1
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Wagner WJ, Gross ML. Using mass spectrometry-based methods to understand amyloid formation and inhibition of alpha-synuclein and amyloid beta. MASS SPECTROMETRY REVIEWS 2024; 43:782-825. [PMID: 36224716 PMCID: PMC10090239 DOI: 10.1002/mas.21814] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Amyloid fibrils, insoluble β-sheets structures that arise from protein misfolding, are associated with several neurodegenerative disorders. Many small molecules have been investigated to prevent amyloid fibrils from forming; however, there are currently no therapeutics to combat these diseases. Mass spectrometry (MS) is proving to be effective for studying the high order structure (HOS) of aggregating proteins and for determining structural changes accompanying protein-inhibitor interactions. When combined with native MS (nMS), gas-phase ion mobility, protein footprinting, and chemical cross-linking, MS can afford regional and sometimes amino acid spatial resolution of the aggregating protein. The spatial resolution is greater than typical low-resolution spectroscopic, calorimetric, and the traditional ThT fluorescence methods used in amyloid research today. High-resolution approaches can struggle when investigating protein aggregation, as the proteins exist as complex oligomeric mixtures of many sizes and several conformations or polymorphs. Thus, MS is positioned to complement both high- and low-resolution approaches to studying amyloid fibril formation and protein-inhibitor interactions. This review covers basics in MS paired with ion mobility, continuous hydrogen-deuterium exchange (continuous HDX), pulsed hydrogen-deuterium exchange (pulsed HDX), fast photochemical oxidation of proteins (FPOP) and other irreversible labeling methods, and chemical cross-linking. We then review the applications of these approaches to studying amyloid-prone proteins with a focus on amyloid beta and alpha-synuclein. Another focus is the determination of protein-inhibitor interactions. The expectation is that MS will bring new insights to amyloid formation and thereby play an important role to prevent their formation.
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Affiliation(s)
- Wesley J Wagner
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, USA
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2
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Bai Y, Zhang S, Dong H, Liu Y, Liu C, Zhang X. Advanced Techniques for Detecting Protein Misfolding and Aggregation in Cellular Environments. Chem Rev 2023; 123:12254-12311. [PMID: 37874548 DOI: 10.1021/acs.chemrev.3c00494] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Protein misfolding and aggregation, a key contributor to the progression of numerous neurodegenerative diseases, results in functional deficiencies and the creation of harmful intermediates. Detailed visualization of this misfolding process is of paramount importance for improving our understanding of disease mechanisms and for the development of potential therapeutic strategies. While in vitro studies using purified proteins have been instrumental in delivering significant insights into protein misfolding, the behavior of these proteins in the complex milieu of living cells often diverges significantly from such simplified environments. Biomedical imaging performed in cell provides cellular-level information with high physiological and pathological relevance, often surpassing the depth of information attainable through in vitro methods. This review highlights a variety of methodologies used to scrutinize protein misfolding within biological systems. This includes optical-based methods, strategies leaning on mass spectrometry, in-cell nuclear magnetic resonance, and cryo-electron microscopy. Recent advancements in these techniques have notably deepened our understanding of protein misfolding processes and the features of the resulting misfolded species within living cells. The progression in these fields promises to catalyze further breakthroughs in our comprehension of neurodegenerative disease mechanisms and potential therapeutic interventions.
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Affiliation(s)
- Yulong Bai
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Shengnan Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Hui Dong
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- University of the Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Xin Zhang
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
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3
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Botamanenko DY, Reitenbach DW, Miller LM, Jarrold MF. Electrostatic Linear Ion Trap Optimization Strategy for High Resolution Charge Detection Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:1731-1740. [PMID: 37466262 PMCID: PMC10842736 DOI: 10.1021/jasms.3c00177] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Single ion mass measurements allow mass distributions to be recorded for heterogeneous samples that cannot be analyzed by conventional mass spectrometry. In charge detection mass spectrometry (CD-MS), ions are detected using a conducting cylinder coupled to a charge sensitive amplifier. For optimum performance, the detection cylinder is embedded in an electrostatic linear ion trap (ELIT) where trapped ions oscillate between end-caps that act as opposing ion mirrors. The oscillating ions generate a periodic signal that is analyzed by fast Fourier transforms. The frequency yields the m/z, and the magnitude provides the charge. With a charge precision of 0.2 elementary charges, ions can be assigned to their correct charge states with a low error rate, and the m/z resolving power determines the mass resolving power. Previously, the best mass resolving power achieved with CD-MS was 300. We have recently increased the mass resolving power to 700, through the better optimization of the end-cap potentials. To make a more dramatic improvement in the m/z resolving power, it is necessary to find an ELIT geometry and end-cap potentials that can simultaneously make the ion oscillation frequency independent of both the ion energy and ion trajectory (angular divergence and radial offset) of the entering ion. We describe an optimization strategy that allows these conditions to be met while also adjusting the signal duty cycle to 50% to maximize the signal-to-noise ratio for the charge measurement. The optimized ELIT provides an m/z resolving power of over 300 000 in simulations. Coupled with the high precision charge determination available with CD-MS, this will yield a mass resolving power of 300 000. Such a high mass resolving power will be transformative for the analysis of heterogeneous samples.
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Affiliation(s)
- Daniel Y Botamanenko
- Chemistry Department, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405
- Megadalton Solutions Inc., 3750 E Bluebird Lane, Bloomington, Indiana 47401
| | - David W Reitenbach
- Chemistry Department, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405
| | - Lohra M Miller
- Chemistry Department, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405
| | - Martin F Jarrold
- Chemistry Department, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405
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4
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Miller LM, Jarrold MF. Charge detection mass spectrometry for the analysis of viruses and virus-like particles. Essays Biochem 2023; 67:315-323. [PMID: 36062529 PMCID: PMC10842916 DOI: 10.1042/ebc20220101] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/11/2022] [Accepted: 08/19/2022] [Indexed: 11/17/2022]
Abstract
Heterogeneity usually restricts conventional mass spectrometry to molecular weights less than around a megadalton. As a single-particle technique, charge detection mass spectrometry (CDMS) overcomes this limitation. In CDMS, the mass-to-charge (m/z) ratio and charge are measured simultaneously for individual ions, giving a direct mass measurement for each ion. Recent applications include the analysis of viruses, virus-like particles, vaccines, heavily glycosylated proteins, and gene therapy vectors.
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Affiliation(s)
- Lohra M Miller
- Department of Chemistry, Indiana University, 800 E Kirkwood Ave, Bloomington 47401, Indiana
| | - Martin F Jarrold
- Department of Chemistry, Indiana University, 800 E Kirkwood Ave, Bloomington 47401, Indiana
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5
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Mass spectrometric insights into protein aggregation. Essays Biochem 2023; 67:243-253. [PMID: 36636963 PMCID: PMC10070474 DOI: 10.1042/ebc20220103] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/11/2022] [Accepted: 12/14/2022] [Indexed: 01/14/2023]
Abstract
Protein aggregation is now recognized as a generic and significant component of the protein energy landscape. Occurring through a complex and dynamic pathway of structural interconversion, the assembly of misfolded proteins to form soluble oligomers and insoluble aggregates remains a challenging topic of study, both in vitro and in vivo. Since the etiology of numerous human diseases has been associated with protein aggregation, and it has become a field of increasing importance in the biopharmaceutical industry, the biophysical characterization of protein misfolded states and their aggregation mechanisms continues to receive increased attention. Mass spectrometry (MS) has firmly established itself as a powerful analytical tool capable of both detection and characterization of proteins at all levels of structure. Given inherent advantages of biological MS, including high sensitivity, rapid timescales of analysis, and the ability to distinguish individual components from complex mixtures with unrivalled specificity, it has found widespread use in the study of protein aggregation, importantly, where traditional structural biology approaches are often not amenable. The present review aims to provide a brief overview of selected MS-based approaches that can provide a range of biophysical descriptors associated with protein conformation and the aggregation pathway. Recent examples highlight where this technology has provided unique structural and mechanistic understanding of protein aggregation.
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6
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Krzek M, Stroobants S, Gelin P, De Malsche W, Maes D. Influence of Centrifugation and Shaking on the Self-Assembly of Lysozyme Fibrils. Biomolecules 2022; 12:biom12121746. [PMID: 36551175 PMCID: PMC9775142 DOI: 10.3390/biom12121746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/15/2022] [Accepted: 11/19/2022] [Indexed: 11/25/2022] Open
Abstract
Protein self-assembly into fibrils and oligomers plays a key role in the etiology of degenerative diseases. Several pathways for this self-assembly process have been described and shown to result in different types and ratios of final assemblies, therewith defining the effective physiological response. Known factors that influence assembly pathways are chemical conditions and the presence or lack of agitation. However, in natural and industrial systems, proteins are exposed to a sequence of different and often complex mass transfers. In this paper, we compare the effect of two fundamentally different mass transfer processes on the fibrilization process. Aggregation-prone solutions of hen egg white lysozyme were subjected to predominantly non-advective mass transfer by employing centrifugation and to advective mass transport represented by orbital shaking. In both cases, fibrilization was triggered, while in quiescent only oligomers were formed. The fibrils obtained by shaking compared to fibrils obtained through centrifugation were shorter, thicker, and more rigid. They had rod-like protofibrils as building blocks and a significantly higher β-sheet content was observed. In contrast, fibrils from centrifugation were more flexible and braided. They consisted of intertwined filaments and had low β-sheet content at the expense of random coil. To the best of our knowledge, this is the first evidence of a fibrilization pathway selectivity, with the fibrilization route determined by the mass transfer and mixing configuration (shaking versus centrifugation). This selectivity can be potentially employed for directed protein fibrilization.
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Affiliation(s)
- Marzena Krzek
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Sander Stroobants
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Pierre Gelin
- μFlow Group, Department of Chemical Engineering, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Wim De Malsche
- μFlow Group, Department of Chemical Engineering, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Dominique Maes
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
- Correspondence:
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7
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Tsirkou A, Kaczorowski F, Verdurand M, Raffoul R, Pansieri J, Quadrio I, Chauveau F, Antoine R. Charge detection mass spectrometry on human-amplified fibrils from different synucleinopathies. Chem Commun (Camb) 2022; 58:7192-7195. [PMID: 35670578 DOI: 10.1039/d2cc00200k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Amyloid fibrils are self-assembled mesoscopic protein aggregates, which can accumulate to form deposits or plaques in the brain. In vitro amplification of fibrils can be achieved with real-time quaking-induced conversion (RT-QuIC). However, this emerging technique would benefit from a complementary method to assess structural properties of the amplification products. This work demonstrates the feasibility of nanospray-charge-detection-mass-spectrometry (CDMS) performed on α-synuclein (αSyn) fibrils amplified from human brains with Parkinson's disease (PD) or Dementia with Lewy bodies (DLB) and its synergistic combination with RT-QuIC.
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Affiliation(s)
- Aikaterini Tsirkou
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Lyon, France.
| | - Flora Kaczorowski
- Laboratory of Neurobiology and Neurogenetics, Department of Biochemistry and Molecular Biology, Lyon University Hospital, 69677 BRON Cedex, France.,Center for Memory Resources and Research, Lyon University Hospital, Lyon 1 University, Villeurbanne, France.,Univ Lyon, Centre de Recherche en Neurosciences de Lyon, Equipe BIORAN, Inserm U1028 - CNRS UMR5292, Université Claude Bernard Lyon 1, Groupement Hospitalier Est - CERMEP, 69677 BRON Cedex, France.
| | - Mathieu Verdurand
- Laboratory of Neurobiology and Neurogenetics, Department of Biochemistry and Molecular Biology, Lyon University Hospital, 69677 BRON Cedex, France.,Center for Memory Resources and Research, Lyon University Hospital, Lyon 1 University, Villeurbanne, France.,Univ Lyon, Centre de Recherche en Neurosciences de Lyon, Equipe BIORAN, Inserm U1028 - CNRS UMR5292, Université Claude Bernard Lyon 1, Groupement Hospitalier Est - CERMEP, 69677 BRON Cedex, France.
| | - Rana Raffoul
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Lyon, France.
| | - Jonathan Pansieri
- Oxford University, Nuffield Department of Clinical Neurosciences, Oxford University, UK
| | - Isabelle Quadrio
- Laboratory of Neurobiology and Neurogenetics, Department of Biochemistry and Molecular Biology, Lyon University Hospital, 69677 BRON Cedex, France.,Center for Memory Resources and Research, Lyon University Hospital, Lyon 1 University, Villeurbanne, France.,Univ Lyon, Centre de Recherche en Neurosciences de Lyon, Equipe BIORAN, Inserm U1028 - CNRS UMR5292, Université Claude Bernard Lyon 1, Groupement Hospitalier Est - CERMEP, 69677 BRON Cedex, France.
| | - Fabien Chauveau
- Univ Lyon, Centre de Recherche en Neurosciences de Lyon, Equipe BIORAN, Inserm U1028 - CNRS UMR5292, Université Claude Bernard Lyon 1, Groupement Hospitalier Est - CERMEP, 69677 BRON Cedex, France.
| | - Rodolphe Antoine
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Lyon, France.
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8
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Abstract
Charge detection mass spectrometry (CDMS) is a single-particle technique where the masses of individual ions are determined from simultaneous measurement of their mass-to-charge ratio (m/z) and charge. Masses are determined for thousands of individual ions, and then the results are binned to give a mass spectrum. Using this approach, accurate mass distributions can be measured for heterogeneous and high-molecular-weight samples that are usually not amenable to analysis by conventional mass spectrometry. Recent applications include heavily glycosylated proteins, protein complexes, protein aggregates such as amyloid fibers, infectious viruses, gene therapies, vaccines, and vesicles such as exosomes.
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Affiliation(s)
- Martin F Jarrold
- Chemistry Department, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47404, United States
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9
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Vallejo DD, Ramírez CR, Parson KF, Han Y, Gadkari VG, Ruotolo BT. Mass Spectrometry Methods for Measuring Protein Stability. Chem Rev 2022; 122:7690-7719. [PMID: 35316030 PMCID: PMC9197173 DOI: 10.1021/acs.chemrev.1c00857] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Mass spectrometry is a central technology in the life sciences, providing our most comprehensive account of the molecular inventory of the cell. In parallel with developments in mass spectrometry technologies targeting such assessments of cellular composition, mass spectrometry tools have emerged as versatile probes of biomolecular stability. In this review, we cover recent advancements in this branch of mass spectrometry that target proteins, a centrally important class of macromolecules that accounts for most biochemical functions and drug targets. Our efforts cover tools such as hydrogen-deuterium exchange, chemical cross-linking, ion mobility, collision induced unfolding, and other techniques capable of stability assessments on a proteomic scale. In addition, we focus on a range of application areas where mass spectrometry-driven protein stability measurements have made notable impacts, including studies of membrane proteins, heat shock proteins, amyloidogenic proteins, and biotherapeutics. We conclude by briefly discussing the future of this vibrant and fast-moving area of research.
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Affiliation(s)
- Daniel D. Vallejo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Carolina Rojas Ramírez
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kristine F. Parson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yilin Han
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Varun G. Gadkari
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brandon T. Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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10
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Strazdaite S, Roeters SJ, Sakalauskas A, Sneideris T, Kirschner J, Pedersen KB, Schiøtt B, Jensen F, Weidner T, Smirnovas V, Niaura G. Interaction of Amyloid-β-(1-42) Peptide and Its Aggregates with Lipid/Water Interfaces Probed by Vibrational Sum-Frequency Generation Spectroscopy. J Phys Chem B 2021; 125:11208-11218. [PMID: 34597059 DOI: 10.1021/acs.jpcb.1c04882] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this study, we use surface-sensitive vibrational sum-frequency generation (VSFG) spectroscopy to investigate the interaction between model lipid monolayers and Aβ(1-42) in its monomeric and aggregated states. Combining VSFG with atomic force microscopy (AFM) and thioflavin T (ThT) fluorescence measurements, we found that only small aggregates with probably a β-hairpin-like structure adsorbed to the zwitterionic lipid monolayer (DOPC). In contrast, larger aggregates with an extended β-sheet structure adsorbed to a negatively charged lipid monolayer (DOPG). The adsorption of small, initially formed aggregates strongly destabilized both monolayers, but only the DOPC monolayer was completely disrupted. We showed that the intensity of the amide-II' band in achiral (SSP) and chiral (SPP) polarization combinations increased in time when Aβ(1-42) aggregates accumulated at the DOPG monolayer. Nevertheless, almost no adsorption of preformed mature fibrils to DOPG monolayers was detected. By performing spectral VSFG calculations, we revealed a clear correlation between the amide-II' signal and the degree of amyloid aggregates (e.g., oligomers or (proto)fibrils) of various Aβ(1-42) structures. The calculations showed that only structures with a significant amyloid β-sheet content have a strong amide-II' intensity, in line with previous Raman studies. The combination of the presented results substantiates the amide-II(') band as a legitimate amyloid marker.
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Affiliation(s)
- S Strazdaite
- Department of Organic Chemistry, Center for Physical Sciences and Technology, Sauletekio Ave. 3, Vilnius LT-10257, Lithuania
| | - S J Roeters
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - A Sakalauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio 7, LT-10257 Vilnius, Lithuania
| | - T Sneideris
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio 7, LT-10257 Vilnius, Lithuania
| | - J Kirschner
- Institute of Solid State Physics, TU Wien, Wiedner Hauptstrasse 8-10, 1040 Vienna, Austria
| | - K B Pedersen
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - B Schiøtt
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - F Jensen
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - T Weidner
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - V Smirnovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio 7, LT-10257 Vilnius, Lithuania
| | - G Niaura
- Department of Organic Chemistry, Center for Physical Sciences and Technology, Sauletekio Ave. 3, Vilnius LT-10257, Lithuania
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11
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Kummer N, Wu T, De France KJ, Zuber F, Ren Q, Fischer P, Campioni S, Nyström G. Self-Assembly Pathways and Antimicrobial Properties of Lysozyme in Different Aggregation States. Biomacromolecules 2021; 22:4327-4336. [PMID: 34533934 DOI: 10.1021/acs.biomac.1c00870] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Antimicrobial resistance in microorganisms will cause millions of deaths and pose a vast burden on health systems; therefore, alternatives to existing small-molecule antibiotics have to be developed. Lysozyme is an antimicrobial enzyme and has broad-spectrum antimicrobial activity in different aggregated forms. Here, we propose a reductive pathway to obtain colloidally stable amyloid-like worm-shaped lysozyme nanoparticles (worms) from hen egg white lysozyme (HEWL) and compare them to amyloid fibrils made in an acid hydrolysis pathway. The aggregation of HEWL into worms follows strongly pH-dependent kinetics and induces a structural transition from α-helices to β-sheets. Both HEWL worms and amyloid fibrils show broad-spectrum antimicrobial activity against the bacteria Staphylococcus aureus (Gram-positive), Escherichia coli (Gram-negative), and the fungus Candida albicans. The colloidal stability of the worms allows the determination of minimum inhibitory concentrations, which are lower than that for native HEWL in the case of S. aureus. Overall, amyloid fibrils have the strongest antimicrobial effect, likely due to the increased positive charge compared to native HEWL. The structural and functional characterizations of HEWL worms and amyloids investigated herein are critical for understanding the detailed mechanisms of antimicrobial activity and opens up new avenues for the design of broad-spectrum antimicrobial materials for use in various applications.
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Affiliation(s)
- Nico Kummer
- Laboratory for Cellulose & Wood Materials, Empa-Swiss Federal Laboratories for Materials Science and Technology, Überlandstrasse 129, 8600 Dübendorf, Switzerland.,Institute of Food Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Tingting Wu
- Laboratory for Cellulose & Wood Materials, Empa-Swiss Federal Laboratories for Materials Science and Technology, Überlandstrasse 129, 8600 Dübendorf, Switzerland.,State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, 201620 Shanghai, P. R. China
| | - Kevin J De France
- Laboratory for Cellulose & Wood Materials, Empa-Swiss Federal Laboratories for Materials Science and Technology, Überlandstrasse 129, 8600 Dübendorf, Switzerland
| | - Flavia Zuber
- Laboratory for Biointerfaces, Empa-Swiss Federal Laboratories for Materials Science and Technology, Lerchenfeldstrasse 5, 9014 St. Gallen, Switzerland
| | - Qun Ren
- Laboratory for Biointerfaces, Empa-Swiss Federal Laboratories for Materials Science and Technology, Lerchenfeldstrasse 5, 9014 St. Gallen, Switzerland
| | - Peter Fischer
- Institute of Food Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Silvia Campioni
- Laboratory for Cellulose & Wood Materials, Empa-Swiss Federal Laboratories for Materials Science and Technology, Überlandstrasse 129, 8600 Dübendorf, Switzerland
| | - Gustav Nyström
- Laboratory for Cellulose & Wood Materials, Empa-Swiss Federal Laboratories for Materials Science and Technology, Überlandstrasse 129, 8600 Dübendorf, Switzerland.,Institute of Food Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
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12
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Lutter L, Aubrey LD, Xue WF. On the Structural Diversity and Individuality of Polymorphic Amyloid Protein Assemblies. J Mol Biol 2021; 433:167124. [PMID: 34224749 DOI: 10.1016/j.jmb.2021.167124] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/20/2021] [Accepted: 06/26/2021] [Indexed: 12/24/2022]
Abstract
The prediction of highly ordered three-dimensional structures of amyloid protein fibrils from the amino acid sequences of their monomeric self-assembly precursors constitutes a challenging and unresolved aspect of the classical protein folding problem. Because of the polymorphic nature of amyloid assembly whereby polypeptide chains of identical amino acid sequences under identical conditions are capable of self-assembly into a spectrum of different fibril structures, the prediction of amyloid structures from an amino acid sequence requires a detailed and holistic understanding of its assembly free energy landscape. The full extent of the structure space accessible to the cross-β molecular architecture of amyloid must also be resolved. Here, we review the current understanding of the diversity and the individuality of amyloid structures, and how the polymorphic landscape of amyloid links to biology and disease phenotypes. We present a comprehensive review of structural models of amyloid fibrils derived by cryo-EM, ssNMR and AFM to date, and discuss the challenges ahead for resolving the structural basis and the biological consequences of polymorphic amyloid assemblies.
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Affiliation(s)
- Liisa Lutter
- School of Biosciences, Division of Natural Sciences, University of Kent, CT2 7NJ Canterbury, UK
| | - Liam D Aubrey
- School of Biosciences, Division of Natural Sciences, University of Kent, CT2 7NJ Canterbury, UK
| | - Wei-Feng Xue
- School of Biosciences, Division of Natural Sciences, University of Kent, CT2 7NJ Canterbury, UK.
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13
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Morzy D, Rubio-Sánchez R, Joshi H, Aksimentiev A, Di Michele L, Keyser UF. Cations Regulate Membrane Attachment and Functionality of DNA Nanostructures. J Am Chem Soc 2021; 143:7358-7367. [PMID: 33961742 PMCID: PMC8154537 DOI: 10.1021/jacs.1c00166] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
The interplay between nucleic acids
and lipids underpins several
key processes in molecular biology, synthetic biotechnology, vaccine
technology, and nanomedicine. These interactions are often electrostatic
in nature, and much of their rich phenomenology remains unexplored
in view of the chemical diversity of lipids, the heterogeneity of
their phases, and the broad range of relevant solvent conditions.
Here we unravel the electrostatic interactions between zwitterionic
lipid membranes and DNA nanostructures in the presence of physiologically
relevant cations, with the purpose of identifying new routes to program
DNA–lipid complexation and membrane-active nanodevices. We
demonstrate that this interplay is influenced by both the phase of
the lipid membranes and the valency of the ions and observe divalent
cation bridging between nucleic acids and gel-phase bilayers. Furthermore,
even in the presence of hydrophobic modifications on the DNA, we find
that cations are still required to enable DNA adhesion to liquid-phase
membranes. We show that the latter mechanism can be exploited to control
the degree of attachment of cholesterol-modified DNA nanostructures
by modifying their overall hydrophobicity and charge. Besides their
biological relevance, the interaction mechanisms we explored hold
great practical potential in the design of biomimetic nanodevices,
as we show by constructing an ion-regulated DNA-based synthetic enzyme.
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Affiliation(s)
- Diana Morzy
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Roger Rubio-Sánchez
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Himanshu Joshi
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Lorenzo Di Michele
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom.,Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, United Kingdom
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
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14
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Fibrilar Polymorphism of the Bacterial Extracellular Matrix Protein TasA. Microorganisms 2021; 9:microorganisms9030529. [PMID: 33806534 PMCID: PMC8000256 DOI: 10.3390/microorganisms9030529] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/23/2021] [Accepted: 03/01/2021] [Indexed: 12/25/2022] Open
Abstract
Functional amyloid proteins often appear as fibers in extracellular matrices of microbial soft colonies. In contrast to disease-related amyloid structures, they serve a functional goal that benefits the organism that secretes them, which is the reason for the title “functional”. Biofilms are a specific example of a microbial community in which functional amyloid fibers play a role. Functional amyloid proteins contribute to the mechanical stability of biofilms and mediate the adhesion of the cells to themselves as well as to surfaces. Recently, it has been shown that functional amyloid proteins also play a regulatory role in biofilm development. TasA is the major proteinaceous fibrilar component of the extracellular matrix of biofilms made of the soil bacterium and Gram-positive Bacillus subtilis. We have previously shown, as later corroborated by others, that in acidic solutions, TasA forms compact aggregates that are composed of tangled fibers. Here, we show that in a neutral pH and above a certain TasA concentration, the fibers of TasA are elongated and straight and that they bundle up in highly concentrated salt solutions. TasA fibers resemble the canonic amyloid morphology; however, these fibers also bear an interesting nm-scale periodicity along the fiber axis. At the molecular level, TasA fibers contain a twisted β-sheet structure, as indicated by circular dichroism measurements. Our study shows that the morphology of TasA fibers depends on the environmental conditions. Different fibrilar morphologies may be related with different functional roles in biofilms, ranging from granting biofilms with a mechanical support to acting as antibiotic agents.
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15
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Gustafson EL, Murray HV, Caldwell T, Austin DE. Accurately Mapping Image Charge and Calibrating Ion Velocity in Charge Detection Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2161-2170. [PMID: 32856905 DOI: 10.1021/jasms.0c00263] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Image charge detection is the foundation of charge detection mass spectrometry (CDMS). The mass-to-charge ratio, m/z, of a highly charged ion or particle is determined by measuring the particle's charge and velocity. Charge is typically determined from a calibrated image charge signal, and the particle velocity is calculated using the peaks from the shaped signal as they relate to the particle position and time-of-flight through a detector of known length. Although much has been done to improve the charge accuracy in CDMS, little has been done to address the inconsistencies in the particle velocity measurements and the interpretation of peak position and effective electrode length. In this work, we combine SIMION ion trajectory software and the Shockley-Ramo theorem to accurately determine the effective electrode length, peak position, and shape of the signal peaks. Six model charge detector geometries were examined with this method and evaluated in laboratory experiments. Experimental results in all cases agreed with the simulations. Using a charge detector with multiple, 12.7 mm-long cylindrical electrodes, experimental velocities across and between electrodes agreed within 0.25% relative standard deviation (RSD) when this method was used to correct for effective electrode lengths, corresponding to an uncertainty in the effective electrode length of only 40 μm. For a detector with multiple electrodes and varied electrode spacing, experiments showed that the peak amplitude and shape vary with the geometry and with the particle path through the detector, whereas all peak areas agreed to within 2.3% RSD. For a charge detector made of two printed circuit boards, the velocities agreed within 0.44% RSD using the calculated effective electrode length.
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Affiliation(s)
- Elaura L Gustafson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Halle V Murray
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Tabitha Caldwell
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Daniel E Austin
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
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16
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Antoine R. Weighing synthetic polymers of ultra-high molar mass and polymeric nanomaterials: What can we learn from charge detection mass spectrometry? RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34 Suppl 2:e8539. [PMID: 31353622 DOI: 10.1002/rcm.8539] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/19/2019] [Accepted: 07/19/2019] [Indexed: 06/10/2023]
Abstract
Advances in soft ionization techniques for mass spectrometry (MS) of polymeric materials make it possible to determine the masses of intact molecular ions exceeding megadaltons. Interfacing MS with separation and fragmentation methods has additionally led to impressive advances in the ability to structurally characterize polymers. Even if the gap to the megadalton range has been bridged by MS for polymers standards, the MS-based analysis for more complex polymeric materials is still challenging. Charge detection mass spectrometry (CDMS) is a single-molecule method where the mass and the charge of each ion are directly determined from individual measurements. The entire molecular mass distribution of a polymer sample can be thus accurately measured. Described in this perspective paper is how molecular weight distribution as well as charge distribution can provide new insights into the structural and compositional studies of synthetic polymers and polymeric nanomaterials in the megadalton to gigadalton range of molecular weight. The recent multidimensional CDMS studies involving couplings with separation and dissociation techniques will be presented. And, finally, an outlook for the future avenues of the CDMS technique in the field of synthetic polymers of ultra-high molar mass and polymeric nanomaterials will be provided.
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Affiliation(s)
- Rodolphe Antoine
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, UMR 5306, F-69622, Lyon, France
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17
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Pansieri J, Iashchishyn IA, Fakhouri H, Ostojić L, Malisauskas M, Musteikyte G, Smirnovas V, Schneider MM, Scheidt T, Xu CK, Meisl G, Knowles TPJ, Gazit E, Antoine R, Morozova-Roche LA. Templating S100A9 amyloids on Aβ fibrillar surfaces revealed by charge detection mass spectrometry, microscopy, kinetic and microfluidic analyses. Chem Sci 2020; 11:7031-7039. [PMID: 34122996 PMCID: PMC8159403 DOI: 10.1039/c9sc05905a] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 06/16/2020] [Indexed: 12/16/2022] Open
Abstract
The mechanism of amyloid co-aggregation and its nucleation process are not fully understood in spite of extensive studies. Deciphering the interactions between proinflammatory S100A9 protein and Aβ42 peptide in Alzheimer's disease is fundamental since inflammation plays a central role in the disease onset. Here we use innovative charge detection mass spectrometry (CDMS) together with biophysical techniques to provide mechanistic insight into the co-aggregation process and differentiate amyloid complexes at a single particle level. Combination of mass and charge distributions of amyloids together with reconstruction of the differences between them and detailed microscopy reveals that co-aggregation involves templating of S100A9 fibrils on the surface of Aβ42 amyloids. Kinetic analysis further corroborates that the surfaces available for the Aβ42 secondary nucleation are diminished due to the coating by S100A9 amyloids, while the binding of S100A9 to Aβ42 fibrils is validated by a microfluidic assay. We demonstrate that synergy between CDMS, microscopy, kinetic and microfluidic analyses opens new directions in interdisciplinary research.
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Affiliation(s)
- Jonathan Pansieri
- Department of Medical Biochemistry and Biophysics, Umeå University SE-90187 Umeå Sweden
| | - Igor A Iashchishyn
- Department of Medical Biochemistry and Biophysics, Umeå University SE-90187 Umeå Sweden
| | - Hussein Fakhouri
- Institut Lumière Matière, UMR 5306, Université Claude Bernard Lyon 1, CNRS, Univ Lyon F-69100 Villeurbanne France
| | - Lucija Ostojić
- Department of Medical Biochemistry and Biophysics, Umeå University SE-90187 Umeå Sweden
| | - Mantas Malisauskas
- Department of Medical Biochemistry and Biophysics, Umeå University SE-90187 Umeå Sweden
| | - Greta Musteikyte
- Institute of Biotechnology, Life Sciences Center, Vilnius University Vilnius Lithuania
| | - Vytautas Smirnovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University Vilnius Lithuania
| | - Matthias M Schneider
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Tom Scheidt
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Catherine K Xu
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Georg Meisl
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
- Cavendish Laboratory, Department of Physics, University of Cambridge JJ Thompson Ave CB3 0HE Cambridge UK
| | - Ehud Gazit
- Department of Medical Biochemistry and Biophysics, Umeå University SE-90187 Umeå Sweden
- School of Molecular Cell Biology and Biotechnology, Tel Aviv University Tel Aviv 69978 Israel
| | - Rodolphe Antoine
- Institut Lumière Matière, UMR 5306, Université Claude Bernard Lyon 1, CNRS, Univ Lyon F-69100 Villeurbanne France
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18
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Exploring the structure and dynamics of macromolecular complexes by native mass spectrometry. J Proteomics 2020; 222:103799. [DOI: 10.1016/j.jprot.2020.103799] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 03/23/2020] [Accepted: 04/25/2020] [Indexed: 12/15/2022]
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19
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Strazdaite S, Navakauskas E, Kirschner J, Sneideris T, Niaura G. Structure Determination of Hen Egg-White Lysozyme Aggregates Adsorbed to Lipid/Water and Air/Water Interfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:4766-4775. [PMID: 32251594 DOI: 10.1021/acs.langmuir.9b03826] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We use vibrational sum-frequency generation (VSFG) spectroscopy to study the structure of hen egg-white lysozyme (HEWL) aggregates adsorbed to DOPG/D2O and air/D2O interfaces. We find that aggregates with a parallel and antiparallel β-sheet structure together with smaller unordered aggregates and a denaturated protein are adsorbed to both interfaces. We demonstrate that to retrieve this information, fitting of the VSFG spectra is essential. The number of bands contributing to the VSFG spectrum might be misinterpreted, due to interference between peaks with opposite orientation and a nonresonant background. Our study identified hydrophobicity as the main driving force for adsorption to the air/D2O interface. Adsorption to the DOPG/D2O interface is also influenced by hydrophobic interaction; however, electrostatic interaction between the charged protein's groups and the lipid's headgroups has the most significant effect on the adsorption. We find that the intensity of the VSFG spectrum at the DOPG/D2O interface is strongly enhanced by varying the pH of the solution. We show that this change is not due to a change of lysozyme's and its aggregates' charge but due to dipole reorientation at the DOPG/D2O interface. This finding suggests that extra care must be taken when interpreting the VSFG spectrum of proteins adsorbed at the lipid/water interface.
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Affiliation(s)
- S Strazdaite
- Department of Organic Chemistry, Center for Physical Sciences and Technology, Sauletekio Ave. 3, Vilnius LT-10257, Lithuania
| | - E Navakauskas
- Department of Organic Chemistry, Center for Physical Sciences and Technology, Sauletekio Ave. 3, Vilnius LT-10257, Lithuania
| | - J Kirschner
- Institute of Solid State Physics, Vienna Technical University, Wiedner Hauptstrasse 8-10, 1040 Vienna, Austria
| | - T Sneideris
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio 7, LT-10257 Vilnius, Lithuania
| | - G Niaura
- Department of Organic Chemistry, Center for Physical Sciences and Technology, Sauletekio Ave. 3, Vilnius LT-10257, Lithuania
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20
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Maiolo D, Pizzi A, Gori A, Gazzera L, Demitri N, Genoni A, Baggi F, Moda F, Terraneo G, Baldelli Bombelli F, Metrangolo P, Resnati G. Halogenation of the N-Terminus Tyrosine 10 Promotes Supramolecular Stabilization of the Amyloid-β Sequence 7-12. ChemistryOpen 2020; 9:253-260. [PMID: 32110506 PMCID: PMC7041548 DOI: 10.1002/open.201900350] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/07/2020] [Indexed: 12/16/2022] Open
Abstract
Here, we demonstrate that introduction of halogen atoms at the tyrosine 10 phenol ring of the DSGYEV sequence derived from the flexible amyloid-β N-terminus, promotes its self-assembly in the solid state. In particular, we report the crystal structures of two halogen-modified sequences, which we found to be stabilized in the solid state by halogen-mediated interactions. The structural study is corroborated by Non-Covalent Interaction (NCI) analysis. Our results prove that selective halogenation of an amino acid enhances the supramolecular organization of otherwise unstructured biologically-relevant sequences. This method may develop as a general strategy for stabilizing highly polymorphic peptide regions.
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Affiliation(s)
- Daniele Maiolo
- Dept. Chem., Mater., and Chem. Eng. “Giulio Natta”Politecnico di MilanoVia L. Mancinelli 720131MilanoItaly
| | - Andrea Pizzi
- Dept. Chem., Mater., and Chem. Eng. “Giulio Natta”Politecnico di MilanoVia L. Mancinelli 720131MilanoItaly
| | - Alessandro Gori
- Istituto di Scienze e Tecnologie ChimicheNational Research Council of ItalyVia M. Bianco 920131MilanoItaly
| | - Lara Gazzera
- Dept. Chem., Mater., and Chem. Eng. “Giulio Natta”Politecnico di MilanoVia L. Mancinelli 720131MilanoItaly
| | - Nicola Demitri
- Elettra – Sincrotrone TriesteS.S. 14 Km 163.5 in Area Science Park34149Basovizza – TriesteItaly
| | - Alessandro Genoni
- Laboratoire de Physique et Chimie ThéoriquesUniversité de Lorraine and CNRS UMR CNRS 70191 Boulevard Arago57078MetzFrance
| | - Fulvio Baggi
- Fondazione IRCCS Istituto Neurologico “Carlo Besta”Via G. Celoria 1120133MilanItaly
| | - Fabio Moda
- Fondazione IRCCS Istituto Neurologico “Carlo Besta”Via G. Celoria 1120133MilanItaly
| | - Giancarlo Terraneo
- Dept. Chem., Mater., and Chem. Eng. “Giulio Natta”Politecnico di MilanoVia L. Mancinelli 720131MilanoItaly
- Istituto di Scienze e Tecnologie ChimicheNational Research Council of ItalyVia M. Bianco 920131MilanoItaly
| | | | - Pierangelo Metrangolo
- Dept. Chem., Mater., and Chem. Eng. “Giulio Natta”Politecnico di MilanoVia L. Mancinelli 720131MilanoItaly
| | - Giuseppe Resnati
- Dept. Chem., Mater., and Chem. Eng. “Giulio Natta”Politecnico di MilanoVia L. Mancinelli 720131MilanoItaly
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21
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Halim MA, Bertorelle F, Doussineau T, Antoine R. Direct determination of molecular weight distribution of calf-thymus DNAs and study of their fragmentation under ultrasonic and low-energy infrared irradiations. A charge detection mass spectrometry investigation. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33 Suppl 1:35-39. [PMID: 29885254 DOI: 10.1002/rcm.8204] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/04/2018] [Accepted: 06/04/2018] [Indexed: 06/08/2023]
Abstract
RATIONALE Calf-thymus (CT-DNA) is widely used as a binding agent. The commercial samples are known to be "highly polymerized DNA" samples. CT-DNA is known to be fragile in particular upon ultrasonic wave irradiation. Degradation products could have dramatic consequences on its bio-sensing activity, and an accurate determination of the molecular weight distribution and stability of commercial samples is highly demanded. METHODS We investigated the sensitivity of charge detection mass spectrometry (CDMS), a single-molecule MS method, both with single-pass and ion trap CDMS ("Benner" trap) modes to the determination of the composition and stability (under multiphoton IR irradiation) of calf-thymus DNAs. We also investigated the changes in molecular weight distributions in the course of sonication by irradiating ultrasonic waves to CT-DNA. RESULTS We report, for the first time, the direct molecular weight (MW) distribution of DNA sodium salt from calf-thymus revealing two populations at high (~10 MDa) and low (~3 MDa) molecular weights. We evidence a transition between the high-MW to the low-MW distribution, confirming that the low-MW distribution results from degradation of CT-DNA. Finally, we report also IRMPD experiments carried out on trapped single-stranded linear DNAs from calf-thymus allowing extraction of their activation energy for unimolecular dissociation. CONCLUSIONS We show that single-pass CDMS is a direct, efficient and accurate MS-based approach to determine the composition of calf-thymus DNAs. Furthermore, ion trap CDMS allows us to evaluate the stability (both under multiphoton IR irradiation and in the course of sonication by irradiating ultrasonic wave) of calf-thymus DNAs.
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Affiliation(s)
- Mohammad A Halim
- Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, UMR 5306, Univ Lyon, F-69622, Lyon, France
| | - Franck Bertorelle
- Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, UMR 5306, Univ Lyon, F-69622, Lyon, France
| | - Tristan Doussineau
- Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, UMR 5306, Univ Lyon, F-69622, Lyon, France
| | - Rodolphe Antoine
- Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, UMR 5306, Univ Lyon, F-69622, Lyon, France
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22
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Fakhouri H, Perić M, Bertorelle F, Dugourd P, Dagany X, Russier-Antoine I, Brevet PF, Bonačić-Koutecký V, Antoine R. Sub-100 nanometer silver doped gold–cysteine supramolecular assemblies with enhanced nonlinear optical properties. Phys Chem Chem Phys 2019; 21:12091-12099. [DOI: 10.1039/c9cp00829b] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The ability of gold(i) thiolates to self-assemble into supramolecular architectures opens the route for a new class of nanomaterials with a unique structure–optical property relationship.
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Affiliation(s)
- Hussein Fakhouri
- Univ Lyon
- Université Claude Bernard Lyon 1
- CNRS
- Institut Lumière Matière
- Lyon
| | - Martina Perić
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM) at Interdisciplinary Center for Advanced Sciences and Technology (ICAST)
- University of Split
- 21000 Split
- Croatia
| | - Franck Bertorelle
- Univ Lyon
- Université Claude Bernard Lyon 1
- CNRS
- Institut Lumière Matière
- Lyon
| | - Philippe Dugourd
- Univ Lyon
- Université Claude Bernard Lyon 1
- CNRS
- Institut Lumière Matière
- Lyon
| | - Xavier Dagany
- Univ Lyon
- Université Claude Bernard Lyon 1
- CNRS
- Institut Lumière Matière
- Lyon
| | | | | | - Vlasta Bonačić-Koutecký
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM) at Interdisciplinary Center for Advanced Sciences and Technology (ICAST)
- University of Split
- 21000 Split
- Croatia
- Chemistry Department
| | - Rodolphe Antoine
- Univ Lyon
- Université Claude Bernard Lyon 1
- CNRS
- Institut Lumière Matière
- Lyon
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23
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Magnetic Nanoparticles Applications for Amyloidosis Study and Detection: A Review. NANOMATERIALS 2018; 8:nano8090740. [PMID: 30231587 PMCID: PMC6164038 DOI: 10.3390/nano8090740] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 09/14/2018] [Accepted: 09/16/2018] [Indexed: 12/27/2022]
Abstract
Magnetic nanoparticles (MNPs) have great potential in biomedical and clinical applications because of their many unique properties. This contribution provides an overview of the MNPs mainly used in the field of amyloid diseases. The first part discusses their use in understanding the amyloid mechanisms of fibrillation, with emphasis on their ability to control aggregation of amyloidogenic proteins. The second part deals with the functionalization by various moieties of numerous MNPs’ surfaces (molecules, peptides, antibody fragments, or whole antibodies of MNPs) for the detection and the quantification of amyloid aggregates. The last part of this review focuses on the use of MNPs for magnetic-resonance-based amyloid imaging in biomedical fields, with particular attention to the application of gadolinium-based paramagnetic nanoparticles (AGuIX), which have been recently developed. Biocompatible AGuIX nanoparticles show favorable characteristics for in vivo use, such as nanometric and straightforward functionalization. Their properties have enabled their application in MRI. Here, we report that AGuIX nanoparticles grafted with the Pittsburgh compound B can actively target amyloid aggregates in the brain, beyond the blood–brain barrier, and remain the first step in observing amyloid plaques in a mouse model of Alzheimer’s disease.
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24
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Napp A, Houbart V, Demelenne A, Merville MP, Crommen J, Dumoulin M, Garraux G, Servais AC, Fillet M. Separation and determination of alpha-synuclein monomeric and oligomeric species using two electrophoretic approaches. Electrophoresis 2018; 39:3022-3031. [PMID: 30157293 DOI: 10.1002/elps.201800224] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/11/2018] [Accepted: 07/27/2018] [Indexed: 12/15/2022]
Abstract
Parkinson's disease (PD) is a frequent degenerative disorder that is diagnosed based on clinical symptoms. When the first symptoms appear, more than 70% of the dopaminergic cells are already lost. Therefore, it is of utmost importance to have reliable biomarkers to diagnose much earlier PD. In this context, alpha-synuclein (aSyn) is a protein of high interest because of its tendency to form oligomers and amyloid fibrils. The oligomeric forms seem to play a critical pathological role in PD. To date, most of studies aiming at detecting and quantifying aSyn oligomers were performed by immunoassays, mainly by ELISA using specific antibodies. In this study a capillary gel electrophoresis (CGE) coupled with fluorescence detection method was developed to detect and quantify the oligomeric forms of aSyn formed in vitro. All the results obtained were supported by SDS-PAGE analysis, a widely used and well-known technique but exhibiting a main drawback since it is not an automated technique. The repeatability and the intermediate precision of the method were evaluated, as well as the stability of the labeled and non-labeled aSyn samples. After careful screening and optimization of various labeling reagents, 4-fluoro-7-nitrobenzofurazan (NBD-F) was selected and used to establish a calibration curve with monomeric fluorescently-labeled aSyn. Finally, the method was used to study the effect of doxycycline on the oligomerization process. Altogether, our results show that CGE is a very promising automated technique to analyze aSyn monomers, as well as small oligomers.
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Affiliation(s)
- Aurore Napp
- Laboratory for the Analysis of Medicines, Department of Pharmacy, CIRM, University of Liège, Liège, Belgium
| | - Virginie Houbart
- Laboratory for the Analysis of Medicines, Department of Pharmacy, CIRM, University of Liège, Liège, Belgium
| | - Alice Demelenne
- Laboratory for the Analysis of Medicines, Department of Pharmacy, CIRM, University of Liège, Liège, Belgium
| | - Marie-Paule Merville
- Department of Clinical Chemistry, CIRM, University Hospital Center, University of Liège, Belgium
| | - Jacques Crommen
- Laboratory for the Analysis of Medicines, Department of Pharmacy, CIRM, University of Liège, Liège, Belgium
| | - Mireille Dumoulin
- Laboratory of Enzymology and Protein Folding Centre for Protein Engineering (CIP), University of Liège, Liège, Belgium
| | - Gaëtan Garraux
- Department of Neurology, University Hospital Center, Liège, Belgium
| | - Anne-Catherine Servais
- Laboratory for the Analysis of Medicines, Department of Pharmacy, CIRM, University of Liège, Liège, Belgium
| | - Marianne Fillet
- Laboratory for the Analysis of Medicines, Department of Pharmacy, CIRM, University of Liège, Liège, Belgium
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