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Szczęśniak K, Veillard F, Scavenius C, Chudzik K, Ferenc K, Bochtler M, Potempa J, Mizgalska D. The Bacteroidetes Q-rule and glutaminyl cyclase activity increase the stability of extracytoplasmic proteins. mBio 2023; 14:e0098023. [PMID: 37750700 PMCID: PMC10653852 DOI: 10.1128/mbio.00980-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 08/07/2023] [Indexed: 09/27/2023] Open
Abstract
IMPORTANCE Exclusively in the Bacteroidetes phylum, most proteins exported across the inner membrane via the Sec system and released into the periplasm by type I signal peptidase have N-terminal glutamine converted to pyroglutamate. The reaction is catalyzed by the periplasmic enzyme glutaminyl cyclase (QC), which is essential for the growth of Porphyromonas gingivalis and other periodontopathogens. Apparently, pyroglutamyl formation stabilizes extracytoplasmic proteins and/or protects them from proteolytic degradation in the periplasm. Given the role of P. gingivalis as the keystone pathogen in periodontitis, P. gingivalis QC is a promising target for the development of drugs to treat and/or prevent this highly prevalent chronic inflammatory disease leading to tooth loss and associated with severe systemic diseases.
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Affiliation(s)
- Katarzyna Szczęśniak
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Florian Veillard
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Carsten Scavenius
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Kamila Chudzik
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Kinga Ferenc
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Matthias Bochtler
- International Institute of Molecular and Cell Biology, Warsaw, Poland
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Warsaw, Poland
| | - Jan Potempa
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, Kentucky, USA
| | - Danuta Mizgalska
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
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2
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Ferreira MML, de Souza SEG, da Silva CC, Souza LEA, Bicev RN, da Silva ER, Nakaie CR. Pyroglutamination-Induced Changes in the Physicochemical Features of a CXCR4 Chemokine Peptide: Kinetic and Structural Analysis. Biochemistry 2023; 62:2530-2540. [PMID: 37540799 DOI: 10.1021/acs.biochem.3c00124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/06/2023]
Abstract
We investigate the physicochemical effects of pyroglutamination on the QHALTSV-NH2 peptide, a segment of cytosolic helix 8 of the human C-X-C chemokine G-protein-coupled receptor type 4 (CXCR4). This modification, resulting from the spontaneous conversion of glutamine to pyroglutamic acid, has significant impacts on the physicochemical features of peptides. Using a static approach, we compared the transformation in different conditions and experimentally found that the rate of product formation increases with temperature, underscoring the need for caution during laboratory experiments to prevent glutamine cyclization. Circular dichroism experiments revealed that the QHALTSV-NH2 segment plays a minor role in the structuration of H8 CXCR4; however, its pyroglutaminated analogue interacts differently with its chemical environment, showing increased susceptibility to solvent variations compared to the native form. The pyroglutaminated analogue exhibits altered behavior when interacting with lipid models, suggesting a significant impact on its interaction with cell membranes. A unique combination of atomic force microscopy and infrared nanospectroscopy revealed that pyroglutamination affects supramolecular self-assembly, leading to highly packed molecular arrangements and a crystalline structure. Moreover, the presence of pyroglumatic acid has been found to favor the formation of amyloidogenic aggregates. Our findings emphasize the importance of considering pyroglutamination in peptide synthesis and proteomics and its potential significance in amyloidosis.
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Affiliation(s)
- Mariana M L Ferreira
- Departamento de Biofísica─Escola Paulista de Medicina, Universidade Federal de São Paulo─São Paulo, São Paulo 04023-062, Brazil
| | - Sinval E G de Souza
- Departamento de Biofísica─Escola Paulista de Medicina, Universidade Federal de São Paulo─São Paulo, São Paulo 04023-062, Brazil
| | - Caroline C da Silva
- Departamento de Biofísica─Escola Paulista de Medicina, Universidade Federal de São Paulo─São Paulo, São Paulo 04023-062, Brazil
| | - Louise E A Souza
- Departamento de Biofísica─Escola Paulista de Medicina, Universidade Federal de São Paulo─São Paulo, São Paulo 04023-062, Brazil
| | - Renata N Bicev
- Departamento de Biofísica─Escola Paulista de Medicina, Universidade Federal de São Paulo─São Paulo, São Paulo 04023-062, Brazil
| | - Emerson R da Silva
- Departamento de Biofísica─Escola Paulista de Medicina, Universidade Federal de São Paulo─São Paulo, São Paulo 04023-062, Brazil
| | - Clovis R Nakaie
- Departamento de Biofísica─Escola Paulista de Medicina, Universidade Federal de São Paulo─São Paulo, São Paulo 04023-062, Brazil
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3
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Zhang Y, Wang Y, Zhao Z, Peng W, Wang P, Xu X, Zhao C. Glutaminyl cyclases, the potential targets of cancer and neurodegenerative diseases. Eur J Pharmacol 2022; 931:175178. [DOI: 10.1016/j.ejphar.2022.175178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 07/20/2022] [Accepted: 07/25/2022] [Indexed: 11/03/2022]
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4
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Bersin LM, Patel SM, Topp EM. Effect of 'pH' on the Rate of Pyroglutamate Formation in Solution and Lyophilized Solids. Mol Pharm 2021; 18:3116-3124. [PMID: 34232660 DOI: 10.1021/acs.molpharmaceut.1c00338] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
N-terminal glutamate can cyclize to form pyroglutamate (pGlu) in pharmaceutically relevant peptides and proteins. The reaction occurs nonenzymatically during storage for monoclonal antibodies and shows a strong 'pH' dependence in solution, but the solid-state reaction has not been studied in detail. This work investigates the effect of 'pH' and buffer species on pGlu formation for a model peptide (EVQLVESGGGLVQPGGSLR) in lyophilized solids and in solution. The model peptide was formulated from 'pH' 4 to 'pH' 9 in citrate, citrate-phosphate, phosphate, and carbonate buffers and stored at 50 °C for at least 10 weeks. pGlu formation and loss of the parent peptide were monitored by reversed-phase high-performance liquid chromatography. The apparent 'pH' dependence of the reaction rate in the solid state differed markedly from that in solution. Interestingly, in the 'pH' range often used to formulate mAbs ('pH' 5.5-6), the rate of pGlu formation in the solid state was greater than that in solution. The results have implications for the rational design of stable formulations of peptides and proteins, and for the transition from solid to solution formulations during development.
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Affiliation(s)
- Lia M Bersin
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907-2091, United States
| | - Sajal M Patel
- Dosage Form Design & Development, Biopharmaceutical Development, Biopharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | - Elizabeth M Topp
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907-2091, United States.,National Institute for Bioprocessing Research and Training, Belfield, Blackrock, County Dublin A94 X099, Ireland
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5
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Xu C, Wang YN, Wu H. Glutaminyl Cyclase, Diseases, and Development of Glutaminyl Cyclase Inhibitors. J Med Chem 2021; 64:6549-6565. [PMID: 34000808 DOI: 10.1021/acs.jmedchem.1c00325] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pyroglutamate (pE) modification, catalyzed mainly by glutaminyl cyclase (QC), is prevalent throughout nature and is particularly important in mammals including humans for the maturation of hormones, peptides, and proteins. In humans, the upregulation of QC is involved in multiple diseases and conditions including Alzheimer's disease, Huntington's disease, melanomas, thyroid carcinomas, accelerated atherosclerosis, septic arthritics, etc. This upregulation catalyzes the generation of modified mediators such as pE-amyloid beta (Aß) and pE-chemokine ligand 2 (CCL2) peptides. Not surprisingly, QC has emerged as a reasonable target for the development of therapeutics to combat these diseases and conditions. In this manuscript the deleterious effects of upregulated QC resulting in disease manifestation are reviewed, along with progress on the development of QC inhibitors.
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Affiliation(s)
- Chenshu Xu
- School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Yi-Nan Wang
- School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Haiqiang Wu
- School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, China
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7
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Kupski O, Funk LM, Sautner V, Seifert F, Worbs B, Ramsbeck D, Meyer F, Diederichsen U, Buchholz M, Schilling S, Demuth HU, Tittmann K. Hydrazides Are Potent Transition-State Analogues for Glutaminyl Cyclase Implicated in the Pathogenesis of Alzheimer's Disease. Biochemistry 2020; 59:2585-2591. [PMID: 32551535 DOI: 10.1021/acs.biochem.0c00337] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Amyloidogenic plaques are hallmarks of Alzheimer's disease (AD) and typically consist of high percentages of modified Aβ peptides bearing N-terminally cyclized glutamate residues. The human zinc(II) enzyme glutaminyl cyclase (QC) was shown in vivo to catalyze the cyclization of N-terminal glutamates of Aβ peptides in a pathophysiological side reaction establishing QC as a druggable target for therapeutic treatment of AD. Here, we report crystallographic snapshots of human QC catalysis acting on the neurohormone neurotensin that delineate the stereochemical course of catalysis and suggest that hydrazides could mimic the transition state of peptide cyclization and deamidation. This hypothesis is validated by a sparse-matrix inhibitor screening campaign that identifies hydrazides as the most potent metal-binding group compared to classic Zn binders. The structural basis of hydrazide inhibition is illuminated by X-ray structure analysis of human QC in complex with a hydrazide-bearing peptide inhibitor and reveals a pentacoordinated Zn complex. Our findings inform novel strategies in the design of potent and highly selective QC inhibitors by employing hydrazides as the metal-binding warhead.
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Affiliation(s)
- Oliver Kupski
- Department of Molecular Enzymology, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, 37077 Göttingen, Germany.,Department of Structural Dynamics, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Lisa-Marie Funk
- Department of Molecular Enzymology, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, 37077 Göttingen, Germany.,Department of Structural Dynamics, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Viktor Sautner
- Department of Molecular Enzymology, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, 37077 Göttingen, Germany.,Department of Structural Dynamics, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Franziska Seifert
- Department of Molecular Enzymology, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, 37077 Göttingen, Germany
| | - Brigitte Worbs
- Institute for Organic and Biomolecular Chemistry, Georg-August University Göttingen, Tammannstraß 2, 37077 Göttingen, Germany
| | - Daniel Ramsbeck
- Fraunhofer Institute for Cell Therapy und Immunology IZI, Department of Drug Design and Target Validation, Weinbergweg 22, 06120 Halle/Saale, Germany
| | - Franc Meyer
- Institute for Inorganic Chemistry, Georg-August University Göttingen, Tammannstraße 4, 37077 Göttingen, Germany
| | - Ulf Diederichsen
- Institute for Organic and Biomolecular Chemistry, Georg-August University Göttingen, Tammannstraß 2, 37077 Göttingen, Germany
| | - Mirko Buchholz
- Fraunhofer Institute for Cell Therapy und Immunology IZI, Department of Drug Design and Target Validation, Weinbergweg 22, 06120 Halle/Saale, Germany
| | - Stephan Schilling
- Fraunhofer Institute for Cell Therapy und Immunology IZI, Department of Drug Design and Target Validation, Weinbergweg 22, 06120 Halle/Saale, Germany
| | - Hans-Ulrich Demuth
- Fraunhofer Institute for Cell Therapy und Immunology IZI, Department of Drug Design and Target Validation, Weinbergweg 22, 06120 Halle/Saale, Germany
| | - Kai Tittmann
- Department of Molecular Enzymology, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, 37077 Göttingen, Germany.,Department of Structural Dynamics, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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8
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Nakayoshi T, Kato K, Kurimoto E, Oda A. Computational Studies on the Mechanisms of Nonenzymatic Intramolecular Cyclization of the Glutamine Residues Located at N-Termini Catalyzed by Inorganic Phosphate Species. ACS OMEGA 2020; 5:9162-9170. [PMID: 32363268 PMCID: PMC7191561 DOI: 10.1021/acsomega.9b04384] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 04/02/2020] [Indexed: 05/13/2023]
Abstract
Glutamine (Gln) residues located at N-termini undergo spontaneous intramolecular cyclization, causing the formation of pyroglutamic acid (pGlu) residues. pGlu residues have been detected at the N-termini in various peptides and proteins. The formation of pGlu residues during the fermentation and purification processes of antibody drugs is one of the concerns in the design and formulation of these drugs and has been reported to proceed rapidly in a phosphate buffer. In this study, we have examined the phosphate-catalyzed mechanisms of the pGlu residue formation from N-terminal Gln residues via quantum chemical calculations using B3LYP density functional methods. Single-point energies were calculated using the second-order Møller-Plesset perturbation theory. We performed the calculations for the model compound in which an uncharged N-terminal Gln residue is capped with a methyl amino group on the C-terminal. The activation energy of the formation of pGlu residues was calculated as 83.8 kJ mol-1, which was lower than that of the typical nonenzymatic reaction of amino acid residues. In addition, the computational results indicate that the flexibility of the main and side chains in N-terminal Gln residues was necessary for the formation of pGlu residues to proceed. In the obtained pathway, inorganic phosphate species act as the catalyst by mediating the proton transfer.
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Affiliation(s)
- Tomoki Nakayoshi
- Graduate
School of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
- Institute
of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Koichi Kato
- Graduate
School of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
- Department
of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi 463-8521, Japan
| | - Eiji Kurimoto
- Graduate
School of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
| | - Akifumi Oda
- Graduate
School of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
- Institute
of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- Institute
for Protein Research, Osaka University, 3-2 Yamadaoka,
Suita, Osaka 565-0871, Japan
- . Phone: +81-52-832-1151
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Bochtler M, Mizgalska D, Veillard F, Nowak ML, Houston J, Veith P, Reynolds EC, Potempa J. The Bacteroidetes Q-Rule: Pyroglutamate in Signal Peptidase I Substrates. Front Microbiol 2018; 9:230. [PMID: 29545777 PMCID: PMC5837995 DOI: 10.3389/fmicb.2018.00230] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 01/30/2018] [Indexed: 11/17/2022] Open
Abstract
Bacteroidetes feature prominently in the human microbiome, as major colonizers of the gut and clinically relevant pathogens elsewhere. Here, we reveal a new Bacteroidetes specific feature in the otherwise widely conserved Sec/SPI (Sec translocase/signal peptidase I) pathway. In Bacteroidetes, but not the entire FCB group or related phyla, signal peptide cleavage exposes N-terminal glutamine residues in most SPI substrates. Reanalysis of published mass spectrometry data for five Bacteroidetes species shows that the newly exposed glutamines are cyclized to pyroglutamate (also termed 5-oxoproline) residues. Using the dental pathogen Porphyromonas gingivalis as a model, we identify the PG2157 (also called PG_RS09565, Q7MT37) as the glutaminyl cyclase in this species, and map the catalytic activity to the periplasmic face of the inner membrane. Genetic manipulations that alter the glutamine residue immediately after the signal peptide in the pre-pro-forms of the gingipains affect the extracellular proteolytic activity of RgpA, but not RgpB and Kgp. Glutamine statistics, mass spectrometry data and the mutagenesis results show that the N-terminal glutamine residues or their pyroglutamate cyclization products do not act as generic sorting signals.
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Affiliation(s)
- Matthias Bochtler
- International Institute of Molecular and Cell Biology, Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Danuta Mizgalska
- Department of Microbiology, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Florian Veillard
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, KY, United States
| | - Magdalena L. Nowak
- Department of Microbiology, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Krakow, Poland
| | - John Houston
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, KY, United States
| | - Paul Veith
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Eric C. Reynolds
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Jan Potempa
- Department of Microbiology, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Krakow, Poland
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, KY, United States
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Borghesani V, Alies B, Hureau C. Cu(II) binding to various forms of amyloid-β peptides. Are they friends or foes? Eur J Inorg Chem 2018; 2018:7-15. [PMID: 30186035 PMCID: PMC6120674 DOI: 10.1002/ejic.201700776] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Indexed: 01/25/2023]
Abstract
In the present micro-review, we describe the Cu(II) binding to several forms of amyloid-β peptides, the peptides involved in Alzheimer's disease. It has indeed been shown that in addition to the "full-length" peptide originating from the precursor protein after cleavage at position 1, several other shorter peptides do exist in large proportion and may be involved in the disease as well. Cu(II) binding to amyloid-β peptides is one of the key interactions that impact both the aggregating properties of the amyloid peptides and the Reactive Oxygen Species (ROS) production, two events linked to the etiology of the disease. Binding sites and affinity are described in correlation with Cu(II) induced ROS formation and Cu(II) altered aggregation, for amyloid peptides starting at position 1, 3, 4, 11 and for the corresponding pyroglutamate forms when they could be obtained (i.e. for peptides cleaved at positions 3 and 11). It appears that the current paradigm which points out a toxic role of the Cu(II) - amyloid-β interaction might well be shifted towards a possible protective role when the peptides considered are the N-terminally truncated ones.
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Affiliation(s)
- Valentina Borghesani
- CNRS, LCC (Laboratoire de Chimie de Coordination), 205 route de Narbonne, BP 44099 31077 Toulouse Cedex 4, France
- University of Toulouse, UPS, INPT, 31077 Toulouse Cedex 4, France
| | | | - Christelle Hureau
- CNRS, LCC (Laboratoire de Chimie de Coordination), 205 route de Narbonne, BP 44099 31077 Toulouse Cedex 4, France
- University of Toulouse, UPS, INPT, 31077 Toulouse Cedex 4, France
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