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Ludwiczak J, Iłowska E, Wilkowska M, Szymańska A, Kempka M, Dobies M, Szutkowski K, Kozak M. The influence of a dicationic surfactant on the aggregation process of the IVAGVN peptide derived from the human cystatin C sequence (56-61). RSC Adv 2025; 15:3237-3249. [PMID: 39896427 PMCID: PMC11784886 DOI: 10.1039/d4ra08377f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2024] [Accepted: 01/12/2025] [Indexed: 02/04/2025] Open
Abstract
Human cystatin C (hCC) undergoes domain swapping and forms amyloid structures. Steric zipper motifs, which are important for hCC fibrillization, have been identified and studied in our previous work. In the present study, we analysed the influence of the selected dicationic surfactant (a derivative of dodecylimidazolium chloride: 3,3'-[α,ω-(dioxahexane)]bis(1-dodecylimidazolium)dichloride) on the structure of the aggregates formed by one such fragment, a peptide with the sequence IVAGVN, corresponding to residues 56-61 in the full-length protein. Changes in the secondary structure of the peptide induced by the surfactant were studied using circular dichroism (CD) and FTIR, and the aggregates were characterised using microscopic techniques (AFM and TEM) and NMR.
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Affiliation(s)
- Julia Ludwiczak
- Department of Biomedical Physics, Adam Mickiewicz University Poznan Poland
| | - Emilia Iłowska
- Department of Organic Chemistry, University of Gdansk Gdansk Poland
| | | | - Aneta Szymańska
- Department of Biomedical Chemistry, University of Gdansk Gdansk Poland
| | - Marek Kempka
- Department of Biomedical Physics, Adam Mickiewicz University Poznan Poland
| | - Maria Dobies
- Department of Biomedical Physics, Adam Mickiewicz University Poznan Poland
| | | | - Maciej Kozak
- Department of Biomedical Physics, Adam Mickiewicz University Poznan Poland
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Zahraee H, Mohammadi F, Parvaee E, Khoshbin Z, Arab SS. Reducing the assemblies of amyloid-beta multimers by sodium dodecyl sulfate surfactant at concentrations lower than critical micelle concentration: molecular dynamics simulation exploration. J Biomol Struct Dyn 2024; 42:8673-8687. [PMID: 37599504 DOI: 10.1080/07391102.2023.2247086] [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: 03/09/2023] [Accepted: 08/05/2023] [Indexed: 08/22/2023]
Abstract
Amyloid-β peptide, the predominant proteinaceous component of senile plaques, is responsible for the incidence of Alzheimer's disease (AD), an age-associated neurodegenerative disorder. Specifically, the amyloid-β(1-42) (Aβ1-42) isoform, known for its high toxicity, is the predominant biomarker for the preliminary diagnosis of AD. The aggregation of the Aβ1-42 peptides can be affected by the components of the cellular medium through changing their structures and molecular interactions. In this study, we investigated the effect of sodium dodecyl sulfate (SDS) at much lower concentrations than the critical micelle concentration (CMC) on Aβ1-42 aggregation. For this purpose, we studied mono-, di-, tri- and tetramers of Aβ1-42 peptide in two different concentrations of SDS molecules (10 and 40 molecules) using a 300 ns molecular dynamics simulation for each system. The distance between the center of mass (COM) of Aβ1-42 peptides confirms that an increase in the number of SDS molecules decreases their aggregation probability due to greater interaction with SDS molecules. Besides, the less compactness parameter reveals the reduced aggregation probability of Aβ1-42 peptides. Based on the energetic FEL landscapes, SDS molecules with the concentration closer to the CMC are an effective inhibitory agent to prevent the formation of Aβ1-42 fibrils. Also, the aggregation direction of the peptide pairs can be predicted by determining the direction of the accumulation-deterrent forces.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hamed Zahraee
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fatemeh Mohammadi
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Elahe Parvaee
- Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Zahra Khoshbin
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Shahriar Arab
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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Corrigan RR, Labrador L, Grizzanti J, Mey M, Piontkivska H, Casadesús G. Neuroprotective Mechanisms of Amylin Receptor Activation, Not Antagonism, in the APP/PS1 Mouse Model of Alzheimer's Disease. J Alzheimers Dis 2023; 91:1495-1514. [PMID: 36641678 DOI: 10.3233/jad-221057] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
BACKGROUND Amylin, a pancreatic amyloid peptide involved in energy homeostasis, is increasingly studied in the context of Alzheimer's disease (AD) etiology. To date, conflicting pathogenic and neuroprotective roles for this peptide and its analogs for AD pathogenesis have been described. OBJECTIVE Whether the benefits of amylin are associated with peripheral improvement of metabolic tone/function or directly through the activation of central amylin receptors is also unknown and downstream signaling mechanisms of amylin receptors are major objectives of this study. METHODS To address these questions more directly we delivered the amylin analog pramlintide systemically (IP), at previously identified therapeutic doses, while centrally (ICV) inhibiting the receptor using an amylin receptor antagonist (AC187), at doses known to impact CNS function. RESULTS Here we show that pramlintide improved cognitive function independently of CNS receptor activation and provide transcriptomic data that highlights potential mechanisms. Furthermore, we show than inhibition of the amylin receptor increased amyloid-beta pathology in female APP/PS1 mice, an effect than was mitigated by peripheral delivery of pramlintide. Through transcriptomic analysis of pramlintide therapy in AD-modeled mice we found sexual dimorphic modulation of neuroprotective mechanisms: oxidative stress protection in females and membrane stability and reduced neuronal excitability markers in males. CONCLUSION These data suggest an uncoupling of functional and pathology-related events and highlighting a more complex receptor system and pharmacological relationship that must be carefully studied to clarify the role of amylin in CNS function and AD.
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Affiliation(s)
| | - Luis Labrador
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL, USA
| | - John Grizzanti
- School of Biomedical Sciences, Kent State University, Kent, OH, USA
| | - Megan Mey
- School of Biomedical Sciences, Kent State University, Kent, OH, USA
| | - Helen Piontkivska
- Department of Biological Sciences, Kent State University, Kent, OH, USA
| | - Gemma Casadesús
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL, USA
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4
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Sedov I, Khaibrakhmanova D. Molecular Mechanisms of Inhibition of Protein Amyloid Fibril Formation: Evidence and Perspectives Based on Kinetic Models. Int J Mol Sci 2022; 23:13428. [PMID: 36362217 PMCID: PMC9657184 DOI: 10.3390/ijms232113428] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 10/29/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022] Open
Abstract
Inhibition of fibril formation is considered a possible treatment strategy for amyloid-related diseases. Understanding the molecular nature of inhibitor action is crucial for the design of drug candidates. In the present review, we describe the common kinetic models of fibril formation and classify known inhibitors by the mechanism of their interactions with the aggregating protein and its oligomers. This mechanism determines the step or steps of the aggregation process that become inhibited and the observed changes in kinetics and equilibrium of fibril formation. The results of numerous studies indicate that possible approaches to antiamyloid inhibitor discovery include the search for the strong binders of protein monomers, cappers blocking the ends of the growing fibril, or the species absorbing on the surface of oligomers preventing nucleation. Strongly binding inhibitors stabilizing the native state can be promising for the structured proteins while designing the drug candidates targeting disordered proteins is challenging.
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Affiliation(s)
- Igor Sedov
- Chemical Institute, Kazan Federal University, Kremlevskaya 18, 420008 Kazan, Russia
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, 420111 Kazan, Russia
- Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russia
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5
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Morris DL, Tjandra N. Inducible fold-switching as a mechanism to fibrillate pro-apoptotic BCL-2 proteins. Biopolymers 2021; 112:e23424. [PMID: 33764501 PMCID: PMC11822676 DOI: 10.1002/bip.23424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/18/2021] [Accepted: 03/05/2021] [Indexed: 12/12/2022]
Abstract
Neurodegenerative diseases often are associated with cellular dysregulation that results in premature cell death or apoptosis. A common example is the accumulation of amyloid plaques that promotes the excessive expression of p38 mitogen-activated protein kinase. The increased abundance of this enzyme leads to mass phosphorylation and activation of a protein from the B-cell lymphoma 2 (BCL-2) family, BAX. BAX is the central regulatory protein for mitochondrial outer membrane permeabilization (MOMP), a poration process that commits cells to apoptosis by releasing death-propagating factors from the mitochondria. Recent reports identify a naturally occurring peptide, Humanin (HN), that could block amyloid-beta-associated neuronal apoptosis by interacting with BCL-2 proteins. We recently showed humanin interaction leads to the amyloid-like fibrillation of BAX and a second BCL-2 family member, BID. We proposed this as a novel anti-apoptotic mechanism that inhibits pro-apoptotic BCL-2 proteins from initiating MOMP by sequestering them into fibrils, a heretofore unprecedented phenomenon that involves refolding globular BCL-2 proteins rapidly into fibrils where they undergo significant alpha-helix to beta-sheet fold-switching. Here we seek to further characterize the fibrillation and fold-switch in conditions that are known to induce amyloid fibrillation.
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Affiliation(s)
- Daniel L Morris
- Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Nico Tjandra
- Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
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6
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Zurlo E, Kumar P, Meisl G, Dear AJ, Mondal D, Claessens MMAE, Knowles TPJ, Huber M. In situ kinetic measurements of α-synuclein aggregation reveal large population of short-lived oligomers. PLoS One 2021; 16:e0245548. [PMID: 33481908 PMCID: PMC7822277 DOI: 10.1371/journal.pone.0245548] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 01/04/2021] [Indexed: 11/19/2022] Open
Abstract
Knowledge of the mechanisms of assembly of amyloid proteins into aggregates is of central importance in building an understanding of neurodegenerative disease. Given that oligomeric intermediates formed during the aggregation reaction are believed to be the major toxic species, methods to track such intermediates are clearly needed. Here we present a method, electron paramagnetic resonance (EPR), by which the amount of intermediates can be measured over the course of the aggregation, directly in the reacting solution, without the need for separation. We use this approach to investigate the aggregation of α-synuclein (αS), a synaptic protein implicated in Parkinson’s disease and find a large population of oligomeric species. Our results show that these are primary oligomers, formed directly from monomeric species, rather than oligomers formed by secondary nucleation processes, and that they are short-lived, the majority of them dissociates rather than converts to fibrils. As demonstrated here, EPR offers the means to detect such short-lived intermediate species directly in situ. As it relies only on the change in size of the detected species, it will be applicable to a wide range of self-assembling systems, making accessible the kinetics of intermediates and thus allowing the determination of their rates of formation and conversion, key processes in the self-assembly reaction.
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Affiliation(s)
- Enrico Zurlo
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Leiden, The Netherlands
| | - Pravin Kumar
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Leiden, The Netherlands
| | - Georg Meisl
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, United Kingdom
| | - Alexander J. Dear
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, United Kingdom
| | - Dipro Mondal
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Leiden, The Netherlands
| | | | - Tuomas P. J. Knowles
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, United Kingdom
- Cavendish Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Martina Huber
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Leiden, The Netherlands
- * E-mail:
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Li Y, Tang H, Andrikopoulos N, Javed I, Cecchetto L, Nandakumar A, Kakinen A, Davis TP, Ding F, Ke PC. The membrane axis of Alzheimer's nanomedicine. ADVANCED NANOBIOMED RESEARCH 2021; 1:2000040. [PMID: 33748816 PMCID: PMC7971452 DOI: 10.1002/anbr.202000040] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Alzheimer's disease (AD) is a major neurological disorder impairing its carrier's cognitive function, memory and lifespan. While the development of AD nanomedicine is still nascent, the field is evolving into a new scientific frontier driven by the diverse physicochemical properties and theranostic potential of nanomaterials and nanocomposites. Characteristic to the AD pathology is the deposition of amyloid plaques and tangles of amyloid beta (Aβ) and tau, whose aggregation kinetics may be curbed by nanoparticle inhibitors via sequence-specific targeting or nonspecific interactions with the amyloidogenic proteins. As literature implicates cell membrane as a culprit in AD pathogenesis, here we summarize the membrane axis of AD nanomedicine and present a new rationale that the field development may greatly benefit from harnessing our existing knowledge of Aβ-membrane interaction, nanoparticle-membrane interaction and Aβ-nanoparticle interaction.
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Affiliation(s)
- Yuhuan Li
- Zhongshan Hospital, Fudan University, 111 Yixueyuan Rd, Xuhui District, Shanghai, 200032, China
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Huayuan Tang
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Nicholas Andrikopoulos
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Ibrahim Javed
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Luca Cecchetto
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Department of Chemical and Pharmaceutical Science, University of Trieste, Via Licio Giorgieri 1, 34127 Trieste, Italy
| | - Aparna Nandakumar
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Aleksandr Kakinen
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Thomas P. Davis
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Pu Chun Ke
- Zhongshan Hospital, Fudan University, 111 Yixueyuan Rd, Xuhui District, Shanghai, 200032, China
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
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8
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Morris DL, Johnson S, Bleck CKE, Lee DY, Tjandra N. Humanin selectively prevents the activation of pro-apoptotic protein BID by sequestering it into fibers. J Biol Chem 2020; 295:18226-18238. [PMID: 33106313 PMCID: PMC11843584 DOI: 10.1074/jbc.ra120.013023] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 10/23/2020] [Indexed: 03/01/2024] Open
Abstract
Members of the B-cell lymphoma (BCL-2) protein family regulate mitochondrial outer membrane permeabilization (MOMP), a phenomenon in which mitochondria become porous and release death-propagating complexes during the early stages of apoptosis. Pro-apoptotic BCL-2 proteins oligomerize at the mitochondrial outer membrane during MOMP, inducing pore formation. Of current interest are endogenous factors that can inhibit pro-apoptotic BCL-2 mitochondrial outer membrane translocation and oligomerization. A mitochondrial-derived peptide, Humanin (HN), was reported being expressed from an alternate ORF in the mitochondrial genome and inhibiting apoptosis through interactions with the pro-apoptotic BCL-2 proteins. Specifically, it is known to complex with BAX and BID. We recently reported the fibrillation of HN and BAX into β-sheets. Here, we detail the fibrillation between HN and BID. These fibers were characterized using several spectroscopic techniques, protease fragmentation with mass analysis, and EM. Enhanced fibrillation rates were detected with rising temperatures or pH values and the presence of a detergent. BID fibers are similar to those produced using BAX; however, the structures differ in final conformations of the BCL-2 proteins. BID fibers display both types of secondary structure in the fiber, whereas BAX was converted entirely to β-sheets. The data show that two distinct segments of BID are incorporated into the fiber structure, whereas other portions of BID remain solvent-exposed and retain helical structure. Similar analyses show that anti-apoptotic BCL-xL does not form fibers with humanin. These results support a general mechanism of sequestration of pro-apoptotic BCL-2 proteins into fibers by HN to inhibit MOMP.
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Affiliation(s)
- Daniel L Morris
- Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, NHLBI, National Institutes of Health, Bethesda, Maryland, USA
| | - Sabrina Johnson
- Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, NHLBI, National Institutes of Health, Bethesda, Maryland, USA
| | - Christopher K E Bleck
- Electron Microscopy Core Facility, NHLBI, National Institutes of Health, Bethesda, Maryland, USA
| | - Duck-Yeon Lee
- Biochemistry Core Facility, NHLBI, National Institutes of Health, Bethesda, Maryland, USA
| | - Nico Tjandra
- Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, NHLBI, National Institutes of Health, Bethesda, Maryland, USA.
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Khan JM, Ahmed A, Alamery SF, Alghamdi OHA, Azmi S, Malik A. Perturbation of anionic surfactant induced amyloid fibrillation by chemical chaperone: A biophysical study. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113717] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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10
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Mello LR, Hamley IW, Castelletto V, Garcia BBM, Lourenço TC, Vassiliades SV, Alves WA, Han SW, Silva ER. Self-assembly and intracellular delivery of DNA by a truncated fragment derived from the Trojan peptide Penetratin. SOFT MATTER 2020; 16:4746-4755. [PMID: 32329496 DOI: 10.1039/d0sm00347f] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Penetratin is a short Trojan peptide that attracts great interest in biomedical research for its capacity to translocate biological membranes. Herein, we study in detail both self-assembly and intracellular delivery of DNA by the heptamer KIWFQNR, a truncated peptide derived from Penetratin. This shortened sequence possesses a unique design with bolaamphiphilic characteristics that preserves the longest noncationic amino acid portion found in Penetratin. These features convey amphipathicity to assist self-assembly and make it a suitable model for exploring the role of hydrophobic residues for peptide interaction and cell uptake. We show that the fragment forms peptiplexes (i.e., peptide-DNA complexes), and aggregates into long nanofibers with clear β-sheet signature. The supramolecular structure of nanofibers is likely composed of DNA cores surrounded by a peptide shell to which the double helix behaves as a template and induces fibrillization. A nucleation and growth mechanism proceeding through liquid-liquid phase separation of coacervates is proposed for describing the self-assembly of peptiplexes. We also demonstrate that peptiplexes deliver double-stranded 200 bp DNA into HeLa cells, indicating its potential for preparing non-viral vectors for oligonucleotides through noncovalent strategies. Since the main structural features of native Penetratin are conserved in this simpler fragment, our findings also highlight the role of uncharged amino acids for structuration, and thus for the ability of Penetratin to cross cell membranes.
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Affiliation(s)
- Lucas R Mello
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo 04023-062, Brazil.
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11
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Bhattacharya S, Xu L, Thompson D. Long-range Regulation of Partially Folded Amyloidogenic Peptides. Sci Rep 2020; 10:7597. [PMID: 32371882 PMCID: PMC7200734 DOI: 10.1038/s41598-020-64303-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 04/15/2020] [Indexed: 01/20/2023] Open
Abstract
Neurodegeneration involves abnormal aggregation of intrinsically disordered amyloidogenic peptides (IDPs), usually mediated by hydrophobic protein-protein interactions. There is mounting evidence that formation of α-helical intermediates is an early event during self-assembly of amyloid-β42 (Aβ42) and α-synuclein (αS) IDPs in Alzheimer’s and Parkinson’s disease pathogenesis, respectively. However, the driving force behind on-pathway molecular assembly of partially folded helical monomers into helical oligomers assembly remains unknown. Here, we employ extensive molecular dynamics simulations to sample the helical conformational sub-spaces of monomeric peptides of both Aβ42 and αS. Our computed free energies, population shifts, and dynamic cross-correlation network analyses reveal a common feature of long-range intra-peptide modulation of partial helical folds of the amyloidogenic central hydrophobic domains via concerted coupling with their charged terminal tails (N-terminus of Aβ42 and C-terminus of αS). The absence of such inter-domain fluctuations in both fully helical and completely unfolded (disordered) states suggests that long-range coupling regulates the dynamicity of partially folded helices, in both Aβ42 and αS peptides. The inter-domain coupling suggests a form of intra-molecular allosteric regulation of the aggregation trigger in partially folded helical monomers. This approach could be applied to study the broad range of amyloidogenic peptides, which could provide a new path to curbing pathogenic aggregation of partially folded conformers into oligomers, by inhibition of sites far from the hydrophobic core.
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Affiliation(s)
- Shayon Bhattacharya
- Department of Physics, Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland
| | - Liang Xu
- Department of Physics, Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland
| | - Damien Thompson
- Department of Physics, Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland.
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12
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Ahmadzade A, Bozorgmehr MR, Parvaee E. The effect of sodium dodecyl sulfate concentration on the aggregation behavior of Aβ (1–42) peptide: Molecular dynamics simulation approach. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.112651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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13
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Näsström T, Ådén J, Shibata F, Andersson PO, Karlsson BC. A Capped Peptide of the Aggregation Prone NAC 71-82 Amino Acid Stretch of α-Synuclein Folds into Soluble β-Sheet Oligomers at Low and Elevated Peptide Concentrations. Int J Mol Sci 2020; 21:ijms21051629. [PMID: 32120928 PMCID: PMC7084662 DOI: 10.3390/ijms21051629] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/25/2020] [Accepted: 02/25/2020] [Indexed: 12/13/2022] Open
Abstract
Although Lewy bodies and Lewy neurites are hallmarks of Parkinson's disease (PD) and dementia with Lewy bodies (DLB), misfolded α-synuclein oligomers are nowadays believed to be key for the development of these diseases. Attempts to target soluble misfolded species of the full-length protein have been limited so far, probably due to the fast aggregation kinetics and burial of aggregation prone segments in final cross-β-sheet fibrils. A previous characterisation study of fibrils prepared from a capped peptide of the non-amyloid β-component (NAC) 71-82 amino acid stretch of α-synuclein demonstrated an increased aggregation propensity resulting in a cross-β-structure that is also found in prion proteins. From this, it was suggested that capped NAC 71-82 peptide oligomers would provide interesting motifs with a capacity to regulate disease development. Here, we demonstrated, from a series of circular dichroism spectroscopic measurements and molecular dynamics simulations, the molecular-environment-sensitive behaviour of the capped NAC 71-82 peptide in a solution phase and the formation of β-sheet oligomeric structures in the supernatant of a fibrillisation mixture. These results highlighted the use of the capped NAC 71-82 peptide as a motif in the preparation of oligomeric β-sheet structures that potentially could be used in therapeutic strategies in the fight against progressive neurodegenerative disorders, such as PD and DLB.
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Affiliation(s)
- Thomas Näsström
- Physical Pharmacy Laboratory, Linnaeus University Centre for Biomaterials Chemistry, Linnaeus University, SE-392 31 Kalmar, Sweden;
- Correspondence: (T.N.); (B.C.G.K.); Tel.: +46-480-446329 (T.N.); +46-480-446740 (B.C.G.K.)
| | - Jörgen Ådén
- Department of Chemistry, University of Umeå, SE-901 87 Umeå, Sweden;
| | - Fumina Shibata
- Physical Pharmacy Laboratory, Linnaeus University Centre for Biomaterials Chemistry, Linnaeus University, SE-392 31 Kalmar, Sweden;
| | - Per Ola Andersson
- Department of Engineering Sciences: Applied Material Science, Uppsala University, SE-751 21 Uppsala, Sweden;
| | - Björn C.G. Karlsson
- Physical Pharmacy Laboratory, Linnaeus University Centre for Biomaterials Chemistry, Linnaeus University, SE-392 31 Kalmar, Sweden;
- Correspondence: (T.N.); (B.C.G.K.); Tel.: +46-480-446329 (T.N.); +46-480-446740 (B.C.G.K.)
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14
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Metal binding to the amyloid-β peptides in the presence of biomembranes: potential mechanisms of cell toxicity. J Biol Inorg Chem 2019; 24:1189-1196. [PMID: 31562546 DOI: 10.1007/s00775-019-01723-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 09/10/2019] [Indexed: 12/18/2022]
Abstract
The amyloid-β (Aβ) peptides are key molecules in Alzheimer's disease (AD) pathology. They interact with cellular membranes, and can bind metal ions outside the membrane. Certain oligomeric Aβ aggregates are known to induce membrane perturbations and the structure of these oligomers-and their membrane-perturbing effects-can be modulated by metal ion binding. If the bound metal ions are redox active, as e.g., Cu and Fe ions are, they will generate harmful reactive oxygen species (ROS) just outside the membrane surface. Thus, the membrane damage incurred by toxic Aβ oligomers is likely aggravated when redox-active metal ions are present. The combined interactions between Aβ oligomers, metal ions, and biomembranes may be responsible for at least some of the neuronal death in AD patients.
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An analog derived from phenylpropanoids ameliorates Alzheimer's disease–like pathology and protects mitochondrial function. Neurobiol Aging 2019; 80:187-195. [DOI: 10.1016/j.neurobiolaging.2019.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 04/23/2019] [Accepted: 05/01/2019] [Indexed: 01/14/2023]
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Sambasivam D, Sivanesan S, Sultana S, Rajadas J. Conformational Preferences of Aβ25-35 and Aβ35-25 in Membrane Mimicking Environments. Protein Pept Lett 2019; 26:386-390. [PMID: 30836907 DOI: 10.2174/0929866526666190228122849] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 01/03/2019] [Accepted: 02/04/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND The structural transition of aggregating Abeta peptides is the key event in the progression of Alzheimer's Disease (AD). OBJECTIVE In the present work, the structural modifications of toxic Aβ25-35 and the scrambled Aβ35-25 were studied in Trifluoroethanol (TFE) and in aqueous SDS micelles. METHODS Using CD spectroscopic investigations, the conformational transition of Aβ25-35 and Aβ35-25 peptides were determined in different membrane mimicking environments such as TFE and SDS. An interval scan CD of the peptides on evaporation of TFE was performed. TFE titrations were carried out to investigate the intrinsic ability of the structural conformations of peptides. RESULTS We show by spectroscopic evidence that Aβ25-35 prefers beta sheet structures upon increasing TFE concentrations. On the other hand, the non-toxic scrambled Aβ35-25 peptide only undergoes a transition from random coil to α-helix conformation with increasing TFE. In the interval scan studies, Aβ25-35 did not show any structural transitions, whereas Aβ35-25 showed transition from α-helix to β-sheet conformation. In membrane simulating aqueous SDS micelles, Aβ25-35 showed a transition from random coil to α-helix while Aβ35-25 underwent transition from random coil to β-sheet conformation. CONCLUSION Overall, the current results seek new insights into the structural properties of amyloidogenic and the truncated sequence in membrane mimicking solvents.
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Affiliation(s)
- Dhandayuthapani Sambasivam
- Bioorganic Chemistry Laboratory, Central Leather Research Institute, Adyar, Chennai 600 020, India.,Department of Chemistry, St Peter's Institute of Higher Education and Research, Chennai-600054, India
| | - Senthilkumar Sivanesan
- Bioorganic Chemistry Laboratory, Central Leather Research Institute, Adyar, Chennai 600 020, India
| | - Sayeeda Sultana
- Department of Chemistry, St Peter's Institute of Higher Education and Research, Chennai-600054, India
| | - Jayakumar Rajadas
- Bioorganic Chemistry Laboratory, Central Leather Research Institute, Adyar, Chennai 600 020, India.,Biomaterials and Advanced Drug Delivery Laboratory (BioADD), Stanford University School of Medicine, Stanford, CA, United States
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Impact of membrane curvature on amyloid aggregation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1741-1764. [PMID: 29709613 DOI: 10.1016/j.bbamem.2018.04.012] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/23/2018] [Accepted: 04/25/2018] [Indexed: 12/11/2022]
Abstract
The misfolding, amyloid aggregation, and fibril formation of intrinsically disordered proteins/peptides (or amyloid proteins) have been shown to cause a number of disorders. The underlying mechanisms of amyloid fibrillation and structural properties of amyloidogenic precursors, intermediates, and amyloid fibrils have been elucidated in detail; however, in-depth examinations on physiologically relevant contributing factors that induce amyloidogenesis and lead to cell death remain challenging. A large number of studies have attempted to characterize the roles of biomembranes on protein aggregation and membrane-mediated cell death by designing various membrane components, such as gangliosides, cholesterol, and other lipid compositions, and by using various membrane mimetics, including liposomes, bicelles, and different types of lipid-nanodiscs. We herein review the dynamic effects of membrane curvature on amyloid generation and the inhibition of amyloidogenic proteins and peptides, and also discuss how amyloid formation affects membrane curvature and integrity, which are key for understanding relationships with cell death. Small unilamellar vesicles with high curvature and large unilamellar vesicles with low curvature have been demonstrated to exhibit different capabilities to induce the nucleation, amyloid formation, and inhibition of amyloid-β peptides and α-synuclein. Polymorphic amyloidogenesis in small unilamellar vesicles was revealed and may be viewed as one of the generic properties of interprotein interaction-dominated amyloid formation. Several mechanical models and phase diagrams are comprehensively shown to better explain experimental findings. The negative membrane curvature-mediated mechanisms responsible for the toxicity of pancreatic β cells by the amyloid aggregation of human islet amyloid polypeptide (IAPP) and binding of the precursors of the semen-derived enhancer of viral infection (SEVI) are also described. The curvature-dependent binding modes of several types of islet amyloid polypeptides with high-resolution NMR structures are also discussed.
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Cieplak AS. Protein folding, misfolding and aggregation: The importance of two-electron stabilizing interactions. PLoS One 2017; 12:e0180905. [PMID: 28922400 PMCID: PMC5603215 DOI: 10.1371/journal.pone.0180905] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 06/22/2017] [Indexed: 12/17/2022] Open
Abstract
Proteins associated with neurodegenerative diseases are highly pleiomorphic and may adopt an all-α-helical fold in one environment, assemble into all-β-sheet or collapse into a coil in another, and rapidly polymerize in yet another one via divergent aggregation pathways that yield broad diversity of aggregates’ morphology. A thorough understanding of this behaviour may be necessary to develop a treatment for Alzheimer’s and related disorders. Unfortunately, our present comprehension of folding and misfolding is limited for want of a physicochemical theory of protein secondary and tertiary structure. Here we demonstrate that electronic configuration and hyperconjugation of the peptide amide bonds ought to be taken into account to advance such a theory. To capture the effect of polarization of peptide linkages on conformational and H-bonding propensity of the polypeptide backbone, we introduce a function of shielding tensors of the Cα atoms. Carrying no information about side chain-side chain interactions, this function nonetheless identifies basic features of the secondary and tertiary structure, establishes sequence correlates of the metamorphic and pH-driven equilibria, relates binding affinities and folding rate constants to secondary structure preferences, and manifests common patterns of backbone density distribution in amyloidogenic regions of Alzheimer’s amyloid β and tau, Parkinson’s α-synuclein and prions. Based on those findings, a split-intein like mechanism of molecular recognition is proposed to underlie dimerization of Aβ, tau, αS and PrPC, and divergent pathways for subsequent association of dimers are outlined; a related mechanism is proposed to underlie formation of PrPSc fibrils. The model does account for: (i) structural features of paranuclei, off-pathway oligomers, non-fibrillar aggregates and fibrils; (ii) effects of incubation conditions, point mutations, isoform lengths, small-molecule assembly modulators and chirality of solid-liquid interface on the rate and morphology of aggregation; (iii) fibril-surface catalysis of secondary nucleation; and (iv) self-propagation of infectious strains of mammalian prions.
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Affiliation(s)
- Andrzej Stanisław Cieplak
- Department of Chemistry, Bilkent University, Ankara, Turkey
- Department of Chemistry, Yale University, New Haven, Connecticut, United States of America
- Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States of America
- * E-mail:
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Khan JM, Khan MS, Alsenaidy MA, Ahmed A, Sen P, Oves M, Al-Shabib NA, Khan RH. Sodium louroyl sarcosinate (sarkosyl) modulate amyloid fibril formation in hen egg white lysozyme (HEWL) at alkaline pH: a molecular insight study. J Biomol Struct Dyn 2017; 36:1550-1565. [DOI: 10.1080/07391102.2017.1329097] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Javed Masood Khan
- Faculty of Food and Agricultural Sciences, Department of Food Science and Nutrition, King Saud University, 2460 Riyadh 11451, Saudi Arabia
| | - Mohd Shahnawaz Khan
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | | - Anwar Ahmed
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Priyankar Sen
- Centre for Bioseparation Technology, VIT University, Vellore 632014, India
| | - Mohammad Oves
- Center of Excellence in Enviromental Studies, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nasser Abdulatif Al-Shabib
- Faculty of Food and Agricultural Sciences, Department of Food Science and Nutrition, King Saud University, 2460 Riyadh 11451, Saudi Arabia
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
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Kinoshita M, Kakimoto E, Terakawa MS, Lin Y, Ikenoue T, So M, Sugiki T, Ramamoorthy A, Goto Y, Lee YH. Model membrane size-dependent amyloidogenesis of Alzheimer's amyloid-β peptides. Phys Chem Chem Phys 2017; 19:16257-16266. [DOI: 10.1039/c6cp07774a] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We herein report the mechanism of amyloid formation of amyloid-β (Aβ) peptides on small (SUV) and large unilamellar vesicles (LUVs), which consist of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipids.
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Affiliation(s)
| | - Erina Kakimoto
- Institute for Protein Research
- Osaka University
- Suita
- Japan
| | - Mayu S. Terakawa
- Institute for Protein Research
- Osaka University
- Suita
- Japan
- Department of Biochemistry
| | - Yuxi Lin
- Institute for Protein Research
- Osaka University
- Suita
- Japan
| | - Tatsuya Ikenoue
- Institute for Protein Research
- Osaka University
- Suita
- Japan
- Department of Chemistry
| | - Masatomo So
- Institute for Protein Research
- Osaka University
- Suita
- Japan
| | | | | | - Yuji Goto
- Institute for Protein Research
- Osaka University
- Suita
- Japan
| | - Young-Ho Lee
- Institute for Protein Research
- Osaka University
- Suita
- Japan
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Tiiman A, Luo J, Wallin C, Olsson L, Lindgren J, Jarvet J, Per R, Sholts SB, Rahimipour S, Abrahams JP, Karlström AE, Gräslund A, Wärmländer SK. Specific Binding of Cu(II) Ions to Amyloid-Beta Peptides Bound to Aggregation-Inhibiting Molecules or SDS Micelles Creates Complexes that Generate Radical Oxygen Species. J Alzheimers Dis 2016; 54:971-982. [DOI: 10.3233/jad-160427] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Ann Tiiman
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, Sweden
| | - Jinghui Luo
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, Sweden
- Chemical Research Laboratory, University of Oxford, UK
| | - Cecilia Wallin
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, Sweden
| | - Lisa Olsson
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, Sweden
| | | | - Jϋri Jarvet
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, Sweden
- The National Institute of Chemical Physics and Biophysics, Tallinn, Estonia
| | - Roos Per
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Physiology, Capio St.Göran Hospital, Stockholm, Sweden
| | - Sabrina B. Sholts
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, Sweden
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Shai Rahimipour
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, Israel
| | - Jan Pieter Abrahams
- Biozentrum, University of Basel, Switzerland & Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland
| | | | - Astrid Gräslund
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, Sweden
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