1
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Ueda T. [Modulation of Aggregation and Immunogenicity of a Protein: Based on the Study of Hen Lysozyme]. YAKUGAKU ZASSHI 2024; 144:299-310. [PMID: 38432940 DOI: 10.1248/yakushi.23-00192] [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] [Indexed: 03/05/2024]
Abstract
This study focuses on the modulation of protein aggregation and immunogenicity. As a starting point for investigating long-range interactions within a non-native protein, the effects of perturbing denatured protein states on their aggregation, including the formation of amyloid fibrils, were evaluated. The effects of adducts, sugar modifications, and stabilization on protein aggregation were then examined. We also investigated how protein immunogenicity was affected by enhancing protein conformational stability and other factors.
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Affiliation(s)
- Tadashi Ueda
- Graduate School of Pharmaceutical Sciences, Kyushu University
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2
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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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3
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Tomiyama R, So M, Yamaguchi K, Miyanoiri Y, Sakurai K. The residual structure of acid-denatured β 2 -microglobulin is relevant to an ordered fibril morphology. Protein Sci 2023; 32:e4487. [PMID: 36321362 PMCID: PMC9793977 DOI: 10.1002/pro.4487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/15/2022] [Accepted: 10/29/2022] [Indexed: 11/09/2022]
Abstract
β2 -Microglobulin (β2m) forms amyloid fibrils in vitro under acidic conditions. Under these conditions, the residual structure of acid-denatured β2m is relevant to seeding and fibril extension processes. Disulfide (SS) bond-oxidized β2m has been shown to form rigid, ordered fibrils, whereas SS bond-reduced β2m forms curvy, less-ordered fibrils. These findings suggest that the presence of an SS bond affects the residual structure of the monomer, which subsequently influences the fibril morphology. To clarify this process, we herein performed NMR experiments. The results obtained revealed that oxidized β2m contained a residual structure throughout the molecule, including the N- and C-termini, whereas the residual structure of the reduced form was localized and other regions had a random coil structure. The range of the residual structure in the oxidized form was wider than that of the fibril core. These results indicate that acid-denatured β2m has variable conformations. Most conformations in the ensemble cannot participate in fibril formation because their core residues are hidden by residual structures. However, when hydrophobic residues are exposed, polypeptides competently form an ordered fibril. This conformational selection phase may be needed for the ordered assembly of amyloid fibrils.
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Affiliation(s)
- Ryosuke Tomiyama
- Graduate School of Biology‐oriented Science and TechnologyKindai UniversityWakayamaJapan
| | - Masatomo So
- Institute for Protein ResearchOsaka UniversityOsakaJapan,Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsUK
| | - Keiichi Yamaguchi
- Global Center for Medical Engineering and InformaticsOsaka UniversitySuitaJapan
| | | | - Kazumasa Sakurai
- Graduate School of Biology‐oriented Science and TechnologyKindai UniversityWakayamaJapan,High Pressure Protein Research Center, Institute of Advanced TechnologyKindai UniversityWakayamaJapan
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4
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Rezaei M, Kalhor HR. Amyloid fibril reduction through covalently modified lysine in HEWL and insulin. Arch Biochem Biophys 2022; 727:109350. [PMID: 35830943 DOI: 10.1016/j.abb.2022.109350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 11/28/2022]
Abstract
Proteins possess a variety of nucleophiles, which can carry out different reactions in the functioning cells. Proteins endogenously and synthetically can be modified through their nucleophilic sites. The roles of these chemical modifications have not been completely revealed. These modifications can alter the protein folding process. Protein folding directly affects the function of proteins. If an error in protein folding occurs, it may cause protein malfunction leading to several neurodegenerative disorders such as Alzheimer's and Parkinson's. In this study, Hen Egg White Lysozyme (HEWL) and bovine insulin, as model proteins for studying the amyloid formation, were covalently attached with 5(6)-thiophenolfluorescein. The amyloid formation of the covalently labeled lysozyme and insulin were compared with the native proteins. Interestingly, the results indicated that the covalent attachment of fluorescein slowed down the amyloid formation of HEWL and insulin significantly. The amyloid formation was examined using Thioflavin T (ThT) fluorescence assay, circular dichroism, FTIR, and gel electrophoresis. Tandem mass spectrometry was employed to identify the sites of covalent modifications in HEWL. It turned out that two surface lysine residues (K97 and K 116) in HEWL were modified. Computational studies, including docking and molecular simulations, revealed that 5(6)-thiophenolfluorescein makes several non-covalent interactions with HEWL residues, including Lys 97, leading to the reduction of the β-sheet in the protein. Additionally, AFM analysis confirmed the amyloid fibril reduction of lysine-modified bovine insulin and HEWL. Altogether, our results expand mechanistic insights into preventing amyloid formation by providing an approach for reducing amyloid formation by modifying specific lysine residues in the proteins.
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Affiliation(s)
- Mohsen Rezaei
- Biochemistry and Chemical Biology Research Laboratory, Chemistry Department, Sharif University of Technology, P.O. Box 11155-3516, Tehran, Iran
| | - Hamid Reza Kalhor
- Biochemistry and Chemical Biology Research Laboratory, Chemistry Department, Sharif University of Technology, P.O. Box 11155-3516, Tehran, Iran.
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5
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Zein HF, Alam I, Asanithi P, Sutthibutpong T. Molecular dynamics study on the effects of charged amino acid distribution under low pH condition to the unfolding of hen egg white lysozyme and formation of beta strands. PLoS One 2022; 17:e0249742. [PMID: 35324907 PMCID: PMC8946743 DOI: 10.1371/journal.pone.0249742] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 02/23/2022] [Indexed: 11/19/2022] Open
Abstract
Aggregation of unfolded or misfolded proteins into amyloid fibrils can cause various diseases in humans. However, the fibrils synthesized in vitro can be developed toward useful biomaterials under some physicochemical conditions. In this study, atomistic molecular dynamics simulations were performed to address the mechanism of beta-sheet formation of the unfolded hen egg-white lysozyme (HEWL) under a high temperature and low pH. Simulations of the protonated HEWL at pH 2 and the non-protonated HEWL at pH 7 were performed at the highly elevated temperature of 450 K to accelerate the unfolding, followed by the 333 K temperature to emulate some previous in vitro studies. The simulations showed that HEWL unfolded faster, and higher beta-strand contents were observed at pH 2. In addition, one of the simulation replicas at pH 2 showed that the beta-strand forming sequence was consistent with the 'K-peptide', proposed as the core region for amyloidosis in previous experimental studies. Beta-strand formation mechanisms at the earlier stage of amyloidosis were explained in terms of the radial distribution of the amino acids. The separation between groups of positively charged sidechains from the hydrophobic core corresponded to the clustering of the hydrophobic residues and beta-strand formation.
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Affiliation(s)
- Husnul Fuad Zein
- Nanoscience and Nanotechnology Program, Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), Thung Khru, Bangkok, Thailand
- Department of Physics, Theoretical and Computational Physics Group, KMUTT, Thung Khru, Bangkok, Thailand
- Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), Thung Khru, Bangkok, Thailand
| | - Ibrar Alam
- Nanoscience and Nanotechnology Program, Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), Thung Khru, Bangkok, Thailand
| | - Piyapong Asanithi
- Nanoscience and Nanotechnology Program, Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), Thung Khru, Bangkok, Thailand
| | - Thana Sutthibutpong
- Nanoscience and Nanotechnology Program, Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), Thung Khru, Bangkok, Thailand
- Department of Physics, Theoretical and Computational Physics Group, KMUTT, Thung Khru, Bangkok, Thailand
- Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), Thung Khru, Bangkok, Thailand
- Center of Excellence in Theoretical and Computational Science (TaCS-CoE), Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), Thung Khru, Bangkok, Thailand
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6
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Kushwaha P, Prabhu NP. Imidazolium-based ionic liquids with increasing alkyl chain length of cations decrease the stability and fibrillation propensity of lysozyme. NEW J CHEM 2022. [DOI: 10.1039/d2nj00559j] [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
Imidazolium ionic liquids with longer alkyl side chains show a larger destabilization effect on lysozyme. Increased hydrophobicity of the IL increases its binding affinity and inhibits the fibril formation of lysozyme.
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Affiliation(s)
- Pratibha Kushwaha
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad – 500 046, India
| | - N. Prakash Prabhu
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad – 500 046, India
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7
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Bioactive Phytocompounds: Anti-amyloidogenic Effects Against Hen Egg-White Lysozyme Aggregation. Protein J 2021; 40:78-86. [PMID: 33392981 DOI: 10.1007/s10930-020-09946-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2020] [Indexed: 10/22/2022]
Abstract
Amyloidosis is the process of fibril formation responsible for causing several diseases in the human being that involve protein aggregation such as Alzheimer's, Parkinson's, Huntington's disease, and type II diabetes. Natural phytocompounds such as curcumin shown promising anti-amyloidogenic activity. In the present study, selective phytocompounds such as piperine, cinnamaldehyde, eugenol, and cuminaldehyde present in Piper nigrum L, Cinnamomum zeylanicum Blume, Eugenia caryophyllus Thumb, and Cuminum cyminum L, respectively were analyzed for anti-amyloidogenic activity using hen egg white-lysozyme (HEWL) as a model system. Out of the selected phytocompounds, piperine showed the most significant anti-amyloidogenic activity, as evident from in vitro assays that were validated by in silico molecular docking study. Piperine showed 64.7 ± 3.74% inhibition of amyloid formation at 50 μM concentration, as observed by Thioflavin T assay. Subsequently, the anti-amyloidogenic activity of piperine was further validated by congo red, intrinsic fluorescence assay, and transmission electron microscopy analysis. The in silico molecular binding interaction showed piperine with the highest docking score and glide energy. Piperine was found to be interacting with amyloidogenic region residues and Trp62, the most important residue involved in the amyloidogenesis process. In conclusion, piperine can be used as a positive lead for a potential therapeutic role in targeting diseases involved amyloidogenesis.
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8
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Kabir A, Jash C, Payghan PV, Ghoshal N, Kumar GS. Polyamines and its analogue modulates amyloid fibrillation in lysozyme: A comparative investigation. Biochim Biophys Acta Gen Subj 2020; 1864:129557. [PMID: 32045632 DOI: 10.1016/j.bbagen.2020.129557] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 01/03/2020] [Accepted: 02/07/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND Polyamines can induce protein aggregation that can be related to the physiology of the cellular function. Polyamines have been implicated in protein aggregation which may lead to neuropathic and non neuropathic amyloidosis. SCOPE OF REVIEW Change in the level of polyamine concentration has been associated with ageing and neurodegeneration such as Parkinson's disease, Alzheimer's disease. Lysozyme aggregation in the presence of polyamines leads to non neuropathic amyloidosis. Polyamine analogues can suppress or inhibit protein aggregation suggesting their efficacy against amyloidogenic protein aggregates. MAJOR CONCLUSIONS In this study we report the comparative interactions of lysozyme with the polyamine analogue, 1-naphthyl acetyl spermine in comparison with the biogenic polyamines through spectroscopy, calorimetry, imaging and docking techniques. The findings revealed that the affinity of binding varied as spermidine > 1-naphthyl acetyl spermine > spermine. The biogenic polyamines accelerated the rate of fibrillation significantly, whereas the analogue inhibited the rate of fibrillation to a considerable extent. The polyamines bind near the catalytic diad residues viz. Glu35 and Asp52, and in close proximity of Trp62 residue. However, the analogue showed dual nature of interaction where its alkyl amine region bind in same way as the biogenic polyamines bind to the catalytic site, while the naphthyl group makes hydrophobic contacts with Trp62 and Trp63, thereby suggesting its direct influence on fibrillation. GENERAL SIGNIFICANCE This study, thus, potentiates, the development of a polyamine analogue that can perform as an effective inhibitor targeted towards aggregation of amyloidogenic proteins.
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Affiliation(s)
- Ayesha Kabir
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja SC Mullick Road, Kolkata 700 032, India
| | - Chandrima Jash
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja SC Mullick Road, Kolkata 700 032, India
| | - Pavan V Payghan
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja SC Mullick Road, Kolkata 700 032, India
| | - Nanda Ghoshal
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja SC Mullick Road, Kolkata 700 032, India
| | - Gopinatha Suresh Kumar
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja SC Mullick Road, Kolkata 700 032, India.
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9
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Kalhor HR, Jabbary M. Investigating Reliable Conditions for HEWL as an Amyloid Model in Computational Studies and Drug Interactions. J Chem Inf Model 2019; 59:5218-5229. [DOI: 10.1021/acs.jcim.9b00819] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Hamid R. Kalhor
- Biochemistry Research Laboratory, Department of Chemistry, Sharif University of Technology, PO Box: 11365-11155 Tehran, Iran
| | - Mohammadparsa Jabbary
- Biochemistry Research Laboratory, Department of Chemistry, Sharif University of Technology, PO Box: 11365-11155 Tehran, Iran
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10
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Jansens KJA, Lambrecht MA, Rombouts I, Monge Morera M, Brijs K, Rousseau F, Schymkowitz J, Delcour JA. Conditions Governing Food Protein Amyloid Fibril Formation-Part I: Egg and Cereal Proteins. Compr Rev Food Sci Food Saf 2019; 18:1256-1276. [PMID: 33336994 DOI: 10.1111/1541-4337.12462] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/26/2019] [Accepted: 05/13/2019] [Indexed: 12/18/2022]
Abstract
Conditions including heating mode, time, temperature, pH, moisture and protein concentration, shear, and the presence of alcohols, chaotropic/reducing agents, enzymes, and/or salt influence amyloid fibril (AF) formation as they can affect the accessibility of amino acid sequences prone to aggregate. As some conditions applied on model protein resemble conditions in food processing unit operations, we here hypothesize that food processing can lead to formation of protein AFs with a compact cross β-sheet structure. This paper reviews conditions and food constituents that affect amyloid fibrillation of egg and cereal proteins. While egg and cereal proteins often coexist in food products, their impact on each other's fibrillation remains unknown. Hen egg ovalbumin and lysozyme form AFs when subjected to moderate heating at acidic pH separately. AFs can also be formed at higher pH, especially in the presence of alcohols or chaotropic/reducing agents. Tryptic wheat gluten digests can form fibrillar structures at neutral pH and maize and rice proteins do so in aqueous ethanol or at acidic pH, respectively.
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Affiliation(s)
- Koen J A Jansens
- KU Leuven, Laboratory of Food Chemistry and Biochemistry and Leuven Food Science and Nutrition Research Centre (LFoRCe), Kasteelpark Arenberg 20, B-3001, Leuven, Belgium.,Nutrex NV, Achterstenhoek 5, B-2275, Lille, Belgium
| | - Marlies A Lambrecht
- KU Leuven, Laboratory of Food Chemistry and Biochemistry and Leuven Food Science and Nutrition Research Centre (LFoRCe), Kasteelpark Arenberg 20, B-3001, Leuven, Belgium
| | - Ine Rombouts
- KU Leuven, Laboratory of Food Chemistry and Biochemistry and Leuven Food Science and Nutrition Research Centre (LFoRCe), Kasteelpark Arenberg 20, B-3001, Leuven, Belgium.,KU Leuven, ECOVO, Kasteelpark Arenberg 21, B-3001, Leuven, Belgium
| | - Margarita Monge Morera
- KU Leuven, Laboratory of Food Chemistry and Biochemistry and Leuven Food Science and Nutrition Research Centre (LFoRCe), Kasteelpark Arenberg 20, B-3001, Leuven, Belgium
| | - Kristof Brijs
- KU Leuven, Laboratory of Food Chemistry and Biochemistry and Leuven Food Science and Nutrition Research Centre (LFoRCe), Kasteelpark Arenberg 20, B-3001, Leuven, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB, and Dept. of Cellular and Molecular Medicine, KU Leuven, B-3000, Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB, and Dept. of Cellular and Molecular Medicine, KU Leuven, B-3000, Leuven, Belgium
| | - Jan A Delcour
- KU Leuven, Laboratory of Food Chemistry and Biochemistry and Leuven Food Science and Nutrition Research Centre (LFoRCe), Kasteelpark Arenberg 20, B-3001, Leuven, Belgium
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Xie J, Mei L, Huang K, Sun Y, Iris A, Ma B, Qiu Y, Li J, Han G. A photo-inducible protein-inorganic nanoparticle assembly for active targeted tumour theranostics. NANOSCALE 2019; 11:6136-6144. [PMID: 30870552 DOI: 10.1039/c9nr01120j] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The assembly of protein-inorganic nanoparticles is an important yet challenging approach that is utilized to develop functional materials in numerous areas, such as bio-catalysis, drug delivery, and biosensing. In this study, we report on a facile, photo-inducible self-assembly method to generate protein-inorganic hybrid nanoplatforms. More specifically, photo-treated disulfide bond rich proteins of lysozyme (LYS) were able to be used as host materials in order to encapsulate nanoparticles (i.e., as-synthesized hydrophobic NIR quantum dots (QDs)) and anti-cancer small molecule drugs (i.e., paclitaxel (PTX)), constructing functional theranostic protein-inorganic hybrid nanoparticles. The modification of the functional polymer of cRGD-PEG contributes to the active tumour targeting characteristic of this protein-inorganic nanocarrier. This novel PTX loaded protein-inorganic hybrid nanoplatform showed high tumour homing accumulation as well as effective tumour inhibition. We believe that this general approach represents a new direction for the development of a photo-induced assembly of protein-inorganic nanoparticles towards versatile applications in both materials science and biomedical fields.
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Affiliation(s)
- Jinbing Xie
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, 210093, China.
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12
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Kalhor HR, Nazari Khodadadi A. Synthesis and Structure Activity Relationship of Pyridazine-Based Inhibitors for Elucidating the Mechanism of Amyloid Inhibition. Chem Res Toxicol 2018; 31:1092-1104. [DOI: 10.1021/acs.chemrestox.8b00210] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Hamid Reza Kalhor
- Biochemistry Research Laboratory, Department of Chemistry, Sharif University of Technology, Tehran 111559516, Iran
| | - Alireza Nazari Khodadadi
- Biochemistry Research Laboratory, Department of Chemistry, Sharif University of Technology, Tehran 111559516, Iran
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13
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Kalhor HR, Ashrafian H. Identification of an aspidospermine derivative from borage extract as an anti-amyloid compound: A possible link between protein aggregation and antimalarial drugs. PHYTOCHEMISTRY 2017; 140:134-140. [PMID: 28499255 DOI: 10.1016/j.phytochem.2017.05.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 05/02/2017] [Accepted: 05/04/2017] [Indexed: 06/07/2023]
Abstract
A number of human diseases, including Alzheimer's and Parkinson's have been linked to amyloid formation. To search for an anti-amyloidogenic product, alkaloid enriched extract from borage leaves was examined for anti-amyloidogenic activity using Hen Egg White Lysozyme (HEWL) as a model protein. After isolation of the plant extract using rHPLC, only one fraction indicated a significant bioactivity. TEM analysis confirmed a remarkable reduction of amyloid fibrils in the presence of the bioactive fraction. To identify the effective substance in the fraction, mass spectrometry, FTIR, and NMR were performed. Our analyses determined that the bioactive compound as 1-acetyl-19,21-epoxy-15,16-dimethoxyaspidospermidine-17-ol, a derivative of aspidospermine. To investigate the mechanism of the inhibition, ANS binding, intrinsic fluorescence, and amide I content were performed in the presence of the bioactive compound. All the results confirmed the role of the compound in assisting the proper folding of the protein. In addition, molecular docking indicated the aspidospermine derivative binds the amyloidogenic region of the protein. Our results show that the alkaloid extracted from borage leaves reduces protein aggregation mediating through structural elements of the protein, promoting the correct folding of lysozyme. Since a number of aspidospermine compounds have been shown to possess potent antimalarial activities, the action of compound identified in the present study suggests a possible link between protein aggregation and aspidospermine drugs.
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Affiliation(s)
- Hamid R Kalhor
- Biochemistry Research Laboratory, Department of Chemistry, Sharif University of Technology, Tehran, Iran.
| | - Hossein Ashrafian
- Biochemistry Research Laboratory, Department of Chemistry, Sharif University of Technology, Tehran, Iran
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14
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Chong X, Sun L, Sun Y, Chang L, Chang AK, Lu X, Zhou X, Liu J, Zhang B, Jones GW, He J. Insights into the mechanism of how Morin suppresses amyloid fibrillation of hen egg white lysozyme. Int J Biol Macromol 2017; 101:321-325. [PMID: 28341174 DOI: 10.1016/j.ijbiomac.2017.03.107] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Revised: 03/17/2017] [Accepted: 03/20/2017] [Indexed: 12/20/2022]
Abstract
This communication describes the inhibitory effect of Morin on the fibrillation of Hen Egg White Lysozyme (HEWL), a generic amyloid-forming model protein. This effect was dose-dependent and stronger than other small molecules we have tested previously. Spectrofluorometric and computational studies support a model suggesting that Morin inhibits amyloid fibril formation of HEWL by binding to the aggregation prone cleft region of the β-domain of HEWL, thereby stabilizing the molecule in its native-like state. Interestingly, transmission electron microscopy observations suggest that, along with increases in Morin concentration, the observed amorphous aggregates became larger and morphologically different. We propose that following occupation of the binding cleft, excess Morin adheres and coats the HEWL protein surface, thereby minimizing the interaction between the protein surface and water molecules.
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Affiliation(s)
- Xiaoying Chong
- School of Life Science, Liaoning University, Shenyang 110036, China
| | - Luchen Sun
- School of Life Science, Liaoning University, Shenyang 110036, China
| | - Yonghui Sun
- School of Life Science, Liaoning University, Shenyang 110036, China
| | - Lin Chang
- School of Life Science, Liaoning University, Shenyang 110036, China
| | - Alan K Chang
- School of Life Science, Liaoning University, Shenyang 110036, China
| | - Xian Lu
- School of Life Science, Liaoning University, Shenyang 110036, China
| | - Xuejie Zhou
- School of Life Science, Liaoning University, Shenyang 110036, China
| | - Junqing Liu
- School of Life Science, Liaoning University, Shenyang 110036, China
| | - Bing Zhang
- Experimental Center of Functional Subjects, China Medical University, 92 Bei Er Road, Heping District, Shenyang 110001, China
| | - Gary W Jones
- Centre for Biomedical Science Research, School of Clinical and Applied Sciences, Leeds Beckett University, City Campus, Leeds LS1 3HE, United Kingdom
| | - Jianwei He
- School of Life Science, Liaoning University, Shenyang 110036, China.
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15
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Tokunaga Y, Matsumoto M, Sugimoto Y. Amyloid fibril formation from a 9 amino acid peptide, 55th–63rd residues of human lysozyme. Int J Biol Macromol 2015; 80:208-16. [DOI: 10.1016/j.ijbiomac.2015.06.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Revised: 06/09/2015] [Accepted: 06/11/2015] [Indexed: 10/23/2022]
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16
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Jash C, Basu P, Payghan PV, Ghoshal N, Kumar GS. Chelerythrine–lysozyme interaction: spectroscopic studies, thermodynamics and molecular modeling exploration. Phys Chem Chem Phys 2015; 17:16630-45. [DOI: 10.1039/c5cp00424a] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The binding of the iminium and alkanolamine forms of chelerythrine to lysozyme (Lyz) was investigated by spectroscopy and molecular modeling studies.
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Affiliation(s)
- Chandrima Jash
- Biophysical Chemistry Laboratory
- Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700 032
- India
| | - Pritha Basu
- Biophysical Chemistry Laboratory
- Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700 032
- India
| | - Pavan V. Payghan
- Structural Biology and Bioinformatics Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700 032
- India
| | - Nanda Ghoshal
- Structural Biology and Bioinformatics Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700 032
- India
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory
- Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700 032
- India
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17
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Abe M, Abe Y, Ohkuri T, Mishima T, Monji A, Kanba S, Ueda T. Mechanism for retardation of amyloid fibril formation by sugars in Vλ6 protein. Protein Sci 2013; 22:467-74. [PMID: 23389799 DOI: 10.1002/pro.2228] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 01/22/2013] [Accepted: 01/25/2013] [Indexed: 11/08/2022]
Abstract
Sugars, which function as osmolytes within cells, retard the amyloid fibril formation of the amyloidosis peptides and proteins. To examine the mechanism of this retardation in detail, we analyzed the effect of sugars (trehalose, sucrose, and glucose) on the polypeptide chains in 3Hmut Wil, which is formed by the mutation of three His residues in Wil mutant as a cause of amyloid light-chain (AL) amyloidosis, at pH 2, a pH condition under which 3Hmut Wil was almost denatured. Sugars caused the folding of 3Hmut Wil so that its polypeptide chains adopted a native-like rather than a denatured conformation, as suggested by tryptophan fluorescence, CD spectroscopy, and heteronuclear NMR. Furthermore, these sugars promoted the folding to a native-like conformation according to the effect of preferential hydration rather than direct interaction. However, the type of sugar had no effect on the elongation of amyloid fibrils. Therefore, it was concluded that sugar affected the thermodynamic stability of 3Hmut Wil but not the elongation of amyloid fibrils.
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Affiliation(s)
- Masahiro Abe
- Department of Protein Structure, Function and Design, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
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18
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Tokunaga Y, Sakakibara Y, Kamada Y, Watanabe KI, Sugimoto Y. Analysis of core region from egg white lysozyme forming amyloid fibrils. Int J Biol Sci 2013; 9:219-27. [PMID: 23459392 PMCID: PMC3584918 DOI: 10.7150/ijbs.5380] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2012] [Accepted: 12/21/2012] [Indexed: 12/30/2022] Open
Abstract
Some of the lysozyme mutants in humans cause systemic amyloidosis. Hen egg white lysozyme (HEWL) has been well studied as a model protein of amyloid fibrils formation. We previously identified an amyloid core region consisting of nine amino acids (designated as the K peptide), which is present at 54-62 in HEWL. The K peptide, with tryptophan at its C- terminus, has the ability of self-aggregation. In the present work we focused on its structural properties in relation to the formation of fibrils. The K peptide alone formed definite fibrils having β-sheet structures by incubation of 7 days under acidic conditions at 37°C. A substantial number of fibrils were generated under this pH condition and incubation period. Deletion and substitution of tryptophan in the K peptide resulted in no formation of fibrils. Tryptophan 62 in lysozyme was suggested to be especially crucial to forming amyloid fibrils. We also show that amyloid fibrils formation of the K peptide requires not only tryptophan 62 but also a certain length containing hydrophobic amino acids. A core region is involved in the significant formation of amyloid fibrils of lysozyme.
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Affiliation(s)
- Yuhei Tokunaga
- Laboratory of Biochemistry and Bioscience The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065 Japan
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19
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Sziegat F, Silvers R, Hähnke M, Jensen MR, Blackledge M, Wirmer-Bartoschek J, Schwalbe H. Disentangling the Coil: Modulation of Conformational and Dynamic Properties by Site-Directed Mutation in the Non-Native State of Hen Egg White Lysozyme. Biochemistry 2012; 51:3361-72. [DOI: 10.1021/bi300222f] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Friederike Sziegat
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Frankfurt a. M., Max-von-Laue-Straße
7, D-60438 Frankfurt, Germany
| | - Robert Silvers
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Frankfurt a. M., Max-von-Laue-Straße
7, D-60438 Frankfurt, Germany
| | - Martin Hähnke
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Frankfurt a. M., Max-von-Laue-Straße
7, D-60438 Frankfurt, Germany
| | - Malene Ringkjøbing Jensen
- Protein Dynamics and Flexibility by NMR, Institut de Biologie Structurale
Jean-Pierre Ebel, CEA-CNRS-UJF UMR 5075, 41 Rue Jules Horowitz, Grenoble 38027, France
| | - Martin Blackledge
- Protein Dynamics and Flexibility by NMR, Institut de Biologie Structurale
Jean-Pierre Ebel, CEA-CNRS-UJF UMR 5075, 41 Rue Jules Horowitz, Grenoble 38027, France
| | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Frankfurt a. M., Max-von-Laue-Straße
7, D-60438 Frankfurt, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Frankfurt a. M., Max-von-Laue-Straße
7, D-60438 Frankfurt, Germany
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20
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Sugimoto Y, Kamada Y, Tokunaga Y, Shinohara H, Matsumoto M, Kusakabe T, Ohkuri T, Ueda T. Aggregates with lysozyme and ovalbumin show features of amyloid-like fibrils. Biochem Cell Biol 2011; 89:533-44. [DOI: 10.1139/o11-041] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The interaction of egg-white lysozyme with N-ovalbumin, the native form of egg-white ovalbumin with the denaturation temperature, Tm, of 78 °C, was investigated by the inhibition of lysozyme muramidase activity, differential scanning calorimetry, and circular dichroism assay as indicators. Signals for the interaction were the most prominent when the mixture of lysozyme and N-ovalbumin was co-heated at 72 °C, slightly lower than the Tm of N-ovalbumin. The interaction was also marked when unheated lysozyme was mixed with N-ovalbumin preheated at 72 °C. Moreover, the mixture rapidly formed fibrous precipitates, which were positive for thioflavin T fluorescent emission, a marker for the amyloid fibril formation. Also electron microscopic observation exhibited features of fibrils. The interaction potency of ovalbumin was ascribed to the tryptic fragment ILELPFASGT MSMLVLLPDE VSGLEQLESIINFEK (residues 229–263), derived from the 2B strands 2 and 3 of ovalbumin. From lysozyme, on the other hand, the chymotryptic peptide RNRCKGTDVQAW (residues 112–123), including cluster 6, and the chymotryptic/tryptic peptide GILQINSRW (residues 54–62), including cluster 3, were responsible for the interaction with N-ovalbumin. Interestingly, this nonamer peptide was found to have the ability to self-aggregate. To the authors knowledge, this may be the first report to document the possible involvement of dual proteins in the formation of amyloid-like fibrils.
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Affiliation(s)
- Yasushi Sugimoto
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065 Japan
| | - Yoshiki Kamada
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065 Japan
| | - Yuhei Tokunaga
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065 Japan
| | - Hiroshi Shinohara
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065 Japan
- Laboratory of Anatomy, Tokyo Medical School, Japan
| | | | - Takahiro Kusakabe
- Graduate School of Agricultural Sciences, Kyushu University, Fukuoka 812-8581 Japan
| | - Takatoshi Ohkuri
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582 Japan
| | - Tadashi Ueda
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582 Japan
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Xie J, Qin M, Cao Y, Wang W. Mechanistic insight of photo-induced aggregation of chicken egg white lysozyme: the interplay between hydrophobic interactions and formation of intermolecular disulfide bonds. Proteins 2011; 79:2505-16. [PMID: 21661057 DOI: 10.1002/prot.23074] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Revised: 04/21/2011] [Accepted: 04/26/2011] [Indexed: 11/05/2022]
Abstract
Recently, it was reported that ultraviolet (UV) illumination could trigger the unfolding of proteins by disrupting the buried disulfide bonds. However, the consequence of such unfolding has not been adequately evaluated. Here, we report that unfolded chicken egg white lysozyme (CEWL) triggered by UV illumination can form uniform globular aggregates as confirmed by dynamic light scattering, atomic force microscopy, and transmission electron microscopy. The assembling process of such aggregates was also monitored by several other methods, such as circular dichroism, fluorescence spectroscopy, mass spectrometry based on chymotrypsin digestion, ANS-binding assay, Ellman essay, and SDS-PAGE. Our finding is that due to the dissociation of the native disulfide bonds by UV illumination, CEWL undergoes drastic conformational changes resulting in the exposure of some hydrophobic residues and free thiols. Subsequently, these partially unfolded molecules self-assemble into small granules driven by intermolecular hydrophobic interaction. With longer UV illumination or longer incubation time, these granules can further self-assemble into larger globular aggregates. The combined effects from both the hydrophobic interaction and the formation of intermolecular disulfide bonds dominate this process. Additionally, similar aggregation behavior can also be found in other three typical disulfide-bonded proteins, that is, α-lactalbumin, RNase A, and bovine serum albumin. Thus, we propose that such aggregation behavior might be a general mechanism for some disulfide-bonded proteins under UV irradiation.
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Affiliation(s)
- Jinbing Xie
- National Laboratory of Solid State Microstructure, Nanjing University, Nanjing, China
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22
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Konuma T, Chatani E, Yagi M, Sakurai K, Ikegami T, Naiki H, Goto Y. Kinetic intermediates of β(2)-microglobulin fibril elongation probed by pulse-labeling H/D exchange combined with NMR analysis. J Mol Biol 2010; 405:851-62. [PMID: 21108949 DOI: 10.1016/j.jmb.2010.11.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2010] [Revised: 11/15/2010] [Accepted: 11/16/2010] [Indexed: 10/18/2022]
Abstract
Amyloid fibril elongation in denatured proteins involves cycles of coupled binding and misfolding. To gain insights into possible kinetic intermediates, we performed hydrogen/deuterium exchange of amide protons during fibril elongation with β(2)-microglobulin (β(2)-m) at pD=2.5, under which conditions β(2)-m is acid denatured. To study the conformational change in monomeric β(2)-m monitored by NMR spectroscopy, we used (15)N-labeled monomers and nonlabeled seeds. Pulse-labeling hydrogen/deuterium exchange with a quenched-flow apparatus indicated that the rate-limiting intermediate at pD=2.5 is not protected from the exchange, even disrupting a hydrophobic cluster present in the acid-denatured β(2)-m. Significant protection was acquired upon transition to the fibrils. In view of the suggestion that the rate-limiting intermediates are bound to the lateral surface of seed fibrils, weak interactions with a largely unfolded conformation might be useful for their dynamic sliding to the growing ends. The results support a new model of fibril elongation with intermediates bound to the lateral surface of seeds.
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Affiliation(s)
- Tsuyoshi Konuma
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
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Mishima T, Ohkuri T, Monji A, Kanemaru T, Abe Y, Ueda T. Residual Structures in the Acid-Unfolded States of Vλ6 Proteins Affect Amyloid Fibrillation. J Mol Biol 2009; 392:1033-43. [DOI: 10.1016/j.jmb.2009.07.078] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2009] [Revised: 06/27/2009] [Accepted: 07/27/2009] [Indexed: 10/20/2022]
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24
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Matsuoka T, Hamada H, Matsumoto K, Shiraki K. Indispensable structure of solution additives to prevent inactivation of lysozyme for heating and refolding. Biotechnol Prog 2009; 25:1515-24. [DOI: 10.1002/btpr.245] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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25
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Routledge KE, Tartaglia GG, Platt GW, Vendruscolo M, Radford SE. Competition between intramolecular and intermolecular interactions in an amyloid-forming protein. J Mol Biol 2009; 389:776-86. [PMID: 19393661 PMCID: PMC2722902 DOI: 10.1016/j.jmb.2009.04.042] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2009] [Revised: 04/09/2009] [Accepted: 04/20/2009] [Indexed: 11/30/2022]
Abstract
Despite much progress in understanding the folding and the aggregation processes of proteins, the rules defining their interplay have yet to be fully defined. This problem is of particular importance since many diseases are initiated by protein unfolding and hence the propensity to aggregate competes with intramolecular collapse and other folding events. Here, we describe the roles of intramolecular and intermolecular interactions in defining the length of the lag time and the apparent rate of elongation of the 100-residue protein human β2-microglobulin at pH 2.5, commencing from an acid-denatured state that lacks persistent structure but contains significant non-random hydrophobic interactions. Using a combination of site-directed mutagenesis, quantitative kinetic analysis and computational methods, we show that only a single region of about 10 residues in length, determines the rate of fibril formation, despite the fact that other regions exhibit a significant intrinsic propensity for aggregation. We rationalise these results by analysing the effect of incorporating the conformational properties of acid-unfolded β2-microglobulin and its variants at pH 2.5 as measured by NMR spectroscopy into the Zyggregator aggregation prediction algorithm. These results demonstrate that residual structure in the precursor state modulates the intrinsic propensity of the polypeptide chain to aggregate and that the algorithm developed here allows the key regions for aggregation to be more clearly identified and the rates of their self-association to be predicted. Given the common propensity of unfolded chains to form non-random intramolecular interactions as monomers and to self-assemble subsequently into amyloid fibrils, the approach developed should find widespread utility for the prediction of regions important in amyloid formation and their rates of self-assembly.
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Affiliation(s)
- Katy E. Routledge
- Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | | | - Geoffrey W. Platt
- Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
- Corresponding authors.
| | - Sheena E. Radford
- Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
- Corresponding authors.
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Rana A, Gupta TP, Bansal S, Kundu B. Formation of amyloid fibrils by bovine carbonic anhydrase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:930-5. [PMID: 18395531 DOI: 10.1016/j.bbapap.2008.02.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2007] [Revised: 02/25/2008] [Accepted: 02/26/2008] [Indexed: 11/17/2022]
Abstract
Amyloids are typically characterized by extensive aggregation of proteins where the participating polypeptides are involved in formation of intermolecular cross beta-sheet structures. Alternate structure attainment and amyloid formation has been hypothesized to be a generic property of a polypeptide, the propensities of which vary widely depending on the polypeptide involved and the physicochemical conditions it encounters. Many proteins that exist in the normal form in-vivo have been shown to form amyloid when incubated in partially denaturing conditions. The protein bovine carbonic anhydrase II (BCA II) when incubated in mildly denaturing conditions showed that the partially unfolded conformers assemble together and form ordered amyloid aggregates. The properties of these aggregates were tested using the traditional Congo-Red (CR) and Thioflavin-T (ThT) assays along with fluorescence microscopy, transmission electron microscopy (TEM), and circular dichroism (CD) spectroscopy. The aggregates were found to possess most of the characteristics ascribed to amyloid fibers. Thus, we report here that the single-domain globular protein, BCA II, is capable of forming amyloid fibrils. The primary sequence of BCA II was also analyzed using recurrence quantification analysis in order to suggest the probable residues responsible for amyloid formation.
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Affiliation(s)
- Anshul Rana
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas. New Delhi 110016, India
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Abstract
Recent NMR experiments have revealed that a single residue mutation W62G on protein hen's-egg white lysozyme can cause a dramatic loss of long-range interactions and protein stability; however, the molecular mechanism for this surprising phenomenon is not completely clear. In this mini-review, we have summarized some of our recent work on the molecular mechanism with large-scale molecular modelling, and also utilized a new wavelet method to analyse the local structural clusters present in both the wild-type and mutant folding trajectories. These extensive MD (Molecular Dynamics) simulations (10+ μs) were performed in 8 M urea, mimicking the experimental condition. Detailed analyses revealed that the Trp62 residue is the key to a co-operative long-range interaction within the wild-type protein: it acts as a bridge between neighbouring basic residues, mainly arginine residues, through π-type hydrogen bonds or π-cation interactions to form an Arg-Trp-Arg ‘sandwich-like’ local structure. The local cluster near Trp62 further extends its interaction to other clusters, such as the one near Trp111, through Arg112, which is involved in such an Arg-Trp-Arg bridging structure, thus achieving the long-range interactions for the wild-type. On the other hand, the mutant does not have this bridging effect and forms much less local clusters or contacts, and therefore results in a much less stable structure. Overall, these findings not only support the general conclusions of the experiment, but also provide a detailed but somewhat different molecular picture of the disruption of the long-range interactions.
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