST), Barcelona, Spain
| | - James Tolchard
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute Science and Technology (BIST), Barcelona, Spain.,CBMN (UMR 5248), Centre National de la Recherche Scientifique - IPB, Institut Européen de Chimie et Biologie, University of Bordeaux, Pessac, France
| | - Fabrice Giusti
- Laboratoire de Physico-Chimie Moléculaire des Protéines Membranaires (UMR 7099), Université Paris-7 - Centre National de la Recherche Scientifique, Institut de Biologie Physico-Chimique, Paris, France
| | - Manuela Zoonens
- Laboratoire de Physico-Chimie Moléculaire des Protéines Membranaires (UMR 7099), Université Paris-7 - Centre National de la Recherche Scientifique, Institut de Biologie Physico-Chimique, Paris, France
| | - Natàlia Carulla
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute Science and Technology (BIST), Barcelona, Spain.,CBMN (UMR 5248), Centre National de la Recherche Scientifique - IPB, Institut Européen de Chimie et Biologie, University of Bordeaux, Pessac, France
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5
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Vázquez de la Torre A, Gay M, Vilaprinyó-Pascual S, Mazzucato R, Serra-Batiste M, Vilaseca M, Carulla N. Direct Evidence of the Presence of Cross-Linked Aβ Dimers in the Brains of Alzheimer’s Disease Patients. Anal Chem 2018. [DOI: 10.1021/acs.analchem.7b04936] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Aurelio Vázquez de la Torre
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Marina Gay
- Mass Spectrometry and Proteomics Core Facility, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Sílvia Vilaprinyó-Pascual
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Roberta Mazzucato
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Montserrat Serra-Batiste
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Marta Vilaseca
- Mass Spectrometry and Proteomics Core Facility, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Natàlia Carulla
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain
- CBMN (UMR 5248), University of Bordeaux − CNRS − IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600 Pessac, France
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6
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Pujol-Pina R, Vilaprinyó-Pascual S, Mazzucato R, Arcella A, Vilaseca M, Orozco M, Carulla N. SDS-PAGE analysis of Aβ oligomers is disserving research into Alzheimer´s disease: appealing for ESI-IM-MS. Sci Rep 2015; 5:14809. [PMID: 26450154 PMCID: PMC4598734 DOI: 10.1038/srep14809] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 09/09/2015] [Indexed: 12/20/2022] Open
Abstract
The characterization of amyloid-beta peptide (Aβ) oligomer forms and structures is crucial to the advancement in the field of Alzheimer´s disease (AD). Here we report a critical evaluation of two methods used for this purpose, namely sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), extensively used in the field, and ion mobility coupled to electrospray ionization mass spectrometry (ESI-IM-MS), an emerging technique with great potential for oligomer characterization. To evaluate their performance, we first obtained pure cross-linked Aβ40 and Aβ42 oligomers of well-defined order. Analysis of these samples by SDS-PAGE revealed that SDS affects the oligomerization state of Aβ42 oligomers, thus providing flawed information on their order and distribution. In contrast, ESI-IM-MS provided accurate information, while also reported on the chemical nature and on the structure of the oligomers. Our findings have important implications as they challenge scientific paradigms in the AD field built upon SDS-PAGE characterization of Aβ oligomer samples.
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Affiliation(s)
- Rosa Pujol-Pina
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona 08028, Spain
| | | | - Roberta Mazzucato
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona 08028, Spain
| | - Annalisa Arcella
- Joint IRB-BSC Research Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona 08028, Spain
| | - Marta Vilaseca
- Mass Spectrometry Core Facility, Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona 08028, Spain
| | - Modesto Orozco
- Joint IRB-BSC Research Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona 08028, Spain.,Department of Biochemistry and Molecular Biology, University of Barcelona, Diagonal 647, Barcelona 08028, Spain
| | - Natàlia Carulla
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona 08028, Spain
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7
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Serra-Vidal B, Pujadas L, Rossi D, Soriano E, Madurga S, Carulla N. Hydrogen/deuterium exchange-protected oligomers populated during Aβ fibril formation correlate with neuronal cell death. ACS Chem Biol 2014; 9:2678-85. [PMID: 25265274 DOI: 10.1021/cb500621x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The aggregation of the amyloid-β peptide (Aβ) to form fibrils and plaques is strongly associated with Alzheimer's disease (AD). Although it is well established that this process generates neurotoxicity, it is also heterogeneous with a variety of species being formed during the conversion process. This heterogeneity makes it difficult to detect and characterize each of the aggregates formed, which precludes establishing the specific features responsible for the neurotoxicity observed. Here we use pulse-labeling hydrogen-deuterium exchange experiments analyzed by electrospray ionization mass spectrometry (PL-HDX-ESI-MS) to distinguish three ensembles populated during the aggregation of the 40 and 42 residue forms of the Aβ peptide, Aβ40 and Aβ42, on the basis of differences in their persistent structure. Noticeably, two of them are more abundant at the beginning and at the end of the lag phase and are therefore not detectable by conventional assays such as Thioflavin T (ThT). The ensembles populated at different stages of the aggregation process have a surprisingly consistent average degree of exchange, indicating that there are definite structural transitions between the different stages of aggregation. To determine whether an ensemble of species with a given hydrogen exchange pattern correlates with neurotoxicity, we combined PL-HDX-ESI-MS experiments with parallel measurements of the neurotoxicity of the samples under study. The results of this dual approach show that the maximum toxicity correlates with the ensemble comprising HDX protected oligomers, indicating that development of persistent structure within Aβ oligomers is a determinant of neurotoxicity.
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Affiliation(s)
- Bernat Serra-Vidal
- Institute for
Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona 08028, Spain
| | - Lluís Pujadas
- Department
of Cell Biology, University of Barcelona and Centro de Investigación en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Diagonal
647, Barcelona 08028, Spain
| | - Daniela Rossi
- Department
of Cell Biology, University of Barcelona and Centro de Investigación en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Diagonal
647, Barcelona 08028, Spain
| | - Eduardo Soriano
- Department
of Cell Biology, University of Barcelona and Centro de Investigación en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Diagonal
647, Barcelona 08028, Spain
- CIEN Foundation, Madrid 28031, Spain
| | - Sergio Madurga
- Department
of Physical Chemistry and Research Institute of Theoretical and Computational
Chemistry (IQTCUB), University of Barcelona, Martí i Franquès 1, Barcelona 08028, Spain
| | - Natàlia Carulla
- Institute for
Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona 08028, Spain
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8
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Pujadas L, Rossi D, Andrés R, Teixeira CM, Serra-Vidal B, Parcerisas A, Maldonado R, Giralt E, Carulla N, Soriano E. Reelin delays amyloid-beta fibril formation and rescues cognitive deficits in a model of Alzheimer's disease. Nat Commun 2014; 5:3443. [PMID: 24599114 DOI: 10.1038/ncomms4443] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 02/13/2014] [Indexed: 12/22/2022] Open
Abstract
Reelin is an extracellular matrix protein that is crucial for neural development and adult brain plasticity. While the Reelin signalling cascade has been reported to be associated with Alzheimer's disease (AD), the role of Reelin in this pathology is not understood. Here we use an in vitro approach to show that Reelin interacts with amyloid-β (Aβ42) soluble species, delays Aβ42 fibril formation and is recruited into amyloid fibrils. Furthermore, Reelin protects against both the neuronal death and dendritic spine loss induced by Aβ42 oligomers. In mice carrying the APP(Swe/Ind) mutation (J20 mice), Reelin overexpression delays amyloid plaque formation and rescues the recognition memory deficits. Our results indicate that by interacting with Aβ42 soluble species, delaying Aβ plaque formation, protecting against neuronal death and dendritic spine loss and preventing AD cognitive deficits, the Reelin pathway deserves consideration as a therapeutic target for the treatment of AD pathogenesis.
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Affiliation(s)
- Lluís Pujadas
- 1] Department of Cell Biology, University of Barcelona, Barcelona 08028, Spain [2] Centro de Investigación en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid 28031, Spain [3] Institute for Research in Biomedicine, Barcelona (IRB Barcelona), Barcelona 08028, Spain [4] Vall D'Hebrón Institut de Recerca (VHIR), Barcelona 08035, Spain [5]
| | - Daniela Rossi
- 1] Department of Cell Biology, University of Barcelona, Barcelona 08028, Spain [2] Centro de Investigación en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid 28031, Spain [3] Institute for Research in Biomedicine, Barcelona (IRB Barcelona), Barcelona 08028, Spain [4]
| | - Rosa Andrés
- 1] Department of Cell Biology, University of Barcelona, Barcelona 08028, Spain [2] Centro de Investigación en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid 28031, Spain [3] Institute for Research in Biomedicine, Barcelona (IRB Barcelona), Barcelona 08028, Spain
| | - Cátia M Teixeira
- 1] Department of Cell Biology, University of Barcelona, Barcelona 08028, Spain [2] Centro de Investigación en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid 28031, Spain [3] Institute for Research in Biomedicine, Barcelona (IRB Barcelona), Barcelona 08028, Spain
| | - Bernat Serra-Vidal
- Institute for Research in Biomedicine, Barcelona (IRB Barcelona), Barcelona 08028, Spain
| | - Antoni Parcerisas
- 1] Department of Cell Biology, University of Barcelona, Barcelona 08028, Spain [2] Centro de Investigación en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid 28031, Spain [3] Institute for Research in Biomedicine, Barcelona (IRB Barcelona), Barcelona 08028, Spain [4] CIEN Foundation, Madrid 28031, Spain
| | - Rafael Maldonado
- Department of Experimental Sciences and Health, University Pompeu Fabra, Barcelona 08003, Spain
| | - Ernest Giralt
- 1] Institute for Research in Biomedicine, Barcelona (IRB Barcelona), Barcelona 08028, Spain [2] Department of Organic Chemistry, University of Barcelona, Barcelona 08028, Spain
| | - Natàlia Carulla
- Institute for Research in Biomedicine, Barcelona (IRB Barcelona), Barcelona 08028, Spain
| | - Eduardo Soriano
- 1] Department of Cell Biology, University of Barcelona, Barcelona 08028, Spain [2] Centro de Investigación en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid 28031, Spain [3] Institute for Research in Biomedicine, Barcelona (IRB Barcelona), Barcelona 08028, Spain [4] Vall D'Hebrón Institut de Recerca (VHIR), Barcelona 08035, Spain [5] CIEN Foundation, Madrid 28031, Spain
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9
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Arimon M, Sanz F, Giralt E, Carulla N. Template-Assisted Lateral Growth of Amyloid-β42 Fibrils Studied by Differential Labeling with Gold Nanoparticles. Bioconjug Chem 2011; 23:27-32. [DOI: 10.1021/bc200077s] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Muriel Arimon
- Institute for Bioengineering of Catalonia (IBEC), Baldiri Reixac 15, Barcelona 08028,
Spain
- CIBER-BBN, Zaragoza, Spain
| | - Fausto Sanz
- Institute for Bioengineering of Catalonia (IBEC), Baldiri Reixac 15, Barcelona 08028,
Spain
- CIBER-BBN, Zaragoza, Spain
| | - Ernest Giralt
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 1-10,
Barcelona 08028, Spain
| | - Natàlia Carulla
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 1-10,
Barcelona 08028, Spain
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10
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Sánchez L, Madurga S, Pukala T, Vilaseca M, López-Iglesias C, Robinson CV, Giralt E, Carulla N. Aβ40 and Aβ42 amyloid fibrils exhibit distinct molecular recycling properties. J Am Chem Soc 2011; 133:6505-8. [PMID: 21486030 DOI: 10.1021/ja1117123] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A critical aspect to understanding the molecular basis of Alzheimer's disease (AD) is the characterization of the kinetics of interconversion between the different species present during amyloid-β protein (Aβ) aggregation. By monitoring hydrogen/deuterium exchange in Aβ fibrils using electrospray ionization mass spectrometry, we demonstrate that the Aβ molecules comprising the fibril continuously dissociate and reassociate, resulting in molecular recycling within the fibril population. Investigations on Aβ40 and Aβ42 amyloid fibrils reveal that molecules making up Aβ40 fibrils recycle to a much greater extent than those of Aβ42. By examining factors that could influence molecular recycling and by running simulations, we show that the rate constant for dissociation of molecules from the fibril (k(off)) is much greater for Aβ40 than that for Aβ42. Importantly, the k(off) values obtained for Aβ40 and Aβ42 reveal that recycling occurs on biologically relevant time scales. These results have implications for understanding the role of Aβ fibrils in neurotoxicity and for designing therapeutic strategies against AD.
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Affiliation(s)
- Laia Sánchez
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona 08028, Spain
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Carulla N, Zhou M, Giralt E, Robinson CV, Dobson CM. Structure and intermolecular dynamics of aggregates populated during amyloid fibril formation studied by hydrogen/deuterium exchange. Acc Chem Res 2010; 43:1072-9. [PMID: 20557067 DOI: 10.1021/ar9002784] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The aggregation of proteins into amyloid fibrils is a complex and fascinating process associated with debilitating clinical disorders such as Alzheimer's and Parkinson's diseases. The process of aggregation involves a series of steps during which many intermediate aggregation states are populated. Recent evidence points to these intermediate states as the toxic moieties primarily responsible for cell damage or cell death, which are critical steps in the origin and progression of these disorders. To understand the molecular basis of these diseases, it is crucial to investigate and define the details of the aggregation process, and to achieve this objective, researchers need the tools to characterize the structure and kinetics of interconversion of the various species present during amyloid fibril formation. Hydrogen-deuterium (HD) exchange experiments are based on solvent accessibilities and provide one means by which this kind of information may be acquired. In this Account, we describe research based on HD exchange processes that is directed toward better understanding the dynamics and structural reorganizations involved in the formation of amyloid fibrils. Amide hydrogens that normally undergo rapid exchange with solvent hydrogens experience much slower exchange when involved in H-bonded structures or when sterically inaccessible to the solvent. The rates of exchange can be monitored by replacing some hydrogens with deuterons. When peptide and protein molecules assemble into amyloid fibrils, the fibrils contain a core region based on repetitive arrays of beta-sheets oriented parallel to the fibril axis. HD experiments have been applied extensively to map such structures in different amyloid fibril systems. By an extension of this approach, we have observed that HD exchange can be governed by a mechanism through which molecules making up the fibrils are continuously dissolving and reforming, revealing that amyloid fibrils are not static but dynamic structures. Under such circumstances, the kinetic parameters that define this "recycling" behavior can be determined, and they contain information that could be of significant value in the design of therapeutic strategies directed against amyloid-related diseases. More recently, to gain insights into the variety of intermediates that are thought to be involved in the aggregation process, we have applied a kinetic pulse labeling HD experiment that is able to characterize such species even if they are only transiently populated. Using this approach, we have been able to obtain structural insights into the different aggregates populated during the process of amyloid fibril formation as well as kinetic and mechanistic information on the structural reorganizations that take place during aggregation. HD exchange experiments, when carefully designed, constitute powerful tools for mapping the core structures of amyloid fibrils, for investigating the recycling of fibril components, and for characterizing the various types of structural reorganization that occur during aggregation. Such information is invaluable for understanding and addressing the molecular origins of the increasingly common and highly debilitating diseases associated with protein misfolding and aggregation.
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Affiliation(s)
- Natàlia Carulla
- ICREA Researcher at Institut de Recerca Biomèdica, Baldiri Reixac 10−12, Barcelona 08028, Spain
| | - Min Zhou
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB21EW, United Kingdom
| | - Ernest Giralt
- Institut de Recerca Biomèdica, Baldiri Reixac 10−12, Barcelona 08028, Spain
- Departament de Química Orgànica, Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain
| | - Carol V. Robinson
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX13QZ, United Kingdom
| | - Christopher M. Dobson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB21EW, United Kingdom
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Grillo-Bosch D, Carulla N, Cruz M, Sánchez L, Pujol-Pina R, Madurga S, Rabanal F, Giralt E. Retro-enantio N-methylated peptides as beta-amyloid aggregation inhibitors. ChemMedChem 2009; 4:1488-94. [PMID: 19591190 DOI: 10.1002/cmdc.200900191] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
An emerging and attractive target for the treatment of Alzheimer's disease is to inhibit the aggregation of beta-amyloid protein (Abeta). We applied the retro-enantio concept to design an N-methylated peptidic inhibitor of the Abeta42 aggregation process. This inhibitor, inrD, as well as the corresponding all-L (inL) and all-D (inD) analogues were assayed for inhibition of Abeta42 aggregation. They were also screened in neuroblastoma cell cultures to assess their capacity to inhibit Abeta42 cytotoxicity and evaluated for proteolytic stability. The results reveal that inrD and inD inhibit Abeta42 aggregation more effectively than inL, that inrD decreases Abeta42 cytotoxicity to a greater extent than inL and inD, and that as expected, both inD and inrD are stable to proteases. Based on these results, we propose that the retro-enantio approach should be considered in future designs of peptide inhibitors of protein aggregation.
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Affiliation(s)
- Dolors Grillo-Bosch
- Institute for Research in Biomedicine, Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain
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Pastor JJ, Granados G, Carulla N, Rabanal F, Giralt E. Redesign of Protein Domains Using One-Bead-One-Compound Combinatorial Chemistry. J Am Chem Soc 2007; 129:14922-32. [DOI: 10.1021/ja073969x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jose J. Pastor
- Contribution from the Institute for Biomedical Research, Barcelona Science Park, 08028 Barcelona, Spain, and Department of Organic Chemistry, University of Barcelona, 08028 Barcelona Spain
| | - Giovanna Granados
- Contribution from the Institute for Biomedical Research, Barcelona Science Park, 08028 Barcelona, Spain, and Department of Organic Chemistry, University of Barcelona, 08028 Barcelona Spain
| | - Natàlia Carulla
- Contribution from the Institute for Biomedical Research, Barcelona Science Park, 08028 Barcelona, Spain, and Department of Organic Chemistry, University of Barcelona, 08028 Barcelona Spain
| | - Francesc Rabanal
- Contribution from the Institute for Biomedical Research, Barcelona Science Park, 08028 Barcelona, Spain, and Department of Organic Chemistry, University of Barcelona, 08028 Barcelona Spain
| | - Ernest Giralt
- Contribution from the Institute for Biomedical Research, Barcelona Science Park, 08028 Barcelona, Spain, and Department of Organic Chemistry, University of Barcelona, 08028 Barcelona Spain
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Carulla N, Caddy GL, Hall DR, Zurdo J, Gairí M, Feliz M, Giralt E, Robinson CV, Dobson CM. Molecular recycling within amyloid fibrils. Nature 2005; 436:554-8. [PMID: 16049488 DOI: 10.1038/nature03986] [Citation(s) in RCA: 285] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2005] [Accepted: 07/04/2005] [Indexed: 11/09/2022]
Abstract
Amyloid fibrils are thread-like protein aggregates with a core region formed from repetitive arrays of beta-sheets oriented parallel to the fibril axis. Such structures were first recognized in clinical disorders, but more recently have also been linked to a variety of non-pathogenic phenomena ranging from the transfer of genetic information to synaptic changes associated with memory. The observation that many proteins can convert into similar structures in vitro has suggested that this ability is a generic feature of polypeptide chains. Here we have probed the nature of the amyloid structure by monitoring hydrogen/deuterium exchange in fibrils formed from an SH3 domain using a combination of nuclear magnetic resonance spectroscopy and electrospray ionization mass spectrometry. The results reveal that under the conditions used in this study, exchange is dominated by a mechanism of dissociation and re-association that results in the recycling of molecules within the fibril population. This insight into the dynamic nature of amyloid fibrils, and the ability to determine the parameters that define this behaviour, have important implications for the design of therapeutic strategies directed against amyloid disease.
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Affiliation(s)
- Natàlia Carulla
- University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK
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Affiliation(s)
- Clare Woodward
- Department of Biochemistry, Biophysics and Molecular Biology, University of Minnesota, St. Paul 55108, USA
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Abstract
A strategy for design of new proteins that mimic folding properties of native proteins is based on peptides modeled on the slow exchange cores of natural proteins. We have synthesized peptides, called core modules, that correspond to the elements of secondary structure that carry the very slowest exchanging amides in a protein. The expectation is that, if soluble in water, core modules will form conformational ensembles that favor native-like structure. Core modules modeled on natural bovine pancreatic trypsin inhibitor have been shown by NMR studies to meet this expectation. The next step toward production of a native state mimic is to further shift the conformational bias of a core module toward more ordered structure by promoting module-module interactions that are mutually stabilizing. For this, two core modules were incorporated into a single molecule by means of a long cross-link. From a panel of several two-module peptides, one very promising lead emerged; it is called BetaCore. BetaCore is monomeric in water and forms a new fold composed of a four-stranded, antiparallel beta-sheet. The single, dominant conformation of BetaCore is characterized by various NMR experiments. Here we compare the individual core module to the two-module BetaCore and discuss the progressive stabilization of intramodule structure and the formation of new intermodule interactions.
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Affiliation(s)
- Natàlia Carulla
- Department of Chemistry, University of Minnesota, 207 Pleasant St SE, Minneapolis, MN 55455, USA
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Abstract
BetaCore is a designed approximately 50-residue protein in which two BPTI-derived core modules, CM I and CM II, are connected by a 22-atom cross-link. At low temperature and pH 3, homo- and heteronuclear NMR data report a dominant folded ('f') conformation with well-dispersed chemical shifts, i, i+1 periodicity, numerous long-range NOEs, and slowed amide hydrogen isotope exchange patterns that is a four-stranded antiparallel beta-sheet with nonsymmetrical and specific association of CM I and CM II. BetaCore 'f' conformations undergo reversible, global, moderately cooperative, non-two-state thermal transitions to an equilibrium ensemble of unfolded 'u' conformations. There is a significant energy barrier between 'f' and 'u' conformations. This is the first designed four-stranded antiparallel beta-sheet that folds in water.
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Affiliation(s)
- Natàlia Carulla
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
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Woodward C, Barbar E, Carulla N, Battiste J, Barany G. Experimental approaches to protein folding based on the concept of a slow hydrogen exchange core. J Mol Graph Model 2002; 19:94-101. [PMID: 11381535 DOI: 10.1016/s1093-3263(00)00131-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In a review of protein hydrogen exchange, we concluded that the slow exchange core is the folding core. By this we mean that the elements of secondary structure carrying the slowest exchanging backbone amides will tend to be the elements of secondary structure to fold first, that partially folded proteins will tend to be most organized in the core, and that peptides made to mimic the slow exchange core will tend to show nativelike structure. These generalizations have led us to ask several experimental questions that will be examined here: (1) In partially folded and unfolded proteins, how do the dynamics and structure of core regions differ from noncore regions? (2) Can we make protein 'core modules' as peptides corresponding to the slow exchange core? Can core modules be covalently linked to make a native state in which one conformation is significantly more stable than all other accessible conformations? (3) In a mutant perturbed outside the core, what are the effects on hydrogen exchange and folding?
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Affiliation(s)
- C Woodward
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Ave. St. Paul, MN 55108, USA.
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Carulla N, Woodward C, Barany G. Toward new designed proteins derived from bovine pancreatic trypsin inhibitor (BPTI): covalent cross-linking of two 'core modules' by oxime-forming ligation. Bioconjug Chem 2001; 12:726-41. [PMID: 11562191 DOI: 10.1021/bc015518m] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A 25-residue disulfide-cross-linked peptide, termed 'oxidized core module' (OxCM), that includes essentially all of the secondary structural elements of bovine pancreatic trypsin inhibitor (BPTI) most refractory to hydrogen exchange, was shown previously to favor nativelike beta-sheet structure [Carulla, N., Woodward, C., and Barany, G. (2000) Synthesis and Characterization of a beta-Hairpin Peptide That Represents a 'Core Module' of Bovine Pancreatic Trypsin Inhibitor (BPTI). Biochemistry 39, 7927-7937]. The present work prepares to explore the hypothesis that the energies of nativelike conformations, relative to other possible conformations, could be decreased further by covalent linkage of two OxCMs. Optimized syntheses of six approximately 50-residue OxCM dimers are reported herein, featuring appropriate monomer modifications followed by oxime-forming ligation chemistry to create covalent cross-links at various positions and with differing lengths. Several side reactions were recognized through this work, and modified procedures to lessen or mitigate their occurrence were developed. Particularly noteworthy, guanidine or urea denaturants that were included as peptide-solubilizing components for some reaction mixtures were proven to form adducts with glyoxylyl moieties, thus affecting rates and outcomes. All six synthetic OxCM dimers were characterized by 1D (1)H NMR; three of them showed considerable chemical shift dispersion suggestive of self-association and mutual stabilization between the monomer units.
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Affiliation(s)
- N Carulla
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
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Carulla N, Woodward C, Barany G. Synthesis and characterization of a beta-hairpin peptide that represents a 'core module' of bovine pancreatic trypsin inhibitor (BPTI). Biochemistry 2000; 39:7927-37. [PMID: 10891073 DOI: 10.1021/bi992927l] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A new strategy for the design and construction of peptide fragments that can achieve defined, nativelike secondary structure is presented. The strategy is based upon the hypothesis that 'core elements' of a protein, synthesized in a single polypeptide molecule, will favor nativelike structure, and that by incorporating a cross-link, nativelike core structure will dominate the ensemble as the more extended conformations are excluded. 'Core elements' are the elements of packed secondary structure that contain the slowest exchanging backbone amide protons in the native protein. The 'core elements' in bovine pancreatic trypsin inhibitor (BPTI) are the two long strands of antiparallel beta-sheet (residues 18-24 and 29-35) and the small beta-bridge (residues 43-44). To test the design strategy, we synthesized an 'oxidized core module', which contains the antiparallel strands connected by a modified reverse turn (A27 replaced by D), a natural disulfide cross-link at the open end of the hairpin, and N- and C-termini blocking groups. A peptide with identical sequence but lacking the disulfide cross-link at the open end was used as the 'reduced core module' control. The conformational behavior of both peptides was examined using (1)H NMR spectroscopy. Chemical shift dispersion, chemical shift deviation from random coil values, sequential and long-range NOEs, and H/D amide exchange rates were compared for the two peptides. We conclude that the ensemble of oxidized and reduced core module conformations samples both nativelike 4:4 and non-native 3:5 beta-hairpin structure, and that the oxidized module samples nativelike structure for a greater fraction of the time than the reduced module.
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Affiliation(s)
- N Carulla
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
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Lloyd-Williams P, Sánchez A, Carulla N, Ochoa T, Giralt E. Synthetic studies on threonines. The preparation of protected derivatives of d-allo- and l-allo-threonine for peptide synthesis. Tetrahedron 1997. [DOI: 10.1016/s0040-4020(97)00059-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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