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Pal S, Udgaonkar JB. Slow Misfolding of a Molten Globule form of a Mutant Prion Protein Variant into a β-rich Dimer. J Mol Biol 2024; 436:168736. [PMID: 39097185 DOI: 10.1016/j.jmb.2024.168736] [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: 05/27/2024] [Revised: 07/13/2024] [Accepted: 07/30/2024] [Indexed: 08/05/2024]
Abstract
Misfolding of the prion protein is linked to multiple neurodegenerative diseases. A better understanding of the process requires the identification and structural characterization of intermediate conformations via which misfolding proceeds. In this study, three conserved aromatic residues (Tyr168, Phe174, and Tyr217) located in the C-terminal domain of mouse PrP (wt moPrP) were mutated to Ala. The resultant mutant protein, 3A moPrP, is shown to adopt a molten globule (MG)-like native conformation. Hydrogen-deuterium exchange studies coupled with mass spectrometry revealed that for 3A moPrP, the free energy gap between the MG-like native conformation and misfolding-prone partially unfolded forms is reduced. Consequently, 3A moPrP misfolds in native conditions even in the absence of salt, unlike wt moPrP, which requires the addition of salt to misfold. 3A moPrP misfolds to a β-rich dimer in the absence of salt, which can rapidly form an oligomer upon the addition of salt. In the presence of salt, 3A moPrP misfolds to a β-rich oligomer about a thousand-fold faster than wt moPrP. Importantly, the misfolded structure of the dimer is similar to that of the salt-induced oligomer. Misfolding to oligomer seems to be induced at the level of the dimeric unit by monomer-monomer association, and the oligomer grows by accretion of misfolded dimeric units. Additionally, it is shown that the conserved aromatic residues collectively stabilize not only monomeric protein, but also the structural core of the β-rich oligomers. Finally, it is also shown that 3A moPrP misfolds much faster to amyloid-fibrils than does the wt protein.
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Affiliation(s)
- Suman Pal
- Indian Institute of Science Education and Research Pune, Pune 411008, India
| | - Jayant B Udgaonkar
- Indian Institute of Science Education and Research Pune, Pune 411008, India.
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2
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John R, Aravindakumar CT, Aravind UK. Delineating the cascade of molecular events in protein aggregation triggered by Glyphosate, aminomethylphosphonic acid, and Roundup in serum albumins. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132158. [PMID: 37567142 DOI: 10.1016/j.jhazmat.2023.132158] [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: 04/18/2023] [Revised: 07/14/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023]
Abstract
The molecular basis of protein unfolding on exposure to the widely used herbicide, Glyphosate (GLY), its metabolite aminomethylphosphonic acid (AMPA), and the commercial formulation Roundup have been probed using human and bovine serum albumins (HSA and BSA). Protein solutions were exposed to chemical stress at set experimental conditions. The study proceeds with spectroscopic and imaging tools. Steady-state and time-resolved fluorescence (TRF) measurements indicated polarity changes with the possibility of forming a ground-state complex. Atomic force microscopy imaging results revealed the formation of fibrils from BSA and dimer, trimer, and tetramer forms of oligomers from HSA under the chemical stress of GLY. In the presence of AMPA, serum albumins (SAs) form a compact network of oligomers. The compact network of oligomers was transformed into fibrils for HSA with increasing concentrations of AMPA. In contrast, Roundup triggered the formation of amorphous aggregates from SAs. Analysis of the Raman amide I band of all aggregates showed a significant increase in antiparallel β-sheet fractions at the expense of α-helix. The highest percentage, 24.6%, of antiparallel β-sheet fractions was present in amorphous aggregate formed from HSA under the influence of Roundup. These results demonstrated protein unfolding, which led to the formation of oligomers and fibrils.
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Affiliation(s)
- Reshmi John
- Inter University Instrumentation Centre (IUIC), India
| | - Charuvila T Aravindakumar
- Inter University Instrumentation Centre (IUIC), India; School of Environmental Sciences, Mahatma Gandhi University, Kottayam 686560, Kerala, India.
| | - Usha K Aravind
- School of Environmental Studies, Cochin University of Science and Technology (CUSAT), Kochi 682022, Kerala, India.
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3
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Esmaili M, Eldeeb M. Cellular toxicity of scrapie prions in prion diseases; a biochemical and molecular overview. Mol Biol Rep 2023; 50:1743-1752. [PMID: 36446981 DOI: 10.1007/s11033-022-07806-2] [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: 08/25/2021] [Revised: 07/15/2022] [Accepted: 07/19/2022] [Indexed: 12/03/2022]
Abstract
Transmissible spongiform encephalopathies (TSEs) or prion diseases consist of a broad range of fatal neurological disorders affecting humans and animals. Contrary to Watson and Crick's 'central dogma', prion diseases are caused by a protein, devoid of DNA involvement. Herein, we briefly review various cellular and biological aspects of prions and prion pathogenesis focusing mainly on historical milestones, biosynthesis, degradation, structure-function of cellular and scrapie forms of prions .
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Affiliation(s)
- Mansoore Esmaili
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.
| | - Mohamed Eldeeb
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC, Canada.
- Department of Chemistry, Faculty of Science, Cairo University, Giza, Egypt.
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4
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Forloni G, La Vitola P, Balducci C. Oligomeropathies, inflammation and prion protein binding. Front Neurosci 2022; 16:822420. [PMID: 36081661 PMCID: PMC9445368 DOI: 10.3389/fnins.2022.822420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
The central role of oligomers, small soluble aggregates of misfolded proteins, in the pathogenesis of neurodegenerative disorders is recognized in numerous experimental conditions and is compatible with clinical evidence. To underline this concept, some years ago we coined the term oligomeropathies to define the common mechanism of action of protein misfolding diseases like Alzheimer, Parkinson or prion diseases. Using simple experimental conditions, with direct application of synthetic β amyloid or α-synuclein oligomers intraventricularly at micromolar concentrations, we could detect differences and similarities in the biological consequences. The two oligomer species affected cognitive behavior, neuronal dysfunction and cerebral inflammatory reactions with distinct mechanisms. In these experimental conditions the proposed mediatory role of cellular prion protein in oligomer activities was not confirmed. Together with oligomers, inflammation at different levels can be important early in neurodegenerative disorders; both β amyloid and α-synuclein oligomers induce inflammation and its control strongly affects neuronal dysfunction. This review summarizes our studies with β-amyloid or α-synuclein oligomers, also considering the potential curative role of doxycycline, a well-known antibiotic with anti-amyloidogenic and anti-inflammatory activities. These actions are analyzed in terms of the therapeutic prospects.
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5
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Serpa JJ, Popov KI, Petrotchenko EV, Dokholyan NV, Borchers CH. Structure of prion β-oligomers as determined by short-distance crosslinking constraint-guided discrete molecular dynamics simulations. Proteomics 2021; 21:e2000298. [PMID: 34482645 PMCID: PMC9285417 DOI: 10.1002/pmic.202000298] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 08/10/2021] [Accepted: 08/27/2021] [Indexed: 11/08/2022]
Abstract
The conversion of the native monomeric cellular prion protein (PrPC ) into an aggregated pathological β-oligomeric form (PrPβ ) and an infectious form (PrPSc ) is the central element in the development of prion diseases. The structure of the aggregates and the molecular mechanisms of the conformational changes involved in the conversion are still unknown. We applied mass spectrometry combined with chemical crosslinking, hydrogen/deuterium exchange, limited proteolysis, and surface modification for the differential characterization of the native and the urea+acid-converted prion β-oligomer structures to obtain insights into the mechanisms of conversion and aggregation. For the determination of the structure of the monomer and the dimer unit of the β-oligomer, we applied a recently-developed approach for de novo protein structure determination which is based on the incorporation of zero-length and short-distance crosslinking data as intra- and inter-protein constraints in discrete molecular dynamics simulations (CL-DMD). Based on all of the structural-proteomics experimental data and the computationally predicted structures of the monomer units, we propose the potential mode of assembly of the β-oligomer. The proposed β-oligomer assembly provides a clue on the β-sheet nucleation site, and how template-based conversion of the native prion molecule occurs, growth of the prion aggregates, and maturation into fibrils may occur.
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Affiliation(s)
- Jason J Serpa
- University of Victoria -Genome British Columbia Proteomics Centre, Victoria, British Columbia, Canada
| | - Konstantin I Popov
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Evgeniy V Petrotchenko
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada.,Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Nikolay V Dokholyan
- Department of Pharmacology, Department of Biochemistry & Molecular Biology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Christoph H Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada.,Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow, Russia.,Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, Quebec, Canada
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6
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Chiou SJ, Ko HJ, Hwang CC, Hong YR. The Double-Edged Sword of Beta2-Microglobulin in Antibacterial Properties and Amyloid Fibril-Mediated Cytotoxicity. Int J Mol Sci 2021; 22:ijms22126330. [PMID: 34199259 PMCID: PMC8231965 DOI: 10.3390/ijms22126330] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/03/2021] [Accepted: 06/09/2021] [Indexed: 11/25/2022] Open
Abstract
Beta2-microglobulin (B2M) a key component of major histocompatibility complex class I molecules, which aid cytotoxic T-lymphocyte (CTL) immune response. However, the majority of studies of B2M have focused only on amyloid fibrils in pathogenesis to the neglect of its role of antimicrobial activity. Indeed, B2M also plays an important role in innate defense and does not only function as an adjuvant for CTL response. A previous study discovered that human aggregated B2M binds the surface protein structure in Streptococci, and a similar study revealed that sB2M-9, derived from native B2M, functions as an antibacterial chemokine that binds Staphylococcus aureus. An investigation of sB2M-9 exhibiting an early lymphocyte recruitment in the human respiratory epithelium with bacterial challenge may uncover previously unrecognized aspects of B2M in the body’s innate defense against Mycobactrium tuberculosis. B2M possesses antimicrobial activity that operates primarily under pH-dependent acidic conditions at which B2M and fragmented B2M may become a nucleus seed that triggers self-aggregation into distinct states, such as oligomers and amyloid fibrils. Modified B2M can act as an antimicrobial peptide (AMP) against a wide range of microbes. Specifically, these AMPs disrupt microbe membranes, a feature similar to that of amyloid fibril mediated cytotoxicity toward eukaryotes. This study investigated two similar but nonidentical effects of B2M: the physiological role of B2M, in which it potentially acts against microbes in innate defense and the role of B2M in amyloid fibrils, in which it disrupts the membrane of pathological cells. Moreover, we explored the pH-governing antibacterial activity of B2M and acidic pH mediated B2M amyloid fibrils underlying such cytotoxicity.
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Affiliation(s)
- Shean-Jaw Chiou
- Department of Biochemistry, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (H.-J.K.); (C.-C.H.)
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
- Correspondence: (S.-J.C.); (Y.-R.H.)
| | - Huey-Jiun Ko
- Department of Biochemistry, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (H.-J.K.); (C.-C.H.)
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| | - Chi-Ching Hwang
- Department of Biochemistry, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (H.-J.K.); (C.-C.H.)
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| | - Yi-Ren Hong
- Department of Biochemistry, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (H.-J.K.); (C.-C.H.)
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung 804, Taiwan
- Correspondence: (S.-J.C.); (Y.-R.H.)
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7
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Transient multimers modulate conformer abundances of prion protein monomer through conformational selection. Sci Rep 2019; 9:12159. [PMID: 31434938 PMCID: PMC6704068 DOI: 10.1038/s41598-019-48377-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 08/01/2019] [Indexed: 01/15/2023] Open
Abstract
Prions are known to be involved in neurodegenerative pathologies such as Creutzfeld-Jakob disease. Current models point to a molecular event which rely on a transmissible structural change that leads to the production of β-sheet-rich prion conformer (PrPSc). PrPSc itself has the capability to trigger the structural rearrangement of the ubiquitously present prion (PrPc) substrate in a self-perpetuating cascade. In this article, we demonstrate that recombinant PrPc exists in a conformational equilibrium. The conformers’ abundances were shown to be dependent on PrPc concentration through the formation of transient multimers leading to conformational selection. The study of PrPc mutants that follow dedicated oligomerization pathways demonstrated that the conformers’ relative abundances are modified, thus reinforcing the assertion that the nature of conformers’ interactions orient the oligomerization pathways. Further this result can be viewed as the “signature” of an aborted oligomerization process. This discovery sheds a new light on the possible origin of prion protein diseases, namely that a change in prion protein structure could be transmitted through the formation of transient multimers having different conformer compositions. This could explain the selection of a transient multimeric type that could be viewed as the precursor of PrPSc responsible for structural information transmission, and strain apparition.
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8
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Amin F, Khan W, Bano B. Oxidation of cystatin imparted by riboflavin generated free radicals: Spectral analysis. Int J Biol Macromol 2019; 124:1281-1291. [PMID: 30521904 DOI: 10.1016/j.ijbiomac.2018.12.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 12/01/2018] [Accepted: 12/01/2018] [Indexed: 10/27/2022]
Abstract
Thiol Protease inhibitors (cystatins) are endogenous natural inhibitors of cysteine proteases. They are present in all mammalians cells and body fluids. Cystatin are allocated into three major families. Family -I stefins, family -II cystatins and family -III kininogens, according to their amino acid sequence, molecular weight, carbohydrate content and disulphide bonds. It has been investigated that thiol proteases (cathepsin) and their endogenous inhibitor, cystatins have been closely associated with diseases like Alzheimer's, Prions, neurodegenerative diseases, cancer and diabetes. Photodynamic effect of various sensitizers' have long been applied to delineate structural and functional properties of biologically active proteins. Flavins are well known to photo oxidize amino acids which effects conformation of proteins. Riboflavin (Vit B2) with a recommended daily requirement of approximately 2-3 mg is a yellow pigment, It is widely distributed in human tissues and blood, in both free and conjugated forms. In the present Study it has been shown that cystatin purified from buffalo brain (BC) is susceptible to reactive oxygen species generated by photo activation of riboflavin. It was observed that Photo activated riboflavin leads to inactivation of BC. Major Loss of tryptophan intensity was observed in the presence of purified thiol protease inhibitor upon incubation with 50 μM of riboflavin. In order to inspect the type of reactive oxygen species involved in inactivation of the inhibitor, different scavenger's were used namely glucose, potassium Iodide, sodium azide, manitol, thiourea, sodium benzoate, curcumin, quercetin, ascorbic acid and uric acid. It was found that Glucose, Potassium Iodide and sodium azide, have preventive effect on photo inactivation of the purified cystatin whilst other scavengers illustrated diminutive defensive effect.
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Affiliation(s)
- Fakhra Amin
- Department of Zoology, Faculty of life sciences, Aligarh Muslim University, Aligarh, UP 202002, India
| | - Wajihullah Khan
- Department of Zoology, Faculty of life sciences, Aligarh Muslim University, Aligarh, UP 202002, India; Department of Biochemistry, Faculty of life sciences, Aligarh Muslim University, Aligarh, UP 202002, India
| | - Bilqees Bano
- Department of Biochemistry, Faculty of life sciences, Aligarh Muslim University, Aligarh, UP 202002, India.
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9
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Amin F, Bano B. Damage of cystatin due to ROS-generation and radical-scavenging activity of antioxidants and associated compounds. Int J Biol Macromol 2018; 119:369-379. [DOI: 10.1016/j.ijbiomac.2018.07.100] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 07/12/2018] [Accepted: 07/16/2018] [Indexed: 01/19/2023]
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10
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Mechanism of aggregation and membrane interactions of mammalian prion protein. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018. [DOI: 10.1016/j.bbamem.2018.02.031] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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11
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Sangeetham SB, Huszár K, Bencsura P, Nyeste A, Hunyadi-Gulyás É, Fodor E, Welker E. Interrogating the Dimerization Interface of the Prion Protein Via Site-Specific Mutations to p-Benzoyl-L-Phenylalanine. J Mol Biol 2018; 430:2784-2801. [PMID: 29778603 DOI: 10.1016/j.jmb.2018.05.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Revised: 05/07/2018] [Accepted: 05/14/2018] [Indexed: 01/10/2023]
Abstract
Transmissible spongiform encephalopathies are centered on the conformational transition of the prion protein from a mainly helical, monomeric structure to a β-sheet rich ordered aggregate. Experiments indicate that the main infectious and toxic species in this process are however shorter oligomers, formation of which from the monomers is yet enigmatic. Here, we created 25 variants of the mouse prion protein site-specifically containing one genetically-incorporated para-benzoyl-phenylalanine (pBpa), a cross-linkable non-natural amino acid, in order to interrogate the interface of a prion protein-dimer, which might lie on the pathway of oligomerization. Our results reveal that the N-terminal part of the prion protein, especially regions around position 127 and 107, is integral part of the dimer interface. These together with additional pBpa-containing variants of mPrP might also facilitate to gain more structural insights into oligomeric and fibrillar prion protein species including the pathological variants.
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Affiliation(s)
- Sudheer Babu Sangeetham
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Krisztina Huszár
- Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Petra Bencsura
- Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Antal Nyeste
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary; ProteoScientia Ltd., Cserhátszentiván, Hungary
| | - Éva Hunyadi-Gulyás
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Elfrieda Fodor
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Ervin Welker
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary; Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary.
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12
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Xin X, Huang G, An C, Huang C, Weger H, Zhao S, Zhou Y, Rosendahl S. Insights into the Toxicity of Triclosan to Green Microalga Chlorococcum sp. Using Synchrotron-Based Fourier Transform Infrared Spectromicroscopy: Biophysiological Analyses and Roles of Environmental Factors. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:2295-2306. [PMID: 29377676 DOI: 10.1021/acs.est.7b05533] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
This study investigated the toxicity of triclosan to the green microalga Chlorococcum sp. under multiple environmental stressors. The interactions between triclosan and environmental stressors were explored through full two-way factorial, synchrotron-based Fourier transform infrared spectromicroscopy and principal component analyses. Phosphorus concentration, pH * phosphorus concentration, and temperature * pH * NaCl concentration were the most statistically significant factors under triclosan exposure. The variation of those factors would have a huge impact on biophysiological performances. It is interesting to find Chlorococcum sp. may become more resistant against triclosan in phosphorus-enriched environment. Besides, particular significant factors from multiple environmental stressors showed the impacts of triclosan on the corresponding response of Chlorococcum sp. owing to the specific structure and performance of biomolecular components. Moreover, two high-order interactions of temperature * pH * NaCl concentration and temperature * pH * NaCl concentration * phosphorus concentration had more contributions than others at the subcellular level, which could be attributed to the interactive complexity of biomolecular components. Due to cellular self-regulation mechanism and short exposure time, the biophysiological changes of Chlorococcum sp. were undramatic. These findings can help reveal the interactive complexity among triclosan and multiple environmental stressors. It is suggested that multiple environmental stressors should be considered during ecological risk assessment and management of emerging pollutants.
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Affiliation(s)
| | | | - Chunjiang An
- Department of Building, Civil and Environmental Engineering, Concordia University , Montreal, Quebec, Canada H3G 1M8
| | - Charley Huang
- Department of Chemical and Biological Engineering, University of British Columbia , Vancouver, British Columbia, Canada V6T 1Z3
| | | | - Shan Zhao
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University , Jinan, China 250100
| | | | - Scott Rosendahl
- Canadian Light Source, Saskatoon, Saskatchewan, Canada S7N 2 V3
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13
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Methods to Characterize the Nanostructure and Molecular Organization of Amphiphilic Peptide Assemblies. Methods Mol Biol 2018; 1777:3-21. [PMID: 29744826 DOI: 10.1007/978-1-4939-7811-3_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Methods to characterize the nanostructure and molecular organization of aggregates of peptides such as amyloid or amphiphilic peptide assemblies are reviewed. We discuss techniques to characterize conformation and secondary structure including circular and linear dichroism and FTIR and Raman spectroscopies, as well as fluorescence methods to detect aggregation. NMR spectroscopy methods, especially solid-state NMR measurements to probe beta-sheet packing motifs, are also briefly outlined. Also discussed are scattering methods including X-ray diffraction and small-angle scattering techniques including SAXS (small-angle X-ray scattering) and SANS (small-angle neutron scattering) and dynamic light scattering. Imaging methods are direct methods to uncover features of peptide nanostructures, and we provide a summary of electron microscopy and atomic force microscopy techniques. Selected examples are highlighted showing data obtained using these techniques, which provide a powerful suite of methods to probe ordering from the molecular scale to the aggregate superstructure.
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14
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Cieplak AS. Protein folding, misfolding and aggregation: The importance of two-electron stabilizing interactions. PLoS One 2017; 12:e0180905. [PMID: 28922400 PMCID: PMC5603215 DOI: 10.1371/journal.pone.0180905] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 06/22/2017] [Indexed: 12/17/2022] Open
Abstract
Proteins associated with neurodegenerative diseases are highly pleiomorphic and may adopt an all-α-helical fold in one environment, assemble into all-β-sheet or collapse into a coil in another, and rapidly polymerize in yet another one via divergent aggregation pathways that yield broad diversity of aggregates’ morphology. A thorough understanding of this behaviour may be necessary to develop a treatment for Alzheimer’s and related disorders. Unfortunately, our present comprehension of folding and misfolding is limited for want of a physicochemical theory of protein secondary and tertiary structure. Here we demonstrate that electronic configuration and hyperconjugation of the peptide amide bonds ought to be taken into account to advance such a theory. To capture the effect of polarization of peptide linkages on conformational and H-bonding propensity of the polypeptide backbone, we introduce a function of shielding tensors of the Cα atoms. Carrying no information about side chain-side chain interactions, this function nonetheless identifies basic features of the secondary and tertiary structure, establishes sequence correlates of the metamorphic and pH-driven equilibria, relates binding affinities and folding rate constants to secondary structure preferences, and manifests common patterns of backbone density distribution in amyloidogenic regions of Alzheimer’s amyloid β and tau, Parkinson’s α-synuclein and prions. Based on those findings, a split-intein like mechanism of molecular recognition is proposed to underlie dimerization of Aβ, tau, αS and PrPC, and divergent pathways for subsequent association of dimers are outlined; a related mechanism is proposed to underlie formation of PrPSc fibrils. The model does account for: (i) structural features of paranuclei, off-pathway oligomers, non-fibrillar aggregates and fibrils; (ii) effects of incubation conditions, point mutations, isoform lengths, small-molecule assembly modulators and chirality of solid-liquid interface on the rate and morphology of aggregation; (iii) fibril-surface catalysis of secondary nucleation; and (iv) self-propagation of infectious strains of mammalian prions.
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Affiliation(s)
- Andrzej Stanisław Cieplak
- Department of Chemistry, Bilkent University, Ankara, Turkey
- Department of Chemistry, Yale University, New Haven, Connecticut, United States of America
- Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States of America
- * E-mail:
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15
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Mi L, Yu J, He F, Jiang L, Wu Y, Yang L, Han X, Li Y, Liu A, Wei W, Zhang Y, Tian Y, Liu S, Jiang L. Boosting Gas Involved Reactions at Nanochannel Reactor with Joint Gas–Solid–Liquid Interfaces and Controlled Wettability. J Am Chem Soc 2017; 139:10441-10446. [DOI: 10.1021/jacs.7b05249] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Li Mi
- Key
Laboratory of Environmental Medicine Engineering, Ministry of Education,
Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and
Device, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Jiachao Yu
- Key
Laboratory of Environmental Medicine Engineering, Ministry of Education,
Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and
Device, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Fei He
- Key
Laboratory of Environmental Medicine Engineering, Ministry of Education,
Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and
Device, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Ling Jiang
- Key
Laboratory of Environmental Medicine Engineering, Ministry of Education,
Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and
Device, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Yafeng Wu
- Key
Laboratory of Environmental Medicine Engineering, Ministry of Education,
Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and
Device, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Lijun Yang
- Key
Laboratory of Bioinspired Smart Interface Sciences, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Xiaofeng Han
- Key
Laboratory of Environmental Medicine Engineering, Ministry of Education,
Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and
Device, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Ying Li
- Key
Laboratory of Environmental Medicine Engineering, Ministry of Education,
Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and
Device, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Anran Liu
- Key
Laboratory of Environmental Medicine Engineering, Ministry of Education,
Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and
Device, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Wei Wei
- Key
Laboratory of Environmental Medicine Engineering, Ministry of Education,
Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and
Device, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Yuanjian Zhang
- Key
Laboratory of Environmental Medicine Engineering, Ministry of Education,
Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and
Device, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Ye Tian
- Beijing
National Laboratory for Molecular Sciences (BNLMS), Key Laboratory
of Green Printing, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Songqin Liu
- Key
Laboratory of Environmental Medicine Engineering, Ministry of Education,
Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and
Device, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Lei Jiang
- Key
Laboratory of Bioinspired Smart Interface Sciences, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
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16
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Elia F, Cantini F, Chiti F, Dobson CM, Bemporad F. Direct Conversion of an Enzyme from Native-like to Amyloid-like Aggregates within Inclusion Bodies. Biophys J 2017; 112:2540-2551. [PMID: 28636911 PMCID: PMC5479110 DOI: 10.1016/j.bpj.2017.05.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 05/02/2017] [Accepted: 05/08/2017] [Indexed: 01/29/2023] Open
Abstract
The acylphosphatase from Sulfolobus solfataricus (Sso AcP) is a globular protein able to aggregate in vitro from a native-like conformational ensemble without the need for a transition across the major unfolding energy barrier. This process leads to the formation of assemblies in which the protein retains its native-like structure, which subsequently convert into amyloid-like aggregates. Here, we investigate the mechanism by which Sso AcP aggregates in vivo to form bacterial inclusion bodies after expression in E. coli. Shortly after the initiation of expression, Sso AcP is incorporated into inclusion bodies as a native-like protein, still exhibiting small but significant enzymatic activity. Additional experiments revealed that this overall process of aggregation is enhanced by the presence of the unfolded N-terminal region of the sequence and by destabilization of the globular segment of the protein. At later times, the Sso AcP molecules in the inclusion bodies lose their native-like properties and convert into β-sheet-rich amyloid-like structures, as indicated by their ability to bind thioflavin T and Congo red. These results show that the aggregation behavior of this protein is similar in vivo to that observed in vitro, and that, at least for a predominant part of the protein population, the transition from a native to an amyloid-like structure occurs within the aggregate state.
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Affiliation(s)
- Francesco Elia
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio," University of Florence, Firenze, Italy
| | - Francesca Cantini
- Centro Risonanze Magnetiche (CERM) and Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Fabrizio Chiti
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio," University of Florence, Firenze, Italy
| | | | - Francesco Bemporad
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio," University of Florence, Firenze, Italy.
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17
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Sengupta I, Bhate SH, Das R, Udgaonkar JB. Salt-Mediated Oligomerization of the Mouse Prion Protein Monitored by Real-Time NMR. J Mol Biol 2017; 429:1852-1872. [DOI: 10.1016/j.jmb.2017.05.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 05/05/2017] [Accepted: 05/07/2017] [Indexed: 12/11/2022]
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18
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Stroo E, Koopman M, Nollen EAA, Mata-Cabana A. Cellular Regulation of Amyloid Formation in Aging and Disease. Front Neurosci 2017; 11:64. [PMID: 28261044 PMCID: PMC5306383 DOI: 10.3389/fnins.2017.00064] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 01/30/2017] [Indexed: 12/24/2022] Open
Abstract
As the population is aging, the incidence of age-related neurodegenerative diseases, such as Alzheimer and Parkinson disease, is growing. The pathology of neurodegenerative diseases is characterized by the presence of protein aggregates of disease specific proteins in the brain of patients. Under certain conditions these disease proteins can undergo structural rearrangements resulting in misfolded proteins that can lead to the formation of aggregates with a fibrillar amyloid-like structure. Cells have different mechanisms to deal with this protein aggregation, where the molecular chaperone machinery constitutes the first line of defense against misfolded proteins. Proteins that cannot be refolded are subjected to degradation and compartmentalization processes. Amyloid formation has traditionally been described as responsible for the proteotoxicity associated with different neurodegenerative disorders. Several mechanisms have been suggested to explain such toxicity, including the sequestration of key proteins and the overload of the protein quality control system. Here, we review different aspects of the involvement of amyloid-forming proteins in disease, mechanisms of toxicity, structural features, and biological functions of amyloids, as well as the cellular mechanisms that modulate and regulate protein aggregation, including the presence of enhancers and suppressors of aggregation, and how aging impacts the functioning of these mechanisms, with special attention to the molecular chaperones.
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Affiliation(s)
- Esther Stroo
- European Research Institute for the Biology of Aging, University of Groningen, University Medical Center Groningen Groningen, Netherlands
| | - Mandy Koopman
- European Research Institute for the Biology of Aging, University of Groningen, University Medical Center Groningen Groningen, Netherlands
| | - Ellen A A Nollen
- European Research Institute for the Biology of Aging, University of Groningen, University Medical Center Groningen Groningen, Netherlands
| | - Alejandro Mata-Cabana
- European Research Institute for the Biology of Aging, University of Groningen, University Medical Center Groningen Groningen, Netherlands
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19
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Strømland Ø, Handegård ØS, Govasli ML, Wen H, Halskau Ø. Peptides derived from α-lactalbumin membrane binding helices oligomerize in presence of lipids and disrupt bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1029-1039. [PMID: 28069414 DOI: 10.1016/j.bbamem.2017.01.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 12/02/2016] [Accepted: 01/04/2017] [Indexed: 11/16/2022]
Abstract
Helix A and -C of α-lactalbumin, a loosely folded amphitropic protein, perturb lipid monolayers by the formation of amyloid pore-like structures. To investigate whether these helices are able to disrupt fully formed bilayers, we designed peptides comprised of Helix A and -C, and investigated their membrane-perturbing properties. The peptides, designated A-Cage-C and A-Lnk-C, were prepared with tryptophan sites in the helical and the spacer segments in order to monitor which part were involved in membrane association under given conditions. The peptides associate with and disrupt negatively charged bilayers in a pH-dependent manner and α-helical tendencies increased upon membrane association. Both helices and the spacer segment were involved in membrane binding in the case of A-Lnk-C, and there are indications that the two helixes act in synergy to affect the membrane. However, the helices and the spacer segment could not intercalate when present as A-Cage-C at neutral conditions. At acidic pH, both helices could intercalate, but not the central spacer segment. AFM performed on bilayers under aqueous conditions revealed oligomers formed by the peptides. The presence of bilayers and acidic pHs were both drivers for the formation of these, suggestive of models for peptide oligomerization where segments of the peptide are stacked in an electrostatically favorable manner by the surface. Of the two peptides, A-Lnk-C was the more prolific oligomerizer, and also formed amyloid-fibril like structures at acidic pH and elevated concentrations. Our results suggest the peptides perturb membranes not through pore-like structures, but possibly by a thinning mechanism.
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Affiliation(s)
- Øyvind Strømland
- Department of Molecular Biology, University of Bergen, Thormøhlensgt. 55, 5008 Bergen, Norway
| | - Ørjan S Handegård
- Department of Molecular Biology, University of Bergen, Thormøhlensgt. 55, 5008 Bergen, Norway
| | - Morten L Govasli
- Department of Molecular Biology, University of Bergen, Thormøhlensgt. 55, 5008 Bergen, Norway
| | - Hanzhen Wen
- Department of Molecular Biology, University of Bergen, Thormøhlensgt. 55, 5008 Bergen, Norway
| | - Øyvind Halskau
- Department of Molecular Biology, University of Bergen, Thormøhlensgt. 55, 5008 Bergen, Norway.
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20
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Rezza G, Ippolito G. Syrian Hamsters as a Small Animal Model for Emerging Infectious Diseases: Advances in Immunologic Methods. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 972:87-101. [PMID: 27722960 PMCID: PMC7121384 DOI: 10.1007/5584_2016_135] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The use of small animal models for the study of infectious disease is critical for understanding disease progression and for developing prophylactic and therapeutic treatment options. For many diseases, Syrian golden hamsters have emerged as an ideal animal model due to their low cost, small size, ease of handling, and ability to accurately reflect disease progression in humans. Despite the increasing use and popularity of hamsters, there remains a lack of available reagents for studying hamster immune responses. Without suitable reagents for assessing immune responses, researchers are left to examine clinical signs and disease pathology. This becomes an issue for the development of vaccine and treatment options where characterizing the type of immune response generated is critical for understanding protection from disease. Despite the relative lack of reagents for use in hamsters, significant advances have been made recently with several hamster specific immunologic methods being developed. Here we discuss the progress of this development, with focus on classical methods used as well as more recent molecular methods. We outline what methods are currently available for use in hamsters and what is readily used as well as what limitations still exist and future perspectives of reagent and assay development for hamsters. This will provide valuable information to researchers who are deciding whether to use hamsters as an animal model.
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21
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Yu Y, Yu Z, Zheng Z, Wang H, Wu X, Guo C, Lin D. Distinct effects of mutations on biophysical properties of human prion protein monomers and oligomers. Acta Biochim Biophys Sin (Shanghai) 2016; 48:1016-1025. [PMID: 27649893 DOI: 10.1093/abbs/gmw094] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 07/15/2016] [Indexed: 02/05/2023] Open
Abstract
Prion diseases are a group of fatal neurodegenerative illnesses, resulting from the conformational conversion of the cellular prion protein (PrPC) into a misfolded form (PrPSc). The formation of neurotoxic soluble prion protein oligomer (PrPO) is regarded as a key step in the development of prion diseases. About 10%-15% of human prion diseases are caused by mutations in the prion protein gene; however, the underlying molecular mechanisms remain unclear. In the present work, we compared the biophysical properties of wild-type (WT) human prion protein 91-231 (WT HuPrP91-231) and its disease-associated variants (P105L, D178N, V203I, and Q212P) using several biophysical techniques. In comparison with WT HuPrPC, the Q212P and D178N variants possessed greatly increased conversion propensities of PrPC into PrPO, while the V203I variant had dramatically decreased conversion propensity. The P105L variant displayed a similar conversion propensity to WT HuPrPC Guanidine hydrochloride-induced unfolding experiments ranked the thermodynamic stabilities of these proteins as Q212P < D178N < WT ≈ P105L < V203I. It was thus suggested that the conversion propensities of the prion proteins are closely associated with their thermodynamic stabilities. Furthermore, structural comparison illustrated that Q212P, D178N, and V203I variants underwent larger structural changes compared with WT HuPrPC, while the P105L variant adopted a similar structure to the WT HuPrPC The mutation-induced structural perturbations might change the thermodynamic stabilities of the HuPrPC variants, and correspondingly alter the conversion propensities for these prion proteins. Our results extend the mechanistic understanding of prion pathogenesis, and lay the basis for the prevention and treatment of prion diseases.
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Affiliation(s)
- Yuanhui Yu
- MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Ziyao Yu
- MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Zhen Zheng
- MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Huilin Wang
- MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xueji Wu
- MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Chenyun Guo
- MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Donghai Lin
- MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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22
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Sabareesan AT, Udgaonkar JB. Pathogenic Mutations within the Disordered Palindromic Region of the Prion Protein Induce Structure Therein and Accelerate the Formation of Misfolded Oligomers. J Mol Biol 2016; 428:3935-3947. [PMID: 27545411 DOI: 10.1016/j.jmb.2016.08.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/09/2016] [Accepted: 08/12/2016] [Indexed: 12/11/2022]
Abstract
Little is understood about how the intrinsically disordered N-terminal region (NTR) of the prion protein modulates its misfolding and aggregation, which lead to prion disease. In this study, two pathogenic mutations, G113V and A116V, in the palindromic region of the NTR are shown to have no effect on the structure, stability, or dynamics of native mouse prion protein (moPrP) but nevertheless accelerate misfolding and oligomerization. For wild-type moPrP, misfolding and oligomerization appear to occur concurrently, while for both mutant variants, oligomerization is shown to precede misfolding. Kinetic hydrogen-deuterium exchange-mass spectrometry experiments show that sequence segment 89-132 from the NTR becomes structured, albeit weakly, during the oligomerization of both mutant variants. Importantly, this structure formation occurs prior to structural conversion in the C-terminal domain and appears to be the reason that the formation of misfolded oligomers is accelerated by the pathogenic mutations.
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Affiliation(s)
- A T Sabareesan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Jayant B Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India.
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23
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Yu Z, Huang P, Yu Y, Zheng Z, Huang Z, Guo C, Lin D. Unique Properties of the Rabbit Prion Protein Oligomer. PLoS One 2016; 11:e0160874. [PMID: 27529173 PMCID: PMC4987043 DOI: 10.1371/journal.pone.0160874] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 07/26/2016] [Indexed: 11/26/2022] Open
Abstract
Prion diseases, also known as transmissible spongiform encephalopathies (TSEs), are a group of fatal neurodegenerative disorders infecting both humans and animals. Recent works have demonstrated that the soluble prion protein oligomer (PrPO), the intermediate of the conformational transformation from the host-derived cellular form (PrPC) to the disease-associated Scrapie form (PrPSc), exerts the major neurotoxicity in vitro and in vivo. Rabbits show strong resistance to TSEs, the underlying mechanism is unclear to date. It is expected that the relative TSEs-resistance of rabbits is closely associated with the unique properties of rabbit prion protein oligomer which remain to be addressed in detail. In the present work, we prepared rabbit prion protein oligomer (recRaPrPO) and human prion protein oligomer (recHuPrPO) under varied conditions, analyzed the effects of pH, NaCl concentration and incubation temperature on the oligomerization, and compared the properties of recRaPrPO and recHuPrPO. We found that several factors facilitated the formation of prion protein oligomers, including low pH, high NaCl concentration, high incubation temperature and low conformational stability of monomeric prion protein. RecRaPrPO was formed more slowly than recHuPrPO at physiological-like conditions (< 57°C, < 150 mM NaCl). Furthermore, recRaPrPO possessed higher susceptibility to proteinase K and lower cytotoxicity in vitro than recHuPrPO. These unique properties of recRaPrPO might substantially contribute to the TSEs-resistance of rabbits. Our work sheds light on the oligomerization of prion proteins and is of benefit to mechanistic understanding of TSEs-resistance of rabbits.
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Affiliation(s)
- Ziyao Yu
- The Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Pei Huang
- The Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yuanhui Yu
- The Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Zhen Zheng
- The Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Zicheng Huang
- The Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Chenyun Guo
- The Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Donghai Lin
- The Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- * E-mail:
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24
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Singh J, Udgaonkar JB. Unraveling the Molecular Mechanism of pH-Induced Misfolding and Oligomerization of the Prion Protein. J Mol Biol 2016; 428:1345-1355. [PMID: 26854758 DOI: 10.1016/j.jmb.2016.01.030] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 01/27/2016] [Accepted: 01/28/2016] [Indexed: 12/31/2022]
Abstract
The misfolding of the prion protein (PrP) to aggregated forms is linked to several neurodegenerative diseases. Misfolded oligomeric forms of PrP are associated with neurotoxicity and/or infectivity, but the molecular mechanism by which they form is still poorly understood. A reduction in pH is known to be a key factor that triggers misfolded oligomer formation by PrP, but the residues whose protonation is linked with misfolding remain unidentified. The structural consequences of the protonation of these residues also remain to be determined. In the current study, amino acid residues whose protonation is critical for PrP misfolding and oligomerization have been identified using site-directed mutagenesis and misfolding/oligomerization assays. It is shown that the protonation of either H186 or D201, which mimics the effects of pathogenic mutations (H186R and D201N) at both residue sites, is critically linked to the stability, misfolding and oligomerization of PrP. Hydrogen-deuterium exchange studies coupled with mass spectrometry show that the protonation of either H186 or D201 leads to the same common structural change: increased structural dynamics in helix 1 and that in the loop between helix 1 and β-strand 2. It is shown that the protonation of either of these residues is sufficient for accelerating misfolded oligomer formation, most likely because the protonation of either residue causes the same structural perturbation. Hence, the increased structural dynamics in helix 1 and that in the loop between helix 1 and β-strand 2 appear to play an early critical role in acid-induced misfolding of PrP.
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Affiliation(s)
- Jogender Singh
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Jayant B Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India.
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25
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Hammond M, Wik L, Deslys JP, Comoy E, Linné T, Landegren U, Kamali-Moghaddam M. Sensitive detection of aggregated prion protein via proximity ligation. Prion 2015; 8:261-5. [PMID: 25482604 DOI: 10.4161/pri.32231] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The DNA assisted solid-phase proximity ligation assay (SP-PLA) provides a unique opportunity to specifically detect prion protein (PrP) aggregates by investigating the collocation of 3 or more copies of the specific protein. We have developed an SP-PLA that can detect PrP aggregates in brain homogenates from infected hamsters even after a 10(7)-fold dilution. In contrast, brain homogenate from uninfected animals did not generate a detectable signal at 100-fold higher concentration. Using either of the 2 monoclonal anti-PrP antibodies, 3F4 and 6H4, we successfully detected low concentrations of aggregated PrP. The presented results provide a proof of concept that this method might be an interesting tool in the development of diagnostic approaches of prion diseases.
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Key Words
- 263K
- BSE, bovine spongiform encephalopathy
- CJD, Creutzfeldt-Jakob disease
- CSF, cerebrospinal fluid
- FIDA, fluorescence intensity distribution analysis
- PLA, proximity ligation assay
- PMCA, protein misfolding cyclic amplification
- PrP, prion protein
- PrPC, cellular prion protein
- PrPSc, scrapie prion protein
- QuIC, quaking-induced conversion
- SP-PLA, solid phase proximity ligation assay
- diagnosis
- monoclonal antibody
- prion protein
- proximity ligation assay
- qPCR, quantitative real-time PCR
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Affiliation(s)
- Maria Hammond
- a Department of Immunology, Genetics and Pathology; Science for Life Laboratory ; Uppsala University ; Uppsala , Sweden
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26
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Membrane-mediated amyloid formation of PrP 106-126: A kinetic study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015. [PMID: 26215743 DOI: 10.1016/j.bbamem.2015.07.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
PrP 106-126 conserves the pathogenic and physicochemical properties of the Scrapie isoform of the prion protein. PrP 106-126 and other amyloidal proteins are capable of inducing ion permeability through cell membranes, and this property may represent the common primary mechanism of pathogenesis in the amyloid-related degenerative diseases. However, for many amyloidal proteins, despite numerous phenomenological observations of their interactions with membranes, it has been difficult to determine the molecular mechanisms by which the proteins cause ion permeability. One approach that has not been undertaken is the kinetic study of protein-membrane interactions. We found that the reaction time constant of the interaction between PrP 106-126 and membranes is suitable for such studies. The kinetic experiment with giant lipid vesicles showed that the membrane area first increased by peptide binding but then decreased. The membrane area decrease was coincidental with appearance of extramembranous aggregates including lipid molecules. Sometimes, the membrane area would increase again followed by another decrease. The kinetic experiment with small vesicles was monitored by circular dichroism for peptide conformation changes. The results are consistent with a molecular simulation following a simple set of well-defined rules. We deduced that at the molecular level the formation of peptide amyloids incorporated lipid molecules as part of the aggregates. Most importantly the amyloid aggregates desorbed from the lipid bilayer, consistent with the macroscopic phenomena observed with giant vesicles. Thus we conclude that the main effect of membrane-mediated amyloid formation is extraction of lipid molecules from the membrane. We discuss the likelihood of this effect on membrane ion permeability.
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27
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Singh J, Udgaonkar JB. Structural Effects of Multiple Pathogenic Mutations Suggest a Model for the Initiation of Misfolding of the Prion Protein. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201501011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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28
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Singh J, Udgaonkar JB. Structural Effects of Multiple Pathogenic Mutations Suggest a Model for the Initiation of Misfolding of the Prion Protein. Angew Chem Int Ed Engl 2015; 54:7529-33. [DOI: 10.1002/anie.201501011] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 04/17/2015] [Indexed: 12/17/2022]
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29
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Wustoni S, Hideshima S, Kuroiwa S, Nakanishi T, Hashimoto M, Mori Y, Osaka T. Sensitive electrical detection of human prion proteins using field effect transistor biosensor with dual-ligand binding amplification. Biosens Bioelectron 2015; 67:256-62. [DOI: 10.1016/j.bios.2014.08.028] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 08/08/2014] [Accepted: 08/08/2014] [Indexed: 11/16/2022]
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30
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Cairns LS, Hobley L, Stanley-Wall NR. Biofilm formation by Bacillus subtilis: new insights into regulatory strategies and assembly mechanisms. Mol Microbiol 2014; 93:587-98. [PMID: 24988880 PMCID: PMC4238804 DOI: 10.1111/mmi.12697] [Citation(s) in RCA: 150] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2014] [Indexed: 12/16/2022]
Abstract
Biofilm formation is a social behaviour that generates favourable conditions for sustained survival in the natural environment. For the Gram-positive bacterium Bacillus subtilis the process involves the differentiation of cell fate within an isogenic population and the production of communal goods that form the biofilm matrix. Here we review recent progress in understanding the regulatory pathways that control biofilm formation and highlight developments in understanding the composition, function and structure of the biofilm matrix.
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Affiliation(s)
- Lynne S Cairns
- Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
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31
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Zhang H, Griggs A, Rochet JC, Stanciu LA. In vitro study of α-synuclein protofibrils by cryo-EM suggests a Cu(2+)-dependent aggregation pathway. Biophys J 2014; 104:2706-13. [PMID: 23790379 DOI: 10.1016/j.bpj.2013.04.050] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 04/16/2013] [Accepted: 04/23/2013] [Indexed: 01/25/2023] Open
Abstract
The aggregation of α-synuclein is thought to play a role in the death of dopamine neurons in Parkinson's disease (PD). Alpha-synuclein transitions itself through an aggregation pathway consisting of pathogenic species referred to as protofibrils (or oligomer), which ultimately convert to mature fibrils. The structural heterogeneity and instability of protofibrils has significantly impeded advance related to the understanding of their structural characteristics and the amyloid aggregation mystery. Here, we report, to our knowledge for the first time, on α-synuclein protofibril structural characteristics with cryo-electron microscopy. Statistical analysis of annular protofibrils revealed a constant wall thickness as a common feature. The visualization of the assembly steps enabled us to propose a novel, to our knowledge, mechanisms for α-synuclein aggregation involving ring-opening and protofibril-protofibril interaction events. The ion channel-like protofibrils and their membrane permeability have also been found in other amyloid diseases, suggesting a common molecular mechanism of pathological aggregation. Our direct visualization of the aggregation pathway of α-synuclein opens up fresh opportunities to advance the understanding of protein aggregation mechanisms relevant to many amyloid diseases. In turn, this information would enable the development of additional therapeutic strategies aimed at suppressing toxic protofibrils of amyloid proteins involved in neurological disorders.
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Affiliation(s)
- Hangyu Zhang
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana, USA
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Schlepckow K, Schwalbe H. Molecular mechanism of prion protein oligomerization at atomic resolution. Angew Chem Int Ed Engl 2013; 52:10002-5. [PMID: 23934741 DOI: 10.1002/anie.201305184] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Indexed: 11/08/2022]
Abstract
Prion protein oligomerization: Despite the crucial role of oligomers during prion protein (PrP) pathogenesis the molecular mechanism of their formation has remained largely elusive. A 2D time-resolved NMR study which made it possible to characterize the oligomerization kinetics with unprecedented site-specificity is reported.
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Affiliation(s)
- Kai Schlepckow
- Institut für Organische Chemie und Chemische Biologie, Zentrum für Biomolekulare Magnetische Resonanz (BMRZ), Johann Wolfgang Goethe-Universität Frankfurt am Main, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main (Germany) http://schwalbe.org.chemie.uni-frankfurt.de
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Schlepckow K, Schwalbe H. Molecular Mechanism of Prion Protein Oligomerization at Atomic Resolution. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201305184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Larda ST, Simonetti K, Al-Abdul-Wahid MS, Sharpe S, Prosser RS. Dynamic Equilibria between Monomeric and Oligomeric Misfolded States of the Mammalian Prion Protein Measured by 19F NMR. J Am Chem Soc 2013; 135:10533-41. [DOI: 10.1021/ja404584s] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Sacha Thierry Larda
- Department of Chemistry, University of Toronto, Toronto, Ontario,
Canada M5S 3H6
| | - Karen Simonetti
- Molecular
Structure and Function
Program, The Hospital for Sick Children, Toronto, Ontario, Canada M5G 1X8
| | | | - Simon Sharpe
- Molecular
Structure and Function
Program, The Hospital for Sick Children, Toronto, Ontario, Canada M5G 1X8
- Department of Biochemistry, University of Toronto, Toronto, Ontario,
Canada M5S 1A8
| | - R. Scott Prosser
- Department of Chemistry, University of Toronto, Toronto, Ontario,
Canada M5S 3H6
- Department of Biochemistry, University of Toronto, Toronto, Ontario,
Canada M5S 1A8
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Hu PP, Huang CZ. Prion protein: structural features and related toxicity. Acta Biochim Biophys Sin (Shanghai) 2013; 45:435-41. [PMID: 23615535 DOI: 10.1093/abbs/gmt035] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Transmissible spongiform encephalopathies, or prion diseases, is a group of infectious neurodegenerative disorders. The conformational conversion from cellular form (PrP(C)) to disease-causing isoform (PrP(Sc)) is considered to be the most important and remarkable event in these diseases, while accumulation of PrP(Sc) is thought to be the main reason for cell death, inflammation and spongiform degeneration observed in infected individuals. Although these rare but unique neurodegenerative disorders have attracted much attention, there are still many questions that remain to be answered. Knowledge of the scrapie agent structures and the toxic species may have significance for understanding the causes of the diseases, and could be helpful for rational design of novel therapeutic and diagnostic methods. In this review, we summarized the available experimental evidence concerning the relationship among the structural features, aggregation status of misfolded PrP and related neurotoxicity in the course of prion diseases development. In particular, most data supports the idea that the smaller oligomeric PrP(Sc) aggregates, rather than the mature amyloid fibers, exhibit the highest toxicity to the host.
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Affiliation(s)
- Ping Ping Hu
- Ministry of Education Key Laboratory on Luminescence and Real-Time Analysis, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
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36
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Drenski MF, Brader ML, Alston RW, Reed WF. Monitoring protein aggregation kinetics with simultaneous multiple sample light scattering. Anal Biochem 2013; 437:185-97. [DOI: 10.1016/j.ab.2013.02.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 02/15/2013] [Accepted: 02/19/2013] [Indexed: 10/27/2022]
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Schreck JS, Yuan JM. A Kinetic Study of Amyloid Formation: Fibril Growth and Length Distributions. J Phys Chem B 2013; 117:6574-83. [DOI: 10.1021/jp401586p] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- John S. Schreck
- Department
of Physics, Drexel University, Philadelphia,
Pennsylvania 19104, United States
| | - Jian-Min Yuan
- Department
of Physics, Drexel University, Philadelphia,
Pennsylvania 19104, United States
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Chai L, Romero D, Kayatekin C, Akabayov B, Vlamakis H, Losick R, Kolter R. Isolation, characterization, and aggregation of a structured bacterial matrix precursor. J Biol Chem 2013; 288:17559-68. [PMID: 23632024 DOI: 10.1074/jbc.m113.453605] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Biofilms are surface-associated groups of microbial cells that are embedded in an extracellular matrix (ECM). The ECM is a network of biopolymers, mainly polysaccharides, proteins, and nucleic acids. ECM proteins serve a variety of structural roles and often form amyloid-like fibers. Despite the extensive study of the formation of amyloid fibers from their constituent subunits in humans, much less is known about the assembly of bacterial functional amyloid-like precursors into fibers. Using dynamic light scattering, atomic force microscopy, circular dichroism, and infrared spectroscopy, we show that our unique purification method of a Bacillus subtilis major matrix protein component results in stable oligomers that retain their native α-helical structure. The stability of these oligomers enabled us to control the external conditions that triggered their aggregation. In particular, we show that stretched fibers are formed on a hydrophobic surface, whereas plaque-like aggregates are formed in solution under acidic pH conditions. TasA is also shown to change conformation upon aggregation and gain some β-sheet structure. Our studies of the aggregation of a bacterial matrix protein from its subunits shed new light on assembly processes of the ECM within bacterial biofilms.
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Affiliation(s)
- Liraz Chai
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, USA
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Abstract
The structural conversion of the prion protein PrP into a transmissible, misfolded form is the central element of prion disease, yet there is little consensus as to how it occurs. Key aspects of conversion into the diseased state remain unsettled, from details about the earliest stages of misfolding such as the involvement of partially- or fully-unfolded intermediates to the structure of the infectious state. Part of the difficulty in understanding the structural conversion arises from the complexity of the underlying energy landscapes. Single molecule methods provide a powerful tool for probing complex folding pathways as in prion misfolding, because they allow rare and transient events to be observed directly. We discuss recent work applying single-molecule probes to study misfolding in prion proteins, and what it has revealed about the folding dynamics of PrP that may underlie its unique behavior. We also discuss single-molecule studies probing the interactions that stabilize non-native structures within aggregates, pointing the way to future work that may help identify the microscopic events triggering pathogenic conversion. Although single-molecule approaches to misfolding are relatively young, they have a promising future in prion science.
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Affiliation(s)
- Hao Yu
- Department of Physics, University of Alberta, Edmonton, AB Canada
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40
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Sang JC, Lee CY, Luh FY, Huang YW, Chiang YW, Chen RPY. Slow spontaneous α-to-β structural conversion in a non-denaturing neutral condition reveals the intrinsically disordered property of the disulfide-reduced recombinant mouse prion protein. Prion 2012; 6:489-97. [PMID: 22987112 PMCID: PMC3510854 DOI: 10.4161/pri.22217] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In prion diseases, the normal prion protein is transformed by an unknown mechanism from a mainly α-helical structure to a β-sheet-rich, disease-related isomer. In this study, we surprisingly found that a slow, spontaneous α-to-coil-to-β transition could be monitored by circular dichroism spectroscopy in one full-length mouse recombinant prion mutant protein, denoted S132C/N181C, in which the endogenous cysteines C179 and C214 were replaced by Ala and S132 and N181 were replaced by Cys, during incubation in a non-denaturing neutral buffer. No denaturant was required to destabilize the native state for the conversion. The product after this structural conversion is toxic β-oligomers with high fluorescence intensity when binding with thioflavin T. Site-directed spin-labeling ESR data suggested that the structural conversion involves the unfolding of helix 2. After examining more protein mutants, it was found that the spontaneous structural conversion is due to the disulfide-deletion (C to A mutations). The recombinant wild-type mouse prion protein could also be transformed into β-oligomers and amyloid fibrils simply by dissolving and incubating the protein in 0.5 mM NaOAc (pH 7) and 1 mM DTT at 25°C with no need of adding any denaturant to destabilize the prion protein. Our findings indicate the important role of disulfide bond reduction on the structural conversion of the recombinant prion protein, and highlight the special “intrinsically disordered” conformational character of the recombinant prion protein.
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Affiliation(s)
- Jason C Sang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
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41
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Pires RH, Karsai Á, Saraiva MJ, Damas AM, Kellermayer MSZ. Distinct annular oligomers captured along the assembly and disassembly pathways of transthyretin amyloid protofibrils. PLoS One 2012; 7:e44992. [PMID: 22984597 PMCID: PMC3440338 DOI: 10.1371/journal.pone.0044992] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 08/15/2012] [Indexed: 11/20/2022] Open
Abstract
Background Defects in protein folding may lead to severe degenerative diseases characterized by the appearance of amyloid fibril deposits. Cytotoxicity in amyloidoses has been linked to poration of the cell membrane that may involve interactions with amyloid intermediates of annular shape. Although annular oligomers have been detected in many amyloidogenic systems, their universality, function and molecular mechanisms of appearance are debated. Methodology/Principal Findings We investigated with high-resolution in situ atomic force microscopy the assembly and disassembly of transthyretin (TTR) amyloid protofibrils formed of the native protein by pH shift. Annular oligomers were the first morphologically distinct intermediates observed in the TTR aggregation pathway. Morphological analysis suggests that they can assemble into a double-stack of octameric rings with a 16±2 nm diameter, and displaying the tendency to form linear structures. According to light scattering data coupled to AFM imaging, annular oligomers appeared to undergo a collapse type of structural transition into spheroid oligomers containing 8–16 monomers. Disassembly of TTR amyloid protofibrils also resulted in the rapid appearance of annular oligomers but with a morphology quite distinct from that observed in the assembly pathway. Conclusions/Significance Our observations indicate that annular oligomers are key dynamic intermediates not only in the assembly but also in the disassembly of TTR protofibrils. The balance between annular and more compact forms of aggregation could be relevant for cytotoxicity in amyloidogenic disorders.
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Affiliation(s)
- Ricardo H. Pires
- Department of Biophysics and Radiation Biology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
- Institute for Molecular and Cell Biology, University of Porto, Porto, Portugal
- * E-mail: (RHP); (AMD); (MSZK)
| | - Árpád Karsai
- Department of Biophysics, University of Pécs, Pécs, Hungary
| | - Maria J. Saraiva
- Institute for Molecular and Cell Biology, University of Porto, Porto, Portugal
- Instituto de Ciências Biomédicas de Abel Salazar, University of Porto, Porto, Portugal
| | - Ana M. Damas
- Institute for Molecular and Cell Biology, University of Porto, Porto, Portugal
- Instituto de Ciências Biomédicas de Abel Salazar, University of Porto, Porto, Portugal
- * E-mail: (RHP); (AMD); (MSZK)
| | - Miklós S. Z. Kellermayer
- Department of Biophysics and Radiation Biology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
- * E-mail: (RHP); (AMD); (MSZK)
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Pastore A, Temussi P. Protein aggregation and misfolding: good or evil? JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2012; 24:244101. [PMID: 22595337 DOI: 10.1088/0953-8984/24/24/244101] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Protein aggregation and misfolding have important implications in an increasing number of fields ranging from medicine to biology to nanotechnology and material science. The interest in understanding this field has accordingly increased steadily over the last two decades. During this time the number of publications that have been dedicated to protein aggregation has increased exponentially, tackling the problem from several different and sometime contradictory perspectives. This review is meant to summarize some of the highlights that come from these studies and introduce this topical issue on the subject. The factors that make a protein aggregate and the cellular strategies that defend from aggregation are discussed together with the perspectives that the accumulated knowledge may open.
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Ladner CL, Wishart DS. Resolution-enhanced native acidic gel electrophoresis: a method for resolving, sizing, and quantifying prion protein oligomers. Anal Biochem 2012; 426:54-62. [PMID: 22490465 DOI: 10.1016/j.ab.2012.04.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Revised: 03/31/2012] [Accepted: 04/02/2012] [Indexed: 11/17/2022]
Abstract
The formation of β-sheet-rich prion protein (PrP(β)) oligomers from native or cellular PrP(c) is thought to be a key step in the development of prion diseases. To assist in this characterization process we have developed a rapid and remarkably high resolution gel electrophoresis technique called RENAGE (resolution-enhanced native acidic gel electrophoresis) for separating, sizing, and quantifying oligomeric PrP(β) complexes. PrP(β) oligomers formed via either urea/salt or acid conversion can be resolved by RENAGE into a clear set of oligomeric bands differing by just one subunit. Calibration of the size of the PrP(β) oligomer bands was made possible with a cross-linked mouse PrP(90-232) ladder (1- to 11-mer) generated using ruthenium bipyridyl-based photoinduced cross-linking of unmodified proteins (PICUP). This PrP PICUP ladder allowed the size and abundance of PrP(β) oligomers formed from urea/salt and acid conversion to be determined. This distribution consists of 7-, 8-, 9-, 10-, and 11-mers, with the most abundant species being the 8-mer. The high-resolution separation afforded by RENAGE has allowed us to investigate distinctive size and population changes in PrP(β) oligomers formed under various conversion conditions, with various construct lengths, from various species or in the presence of anti-prion compounds.
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Affiliation(s)
- Carol L Ladner
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E8
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Kagan BL, Jang H, Capone R, Arce FT, Ramachandran S, Lal R, Nussinov R. Antimicrobial properties of amyloid peptides. Mol Pharm 2012; 9:708-17. [PMID: 22081976 PMCID: PMC3297685 DOI: 10.1021/mp200419b] [Citation(s) in RCA: 166] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
More than two dozen clinical syndromes known as amyloid diseases are characterized by the buildup of extended insoluble fibrillar deposits in tissues. These amorphous Congo red staining deposits known as amyloids exhibit a characteristic green birefringence and cross-β structure. Substantial evidence implicates oligomeric intermediates of amyloids as toxic species in the pathogenesis of these chronic disease states. A growing body of data has suggested that these toxic species form ion channels in cellular membranes causing disruption of calcium homeostasis, membrane depolarization, energy drainage, and in some cases apoptosis. Amyloid peptide channels exhibit a number of common biological properties including the universal U-shape β-strand-turn-β-strand structure, irreversible and spontaneous insertion into membranes, production of large heterogeneous single-channel conductances, relatively poor ion selectivity, inhibition by Congo red, and channel blockade by zinc. Recent evidence has suggested that increased amounts of amyloids not only are toxic to its host target cells but also possess antimicrobial activity. Furthermore, at least one human antimicrobial peptide, protegrin-1, which kills microbes by a channel-forming mechanism, has been shown to possess the ability to form extended amyloid fibrils very similar to those of classic disease-forming amyloids. In this paper, we will review the reported antimicrobial properties of amyloids and the implications of these discoveries for our understanding of amyloid structure and function.
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Affiliation(s)
- Bruce L. Kagan
- Department of Psychiatry, David Geffen School of Medicine, Semel Institute for Neuroscience & Human Behavior, University of California, Los Angeles, California 90024, U.S.A
| | - Hyunbum Jang
- Center for Cancer Research Nanobiology Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, U.S.A
| | - Ricardo Capone
- Departments of Bioengineering and of Mechanical and Aerospace Engineering and Material Science Program, University of California, San Diego, La Jolla, California 92093, U.S.A
| | - Fernando Teran Arce
- Departments of Bioengineering and of Mechanical and Aerospace Engineering and Material Science Program, University of California, San Diego, La Jolla, California 92093, U.S.A
| | - Srinivasan Ramachandran
- Departments of Bioengineering and of Mechanical and Aerospace Engineering and Material Science Program, University of California, San Diego, La Jolla, California 92093, U.S.A
| | - Ratnesh Lal
- Departments of Bioengineering and of Mechanical and Aerospace Engineering and Material Science Program, University of California, San Diego, La Jolla, California 92093, U.S.A
| | - Ruth Nussinov
- Center for Cancer Research Nanobiology Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, U.S.A
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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Abstract
Molecular parameters such as size, molar mass, and intermolecular interactions, which are important to identify and characterize intrinsically disordered proteins (IDPs), can be obtained from light scattering measurements. In this chapter, we discuss the physical basis of light scattering, experimental techniques, sample treatment, and data evaluation with special emphasis on studies on proteins. Static light scattering (SLS) is capable of measuring molar masses within the range 10(3)-10(8) g/mol and is therefore ideal for determining the state of association of proteins in solution. Since proteins are in general too small to obtain the geometric radius of gyration R (G) from SLS, it is more useful to determine the hydrodynamic Stokes radius, R (S), which can be obtained easily and quickly from dynamic light scattering (DLS) experiments. Accordingly, DLS is an appropriate technique to monitor expansion or compaction of protein molecules. This is especially important for IDPs, which can be recognized and characterized by comparing the measured Stokes radii with those calculated for particular reference states, such as the compactly folded and the fully unfolded states. The combined application of DLS and SLS improves measurements of the molar mass and is essential when changes in the molecular dimensions and molecular association/dissociation take place simultaneously.
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Affiliation(s)
- Klaus Gast
- Institut für Biochemie und Biologie, Physikalische Biochemie, Universität Potsdam, Potsdam, Germany.
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46
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Bromley KM, Kiss AS, Lokappa SB, Lakshminarayanan R, Fan D, Ndao M, Evans JS, Moradian-Oldak J. Dissecting amelogenin protein nanospheres: characterization of metastable oligomers. J Biol Chem 2011; 286:34643-53. [PMID: 21840988 DOI: 10.1074/jbc.m111.250928] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Amelogenin self-assembles to form an extracellular protein matrix, which serves as a template for the continuously growing enamel apatite crystals. To gain further insight into the molecular mechanism of amelogenin nanosphere formation, we manipulated the interactions between amelogenin monomers by altering pH, temperature, and protein concentration to create isolated metastable amelogenin oligomers. Recombinant porcine amelogenins (rP172 and rP148) and three different mutants containing only a single tryptophan (Trp(161), Trp(45), and Trp(25)) were used. Dynamic light scattering and fluorescence studies demonstrated that oligomers were metastable and in constant equilibrium with monomers. Stable oligomers with an average hydrodynamic radius (R(H)) of 7.5 nm were observed at pH 5.5 between 4 and 10 mg · ml(-1). We did not find any evidence of a significant increase in folding upon self-association of the monomers into oligomers, indicating that they are disordered. Fluorescence experiments with single tryptophan amelogenins revealed that upon oligomerization the C terminus of amelogenin (around residue Trp(161)) is exposed at the surface of the oligomers, whereas the N-terminal region around Trp(25) and Trp(45) is involved in protein-protein interaction. The truncated rP148 formed similar but smaller oligomers, suggesting that the C terminus is not critical for amelogenin oligomerization. We propose a model for nanosphere formation via oligomers, and we predict that nanospheres will break up to form oligomers in mildly acidic environments via histidine protonation. We further suggest that oligomeric structures might be functional components during maturation of enamel apatite.
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Affiliation(s)
- Keith M Bromley
- Center for Craniofacial Molecular Biology, Ostrow School of Dentistry, University of Southern California, Los Angeles, California 90033, USA
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Misfolded PrP impairs the UPS by interaction with the 20S proteasome and inhibition of substrate entry. EMBO J 2011; 30:3065-77. [PMID: 21743439 DOI: 10.1038/emboj.2011.224] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Accepted: 06/16/2011] [Indexed: 01/07/2023] Open
Abstract
Prion diseases are associated with the conversion of cellular prion protein (PrP(C)) to toxic β-sheet isoforms (PrP(Sc)), which are reported to inhibit the ubiquitin-proteasome system (UPS). Accordingly, UPS substrates accumulate in prion-infected mouse brains, suggesting impairment of the 26S proteasome. A direct interaction between its 20S core particle and PrP isoforms was demonstrated by immunoprecipitation. β-PrP aggregates associated with the 20S particle, but did not impede binding of the PA26 complex, suggesting that the aggregates do not bind to its ends. Aggregated β-PrP reduced the 20S proteasome's basal peptidase activity, and the enhanced activity induced by C-terminal peptides from the 19S ATPases or by the 19S regulator itself, including when stimulated by polyubiquitin conjugates. However, the 20S proteasome was not inhibited when the gate in the α-ring was open due to a truncation mutation or by association with PA26/PA28. These PrP aggregates inhibit by stabilising the closed conformation of the substrate entry channel. A similar inhibition of substrate entry into the proteasome may occur in other neurodegenerative diseases where misfolded β-sheet-rich proteins accumulate.
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48
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Zou WQ, Zhou X, Yuan J, Xiao X. Insoluble cellular prion protein and its association with prion and Alzheimer diseases. Prion 2011; 5:172-8. [PMID: 21847014 DOI: 10.4161/pri.5.3.16894] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The soluble cellular prion protein (PrP(C)) is best known for its association with prion disease (PrD) through its conversion to a pathogenic insoluble isoform (PrP(Sc)). However, its deleterious effects independent of PrP(Sc) have recently been observed not only in PrD but also in Alzheimer disease (AD), two diseases which mainly affect cognition. At the same time, PrP(C) itself seems to have broad physiologic functions including involvement in cognitive processes. The PrP(C) that is believed to be soluble and monomeric has so far been the only PrP conformer observed in the uninfected brain. In 2006, we identified an insoluble PrP(C) conformer (termed iPrP(C) ) in uninfected human and animal brains. Remarkably, the PrP(Sc) -like iPrPC shares the immunoreactivity behavior and fragmentation with a newly-identified PrP(Sc) species in a novel human PrD termed variably protease-sensitive prionopathy. Moreover, iPrP(C) has been observed as the major PrP species that interacts with amyloid β (Aβ) in AD. This article highlights evidence of PrP involvement in two putatively beneficial and deleterious PrP-implicated pathways in cognition, and hypothesizes first, that beneficial and deleterious effects of PrP(C) are attributable to the chameleon-like conformation of the protein and second, that the iPrP(C) conformer is associated with PrD and AD.
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Affiliation(s)
- Wen-Quan Zou
- Department of Pathology, National Prion Disease Pathology Surveillance Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
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49
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Cho KR, Huang Y, Yu S, Yin S, Plomp M, Qiu SR, Lakshminarayanan R, Moradian-Oldak J, Sy MS, De Yoreo JJ. A multistage pathway for human prion protein aggregation in vitro: from multimeric seeds to β-oligomers and nonfibrillar structures. J Am Chem Soc 2011; 133:8586-93. [PMID: 21534611 PMCID: PMC4505822 DOI: 10.1021/ja1117446] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Aberrant protein aggregation causes numerous neurological diseases including Creutzfeldt-Jakob disease (CJD), but the aggregation mechanisms remain poorly understood. Here, we report AFM results on the formation pathways of β-oligomers and nonfibrillar aggregates from wild-type full-length recombinant human prion protein (WT) and an insertion mutant (10OR) with five additional octapeptide repeats linked to familial CJD. Upon partial denaturing, seeds consisting of 3-4 monomers quickly appeared. Oligomers of ~11-22 monomers then formed through direct interaction of seeds, rather than by subsequent monomer attachment. All larger aggregates formed through association of these β-oligomers. Although both WT and 10OR exhibited identical aggregation mechanisms, the latter oligomerized faster due to lower solubility and, hence, thermodynamic stability. This novel aggregation pathway has implications for prion diseases as well as others caused by protein aggregation.
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Affiliation(s)
- Kang R. Cho
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
- Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Yu Huang
- Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Shuiliang Yu
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Shaoman Yin
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Marco Plomp
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - S. Roger Qiu
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Rajamani Lakshminarayanan
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, California 90033, United States
| | - Janet Moradian-Oldak
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, California 90033, United States
| | - Man-Sun Sy
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - James J. De Yoreo
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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Prion disease susceptibility is affected by beta-structure folding propensity and local side-chain interactions in PrP. Proc Natl Acad Sci U S A 2010; 107:19808-13. [PMID: 21041683 DOI: 10.1073/pnas.1005267107] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Prion diseases occur when the normally α-helical prion protein (PrP) converts to a pathological β-structured state with prion infectivity (PrP(Sc)). Exposure to PrP(Sc) from other mammals can catalyze this conversion. Evidence from experimental and accidental transmission of prions suggests that mammals vary in their prion disease susceptibility: Hamsters and mice show relatively high susceptibility, whereas rabbits, horses, and dogs show low susceptibility. Using a novel approach to quantify conformational states of PrP by circular dichroism (CD), we find that prion susceptibility tracks with the intrinsic propensity of mammalian PrP to convert from the native, α-helical state to a cytotoxic β-structured state, which exists in a monomer-octamer equilibrium. It has been controversial whether β-structured monomers exist at acidic pH; sedimentation equilibrium and dual-wavelength CD evidence is presented for an equilibrium between a β-structured monomer and octamer in some acidic pH conditions. Our X-ray crystallographic structure of rabbit PrP has identified a key helix-capping motif implicated in the low prion disease susceptibility of rabbits. Removal of this capping motif increases the β-structure folding propensity of rabbit PrP to match that of PrP from mouse, a species more susceptible to prion disease.
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