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Wilson DL, Carreon A, Chinnam S, Sharifan H, Ahlawat J, Narayan M. Screening Carbon Nano Materials for Preventing Amyloid Protein Aggregation by Adopting a Facile Method. Cell Biochem Biophys 2024; 82:1389-1395. [PMID: 38802601 DOI: 10.1007/s12013-024-01293-x] [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] [Accepted: 04/24/2024] [Indexed: 05/29/2024]
Abstract
The soluble-to-toxic transformation of intrinsically disordered amyloidogenic proteins such as amyloid beta (Aβ), α-synuclein, mutant Huntingtin Protein (mHTT) and islet amyloid polypeptide (IAPP) among others are associated with disorders such as Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD) and Type 2 Diabetes (T2D), respectively. The dissolution of mature fibrils and toxic amyloidogenic intermediates, including oligomers, continues to be the pinnacle in the treatment of neurodegenerative disorders. Yet, methods to effectively and quantitatively report on the interconversion between amyloid monomers, oligomers and mature fibrils fall short. Here we describe a simplified method that implements the use of gel electrophoresis to address the transformation between soluble monomeric amyloid proteins and mature amyloid fibrils. The technique implements an optimized but well-known, simple, inexpensive, and quantitative assessment previously used to assess the oligomerization of amyloid monomers and subsequent amyloid fibrils. This method facilitates the screening of small molecules that disintegrate oligomers and fibrils into monomers, dimers, and trimers and/or retain amyloid proteins in their monomeric forms. Most importantly, our optimized method diminishes existing barriers associated with existing (alternative) techniques to evaluate fibril formation and intervention.
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Affiliation(s)
- Daisy L Wilson
- The Environmental Science & Engineering Program, The University of Texas at El Paso, El Paso, TX, 79968, USA
| | - Ana Carreon
- Department of Chemistry and Biochemistry, the University of Texas at El Paso (UTEP), El Paso, TX, 79968, USA
| | - Sampath Chinnam
- Department of Chemistry, M.S. Ramaiah Institute of Technology (Autonoumous Institution, Affiliated to Visvesvaraya Technological University, Belgaum), Bengaluru, Karnataka, 560054, India
| | - Hamidreza Sharifan
- Department of Chemistry and Biochemistry, the University of Texas at El Paso (UTEP), El Paso, TX, 79968, USA
| | - Jyoti Ahlawat
- Department of Chemistry and Biochemistry, the University of Texas at El Paso (UTEP), El Paso, TX, 79968, USA.
| | - Mahesh Narayan
- Department of Chemistry and Biochemistry, the University of Texas at El Paso (UTEP), El Paso, TX, 79968, USA.
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2
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Wilson DL, Carreon A, Chinnam S, Sharifan H, Ahlawat J, Narayan M. Screening Carbon Nano Materials for preventing amyloid protein aggregation by adopting a facile method. RESEARCH SQUARE 2024:rs.3.rs-4164618. [PMID: 38585783 PMCID: PMC10996794 DOI: 10.21203/rs.3.rs-4164618/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The soluble-to-toxic transformation of intrinsically disordered amyloidogenic proteins such as amyloid beta (Aβ), α-synuclein, mutant Huntingtin Protein (mHTT) and islet amyloid polypeptide (IAPP) among others is associated with disorders such as Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD) and Type 2 Diabetes (T2D), respectively. The dissolution of mature fibrils and toxic amyloidogenic intermediates including oligomers continues to be the pinnacle in the treatment of neurodegenerative disorders. Yet, methods to effectively, and quantitatively, report on the interconversion between amyloid monomers, oligomers and mature fibrils fall short. Here we describe a simplified method that implements the use of gel electrophoresis to address the transformation between soluble monomeric amyloid proteins and mature amyloid fibrils. The technique implements an optimized but well-known, simple, inexpensive and quantitative assessment previously used to assess the oligomerization of amyloid monomers and subsequent amyloid fibrils. This method facilitates the screening of small molecules that disintegrate oligomers and fibrils into monomers, dimers, and trimers and/or retain amyloid proteins in their monomeric forms. Most importantly, our optimized method diminishes existing barriers associated with existing (alternative) techniques to evaluate fibril formation and intervention.
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Affiliation(s)
| | | | - Sampath Chinnam
- M.S. Ramaiah Institute of Technology (Autonoumous Institution, Affiliated to Visvesvaraya Technological University
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Ahlawat J, Wilson DL, Carreon A, Narayan M. Resolving the soluble-to-toxic transformation of amyloidogenic proteins: A method to assess intervention by small-molecules. RESEARCH SQUARE 2023:rs.3.rs-2631727. [PMID: 36945382 PMCID: PMC10029074 DOI: 10.21203/rs.3.rs-2631727/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
The soluble-to-toxic transformation of intrinsically disordered amyloidogenic proteins such as amyloid beta (Aβ), α-synuclein, mutant Huntingtin Protein (mHTT) and islet amyloid polypeptide (IAPP) among others is associated with disorders such as Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD) and Type 2 Diabetes (T2D), respectively. Conversely, the dissolution of mature fibrils and toxic amyloidogenic intermediates including oligomers remains the holy grail in the treatment of neurodegenerative disorders. Yet, methods to effectively, and quantitatively, report on the interconversion between amyloid monomers, oligomers and mature fibrils fall short. For the first time, we describe the use of gel electrophoresis to address the transformation between soluble monomeric amyloid proteins and mature amyloid fibrils. The technique permits rapid, inexpensive and quantitative assessment of the fraction of amyloid monomers that form intermediates and mature fibrils. In addition, the method facilitates the screening of small molecules that disintegrate oligomers and fibrils into monomers or retain amyloid proteins in their monomeric forms. Importantly, our methodological advance diminishes major existing barriers associated with existing (alternative) techniques to evaluate fibril formation and intervention.
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Henriquez G, Ahlawat J, Fairman R, Narayan M. Citric Acid-Derived Carbon Quantum Dots Attenuate Paraquat-Induced Neuronal Compromise In Vitro and In Vivo. ACS Chem Neurosci 2022; 13:2399-2409. [PMID: 35942850 DOI: 10.1021/acschemneuro.2c00099] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The potent environmental herbicide and weedicide paraquat is linked to neuromotor defects and Parkinson's disease (PD). We have evaluated the neuroprotective role of citric acid-sourced carbon quantum dots (Cit-CQDs) on paraquat-insulted human neuroblastoma-derived SH-SY5Y cell lines and on a paraquat-exposed nematode (Caenorhabditis elegans). Our data reveal that Cit-CQDs are able to scavenge free radicals in test tube assays and mitigate paraquat-elevated reactive oxygen species (ROS) levels in SH-SY5Y cells. Furthermore, Cit-CQDs protect the cell line from paraquat, which otherwise elicits cell death. Cit-CQDs-challenged nematodes demonstrate enhanced survival rates 72 h post-paraquat exposure compared to controls. Paraquat ablates dopamine (DA) neurons, which results in compromised locomotor function in nematodes. However, the neurons remained intact when the nematodes were incubated with Cit-CQDs prior to neurotoxicant exposure. The collective data suggest Cit-CQDs offer neuroprotection for cell lines and organisms from xenotoxicant-associated neuronal injury and death. The study suggests Cit-CQDs as a potentially viable green chemistry-synthesized, biobased nanomaterial for intervention in neurodegenerative disorders.
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Affiliation(s)
- Gabriela Henriquez
- Department of Environmental Science and Engineering, The University of Texas at El Paso (UTEP), El Paso, Texas 79968, United States
| | - Jyoti Ahlawat
- Department of Chemistry and Biochemistry, The University of Texas at El Paso (UTEP), El Paso, Texas 79968, United States
| | - Robert Fairman
- Department of Biology, Haverford College, Haverford, Pennsylvania 19041, United States
| | - Mahesh Narayan
- Department of Chemistry and Biochemistry, The University of Texas at El Paso (UTEP), El Paso, Texas 79968, United States
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Damian Guerrero E, Lopez-Velazquez AM, Ahlawat J, Narayan M. Carbon Quantum Dots for Treatment of Amyloid Disorders. ACS APPLIED NANO MATERIALS 2021; 4:2423-2433. [PMID: 33969279 PMCID: PMC8101282 DOI: 10.1021/acsanm.0c02792] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Prion-like amyloids self-template and form toxic oligomers, protofibrils, and fibrils from their soluble monomers; a phenomenon that has been implicated in the onset and progress of neurodegenerative disorders such as Alzheimer's (AD), Parkinson's (PD), Huntington's, and systemic lysozyme amyloidosis. Carbon quantum dots (CQDs), sourced from Na-citrate as a carbon precursor were synthesized and characterized before being tested for their ability to intervene in amyloidogenic (fibril-forming) trajectories. Hen-egg white lysozyme (HEWL) served as a model amyloidogenic protein. A pulse-chase lysozyme fibril-forming assay developed to examine the impact of CQDs on the HEWL amyloid-fibril-forming trajectory used ThT fluorescence as a reporter of mature fibril presence. The results revealed that the Na-citrate-derived CQDs were able to intervene at multiple points along the fibril-forming trajectory by preventing the conversion of both monomeric and oligomeric HEWL intermediates into mature fibrils. In addition, and importantly, the carbon nano material (CNM) was able to dissolve oligomeric HEWL into monomeric HEWL and provoke the disaggregation of mature HEWL fibrils. These results suggest that Na-citrate CQD's intervene in amyloidogenesis by multiple mechanisms. The gathered data, coupled with cell-line results demonstrating the relatively low cytotoxicity of Na-citrate CQDs, suggest that this emerging CNM has the potential to intervene both prophylactically and therapeutically in protein misfolding diseases. The aforementioned findings are likely to enable Na-citrate CQDs to eventually transition to both cell-line and preclinical models of protein-misfolding-related disorders. Importantly, the study outcomes positions Na-citrate CQDs as an important class of chemical, nanotechnological, and biobased interventional tools in neuroscience.
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Affiliation(s)
- Erick Damian Guerrero
- Department of Chemistry and Biochemistry, The University of Texas at El Paso (UTEP), El Paso, Texas 79968, United States
| | - Angela Marlene Lopez-Velazquez
- Department of Biological Sciences, Bioscience Research Building, Border Biomedical Research Center, the Cellular Characterization and Biorepository Core Facility, The University of Texas at El Paso (UTEP), El Paso, Texas 79968, United States
| | - Jyoti Ahlawat
- Department of Chemistry and Biochemistry, The University of Texas at El Paso (UTEP), El Paso, Texas 79968, United States
| | - Mahesh Narayan
- Department of Chemistry and Biochemistry, The University of Texas at El Paso (UTEP), El Paso, Texas 79968, United States
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Pignataro MF, Herrera MG, Dodero VI. Evaluation of Peptide/Protein Self-Assembly and Aggregation by Spectroscopic Methods. Molecules 2020; 25:E4854. [PMID: 33096797 PMCID: PMC7587993 DOI: 10.3390/molecules25204854] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/17/2020] [Accepted: 10/19/2020] [Indexed: 01/08/2023] Open
Abstract
The self-assembly of proteins is an essential process for a variety of cellular functions including cell respiration, mobility and division. On the other hand, protein or peptide misfolding and aggregation is related to the development of Parkinson's disease and Alzheimer's disease, among other aggregopathies. As a consequence, significant research efforts are directed towards the understanding of this process. In this review, we are focused on the use of UV-Visible Absorption Spectroscopy, Fluorescence Spectroscopy and Circular Dichroism to evaluate the self-organization of proteins and peptides in solution. These spectroscopic techniques are commonly available in most chemistry and biochemistry research laboratories, and together they are a powerful approach for initial as well as routine evaluation of protein and peptide self-assembly and aggregation under different environmental stimulus. Furthermore, these spectroscopic techniques are even suitable for studying complex systems like those in the food industry or pharmaceutical formulations, providing an overall idea of the folding, self-assembly, and aggregation processes, which is challenging to obtain with high-resolution methods. Here, we compiled and discussed selected examples, together with our results and those that helped us better to understand the process of protein and peptide aggregation. We put particular emphasis on the basic description of the methods as well as on the experimental considerations needed to obtain meaningful information, to help those who are just getting into this exciting area of research. Moreover, this review is particularly useful to those out of the field who would like to improve reproducibility in their cellular and biomedical experiments, especially while working with peptide and protein systems as an external stimulus. Our final aim is to show the power of these low-resolution techniques to improve our understanding of the self-assembly of peptides and proteins and translate this fundamental knowledge in biomedical research or food applications.
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Affiliation(s)
- María Florencia Pignataro
- Department of Physiology and Molecular and Cellular Biology, Institute of Biosciences, Biotechnology and Translational Biology (iB3), Faculty of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires C1428EG, Argentina;
- Institute of Biological Chemistry and Physical Chemistry, Dr. Alejandro Paladini, University of Buenos Aires-CONICET, Buenos Aires C1113AAD, Argentina
| | - María Georgina Herrera
- Department of Physiology and Molecular and Cellular Biology, Institute of Biosciences, Biotechnology and Translational Biology (iB3), Faculty of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires C1428EG, Argentina;
- Institute of Biological Chemistry and Physical Chemistry, Dr. Alejandro Paladini, University of Buenos Aires-CONICET, Buenos Aires C1113AAD, Argentina
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
| | - Verónica Isabel Dodero
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
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Micsonai A, Wien F, Bulyáki É, Kun J, Moussong É, Lee YH, Goto Y, Réfrégiers M, Kardos J. BeStSel: a web server for accurate protein secondary structure prediction and fold recognition from the circular dichroism spectra. Nucleic Acids Res 2019; 46:W315-W322. [PMID: 29893907 PMCID: PMC6031044 DOI: 10.1093/nar/gky497] [Citation(s) in RCA: 671] [Impact Index Per Article: 134.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 05/22/2018] [Indexed: 12/31/2022] Open
Abstract
Circular dichroism (CD) spectroscopy is a widely used method to study the protein secondary structure. However, for decades, the general opinion was that the correct estimation of β-sheet content is challenging because of the large spectral and structural diversity of β-sheets. Recently, we showed that the orientation and twisting of β-sheets account for the observed spectral diversity, and developed a new method to estimate accurately the secondary structure (PNAS, 112, E3095). BeStSel web server provides the Beta Structure Selection method to analyze the CD spectra recorded by conventional or synchrotron radiation CD equipment. Both normalized and measured data can be uploaded to the server either as a single spectrum or series of spectra. The originality of BeStSel is that it carries out a detailed secondary structure analysis providing information on eight secondary structure components including parallel-β structure and antiparallel β-sheets with three different groups of twist. Based on these, it predicts the protein fold down to the topology/homology level of the CATH protein fold classification. The server also provides a module to analyze the structures deposited in the PDB for BeStSel secondary structure contents in relation to Dictionary of Secondary Structure of Proteins data. The BeStSel server is freely accessible at http://bestsel.elte.hu.
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Affiliation(s)
- András Micsonai
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, ELTE Eötvös Loránd University, Budapest H-1117, Hungary
| | - Frank Wien
- Synchrotron SOLEIL, Gif-sur-Yvette 91192, France
| | - Éva Bulyáki
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, ELTE Eötvös Loránd University, Budapest H-1117, Hungary
| | - Judit Kun
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, ELTE Eötvös Loránd University, Budapest H-1117, Hungary
| | - Éva Moussong
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, ELTE Eötvös Loránd University, Budapest H-1117, Hungary
| | - Young-Ho Lee
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Yuji Goto
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | | | - József Kardos
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, ELTE Eötvös Loránd University, Budapest H-1117, Hungary
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Cámara-Almirón J, Caro-Astorga J, de Vicente A, Romero D. Beyond the expected: the structural and functional diversity of bacterial amyloids. Crit Rev Microbiol 2018; 44:653-666. [PMID: 30354913 DOI: 10.1080/1040841x.2018.1491527] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Intense research has confirmed the formerly theoretical distribution of amyloids in nature, and studies on different systems have illustrated the role of these proteins in microbial adaptation and in interactions with the environment. Two lines of research are expanding our knowledge on functional amyloids: (i) structural studies providing insights into the molecular machineries responsible for the transition from monomer to fibers and (ii) studies showing the way in which these proteins might participate in the microbial fitness in natural settings. Much is known about how amyloids play a role in the social behavior of bacteria, or biofilm formation, and in the adhesion of bacteria to surfaces; however, we are still in the initial stages of understanding a complementary involvement of amyloids in bacteria-host interactions. This review will cover the following two topics: first, the key aspects of the microbial platforms dedicated to the assembly of the fibers, and second, the mechanisms by which bacteria utilize the morphological and biochemical variability of amyloids to modulate the immunological response of the host, plants and humans, contributing to (i) infection, in the case of pathogenic bacteria or (ii) promotion of the health of the host, in the case of beneficial bacteria.
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Affiliation(s)
- Jesús Cámara-Almirón
- a Instituto de Hortofruticultura Subtropical y Mediterránea ''La Mayora'' - Departamento de Microbiología , Universidad de Málaga , Málaga , Spain
| | - Joaquin Caro-Astorga
- a Instituto de Hortofruticultura Subtropical y Mediterránea ''La Mayora'' - Departamento de Microbiología , Universidad de Málaga , Málaga , Spain
| | - Antonio de Vicente
- a Instituto de Hortofruticultura Subtropical y Mediterránea ''La Mayora'' - Departamento de Microbiología , Universidad de Málaga , Málaga , Spain
| | - Diego Romero
- a Instituto de Hortofruticultura Subtropical y Mediterránea ''La Mayora'' - Departamento de Microbiología , Universidad de Málaga , Málaga , Spain
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Kaur G, Kapoor S, Thakur KG. Bacillus subtilis HelD, an RNA Polymerase Interacting Helicase, Forms Amyloid-Like Fibrils. Front Microbiol 2018; 9:1934. [PMID: 30186259 PMCID: PMC6111841 DOI: 10.3389/fmicb.2018.01934] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 07/30/2018] [Indexed: 12/26/2022] Open
Abstract
HelD, an RNA polymerase binding protein from Bacillus subtilis, stimulates transcription and helps in timely adaptation of cells under diverse environmental conditions. At present, no structural information is available for HelD. In the current study, we performed size exclusion chromatography coupled to small angle X-ray scattering (SEC-SAXS) which suggests that HelD is predominantly monomeric and globular in solution. Using combination of size exclusion chromatography and analytical ultracentrifugation, we also show that HelD has a tendency to form higher order oligomers in solution. CD experiments suggest that HelD has both α-helical (∼35%) and β sheet (∼26%) secondary structural elements. Thermal melting experiments suggest that even at 90°C, there is only about 30% loss in secondary structural contents with Tm of 44°C. However, with the increase in temperature, there was a gain in the β-sheet content and significant irreversible loss of α-helical content. Using a combination of X-ray fiber diffraction analysis, and dye based assays including Thioflavin-T based fluorescence and Congo red binding assays, we discovered that HelD forms amyloid-like fibrils at physiologically relevant conditions in vitro. Using confocal imaging, we further show that HelD forms amyloid inclusions in Escherichia coli. Bioinformatics-based sequence analysis performed using three independent web-based servers suggests that HelD has more than 20 hot-spots spread across the sequence that may aid the formation of amyloid-like fibrils. This discovery adds one more member to the growing list of amyloid or amyloid-like fibril forming cytosolic proteins in bacteria. Future studies aimed at resolving the function of amyloid-like fibrils or amyloid inclusions may help better understand their role, if any, in the bacterial physiology.
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Affiliation(s)
- Gundeep Kaur
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Srajan Kapoor
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Krishan G Thakur
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
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Mycobacterium tuberculosis CarD, an essential global transcriptional regulator forms amyloid-like fibrils. Sci Rep 2018; 8:10124. [PMID: 29973616 PMCID: PMC6031611 DOI: 10.1038/s41598-018-28290-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 06/21/2018] [Indexed: 02/06/2023] Open
Abstract
CarD is an essential global transcription regulator from Mycobacterium tuberculosis (Mtb) that binds RNA polymerase and activates transcription by stabilizing the transcription initiation complex. Available crystal structures have captured two distinct, monomeric and domain-swapped homodimeric, oligomeric states of CarD. However, the actual oligomeric state of CarD in solution and its biological relevance has remained unclear. Here, we confirm the presence of the homodimeric state of CarD in solution by using synchrotron-based small-angle X-ray scattering. Furthermore, by using biochemical and biophysical experiments, in addition to mass-spectrometry, transmission electron microscopy, and confocal imaging, we show that CarD is the first soluble cytosolic protein in Mtb which displays the tendency to form amyloid-like fibrils both in vitro as well as in vivo. We demonstrate that the deletion of the fourteen N-terminal residues involved in domain-swapping hampers amyloid formation, thus, suggesting that domain-swapping is crucial in amyloidogenesis. The discovery of the amyloidogenic property of an essential cytosolic global transcription regulator, CarD, in a pathogenic bacteria will further open up new frontiers in research.
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Davies HA, Rigden DJ, Phelan MM, Madine J. Probing Medin Monomer Structure and its Amyloid Nucleation Using 13C-Direct Detection NMR in Combination with Structural Bioinformatics. Sci Rep 2017; 7:45224. [PMID: 28327552 PMCID: PMC5361114 DOI: 10.1038/srep45224] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 02/20/2017] [Indexed: 12/21/2022] Open
Abstract
Aortic medial amyloid is the most prevalent amyloid found to date, but remarkably little is known about it. It is characterised by aberrant deposition of a 5.4 kDa protein called medin within the medial layer of large arteries. Here we employ a combined approach of ab initio protein modelling and 13C-direct detection NMR to generate a model for soluble monomeric medin comprising a stable core of three β-strands and shorter more labile strands at the termini. Molecular dynamics simulations suggested that detachment of the short, C-terminal β-strand from the soluble fold exposes key amyloidogenic regions as a potential site of nucleation enabling dimerisation and subsequent fibril formation. This mechanism resembles models proposed for several other amyloidogenic proteins suggesting that despite variations in sequence and protomer structure these proteins may share a common pathway for amyloid nucleation and subsequent protofibril and fibril formation.
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Affiliation(s)
- Hannah A. Davies
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, L69 7ZB, UK
| | - Daniel J. Rigden
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, L69 7ZB, UK
| | - Marie M. Phelan
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, L69 7ZB, UK
| | - Jillian Madine
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, L69 7ZB, UK
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12
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Harris JR, Soliakov A, Watkinson A, Lakey JH. Recombinant anthrax protective antigen: Observation of aggregation phenomena by TEM reveals specific effects of sterols. Micron 2016; 93:1-8. [PMID: 27883989 DOI: 10.1016/j.micron.2016.10.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Accepted: 10/12/2016] [Indexed: 10/20/2022]
Abstract
Negatively stained transmission electron microscope images are presented that depict the aggregation of recombinant anthrax protective antigen (rPA83 monomer and the PA63 prepore oligomer) under varying in vitro biochemical conditions. Heat treatment (50°C) of rPA83 produced clumped fibrils, but following heating the PA63 prepore formed disordered aggregates. Freeze-thaw treatment of the PA63 prepore generated linear flexuous aggregates of the heptameric oligomers. Aqueous suspensions of cholesterol microcrystals were shown to bind small rPA83 aggregates at the edges of the planar bilayers. With PA63 a more discrete binding of the prepores to the crystalline cholesterol bilayer edges occurs. Sodium deoxycholate (NaDOC) treatment of rPA83 produced quasi helical fibrillar aggregate, similar but not identical to that produced by heat treatment. Remarkably, NaDOC treatment of the PA63 prepores induced transformation into pores, with a characteristic extended ß-barrel. The PA63 pores aggregated as dimers, that aggregated further as angular chains and closed structures in higher NaDOC concentrations. The significance of the sterol interaction is discussed in relation to its likely importance for PA action in vivo.
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Affiliation(s)
- J Robin Harris
- Institute of Zoology, University of Mainz, 55099 Mainz, Germany.
| | - Andrei Soliakov
- Fujifilm Diosynth Biotechnologies, Belasis Avenue, Billingham TS23 1LH, UK
| | - Allan Watkinson
- Envigo, Wooley Road, Alcon bury, Huntingdon, Cambridgeshire PE28 4HS, UK
| | - Jeremy H Lakey
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK
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