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Kaku T, Ikebukuro K, Tsukakoshi K. Structure of cytotoxic amyloid oligomers generated during disaggregation. J Biochem 2024; 175:575-585. [PMID: 38430131 PMCID: PMC11155694 DOI: 10.1093/jb/mvae023] [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] [Received: 08/30/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 03/03/2024] Open
Abstract
Amyloidosis is characterized by the abnormal accumulation of amyloid proteins. The causative proteins aggregate from monomers to oligomers and fibrils, among which some intermediate oligomers are considered as major toxins. Cytotoxic oligomers are generated not only by aggregation but also via fibril disaggregation. However, little is known about the structural characteristics and generation conditions of cytotoxic oligomers produced during disaggregation. Herein, we summarized the structural commonalities of cytotoxic oligomers formed under various disaggregation conditions, including the addition of heat shock proteins or small compounds. In vitro experimental data demonstrated the presence of high-molecular-weight oligomers (protofibrils or protofilaments) that exhibited a fibrous morphology and β-sheet structure. Molecular dynamics simulations indicated that the distorted β-sheet structure contributed to their metastability. The tendency of these cytotoxic oligomers to appear under mild disaggregation conditions, implied formation during the early stages of disaggregation. This review will aid researchers in exploring the characteristics of highly cytotoxic oligomers and developing drugs that target amyloid aggregates.
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Affiliation(s)
- Toshisuke Kaku
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Kaori Tsukakoshi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
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2
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Kuramochi M, Nakamura M, Takahashi H, Komoriya T, Takita T, Pham NTK, Yasukawa K, Yoshimune K. Adenosine triphosphate induces amorphous aggregation of amyloid β by increasing Aβ dynamics. Sci Rep 2024; 14:8134. [PMID: 38584155 PMCID: PMC10999452 DOI: 10.1038/s41598-024-58773-6] [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: 11/24/2023] [Accepted: 04/03/2024] [Indexed: 04/09/2024] Open
Abstract
Amyloid β (Aβ) aggregates into two distinct fibril and amorphous forms in the brains of patients with Alzheimer's disease. Adenosine triphosphate (ATP) is a biological hydrotrope that causes Aβ to form amorphous aggregates and inhibit fibril formation at physiological concentrations. Based on diffracted X-ray blinking (DXB) analysis, the dynamics of Aβ significantly increased immediately after ATP was added compared to those in the absence and presence of ADP and AMP, and the effect diminished after 30 min as the aggregates formed. In the presence of ATP, the β-sheet content of Aβ gradually increased from the beginning, and in the absence of ATP, the content increased rapidly after 180 min incubation, as revealed by a time-dependent thioflavin T fluorescence assay. Images of an atomic force microscope revealed that ATP induces the formation of amorphous aggregates with an average diameter of less than 100 nm, preventing fibrillar formation during 4 days of incubation at 37 °C. ATP may induce amorphous aggregation by increasing the dynamics of Aβ, and as a result, the other aggregation pathway is omitted. Our results also suggest that DXB analysis is a useful method to evaluate the inhibitory effect of fibrillar formation.
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Affiliation(s)
- Masahiro Kuramochi
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, 316-8511, Japan
| | - Momoka Nakamura
- Department of Applied Molecular Chemistry, Graduate School of Industrial Technology, Nihon University, 1-2-1, Izumichou, Narashino, Chiba, 275-8575, Japan
| | - Hiroto Takahashi
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, 316-8511, Japan
| | - Tomoe Komoriya
- Department of Sustainable Engineering, College of Industrial Technology, Nihon University, 1-2-1, Izumichou, Narashino, Chiba, 275-8575, Japan
| | - Teisuke Takita
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Ngan Thi Kim Pham
- Department of Applied Molecular Chemistry, Graduate School of Industrial Technology, Nihon University, 1-2-1, Izumichou, Narashino, Chiba, 275-8575, Japan
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Kazuaki Yoshimune
- Department of Applied Molecular Chemistry, Graduate School of Industrial Technology, Nihon University, 1-2-1, Izumichou, Narashino, Chiba, 275-8575, Japan.
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Chen Y, Zhan C, Li X, Pan T, Yao Y, Tan Y, Wei G. Five similar anthocyanidin molecules display distinct disruptive effects and mechanisms of action on Aβ 1-42 protofibril: A molecular dynamic simulation study. Int J Biol Macromol 2024; 256:128467. [PMID: 38035959 DOI: 10.1016/j.ijbiomac.2023.128467] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 11/23/2023] [Accepted: 11/25/2023] [Indexed: 12/02/2023]
Abstract
Alzheimer's disease (AD) is associated with the deposition of amyloid-β (Aβ) fibrillary aggregates. Disaggregation of Aβ fibrils is considered as one of the promising AD treatments. Recent experimental studies showed that anthocyanidins, one type of flavonoids abundant in fruits/vegetables, can disaggregate Aβ fibrillary aggregates. However, their relative disruptive capacities and underlying mechanisms are largely unknown. Herein, we investigated the detailed interactions between five most common anthocyanidins (cyanidin, aurantinidin, peonidin, delphinidin, and pelargonidin) and Aβ protofibril (an intermediate of Aβ fibrillization) by performing microsecond molecular dynamic simulations. We found that all five anthocyanidins can destroy F4-L34-V36 hydrophobic core and K28-A42 salt bridge, leading to Aβ protofibril destabilization. Aurantinidin exhibits the strongest damage to Aβ protofibril (with the most severe disruption on K28-A42 salt bridges), followed by cyanidin (with the most destructive effect on F4-L34-V36 core). Detailed analyses reveal that the protofibril-destruction capacities of anthocyanidins are subtly modulated by the interplay of anthocyanidin-protofibril hydrogen bonding, hydrophobic, aromatic stacking interactions, which are dictated by the number or location of hydroxyl/methyl groups of anthocyanidins. These findings provide important mechanistic insights into Aβ protofibril disaggregation by anthocyanidins, and suggest that aurantinidin/cyanidin may serve as promising starting-points for the development of new drug candidates against AD.
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Affiliation(s)
- Yujie Chen
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Department of Physics, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Chendi Zhan
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Department of Physics, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Xuhua Li
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Tong Pan
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Department of Physics, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Yifei Yao
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Department of Physics, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Yuan Tan
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Department of Physics, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Guanghong Wei
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Department of Physics, Fudan University, 2005 Songhu Road, Shanghai 200438, China.
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4
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Jahan I, Ahmad A, Deep S. Effect of flavonoids on the destabilization of α-synuclein fibrils and their conversion to amorphous aggregate: A molecular dynamics simulation and experimental study. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140951. [PMID: 37574034 DOI: 10.1016/j.bbapap.2023.140951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/15/2023]
Abstract
The second most prevalent neurodegenerative disease, Parkinson's disease (PD), is caused by the accumulation and deposition of fibrillar aggregates of the α-Syn into the Lewy bodies. To create a potent pharmacological candidate to destabilize the preformed α-Syn fibril, it is important to understand the precise molecular mechanism underlying the destabilization of the α-Syn fibril. Through molecular dynamics simulations and experiments, we have examined the molecular mechanisms causing the destabilization and suppression of a newly discovered α-Syn fibril with a Greek-key-like shape and an aggregation prone state (APS) of α-Syn in the presence and absence of various Flvs. According to MD simulation and experimental evidence, morin, quercetin, and myricetin are the Flvs, most capable of destabilizing the fibrils and converting them into amorphous aggregates. Compared to galangin and kaempferol, they have more hydroxyl groups and form more hydrogen bonds with fibrils.The processes by which morin and myricetin prevent new fibril production from APS and destabilize the fibrils are different. According to linear interaction energy analysis, van der Waals interaction predominates with morin, and electrostatic interaction dominates with myricetin. Our MD simulation and experimental findings provide mechanistic insights into how Flvs destabilize α-Syn fibrils and change their morphology, opening the door to developing structure-based drugs for treating Parkinson's disease.
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Affiliation(s)
- Ishrat Jahan
- Department of Chemistry, Indian Institute of Technology Delhi, Delhi 110016, India
| | - Aziz Ahmad
- Department of Chemistry, Indian Institute of Technology Delhi, Delhi 110016, India
| | - Shashank Deep
- Department of Chemistry, Indian Institute of Technology Delhi, Delhi 110016, India.
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Gupta S, Dasmahapatra AK. Enhanced stability of a disaggregated Aβ fibril on removal of ligand inhibits refibrillation: An all atom Molecular Dynamics simulation study. Int J Biol Macromol 2023; 240:124481. [PMID: 37076062 DOI: 10.1016/j.ijbiomac.2023.124481] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 04/21/2023]
Abstract
The extraneuronally deposited senile plaques, composed of neurotoxic aggregates of Aβ fibril, define Alzheimer's disease (AD). Natural compounds have been tested for their destabilization potential on Aβ fibril, thereby curing AD. However, the resultant destabilized Aβ fibril, needs to be checked for its irreversibility to the native organized state after removal of the ligand. Herein, we assessed the stability of a destabilized fibril after the ligand (ellagic acid represented as REF) is removed from the complex. The study has been conducted via Molecular Dynamics (MD) simulation of 1 μs for both Aβ-Water (control) and Aβ-REF″ (test or REF removed) system. The increased value of RMSD, Rg, SASA, lower β-sheet content and reduced number of H-bonds explains enhanced destabilization observed in Aβ-REF″ system. The increased inter-chain distance demonstrates breaking of the residual contacts, testifying the drift of terminal chains from the pentamer. The increased SASA along with the ∆Gps(polar solvation energy) accounts for the reduced interaction amongst residues, and more with solvent molecules, governing irreversibility to native state. The higher Gibb's free energy of the misaligned structure of Aβ-REF″ ensures irreversibility to the organized structure due to its inability to cross such high energy barrier. The observed stability of the disaggregated structure, despite ligand elimination, establishes the effectiveness of the destabilization technique as a promising therapeutic approach towards treating AD.
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Affiliation(s)
- Shivani Gupta
- Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Ashok Kumar Dasmahapatra
- Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India; Center for Nanotechnology, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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Cho I, Yoon S, Park S, Hong SW, Cho E, Kim E, Kim HY, Kim Y. Immobilized Amyloid Hexamer Fragments to Map Active Sites of Amyloid-Targeting Chemicals. ACS Chem Neurosci 2023; 14:9-18. [PMID: 36445044 DOI: 10.1021/acschemneuro.2c00449] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
As amyloid-β (Aβ) peptide is considered a biomarker and pathological culprit of Alzheimer's disease, Aβ-targeting compounds have been investigated for diagnostics development and drug discovery of the disorder. Unlike amyloid plaque targeting agents, such as clinically available amyloid radiotracers intercalating into the β-sheet structures of the aggregates, monomer and oligomer targeting chemicals are difficult to develop, as the transient and polymorphic nature of these peptides impedes their structural understanding. Here, we report a mapping approach to explore targeting residues of Aβ-imaging probes and Aβ-regulating drug candidates by utilizing a set of fragmented Aβ hexamers immobilized on a 96-well microplate in combination with fluorescent full-length Aβ for on-plate aggregation. To evaluate the mapping potential of the peptide plate, we tested previously reported fluorescent imaging agents (CRANAD-28, bis-ANS), aggregation inhibitors (curcumin, scyllo-inositol), and aggregate dissociators (necrostatin-1, sunitinib) targeting Aβ. Our approach enabled mechanistic understanding of compounds targeting nonfibrillar Aβ on an interacting sequence level.
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Affiliation(s)
- Illhwan Cho
- Department of Pharmacy, College of Pharmacy, Yonsei University, Incheon21983, Republic of Korea.,Yonsei Institute of Pharmaceutical Sciences, College of Pharmacy, Yonsei University, Incheon21983, Republic of Korea
| | - Soljee Yoon
- Department of Pharmacy, College of Pharmacy, Yonsei University, Incheon21983, Republic of Korea.,Yonsei Institute of Pharmaceutical Sciences, College of Pharmacy, Yonsei University, Incheon21983, Republic of Korea.,Department of Integrative Biotechnology and Translational Medicine, Yonsei University, Incheon21983, Republic of Korea
| | - Sunghyun Park
- Department of Integrative Biotechnology and Translational Medicine, Yonsei University, Incheon21983, Republic of Korea
| | - Seung Woo Hong
- Department of Integrative Biotechnology and Translational Medicine, Yonsei University, Incheon21983, Republic of Korea
| | - Eunjung Cho
- Department of Medical Science, Yonsei University College of Medicine, Seoul03722, Republic of Korea.,Department of Psychiatry, Institute of Behavioral Science in Medicine, Yonsei University College of Medicine, Seoul03722, Republic of Korea.,Brain Korea 21 Four Project for Medical Science, Yonsei University College of Medicine, Seoul03722, Republic of Korea
| | - Eosu Kim
- Department of Medical Science, Yonsei University College of Medicine, Seoul03722, Republic of Korea.,Department of Psychiatry, Institute of Behavioral Science in Medicine, Yonsei University College of Medicine, Seoul03722, Republic of Korea
| | - Hye Yun Kim
- Department of Pharmacy, College of Pharmacy, Yonsei University, Incheon21983, Republic of Korea.,Yonsei Institute of Pharmaceutical Sciences, College of Pharmacy, Yonsei University, Incheon21983, Republic of Korea
| | - YoungSoo Kim
- Department of Pharmacy, College of Pharmacy, Yonsei University, Incheon21983, Republic of Korea.,Yonsei Institute of Pharmaceutical Sciences, College of Pharmacy, Yonsei University, Incheon21983, Republic of Korea.,Department of Integrative Biotechnology and Translational Medicine, Yonsei University, Incheon21983, Republic of Korea.,Integrated Science and Engineering Division, Yonsei University, Incheon21983, Republic of Korea.,POSTECH-Yonsei Campus, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk37673, Republic of Korea.,Amyloid Solution, Seongnam, Gyeonggi13486, Republic of Korea
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Ghasemali S, Farajnia S, Barzegar A, Rahmati-Yamchi M, Negahdari B, Rahbarnia L, Yousefi-Nodeh H. Rational Design of Anti-Angiogenic Peptides to Inhibit VEGF/VEGFR2 Interactions for Cancer Therapeutics. Anticancer Agents Med Chem 2021; 22:ACAMC-EPUB-118914. [PMID: 34792006 DOI: 10.2174/1871520621666211118104051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 07/19/2021] [Accepted: 08/26/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Angiogenesis is a critical physiological process that plays a key role in tumor progression, metastatic dissemination, and invasion. In the last two decades, the vascular endothelial growth factor (VEGF) signaling pathway has been the area of extensive researches. VEGF executes its special effects by binding to vascular endothelial growth factor receptors (VEGFRs), particularly VEGFR-2. OBJECTIVE The inhibition of VEGF/VEGFR2 interaction is known as an effective cancer therapy strategy. The current study pointed to design and model an anti-VEGF peptide based on VEGFR2 binding regions. METHOD The large-scale peptide mutation screening was used to achieve a potent peptide with high binding affinity to VEGF for possible application in inhibition of VEGF/VEGFR2 interaction. The AntiCP and Peptide Ranker servers were used to generate the possible peptides library with anticancer activities and prediction of peptides bioactivity. Then, the interaction of VEGF and all library peptides were analyzed using Hex 8.0.0 and ClusPro tools. A number of six peptides with favorable docking scores were achieved. All of the best docking scores of peptides in complexes with VEGF were evaluated to confirm their stability, using molecular dynamics simulation (MD) with the help of the GROMACS software package. RESULTS As a result, two antiangiogenic peptides with 13 residues of PepA (NGIDFNRDFFLGL) and PepC (NGIDFNRDKFLFL) were achieved and introduced to inhibit VEGF/VEGFR2 interactions. CONCLUSIONS In summary, this study provided new insights into peptide-based therapeutics development for targeting VEGF signaling pathway in tumor cells. PepA and PepC are recommended as potentially promising anticancer agents for further experimental evaluations.
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Affiliation(s)
- Samaneh Ghasemali
- Department of Medical Biotechnology, School of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Safar Farajnia
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Abolfazl Barzegar
- Research Center of Bioscience and Biotechnology, University of Tabriz, Tabriz. Iran
| | - Mohammad Rahmati-Yamchi
- Department of Clinical Biochemistry, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Babak Negahdari
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran. Iran
| | - Leila Rahbarnia
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Hamidreza Yousefi-Nodeh
- Research Center for Evidence-Based Medicine, Tabriz University of Medical Sciences, Tabriz. Iran
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Gaudreault R, Hervé V, van de Ven TGM, Mousseau N, Ramassamy C. Polyphenol-Peptide Interactions in Mitigation of Alzheimer's Disease: Role of Biosurface-Induced Aggregation. J Alzheimers Dis 2021; 81:33-55. [PMID: 33749653 DOI: 10.3233/jad-201549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Alzheimer's disease (AD) is the most common age-related neurodegenerative disorder, responsible for nearly two-thirds of all dementia cases. In this review, we report the potential AD treatment strategies focusing on natural polyphenol molecules (green chemistry) and more specifically on the inhibition of polyphenol-induced amyloid aggregation/disaggregation pathways: in bulk and on biosurfaces. We discuss how these pathways can potentially alter the structure at the early stages of AD, hence delaying the aggregation of amyloid-β (Aβ) and tau. We also discuss multidisciplinary approaches, combining experimental and modelling methods, that can better characterize the biochemical and biophysical interactions between proteins and phenolic ligands. In addition to the surface-induced aggregation, which can occur on surfaces where protein can interact with other proteins and polyphenols, we suggest a new concept referred as "confinement stability". Here, on the contrary, the adsorption of Aβ and tau on biosurfaces other than Aβ- and tau-fibrils, e.g., red blood cells, can lead to confinement stability that minimizes the aggregation of Aβ and tau. Overall, these mechanisms may participate directly or indirectly in mitigating neurodegenerative diseases, by preventing protein self-association, slowing down the aggregation processes, and delaying the progression of AD.
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Affiliation(s)
- Roger Gaudreault
- Department of Physics, Université de Montréal, Montreal, QC, Canada
| | - Vincent Hervé
- INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, QC, Canada
| | | | - Normand Mousseau
- Department of Physics, Université de Montréal, Montreal, QC, Canada
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