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Shi L, Pico J, Zamani S, Castellarin SD, Dee DR. Fibrillization of lentil proteins is impacted by the protein extraction conditions and co-extracted phenolics. Food Chem 2024; 448:139104. [PMID: 38547711 DOI: 10.1016/j.foodchem.2024.139104] [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: 06/30/2023] [Revised: 03/08/2024] [Accepted: 03/19/2024] [Indexed: 04/24/2024]
Abstract
Legume proteins can be induced to form amyloid-like fibrils upon heating at low pH, with the exact conditions greatly impacting the fibril characteristics. The protein extraction method may also impact the resulting fibrils, although this effect has not been carefully examined. Here, the fibrillization of lentil protein prepared using various extraction methods and the corresponding fibril morphology were characterized. It was found that an acidic, rather than alkaline, protein extraction method was better suited for producing homogeneous, long, and straight fibrils from lentil proteins. During alkaline extraction, co-extracted phenolic compounds bound proteins through covalent and non-covalent interactions, contributing to the formation of heterogeneous, curly, and tangled fibrils. Recombination of isolated phenolics and proteins (from acidic extracts) at alkaline pH resulted in a distinct morphology, implicating a role for polyphenol oxidase also in modifying proteins during alkaline extraction. These results help disentangle the complex factors affecting legume protein fibrillization.
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Affiliation(s)
- Lanfang Shi
- Food, Nutrition and Health, Faculty of Land and Food Systems, The University of British Columbia, 2205 East Mall, Vancouver, BC V6T 1Z4, Canada
| | - Joana Pico
- Wine Research Centre, Faculty of Land and Food Systems, The University of British Columbia, 2205 East Mall, Vancouver, BC V6T 1Z4, Canada
| | - Sara Zamani
- Food, Nutrition and Health, Faculty of Land and Food Systems, The University of British Columbia, 2205 East Mall, Vancouver, BC V6T 1Z4, Canada
| | - Simone D Castellarin
- Wine Research Centre, Faculty of Land and Food Systems, The University of British Columbia, 2205 East Mall, Vancouver, BC V6T 1Z4, Canada
| | - Derek R Dee
- Food, Nutrition and Health, Faculty of Land and Food Systems, The University of British Columbia, 2205 East Mall, Vancouver, BC V6T 1Z4, Canada.
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2
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Lordifard P, Shariatpanahi SP, Khajeh K, Saboury AA, Goliaei B. Frequency dependence of ultrasonic effects on the kinetics of hen egg white lysozyme fibrillation. Int J Biol Macromol 2024; 254:127871. [PMID: 37952804 DOI: 10.1016/j.ijbiomac.2023.127871] [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: 07/30/2023] [Revised: 10/23/2023] [Accepted: 11/01/2023] [Indexed: 11/14/2023]
Abstract
Our study aimed to investigate the effects of ultrasound on the fibrillation kinetics of HEWL (hen egg white lysozyme) and its physicochemical properties. Ultrasound, a mechanical wave, can induce conformational changes in proteins. To achieve this, we developed an ultrasound exposure system and used various biophysical techniques, including ThT fluorescence spectroscopy, ATR-FTIR, Far-UV CD spectrophotometry, Fluorescence microscopy, UV-spectroscopy, and seeding experiments. Our results revealed that higher frequencies significantly accelerated the fibrillation of lysozyme by unfolding the native protein and promoting the fibrillation process, thereby reducing the lag time. We observed a change in the secondary structure of the sonicated protein change to the β-structure, but there was no difference in the Tm of native and sonicated proteins. Furthermore, we found that higher ultrasound frequencies had a greater seeding effect. We propose that the effect of frequency can be explained by the impact of the Reynolds number, and for the Megahertz frequency range, we are almost at the transition regime of turbulence. Our results suggest that laminar flows may not induce any significant change in the fibrillation kinetics, while turbulent flows may affect the process.
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Affiliation(s)
- Parinaz Lordifard
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
| | | | - Khosro Khajeh
- Department of Biochemistry, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran.
| | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
| | - Bahram Goliaei
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
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3
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Wojciechowski JW, Szczurek W, Szulc N, Szefczyk M, Kotulska M. PACT - Prediction of amyloid cross-interaction by threading. Sci Rep 2023; 13:22268. [PMID: 38097650 PMCID: PMC10721876 DOI: 10.1038/s41598-023-48886-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023] Open
Abstract
Amyloid proteins are often associated with the onset of diseases, including Alzheimer's, Parkinson's and many others. However, there is a wide class of functional amyloids that are involved in physiological functions, e.g., formation of microbial biofilms or storage of hormones. Recent studies showed that an amyloid fibril could affect the aggregation of another protein, even from a different species. This may result in amplification or attenuation of the aggregation process. Insight into amyloid cross-interactions may be crucial for better understanding of amyloid diseases and the potential influence of microbial amyloids on human proteins. However, due to the demanding nature of the needed experiments, knowledge of such interactions is still limited. Here, we present PACT (Prediction of Amyloid Cross-interaction by Threading) - the computational method for the prediction of amyloid cross-interactions. The method is based on modeling of a heterogeneous fibril formed by two amyloidogenic peptides. The resulting structure is assessed by the structural statistical potential that approximates its plausibility and energetic stability. PACT was developed and first evaluated mostly on data collected in the AmyloGraph database of interacting amyloids and achieved high values of Area Under ROC (AUC=0.88) and F1 (0.82). Then, we applied our method to study the interactions of CsgA - a bacterial biofilm protein that was not used in our in-reference datasets, which is expressed in several bacterial species that inhabit the human intestines - with two human proteins. The study included alpha-synuclein, a human protein that is involved in Parkinson's disease, and human islet amyloid polypeptide (hIAPP), which is involved in type 2 diabetes. In both cases, PACT predicted the appearance of cross-interactions. Importantly, the method indicated specific regions of the proteins, which were shown to play a central role in both interactions. We experimentally confirmed the novel results of the indicated CsgA fragments interacting with hIAPP based on the kinetic characteristics obtained with the ThT assay. PACT opens the possibility of high-throughput studies of amyloid interactions. Importantly, it can work with fairly long protein fragments, and as a purely physicochemical approach, it relies very little on scarce training data. The tool is available as a web server at https://pact.e-science.pl/pact/ . The local version can be downloaded from https://github.com/KubaWojciechowski/PACT .
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Affiliation(s)
- Jakub W Wojciechowski
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wrocław University of Science and Technology, 50-370, Wrocław, Poland.
| | - Witold Szczurek
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wrocław University of Science and Technology, 50-370, Wrocław, Poland
| | - Natalia Szulc
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wrocław University of Science and Technology, 50-370, Wrocław, Poland
- Department of Physics and Biophysics, Wrocław University of Environmental and Life Sciences, Norwida 25, 50-375, Wrocław, Poland
- LPCT, CNRS, Université de Lorraine, F-54000, Nancy, France
| | - Monika Szefczyk
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, 50-370, Wrocław, Poland
| | - Malgorzata Kotulska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wrocław University of Science and Technology, 50-370, Wrocław, Poland.
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4
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Hoppenreijs LJG, Overbeck A, Brune SE, Biedendieck R, Kwade A, Krull R, Boom RM, Keppler JK. Amyloid-like aggregation of recombinant β-lactoglobulin at pH 3.5 and 7.0: Is disulfide bond removal the key to fibrillation? Int J Biol Macromol 2023; 242:124855. [PMID: 37187417 DOI: 10.1016/j.ijbiomac.2023.124855] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 04/19/2023] [Accepted: 05/10/2023] [Indexed: 05/17/2023]
Abstract
Functional nanofibrils from globular proteins are usually formed by heating for several hours at pH 2.0, which induces acidic hydrolysis and consecutive self-association. The functional properties of these micro-metre-long anisotropic structures are promising for biodegradable biomaterials and food applications, but their stability at pH > 2.0 is low. The results presented here show that modified β-lactoglobulin can also form nanofibrils by heating at neutral pH without prior acidic hydrolysis; the key is removing covalent disulfide bonds. The aggregation behaviour of various recombinant β-lactoglobulin variants was systemically studied at pH 3.5 and 7.0. The suppression of intra- and intermolecular disulfide bonds by eliminating one to three out of the five cysteines makes the non-covalent interactions more prevalent and allow for structural rearrangement. This stimulated the linear growth of worm-like aggregates. Full elimination of all five cysteines led to the transformation of worm-like aggregates into actual fibril structures (several hundreds of nanometres long) at pH 7.0. This understanding of the role of cysteine in protein-protein interactions will help to identify proteins and protein modifications to form functional aggregates at neutral pH.
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Affiliation(s)
- Loes J G Hoppenreijs
- Laboratory of Food Process Engineering, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Achim Overbeck
- Technische Universität Braunschweig, Institute of Particle Technology, Volkmaroderstrasse 5, 38104 Braunschweig, Germany; Technische Universität Braunschweig, Center of Pharmaceutical Engineering (PVZ), Franz-Liszt-Straße 35a, 38106 Braunschweig, Germany
| | - Sarah E Brune
- Technische Universität Braunschweig, Institute of Biochemical Engineering, Rebenring 56, 38106 Braunschweig, Germany; Technische Universität Braunschweig, Institute of Microbiology, Rebenring 56, 38106 Braunschweig, Germany; Technische Universität Braunschweig, Braunschweig Integrated Centre of Systems Biology (BRICS), Rebenring 56, 38106 Braunschweig, Germany; Technische Universität Braunschweig, Center of Pharmaceutical Engineering (PVZ), Franz-Liszt-Straße 35a, 38106 Braunschweig, Germany
| | - Rebekka Biedendieck
- Technische Universität Braunschweig, Institute of Microbiology, Rebenring 56, 38106 Braunschweig, Germany; Technische Universität Braunschweig, Braunschweig Integrated Centre of Systems Biology (BRICS), Rebenring 56, 38106 Braunschweig, Germany
| | - Arno Kwade
- Technische Universität Braunschweig, Institute of Particle Technology, Volkmaroderstrasse 5, 38104 Braunschweig, Germany; Technische Universität Braunschweig, Center of Pharmaceutical Engineering (PVZ), Franz-Liszt-Straße 35a, 38106 Braunschweig, Germany
| | - Rainer Krull
- Technische Universität Braunschweig, Institute of Biochemical Engineering, Rebenring 56, 38106 Braunschweig, Germany; Technische Universität Braunschweig, Braunschweig Integrated Centre of Systems Biology (BRICS), Rebenring 56, 38106 Braunschweig, Germany; Technische Universität Braunschweig, Center of Pharmaceutical Engineering (PVZ), Franz-Liszt-Straße 35a, 38106 Braunschweig, Germany
| | - Remko M Boom
- Laboratory of Food Process Engineering, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Julia K Keppler
- Laboratory of Food Process Engineering, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands.
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5
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Dudure R, Ganorkar K, Beldar V, Ghosh SK, Panda AK, Jadhao M. Effect of artificial sweetener saccharin on lysozyme aggregation: A combined spectroscopic and in silico approach. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 290:122269. [PMID: 36566534 DOI: 10.1016/j.saa.2022.122269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 12/11/2022] [Accepted: 12/18/2022] [Indexed: 06/17/2023]
Abstract
The use of saccharin in food products attracts much attention as it involves the risk of lethal allergies and many protein aggregation diseases. However, its role in protein aggregation has not been explored to date. This study embodies the effect of artificial sweeteners on HEWL in the absence and presence of commonly available natural products such as curcumin and EGCG. Various techniques have been used to characterize the protein interaction, such as steady-state emission and time-resolved fluorescence, FTIR, gel electrophoresis, TEM, and molecular docking. Steady-state and time-resolved studies revealed the binding strength and concomitant effect of saccharin on HEWL protein. Kinetic measurements revealed that saccharin causes significant enhancement of HEWL aggregation with a considerable reduction in lag phase time i.e. from 37 hr to 08 hr. Whereas in the presence of natural products, the effect of saccharin on HEWL aggregation was significantly reduced specifically in the case of curcumin. The result obtained in the fluorescence experiment were also supported by the gel electrophoresis technique and morphological images taken by TEM. The rapid change in the secondary structure of the protein in the presence of saccharin was confirmed by the FTIR spectroscopy technique. This study is instrumental in understanding the effect of saccharin on protein aggregation and the role of commonly available natural products in curbing its effect.
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Affiliation(s)
- Rushali Dudure
- Institute of Chemical Technology Mumbai-Marathwada Campus, Jalna, Maharashtra 431203, India
| | - Kapil Ganorkar
- Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur, Maharashtra 440010, India
| | - Vishal Beldar
- Institute of Chemical Technology Mumbai-Marathwada Campus, Jalna, Maharashtra 431203, India
| | - Sujit Kumar Ghosh
- Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur, Maharashtra 440010, India
| | - Alok Kumar Panda
- Environmental Science Laboratory, School of Applied Sciences, KIIT Deemed to be University, Bhubaneswar, Odisha 751 024, India
| | - Manojkumar Jadhao
- Institute of Chemical Technology Mumbai-Marathwada Campus, Jalna, Maharashtra 431203, India.
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6
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Zhang Y, Dee DR. Morphology, Formation Kinetics and Core Composition of Pea and Soy 7S and 11S Globulin Amyloid Fibrils. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:4755-4765. [PMID: 36890640 DOI: 10.1021/acs.jafc.2c08704] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Legume seed storage proteins can be induced to form amyloid fibrils upon heating at low pH, which could improve their functionality for use in food and materials. However, the amyloidogenic regions of legume proteins are largely unknown. Here, we used LC-MS/MS to determine the amyloid core regions of fibrils formed by enriched pea and soy 7S and 11S globulins at pH 2, 80 °C, and characterized their hydrolysis, assembly kinetics, and morphology. A lag phase was absent from the fibrillation kinetics of pea and soy 7S globulins, while 11S globulins and crude extracts displayed a similar lag time. Pea and soy protein fibrils differed in morphology, with most pea fibrils being straight and soy fibrils being worm-like. Pea and soy globulins were abundant in amyloid-forming peptides, with over 100 unique fibril-core peptides from pea 7S and around 50 unique fibril-core peptides identified from pea 11S, soy 7S, and soy 11S globulins. Amyloidogenic regions derive predominantly from the homologous core region of 7S globulins and the basic subunit of 11S globulins. Overall, pea and soy 7S and 11S globulins are rich in amyloidogenic regions. This study will help understand their fibrillation mechanism and engineer protein fibrils with specific structures and functionality.
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Affiliation(s)
- Yuran Zhang
- Food, Nutrition and Health, Faculty of Land and Food Systems, The University of British Columbia, 2205 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - Derek R Dee
- Food, Nutrition and Health, Faculty of Land and Food Systems, The University of British Columbia, 2205 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
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7
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Zein HF, Sutthibutpong T. Roles of Tryptophan and Charged Residues on the Polymorphisms of Amyloids Formed by K-Peptides of Hen Egg White Lysozyme Investigated through Molecular Dynamics Simulations. Int J Mol Sci 2023; 24:ijms24032626. [PMID: 36768943 PMCID: PMC9916845 DOI: 10.3390/ijms24032626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 01/31/2023] Open
Abstract
Atomistic molecular dynamics simulations of amyloid models, consisting of the previously reported STDY-K-peptides and K-peptides from the hen egg white lysozyme (HEWL), were performed to address the effects of charged residues and pH observed in an in vitro study. Simulation results showed that amyloid models with antiparallel configurations possessed greater stability and compactness than those with parallel configurations. Then, peptide chain stretching and ordering were measured through the end-to-end distance and the order parameter, for which the amyloid models consisting of K-peptides and the STDY-K-peptides at pH 2 displayed a higher level of chain stretching and ordering. After that, the molecular mechanics energy decomposition and the radial distribution function (RDF) clearly displayed the importance of Trp62 to the K-peptide and the STDY-K-peptide models at pH 2. Moreover, the results also displayed how the negatively charged Asp52 disrupted the interaction networks and prevented the amyloid formation from STDY-K-peptide at pH 7. Finally, this study provided an insight into the interplay between pH conditions and molecular interactions underlying the formation of amyloid fibrils from short peptides contained within the HEWL. This served as a basis of understanding towards the design of other amyloids for biomaterial applications.
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Affiliation(s)
- Husnul Fuad Zein
- Nanoscience and Nanotechnology Program, Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), 126 Pracha Uthit Rd., Bang Mod, Thung Khru, Bangkok 10140, Thailand
- Department of Physics, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok 10140, Thailand
| | - Thana Sutthibutpong
- Nanoscience and Nanotechnology Program, Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), 126 Pracha Uthit Rd., Bang Mod, Thung Khru, Bangkok 10140, Thailand
- Department of Physics, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok 10140, Thailand
- Center of Excellence in Theoretical and Computational Science (TaCS-CoE), Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), 126 Pracha Uthit Rd., Bang Mod, Thung Khru, Bangkok 10140, Thailand
- Correspondence:
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Matsuo T, Peters J. Sub-Nanosecond Dynamics of Pathologically Relevant Bio-Macromolecules Observed by Incoherent Neutron Scattering. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081259. [PMID: 36013438 PMCID: PMC9410404 DOI: 10.3390/life12081259] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/09/2022] [Accepted: 08/12/2022] [Indexed: 01/22/2023]
Abstract
Incoherent neutron scattering (iNS) is one of the most powerful techniques to study the dynamical behavior of bio-macromolecules such as proteins and lipid molecules or whole cells. This technique has widely been used to elucidate the fundamental aspects of molecular motions that manifest in the bio-macromolecules in relation to their intrinsic molecular properties and biological functions. Furthermore, in the last decade, iNS studies focusing on a possible relationship between molecular dynamics and biological malfunctions, i.e., human diseases and disorders, have gained importance. In this review, we summarize recent iNS studies on pathologically relevant proteins and lipids and discuss how the findings are of importance to elucidate the molecular mechanisms of human diseases and disorders that each study targets. Since some diseases such as amyloidosis have become more relevant in the aging society, research in this field will continue to develop further and be more important in the current increasing trend for longevity worldwide.
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Affiliation(s)
- Tatsuhito Matsuo
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, 2-4 Shirakata, Tokai 319-1106, Ibaraki, Japan
- Dept. of Physics, Univ. Grenoble Alpes, CNRS, LiPhy, 38000 Grenoble, France
- Institut Laue-Langevin, 71 Avenue des Martyrs, CEDEX 9, 38042 Grenoble, France
- Correspondence: (T.M.); (J.P.)
| | - Judith Peters
- Dept. of Physics, Univ. Grenoble Alpes, CNRS, LiPhy, 38000 Grenoble, France
- Institut Laue-Langevin, 71 Avenue des Martyrs, CEDEX 9, 38042 Grenoble, France
- Institut Universitaire de France, 75231 Paris, France
- Correspondence: (T.M.); (J.P.)
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9
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Mikalauskaite K, Ziaunys M, Smirnovas V. Lysozyme Amyloid Fibril Structural Variability Dependence on Initial Protein Folding State. Int J Mol Sci 2022; 23:5421. [PMID: 35628230 PMCID: PMC9141980 DOI: 10.3390/ijms23105421] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 05/11/2022] [Accepted: 05/11/2022] [Indexed: 02/05/2023] Open
Abstract
Amyloid fibril formation is associated with several amyloidoses, including neurodegenerative Alzheimer's or Parkinson's diseases. The process of such fibrillar structure formation is still not fully understood, with new mechanistic insights appearing on a regular basis. This, in turn, has limited the development of potential anti-amyloid compounds, with only a handful of effective cures or treatment modalities available. One of the multiple amyloid aggregation factors that requires further examination is the ability of proteins to form multiple, structurally distinct aggregates, based on the environmental conditions. In this work, we examine how the initial folding state affects the fibrilization of lysozyme-an amyloidogenic protein, often used in protein aggregation studies. We show that there is a correlation between the initial state of the protein and the aggregate formation lag time, rate of elongation, resulting aggregate structural variability and dye-binding properties, as well as formation lag time and rate of elongation.
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Affiliation(s)
- Kamile Mikalauskaite
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Mantas Ziaunys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Vytautas Smirnovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
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10
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Using Sugar-Derived Nanoparticles to Mitigate Amyloid Fibril Formation of Lysozyme. J Taiwan Inst Chem Eng 2022. [DOI: 10.1016/j.jtice.2022.104360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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11
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Matsuo T, De Francesco A, Peters J. Molecular Dynamics of Lysozyme Amyloid Polymorphs Studied by Incoherent Neutron Scattering. Front Mol Biosci 2022; 8:812096. [PMID: 35111814 PMCID: PMC8801425 DOI: 10.3389/fmolb.2021.812096] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 12/03/2021] [Indexed: 11/22/2022] Open
Abstract
Lysozyme amyloidosis is a hereditary disease, which is characterized by the deposition of lysozyme amyloid fibrils in various internal organs. It is known that lysozyme fibrils show polymorphism and that polymorphs formed at near-neutral pH have the ability to promote more monomer binding than those formed at acidic pH, indicating that only specific polymorphs become dominant species in a given environment. This is likely due to the polymorph-specific configurational diffusion. Understanding the possible differences in dynamical behavior between the polymorphs is thus crucial to deepen our knowledge of amyloid polymorphism and eventually elucidate the molecular mechanism of lysozyme amyloidosis. In this study, molecular dynamics at sub-nanosecond timescale of two kinds of polymorphic fibrils of hen egg white lysozyme, which has long been used as a model of human lysozyme, formed at pH 2.7 (LP27) and pH 6.0 (LP60) was investigated using elastic incoherent neutron scattering (EINS) and quasi-elastic neutron scattering (QENS). Analysis of the EINS data showed that whereas the mean square displacement of atomic motions is similar for both LP27 and LP60, LP60 contains a larger fraction of atoms moving with larger amplitudes than LP27, indicating that the dynamical difference between the two polymorphs lies not in the averaged amplitude, but in the distribution of the amplitudes. Furthermore, analysis of the QENS data showed that the jump diffusion coefficient of atoms is larger for LP60, suggesting that the atoms of LP60 undergo faster diffusive motions than those of LP27. This study thus characterizes the dynamics of the two lysozyme polymorphs and reveals that the molecular dynamics of LP60 is enhanced compared with that of LP27. The higher molecular flexibility of the polymorph would permit to adjust its conformation more quickly than its counterpart, facilitating monomer binding.
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Affiliation(s)
- Tatsuhito Matsuo
- Univ. Grenoble Alpes, CNRS, LiPhy, Grenoble, France
- Institut Laue-Langevin, Grenoble, France
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Tokai, Japan
- *Correspondence: Tatsuhito Matsuo, ; Judith Peters,
| | - Alessio De Francesco
- Institut Laue-Langevin, Grenoble, France
- CNR-IOM and INSIDE@ILL C/O Operative Group in Grenoble (OGG), Grenoble, France
| | - Judith Peters
- Univ. Grenoble Alpes, CNRS, LiPhy, Grenoble, France
- Institut Laue-Langevin, Grenoble, France
- Institut Universitaire de France, Paris, France
- *Correspondence: Tatsuhito Matsuo, ; Judith Peters,
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