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Chauhan R, Navale GR, Saini S, Panwar A, Kukreti P, Saini R, Roy P, Ghosh K. Modulating the aggregation of human prion protein PrP 106-126 by an indole-based cyclometallated palladium complex. Dalton Trans 2024; 53:11995-12006. [PMID: 38963284 DOI: 10.1039/d4dt00704b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
The spontaneous aggregation of infectious or misfolded forms of prion protein is known to be responsible for neurotoxicity in brain cells, which ultimately leads to the progression of prion disorders. Bovine spongiform encephalopathy (BSE) in animals and Creutzfeldt-Jakob disease (CJD) in humans are glaring examples in this regard. Square-planar complexes with labile ligands and indole-based compounds are found to be efficiently inhibitory against protein aggregation. Herein, we report the synthesis of an indole-based cyclometallated palladium complex. The ligand and complex were characterized by various spectroscopic techniques such as UV-visible, NMR, IR, and HRMS. The molecular structure of the complex was confirmed by single-crystal X-ray crystallography. The interaction of the complex with PrP106-126 was studied using UV-visible spectroscopy, CD spectroscopy, MALDI-TOF MS, and molecular docking. The inhibition effects of the complex on the PrP106-126 aggregation, fibrillization and amyloid formation phenomena were analysed through the ThT assay, CD, TEM and AFM. The effect of the complex on the aggregation process of PrP106-126 was determined kinetically through the ThT assay. The complex presented high binding affinity with the peptide and influenced the peptide's conformation and aggregation in different modes of binding. Furthermore, the MTT assay on neuronal HT-22 cells showed considerable protective properties of the complex against PrP106-126-mediated cytotoxicity. These findings suggest that the compound influences peptide aggregation in different ways, and the anti-aggregation action is primarily associated with the metal's physicochemical properties and the reactivity rather than the ligand. As a result, we propose that this compound be investigated as a potential therapeutic molecule in metallopharmaceutical research to treat prion disease (PD).
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Affiliation(s)
- Rahul Chauhan
- Department of Chemistry, Indian Institute of Technology, Roorkee 247667, Uttarakhand, India.
| | - Govinda R Navale
- Department of Chemistry, Indian Institute of Technology, Roorkee 247667, Uttarakhand, India.
| | - Saakshi Saini
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee 247667, Uttarakhand, India
| | - Abhishek Panwar
- Department of Chemistry, National Institute of Technology Manipur, Langol 795004, India
| | - Prashant Kukreti
- Department of Chemistry, Indian Institute of Technology, Roorkee 247667, Uttarakhand, India.
| | - Rajat Saini
- Department of Chemistry, Indian Institute of Technology, Roorkee 247667, Uttarakhand, India.
| | - Partha Roy
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee 247667, Uttarakhand, India
| | - Kaushik Ghosh
- Department of Chemistry, Indian Institute of Technology, Roorkee 247667, Uttarakhand, India.
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee 247667, Uttarakhand, India
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2
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Homodimeric complexes of the 90-231 human prion: a multilayered computational study based on FMO/GRID-DRY approach. J Mol Model 2022; 28:241. [PMID: 35918494 PMCID: PMC9345805 DOI: 10.1007/s00894-022-05244-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/25/2022] [Indexed: 12/25/2022]
Abstract
The molecular interaction properties and aggregation capabilities disclosed by PrP-E200K, a pathogenic mutant of the human prion protein, were investigated in detail using multilayered computational approaches. In a previous work, we reported that the electrostatic complementarity between region1 (negative) and region3 (positive) has been assumed to lead to a head-to tail interaction between 120 and 231 PrP-E200K units and to initiation of the aggregation process. In this work, we extended the PrP-E200K structure by including the unstructured 90–120 segment which was found to assume different conformations. Plausible models of 90–231 PrP-E200K dimers were calculated and analyzed in depth to identify the nature of the involved protein–protein interactions. The unstructured 90–120 segment was found to extend the positively charged region3 involved in the association of PrP-E200K units which resulted to be driven by hydrophobic interactions. The combination of molecular dynamics, protein–protein docking, grid-based mapping, and fragment molecular orbital approaches allowed us to provide a plausible mechanism of the early state of 90–231 PrP-E200K aggregation, considered a preliminary step of amyloid conversion.
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3
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Hong JM, Moon JH, Oh YM, Park SY. Calcineurin, Calcium-Dependent Serine-Threonine Phosphatase Activation by Prion Peptide 106-126 Enhances Nuclear Factor-κB-Linked Proinflammatory Response through Autophagy Pathway. ACS Chem Neurosci 2021; 12:3277-3283. [PMID: 34424663 DOI: 10.1021/acschemneuro.1c00453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Prion diseases are mortal neurodegenerative pathologies that are caused by the accumulation of abnormal prion protein (PrPSc) in the brain. Recent advances reveal that calcineurin may play a critical role in regulating nuclear factor kappa B (NF-κB) in the calcium-calmodulin pathway. However, the exact mechanism by calcineurin remains unclear. In the present study, we observed that the prion peptide induces calcineurin and autophagy activation. Also, NF-κB and proinflammatory cytokines like interleukin (IL)-6 and tumor necrosis factor (TNF)-α are upregulated upon exposure to prion peptide in human neuroblastoma. The results show that the prion peptide induces calcineurin activation, leading to the activation of NF-κB transcription factor via autophagy signaling. Expression of TNF-α and IL-6 was increased by calcineurin activation and blocked by calcineurin inhibitor and autophagy inhibitor treatments. Collectively, these findings indicate that calcineurin activation mediated by prion protein induces NF-κB-driven neuroinflammation via autophagy pathway, suggesting that calcineurin and autophagy may be possible therapeutic targets for neuroinflammation in neurodegeneration diseases including prion disease.
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Affiliation(s)
- Jeong-Min Hong
- Biosafety Research Institute, College of Veterinary Medicine, Jeonbuk National University, Gobong ro, Iksan, Jeonbuk 54596, Korea
| | - Ji-Hong Moon
- Biosafety Research Institute, College of Veterinary Medicine, Jeonbuk National University, Gobong ro, Iksan, Jeonbuk 54596, Korea
| | - Young Min Oh
- Department of Neurosurgery, Research Institute of Clinical Medicine, Jeonbuk National University Medical School and Hospital, Jeonju 54907, Korea
| | - Sang-Youel Park
- Biosafety Research Institute, College of Veterinary Medicine, Jeonbuk National University, Gobong ro, Iksan, Jeonbuk 54596, Korea
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4
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Rezvani Boroujeni E, Hosseini SM, Fani G, Cecchi C, Chiti F. Soluble Prion Peptide 107-120 Protects Neuroblastoma SH-SY5Y Cells against Oligomers Associated with Alzheimer's Disease. Int J Mol Sci 2020; 21:E7273. [PMID: 33019683 PMCID: PMC7582777 DOI: 10.3390/ijms21197273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/27/2020] [Accepted: 09/28/2020] [Indexed: 12/20/2022] Open
Abstract
Alzheimer's disease (AD) is the most prevalent form of dementia and soluble amyloid β (Aβ) oligomers are thought to play a critical role in AD pathogenesis. Cellular prion protein (PrPC) is a high-affinity receptor for Aβ oligomers and mediates some of their toxic effects. The N-terminal region of PrPC can interact with Aβ, particularly the region encompassing residues 95-110. In this study, we identified a soluble and unstructured prion-derived peptide (PrP107-120) that is external to this region of the sequence and was found to successfully reduce the mitochondrial impairment, intracellular ROS generation and cytosolic Ca2+ uptake induced by oligomeric Aβ42 ADDLs in neuroblastoma SH-SY5Y cells. PrP107-120 was also found to rescue SH-SY5Y cells from Aβ42 ADDL internalization. The peptide did not change the structure and aggregation pathway of Aβ42 ADDLs, did not show co-localization with Aβ42 ADDLs in the cells and showed a partial colocalization with the endogenous cellular PrPC. As a sequence region that is not involved in Aβ binding but in PrP self-recognition, the peptide was suggested to protect against the toxicity of Aβ42 oligomers by interfering with cellular PrPC and/or activating a signaling that protected the cells. These results strongly suggest that PrP107-120 has therapeutic potential for AD.
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Affiliation(s)
- Elham Rezvani Boroujeni
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Science and Biotechnology, Shahid Beheshti University, Tehran 1983969411, Iran;
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Viale G.B Morgagni 50, 50134 Florence, Italy; (G.F.); (C.C.)
| | - Seyed Masoud Hosseini
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Science and Biotechnology, Shahid Beheshti University, Tehran 1983969411, Iran;
| | - Giulia Fani
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Viale G.B Morgagni 50, 50134 Florence, Italy; (G.F.); (C.C.)
| | - Cristina Cecchi
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Viale G.B Morgagni 50, 50134 Florence, Italy; (G.F.); (C.C.)
| | - Fabrizio Chiti
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Viale G.B Morgagni 50, 50134 Florence, Italy; (G.F.); (C.C.)
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Glynn C, Sawaya MR, Ge P, Gallagher-Jones M, Short CW, Bowman R, Apostol M, Zhou ZH, Eisenberg DS, Rodriguez JA. Cryo-EM structure of a human prion fibril with a hydrophobic, protease-resistant core. Nat Struct Mol Biol 2020; 27:417-423. [PMID: 32284600 PMCID: PMC7338044 DOI: 10.1038/s41594-020-0403-y] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 02/28/2020] [Indexed: 01/22/2023]
Abstract
Self-templating assemblies of the human prion protein are clinically associated with transmissible spongiform encephalopathies. Here we present the cryo-EM structure of a denaturant- and protease-resistant fibril formed in vitro spontaneously by a 9.7-kDa unglycosylated fragment of the human prion protein. This human prion fibril contains two protofilaments intertwined with screw symmetry and linked by a tightly packed hydrophobic interface. Each protofilament consists of an extended beta arch formed by residues 106 to 145 of the prion protein, a hydrophobic and highly fibrillogenic disease-associated segment. Such structures of prion polymorphs serve as blueprints on which to evaluate the potential impact of sequence variants on prion disease.
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Affiliation(s)
- Calina Glynn
- Department of Chemistry and Biochemistry; UCLA-DOE Institute for Genomics and Proteomics; STROBE, NSF Science and Technology Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Michael R Sawaya
- Department of Biological Chemistry and Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - Peng Ge
- California NanoSystems Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - Marcus Gallagher-Jones
- Department of Chemistry and Biochemistry; UCLA-DOE Institute for Genomics and Proteomics; STROBE, NSF Science and Technology Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Connor W Short
- Department of Chemistry and Biochemistry; UCLA-DOE Institute for Genomics and Proteomics; STROBE, NSF Science and Technology Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ronquiajah Bowman
- Department of Chemistry and Biochemistry; UCLA-DOE Institute for Genomics and Proteomics; STROBE, NSF Science and Technology Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Marcin Apostol
- Department of Biological Chemistry and Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA, USA
- ADRx, Thousand Oaks, CA, USA
| | - Z Hong Zhou
- California NanoSystems Institute, University of California Los Angeles, Los Angeles, CA, USA
- Department of Microbiology Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA
| | - David S Eisenberg
- Department of Biological Chemistry and Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - Jose A Rodriguez
- Department of Chemistry and Biochemistry; UCLA-DOE Institute for Genomics and Proteomics; STROBE, NSF Science and Technology Center, University of California, Los Angeles, Los Angeles, CA, USA.
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Arad E, Green H, Jelinek R, Rapaport H. Revisiting thioflavin T (ThT) fluorescence as a marker of protein fibrillation - The prominent role of electrostatic interactions. J Colloid Interface Sci 2020; 573:87-95. [PMID: 32272300 DOI: 10.1016/j.jcis.2020.03.075] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 03/07/2020] [Accepted: 03/21/2020] [Indexed: 12/25/2022]
Abstract
Thioflavin T (ThT), a benzothiazole-based fluorophore, is a prominent dye widely employed for monitoring amyloid fibril assembly. Despite the near-universal presumption that ThT binds to β-sheet domains upon fibrillar surface via hydrophobic forces, the contribution of the positive charge of ThT to fibril binding and concomitant fluorescence enhancement have not been thoroughly assessed. Here we demonstrate a considerable interdependence between ThT fluorescence and electrostatic charges of peptide fibrils. Specifically, by analyzing both fibril-forming synthetic peptides and prominent natural fibrillar peptides, we demonstrate pronounced modulations of ThT fluorescence signal that were solely dependent upon electrostatic interactions between ThT and peptide surface. The results further attest to the fact that fibril ζ-potential rather than pH-dependent assembly of the fibrils constitute the primary factor affecting ThT binding and fluorescence. This study provides the first quantitative assessment of electrostatically driven ThT fluorescence upon adsorption to amyloid fibrils.
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Affiliation(s)
- Elad Arad
- Ilse Katz Institute for Nanoscale Science and Technology, Ben Gurion University of the Negev, Beer Sheva 8410501, Israel; Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Hodaya Green
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Raz Jelinek
- Ilse Katz Institute for Nanoscale Science and Technology, Ben Gurion University of the Negev, Beer Sheva 8410501, Israel; Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva 8410501, Israel.
| | - Hanna Rapaport
- Ilse Katz Institute for Nanoscale Science and Technology, Ben Gurion University of the Negev, Beer Sheva 8410501, Israel; Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben Gurion University of the Negev, Beer Sheva 8410501, Israel.
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7
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Human prion protein-mediated calcineurin activation induces neuron cell death via AMPK and autophagy pathway. Int J Biochem Cell Biol 2019; 119:105680. [PMID: 31866508 DOI: 10.1016/j.biocel.2019.105680] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 11/28/2019] [Accepted: 12/16/2019] [Indexed: 12/21/2022]
Abstract
It is usually accepted that prion proteins induce apoptosis in nerve cells. However, the mechanisms of PrPSc-neurotoxicity are not completely clear. Calcineurin is a Ca2+/calmodulin-dependent phosphatase. It activates autophagy, and may represent a link between deregulation of Ca2+ homeostasis and neuronal cell death. In this study, the effect of calcineurin activation mediated by human prion protein induced neuronal cell death via AMPK dephosphorylation and autophagy, was investigated. Synthetic peptides of PrP (PrP 106-126) increased calcineurin activity, without changing the levels of this protein phosphatase. Furthermore, these peptides reduced the levels of AMPK phosphorylation at threonine residue 172 and in autophagy activation. Calcineurin inhibitor, FK506, prevented this effect. The data showed that PrP-treated neurons had lower levels of AMPK than control neurons. This decrease in AMPK levels was matched via activation of autophagy. FK506 prevented the changes in AMPK and autophagy levels induced by PrP peptides. Taken together, the data demonstrated that prion peptides triggered an apoptotic cascade via calcineurin activation, which mediated AMPK dephosphorylation and autophagy activation. Therefore, these data suggest that therapeutic strategies targeting calcineurin inhibition might facilitate the management of neurodegenerative disorders including prion disease.
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Zhou S, Shi D, Liu X, Yao X, Da LT, Liu H. pH-Induced Misfolding Mechanism of Prion Protein: Insights from Microsecond-Accelerated Molecular Dynamics Simulations. ACS Chem Neurosci 2019; 10:2718-2729. [PMID: 31070897 DOI: 10.1021/acschemneuro.8b00582] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The conformational transition of prion protein (PrP) from a native form PrPC to a pathological isoform PrPSc is the main cause of a number of prion diseases in human and animals. Thus, understanding the molecular basis of conformational transition of PrP will be valuable for unveiling the etiology of PrP-related diseases. Here, to explore the potential misfolding mechanism of PrP under the acidic condition, which is known to promote PrP misfolding and trigger its aggregation, the conventional and accelerated molecular dynamics (MD) simulations combined with the Markov state model (MSM) analysis were performed. The conventional MD simulations reveal that, at an acidic pH, the globular domain of PrP is partially unfolded, particularly for the α2 C-terminus. Structural analysis of the key macrostates obtained by MSM indicates that the α2 C-terminus and the β2-α2 loop may serve as important sites for the pH-induced PrP misfolding. Meanwhile, the α1 may also participate in the pH-induced structural conversion by moving away from the α2-α3 subdomain. Notably, dynamical network analysis of the key metastable states indicates that the protonated H187 weakens the interactions between the α2 C-terminus, α1-β2 loop, and α2-α3 loop, leading these domains, especially the α2 C-terminus, to become unstable and to begin to misfold. Therefore, the α2 C-terminus plays a key role in the PrP misfolding process and serves as a potential site for drug targeting. Overall, our findings can deepen the understanding of the pathogenesis related to PrP and provide useful guidance for the future drug discovery.
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Affiliation(s)
- Shuangyan Zhou
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
- Chongqing Key Laboratory on Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Danfeng Shi
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, China
| | - Xuewei Liu
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, China
| | - Xiaojun Yao
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, China
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China
| | - Lin-Tai Da
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai JiaoTong University, Shanghai 200240, China
| | - Huanxiang Liu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
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Tan J, Zhang J, Luo Y, Ye S. Misfolding of a Human Islet Amyloid Polypeptide at the Lipid Membrane Populates through β-Sheet Conformers without Involving α-Helical Intermediates. J Am Chem Soc 2019; 141:1941-1948. [PMID: 30621387 DOI: 10.1021/jacs.8b08537] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Amyloid formation has been implicated in many fatal diseases, but its mechanism remains to be clarified due to a lack of effective methods that can capture the transient intermediates. Here, we experimentally demonstrate that sum frequency generation vibrational spectroscopy can unambiguously discriminate the intermediates during amyloid formation at the lipid membrane in situ and in real time by combining the chiral amide I and achiral amide II and amide III spectral signals of the protein backbone. Such a combination can directly identify the formation of β-hairpin-like monomers and β-sheet oligomers and fibrils. A strong correlation between the amide II signals and the formation of β-sheet oligomers and fibrils was found. With this approach, the structural evolution of human islet amyloid polypeptides (hIAPP) at negative lipid bilayers was elucidated. It was firmly confirmed that hIAPP populates through β-sheet conformers without involving α-helical intermediates. The membrane-associated assembly of hIAPP proceeds by assembling with a β-hairpin-like monomer at the lipid bilayer surface, rather than by inserting the preassembled β-sheet oligomers in solution. This newly established protocol is ready to be utilized in revealing the mechanism of amyloid aggregation at the lipid membrane.
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Affiliation(s)
- Junjun Tan
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Chemical Physics, and Synergetic Innovation Center of Quantum Information & Quantum Physics , University of Science and Technology of China , Hefei , 230026 , China
| | - Jiahui Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Chemical Physics, and Synergetic Innovation Center of Quantum Information & Quantum Physics , University of Science and Technology of China , Hefei , 230026 , China
| | - Yi Luo
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Chemical Physics, and Synergetic Innovation Center of Quantum Information & Quantum Physics , University of Science and Technology of China , Hefei , 230026 , China
| | - Shuji Ye
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Chemical Physics, and Synergetic Innovation Center of Quantum Information & Quantum Physics , University of Science and Technology of China , Hefei , 230026 , China
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10
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Zhou S, Zhu Y, Yao X, Liu H. Carbon Nanoparticles Inhibit the Aggregation of Prion Protein as Revealed by Experiments and Atomistic Simulations. J Chem Inf Model 2018; 59:1909-1918. [DOI: 10.1021/acs.jcim.8b00725] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Shuangyan Zhou
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
- Chongqing Key Laboratory on Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Yongchang Zhu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, China
| | - Xiaojun Yao
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, China
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China
| | - Huanxiang Liu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
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11
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Hecel A, Valensin D, Kozłowski H. How copper ions and membrane environment influence the structure of the human and chicken tandem repeats domain? J Inorg Biochem 2018; 191:143-153. [PMID: 30529722 DOI: 10.1016/j.jinorgbio.2018.11.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 11/19/2018] [Accepted: 11/21/2018] [Indexed: 12/14/2022]
Abstract
Prion proteins (PrPs) from different species have the enormous ability to anchor copper ions. The N-terminal domain of human prion protein (hPrP) contains four tandem repeats of the -PHGGGWGQ- octapeptide sequence. This octarepeat domain can bind up to four Cu2+ ions. Similarly to hPrP, chicken prion protein (chPrP) is able to interact with Cu2+ through the tandem hexapeptide -HNPGYP- region (residues 53-94). In this work, we focused on the human octapeptide repeat (human Octa4, hPrP60-91) (Ac-PHGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQ-NH2) and chicken hexapeptide repeat (chicken Hexa4, chPrP54-77) (Ac-HNPGYPHNPGYPHNPGYPHNPGYP-NH2) prion protein fragments. Due to the fact that PrP is a membrane-anchored glycoprotein and its unstructured and flexible N-terminal domain may interact with the lipid bilayer, our studies were carried out in presence of the surfactant sodium dodecyl sulfate (SDS) mimicking the membrane environment in vitro. The main objective of this work was to understand the effects of copper ion on the structural rearrangements of the human and chicken N-terminal repeat domain. The obtained results provide a fundamental first step in describing the thermodynamic (potentiometric titrations) and structural properties of Cu(II) binding (UV-Vis, NMR, CD spectroscopy) to both human Octa4 and chicken Hexa4 repeats in both a DMSO/water and SDS micelle environment. Interestingly, in SDS environment, both ligands indicate different copper coordination modes, which results of the conformational changes in micelle environment. Our results strongly support that copper binding mode strongly depends on the protein backbone structure. Moreover, we focused on previously obtained results for amyloidogenic human and chicken fragments in membrane mimicking environment.
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Affiliation(s)
- Aleksandra Hecel
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50383 Wroclaw, Poland.
| | - Daniela Valensin
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Henryk Kozłowski
- Opole Medical School in Opole, Katowicka 68, 45060 Opole, Poland
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12
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Sengupta I, Udgaonkar JB. Structural mechanisms of oligomer and amyloid fibril formation by the prion protein. Chem Commun (Camb) 2018; 54:6230-6242. [PMID: 29789820 DOI: 10.1039/c8cc03053g] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Misfolding and aggregation of the prion protein is responsible for multiple neurodegenerative diseases. Works from several laboratories on folding of both the WT and multiple pathogenic mutant variants of the prion protein have identified several structurally dissimilar intermediates, which might be potential precursors to misfolding and aggregation. The misfolded aggregates themselves are morphologically distinct, critically dependent on the solution conditions under which they are prepared, but always β-sheet rich. Despite the lack of an atomic resolution structure of the infectious pathogenic agent in prion diseases, several low resolution models have identified the β-sheet rich core of the aggregates formed in vitro, to lie in the α2-α3 subdomain of the prion protein, albeit with local stabilities that vary with the type of aggregate. This feature article describes recent advances in the investigation of in vitro prion protein aggregation using multiple spectroscopic probes, with particular focus on (1) identifying aggregation-prone conformations of the monomeric protein, (2) conditions which trigger misfolding and oligomerization, (3) the mechanism of misfolding and aggregation, and (4) the structure of the misfolded intermediates and final aggregates.
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Affiliation(s)
- Ishita Sengupta
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
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Martial B, Lefèvre T, Auger M. Understanding amyloid fibril formation using protein fragments: structural investigations via vibrational spectroscopy and solid-state NMR. Biophys Rev 2018; 10:1133-1149. [PMID: 29855812 PMCID: PMC6082320 DOI: 10.1007/s12551-018-0427-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 05/17/2018] [Indexed: 12/11/2022] Open
Abstract
It is well established that amyloid proteins play a primary role in neurodegenerative diseases. Alzheimer's, Parkinson's, type II diabetes, and Creutzfeldt-Jakob's diseases are part of a wider family encompassing more than 50 human pathologies related to aggregation of proteins. Although this field of research is thoroughly investigated, several aspects of fibrillization remain misunderstood, which in turn slows down, or even impedes, advances in treating and curing amyloidoses. To solve this problem, several research groups have chosen to focus on short fragments of amyloid proteins, sequences that have been found to be of great importance for the amyloid formation process. Studying short peptides allows bypassing the complexity of working with full-length proteins and may provide important information relative to critical segments of amyloid proteins. To this end, efficient biophysical tools are required. In this review, we focus on two essential types of spectroscopic techniques, i.e., vibrational spectroscopy and its derivatives (conventional Raman scattering, deep-UV resonance Raman (DUVRR), Raman optical activity (ROA), surface-enhanced Raman spectroscopy (SERS), tip-enhanced Raman spectroscopy (TERS), infrared (IR) absorption spectroscopy, vibrational circular dichroism (VCD)) and solid-state nuclear magnetic resonance (ssNMR). These techniques revealed powerful to provide a better atomic and molecular comprehension of the amyloidogenic process and fibril structure. This review aims at underlining the information that these techniques can provide and at highlighting their strengths and weaknesses when studying amyloid fragments. Meaningful examples from the literature are provided for each technique, and their complementarity is stressed for the kinetic and structural characterization of amyloid fibril formation.
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Affiliation(s)
- Benjamin Martial
- Department of Chemistry, Regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines (PROTEO), Centre de recherche sur les matériaux avancés (CERMA), Centre québécois sur les matériaux fonctionnels (CQMF), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Thierry Lefèvre
- Department of Chemistry, Regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines (PROTEO), Centre de recherche sur les matériaux avancés (CERMA), Centre québécois sur les matériaux fonctionnels (CQMF), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Michèle Auger
- Department of Chemistry, Regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines (PROTEO), Centre de recherche sur les matériaux avancés (CERMA), Centre québécois sur les matériaux fonctionnels (CQMF), Université Laval, Québec, QC, G1V 0A6, Canada.
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14
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Arad E, Bhunia SK, Jopp J, Kolusheva S, Rapaport H, Jelinek R. Lysine-Derived Carbon Dots for Chiral Inhibition of Prion Peptide Fibril Assembly. ADVANCED THERAPEUTICS 2018. [DOI: 10.1002/adtp.201800006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Elad Arad
- Department of Chemistry; Ben Gurion University of the Negev; Beer Sheva 84105 Israel
| | - Susanta Kumar Bhunia
- Department of Chemistry; Ben Gurion University of the Negev; Beer Sheva 84105 Israel
| | - Jürgen Jopp
- Ilse Katz Institute (IKI) for Nanoscale Science and Technology; Ben Gurion University of the Negev; Beer Sheva 84105 Israel
| | - Sofiya Kolusheva
- Ilse Katz Institute (IKI) for Nanoscale Science and Technology; Ben Gurion University of the Negev; Beer Sheva 84105 Israel
| | - Hanna Rapaport
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering and Ilse Katz Institute (IKI) for Nanoscale Science and Technology; Ben Gurion University of the Negev; Beer Sheva 84105 Israel
| | - Raz Jelinek
- Department of Chemistry; Ben Gurion University of the Negev; Beer Sheva 84105 Israel
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15
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Rehbein P, Schwalbe H. Improved high-yield expression, purification and refolding of recombinant mammalian prion proteins under aerosol-free elevated biological safety conditions. Protein Expr Purif 2018; 150:53-60. [PMID: 29751084 DOI: 10.1016/j.pep.2018.04.018] [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: 04/18/2018] [Revised: 04/28/2018] [Accepted: 04/29/2018] [Indexed: 11/28/2022]
Abstract
Production of recombinant prion proteins is of crucial relevance in food technology (analytical standards, assay development) but also in basic research, most importantly structural biology (NMR, X-ray diffraction). Structural approaches conveniently allow for sophisticated investigation of prion disease pathogenesis, but usually require large amounts of sample material. Recently, working with recombinant prion proteins has been recategorized to biosafety levels > S1 as infectious prions may readily be generated de novo and become airborne via aerosols. Heterologous expression should therefore be established with appropriately adjusted safety precautions. We have developed a protocol for high-yield expression, purification and refolding of recombinant mammalian prion proteins at elevated biological safety levels by introducing means of abolishing aerosol formation and propagation.
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Affiliation(s)
- Peter Rehbein
- Institute for Organic Chemistry and Chemical Biology, Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany.
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany.
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16
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Aucoin D, Xia Y, Theint T, Nadaud PS, Surewicz K, Surewicz WK, Jaroniec CP. Protein-solvent interfaces in human Y145Stop prion protein amyloid fibrils probed by paramagnetic solid-state NMR spectroscopy. J Struct Biol 2018; 206:36-42. [PMID: 29679649 DOI: 10.1016/j.jsb.2018.04.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Revised: 03/24/2018] [Accepted: 04/13/2018] [Indexed: 11/16/2022]
Abstract
The C-terminally truncated Y145Stop variant of prion protein (PrP23-144), which is associated with heritable PrP cerebral amyloid angiopathy in humans and also capable of triggering a transmissible prion disease in mice, serves as a useful in vitro model for investigating the molecular and structural basis of amyloid strains and cross-seeding specificities. Here, we determine the protein-solvent interfaces in human PrP23-144 amyloid fibrils generated from recombinant 13C,15N-enriched protein and incubated in aqueous solution containing paramagnetic Cu(II)-EDTA, by measuring residue-specific 15N longitudinal paramagnetic relaxation enhancements using two-dimensional magic-angle spinning solid-state NMR spectroscopy. To further probe the interactions of the amyloid core residues with solvent molecules we perform complementary measurements of amide hydrogen/deuterium exchange detected by solid-state NMR and solution NMR methods. The solvent accessibility data are evaluated in the context of the structural model for human PrP23-144 amyloid.
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Affiliation(s)
- Darryl Aucoin
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Yongjie Xia
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Theint Theint
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Philippe S Nadaud
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Krystyna Surewicz
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Witold K Surewicz
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Christopher P Jaroniec
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.
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17
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Hecel A, Draghi S, Valensin D, Kozlowski H. The effect of a membrane-mimicking environment on the interactions of Cu 2+ with an amyloidogenic fragment of chicken prion protein. Dalton Trans 2018; 46:7758-7769. [PMID: 28589973 DOI: 10.1039/c7dt01069a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Prion proteins (PrP) from different species have the ability to tightly bind Cu2+ ions. Copper coordination sites are located in the disordered and flexible N-terminal region which contains several His anchoring sites. Among them, two His residues are found in the so called amyloidogenic PrP region which is believed to play a key role in the process leading to oligomer and fibril formation. Both chicken and human amyloidogenic regions have a hydrophobic C-terminal region rich in Ala and Val amino acids. Recent findings revealed that this domain undergoes random coil to α-helix structuring upon interaction with membrane models. This interaction might strongly impact metal binding abilities either in terms of donor sets or affinity. In this study we investigated Cu2+ interaction with an amyloidogenic fragment, chPrP105-140, derived from chicken prion protein (chPrP), in different solution environments. The behavior of the peptide and its metal complexes was analyzed in water and in the presence of negative and positive charged membrane mimicking environments formed by sodium dodecyl sulfate (SDS) and dodecyl trimethyl ammonium chloride (DTAC) micelles. The metal coordination sphere, the metal binding affinity and stoichiometry were evaluated by combining spectroscopic and potentiometric methods. Finally we compare copper(ii) interactions with human and chicken amyloidogenic fragments. Our results indicate that the chicken amyloidogenic fragment is a stronger copper ligand than the human amyloidogenic fragment.
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Affiliation(s)
- Aleksandra Hecel
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14., 50-383 Wroclaw, Poland
| | - Sara Draghi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy.
| | - Daniela Valensin
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy.
| | - Henryk Kozlowski
- Public Higher Medical Professional School in Opole, Katowicka 68, 45060 Opole, Poland
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18
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Periole X, Huber T, Bonito-Oliva A, Aberg KC, van der Wel PCA, Sakmar TP, Marrink SJ. Energetics Underlying Twist Polymorphisms in Amyloid Fibrils. J Phys Chem B 2018; 122:1081-1091. [PMID: 29254334 PMCID: PMC5857390 DOI: 10.1021/acs.jpcb.7b10233] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Amyloid fibrils are highly ordered protein aggregates associated with more than 40 human diseases. The exact conditions under which the fibrils are grown determine many types of reported fibril polymorphism, including different twist patterns. Twist-based polymorphs display unique mechanical properties in vitro, and the relevance of twist polymorphism in amyloid diseases has been suggested. We present transmission electron microscopy images of Aβ42-derived (amyloid β) fibrils, which are associated with Alzheimer's disease, demonstrating the presence of twist variability even within a single long fibril. To better understand the molecular underpinnings of twist polymorphism, we present a structural and thermodynamics analysis of molecular dynamics simulations of the twisting of β-sheet protofilaments of a well-characterized cross-β model: the GNNQQNY peptide from the yeast prion Sup35. The results show that a protofilament model of GNNQQNY is able to adopt twist angles from -11° on the left-hand side to +8° on the right-hand side in response to various external conditions, keeping an unchanged peptide structure. The potential of mean force (PMF) of this cross-β structure upon twisting revealed that only ∼2kBT per peptide are needed to stabilize a straight conformation with respect to the left-handed free-energy minimum. The PMF also shows that the canonical structural core of β-sheets, i.e., the hydrogen-bonded backbone β-strands, favors the straight conformation. However, the concerted effects of the side chains contribute to twisting, which provides a rationale to correlate polypeptide sequence, environmental growth conditions and number of protofilaments in a fibril with twist polymorphisms.
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Affiliation(s)
- Xavier Periole
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Groningen 9747 AG, The Netherlands
| | - Thomas Huber
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University , 1230 York Avenue, New York, New York 10065, United States
| | - Alessandra Bonito-Oliva
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University , 1230 York Avenue, New York, New York 10065, United States
| | - Karina C Aberg
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University , 1230 York Avenue, New York, New York 10065, United States
| | - Patrick C A van der Wel
- Department of Structural Biology and Center for Protein Conformational Diseases, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States
| | - Thomas P Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University , 1230 York Avenue, New York, New York 10065, United States
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet , 141 57 Huddinge, Sweden
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Groningen 9747 AG, The Netherlands
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19
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Li L, Zhu Y, Zhou S, An X, Zhang Y, Bai Q, He YX, Liu H, Yao X. Experimental and Theoretical Insights into the Inhibition Mechanism of Prion Fibrillation by Resveratrol and its Derivatives. ACS Chem Neurosci 2017; 8:2698-2707. [PMID: 28817252 DOI: 10.1021/acschemneuro.7b00240] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Resveratrol and its derivatives have been shown to display beneficial effects to neurodegenerative diseases. However, the molecular mechanism of resveratrol and its derivatives on prion conformational conversion is poorly understood. In this work, the interaction mechanism between prion and resveratrol as well as its derivatives was investigated using steady-state fluorescence quenching, Thioflavin T binding assay, Western blotting, and molecular dynamics simulation. Protein fluorescence quenching method and Thioflavin T assay revealed that resveratrol and its derivatives could interact with prion and interrupt prion fibril formation. Molecular dynamics simulation results indicated that resveratrol can stabilize the PrP127-147 peptide mainly through π-π stacking interactions between resveratrol and Tyr128. The hydrogen bonds interactions between resveratrol and the PrP127-147 peptide could further reduce the flexibility and the propensity to aggregate. The results of this study not only can provide useful information about the interaction mechanism between resveratrol and prion, but also can provide useful clues for further design of new inhibitors inhibiting prion aggregation.
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Affiliation(s)
- Lanlan Li
- State
Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, P. R. China
| | - Yongchang Zhu
- School
of Pharmacy, Lanzhou University, Lanzhou 730000, P. R. China
| | - Shuangyan Zhou
- State
Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, P. R. China
- School
of Pharmacy, Lanzhou University, Lanzhou 730000, P. R. China
| | - Xiaoli An
- State
Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, P. R. China
| | - Yan Zhang
- State
Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, P. R. China
- School
of Pharmacy, Lanzhou University, Lanzhou 730000, P. R. China
| | - Qifeng Bai
- State
Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, P. R. China
| | - Yong-Xing He
- School
of Life Sciences, Lanzhou University, Lanzhou 730000, P. R. China
| | - Huanxiang Liu
- School
of Pharmacy, Lanzhou University, Lanzhou 730000, P. R. China
| | - Xiaojun Yao
- State
Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, P. R. China
- State
Key Laboratory of Quality Research in Chinese Medicine, Macau Institute
for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, P. R. China
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20
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Abstract
Prion diseases are characterized by the deposition of amyloids, misfolded conformers of the prion protein. The misfolded conformation is self-replicating, by a mechanism solely enciphered in the conformation of the protein. Because of low solubility and heterogeneous aggregate sizes, the detailed atomic structure of the infectious isoform is still unknown. Progress has, however, been made, and has allowed insights into the structural and disease-related mechanisms of prions. Many structural models have been proposed, and a number of them support a consensus trimeric β-helical model, significantly more complex than simple amyloid models. There is evidence that such complexity may be a necessary property of prion structure. Knowledge of the structure of prions will provide a greater understanding of the protein isoform conversion mechanism, and could eventually lead to rationally designed intervention strategies.
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Affiliation(s)
- Gerald Stubbs
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 53723
| | - Jan Stöhr
- Institute for Neurodegenerative Diseases, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California 94143
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21
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Honda RP, Kuwata K. The native state of prion protein (PrP) directly inhibits formation of PrP-amyloid fibrils in vitro. Sci Rep 2017; 7:562. [PMID: 28373719 PMCID: PMC5429628 DOI: 10.1038/s41598-017-00710-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 03/08/2017] [Indexed: 11/25/2022] Open
Abstract
The conversion of globular proteins into amyloid fibrils is associated with a wide variety of human diseases. One example is the prion protein (PrP), which adopts an α-helical structure in the native state but its amyloid form is implicated in the pathogenesis of prion diseases. Previous evidence has suggested that destabilization of the native state promotes amyloid formation, but the underlying mechanism remains unknown. In this study, we report that the native state of PrP serves as a potent inhibitor in the formation of PrP amyloid fibrils. By monitoring the time courses of thioflavin T fluorescence, the kinetics of amyloid formation was studied in vitro under various concentrations of pre-formed amyloid, monomer, and denaturant. Quantitative analysis of the kinetic data using various models of enzyme kinetics suggested that the native state of PrP is either an uncompetitive or noncompetitive inhibitor of amyloid formation. This study highlights the significant role of the native state in inhibiting amyloid formation, which provides new insights into the pathogenesis of misfolding diseases.
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Affiliation(s)
- Ryo P Honda
- Department of Molecular Pathobiochemistry, Graduate School of Medicine, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan.
| | - Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan. .,Department of Gene and Development, Graduate School of Medicine, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan.
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22
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The Structure of Mammalian Prions and Their Aggregates. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 329:277-301. [PMID: 28109330 DOI: 10.1016/bs.ircmb.2016.08.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Prion diseases, such as Creutzfeldt-Jakob disease in humans, bovine spongiform encephalopathy in cattle, chronic wasting disease in cervids (i.e., deer, elk, moose, and reindeer), and sheep scrapie, are caused by the misfolding of the cellular prion protein (PrPC) into a disease-causing conformer (PrPSc). PrPC is a normal, GPI-anchored protein that is expressed on the surface of neurons and other cell types. The structure of PrPC is well understood, based on studies of recombinant PrP, which closely mimics the structure of native PrPC. In contrast, PrPSc is prone to aggregate into a variety of quaternary structures, such as oligomers, amorphous aggregates, and amyloid fibrils. The propensity of PrPSc to assemble into these diverse forms of aggregates is also responsible for our limited knowledge about its structure. Then again, the repeating nature of certain regular PrPSc aggregates has allowed (lower resolution) insights into the structure of the infectious conformer, establishing a four-rung β-solenoid structure as a key element of its architecture.
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23
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Chan SWS, Yau J, Ing C, Liu K, Farber P, Won A, Bhandari V, Kara-Yacoubian N, Seraphim TV, Chakrabarti N, Kay LE, Yip CM, Pomès R, Sharpe S, Houry WA. Mechanism of Amyloidogenesis of a Bacterial AAA+ Chaperone. Structure 2016; 24:1095-109. [PMID: 27265850 DOI: 10.1016/j.str.2016.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 04/27/2016] [Accepted: 05/01/2016] [Indexed: 10/21/2022]
Abstract
Amyloids are fibrillar protein superstructures that are commonly associated with diseases in humans and with physiological functions in various organisms. The precise mechanisms of amyloid formation remain to be elucidated. Surprisingly, we discovered that a bacterial Escherichia coli chaperone-like ATPase, regulatory ATPase variant A (RavA), and specifically the LARA domain in RavA, forms amyloids under acidic conditions at elevated temperatures. RavA is involved in modulating the proper assembly of membrane respiratory complexes. LARA contains an N-terminal loop region followed by a β-sandwich-like folded core. Several approaches, including nuclear magnetic resonance spectroscopy and molecular dynamics simulations, were used to determine the mechanism by which LARA switches to an amyloid state. These studies revealed that the folded core of LARA is amyloidogenic and is protected by its N-terminal loop. At low pH and high temperatures, the interaction of the N-terminal loop with the folded core is disrupted, leading to amyloid formation.
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Affiliation(s)
- Sze Wah Samuel Chan
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building, Toronto, ON M5S 1A8, Canada
| | - Jason Yau
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building, Toronto, ON M5S 1A8, Canada; Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Christopher Ing
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building, Toronto, ON M5S 1A8, Canada; Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Kaiyin Liu
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building, Toronto, ON M5S 1A8, Canada
| | - Patrick Farber
- Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Amy Won
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Vaibhav Bhandari
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building, Toronto, ON M5S 1A8, Canada
| | - Nareg Kara-Yacoubian
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building, Toronto, ON M5S 1A8, Canada
| | - Thiago V Seraphim
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building, Toronto, ON M5S 1A8, Canada
| | - Nilmadhab Chakrabarti
- Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Lewis E Kay
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building, Toronto, ON M5S 1A8, Canada; Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Christopher M Yip
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building, Toronto, ON M5S 1A8, Canada; Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Régis Pomès
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building, Toronto, ON M5S 1A8, Canada; Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Simon Sharpe
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building, Toronto, ON M5S 1A8, Canada; Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada.
| | - Walid A Houry
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building, Toronto, ON M5S 1A8, Canada.
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24
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Inayathullah M, Rajadas J. Conformational dynamics of a hydrophobic prion fragment (113-127) in different pH and osmolyte solutions. Neuropeptides 2016; 57:9-14. [PMID: 26919915 DOI: 10.1016/j.npep.2016.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 02/09/2016] [Accepted: 02/14/2016] [Indexed: 01/17/2023]
Abstract
Prion diseases are characterized by a conformational change in prion protein from its native state into beta-sheet rich aggregates that are neurotoxic. The central domain that contain a highly conserved hydrophobic region of the protein play an important role in the toxicity. The conformation of the proteins is largely influenced by various solvent environments. Here we report results of study of hydrophobic prion fragment peptide PrP(113-127) under different pH and osmolytes solution conditions. The secondary structure and the folding of PrP(113-127) was determined using circular dichroism and fluorescence spectroscopic methods. The results indicate that PrP(113-127) adopts a random coil conformation in aqueous buffer at neutral pH and that converted into beta sheet on aging. Even though the initial random coil conformation was similar in different pH conditions, the acidic as well as basic pH conditions delays the conformational transition to beta sheet. FRET results indicate that the distance between N and C-terminal regions increased on aging due to unfolding by self-assembly of the peptide into an organized beta sheet structure. Presence of osmolytes, prevented or decelerated the aggregation process of PrP(113-127) peptide.
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Affiliation(s)
- Mohammed Inayathullah
- Biomaterials and Advanced Drug Delivery Laboratory, School of Medicine, Stanford University, Palo Alto, CA 94304, USA; Bioorganic and Neurochemistry Laboratory, Central Leather Research Institute, Adyar, Chennai, Tamil Nadu 600020, India; Cardiovascular Pharmacology Division, Cardiovascular Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Jayakumar Rajadas
- Biomaterials and Advanced Drug Delivery Laboratory, School of Medicine, Stanford University, Palo Alto, CA 94304, USA; Cardiovascular Pharmacology Division, Cardiovascular Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA.
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25
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Wan W, Wille H, Stöhr J, Kendall A, Bian W, McDonald M, Tiggelaar S, Watts JC, Prusiner SB, Stubbs G. Structural studies of truncated forms of the prion protein PrP. Biophys J 2016; 108:1548-1554. [PMID: 25809267 DOI: 10.1016/j.bpj.2015.01.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 01/07/2015] [Accepted: 01/13/2015] [Indexed: 11/19/2022] Open
Abstract
Prions are proteins that adopt self-propagating aberrant folds. The self-propagating properties of prions are a direct consequence of their distinct structures, making the understanding of these structures and their biophysical interactions fundamental to understanding prions and their related diseases. The insolubility and inherent disorder of prions have made their structures difficult to study, particularly in the case of the infectious form of the mammalian prion protein PrP. Many investigators have therefore preferred to work with peptide fragments of PrP, suggesting that these peptides might serve as structural and functional models for biologically active prions. We have used x-ray fiber diffraction to compare a series of different-sized fragments of PrP, to determine the structural commonalities among the fragments and the biologically active, self-propagating prions. Although all of the peptides studied adopted amyloid conformations, only the larger fragments demonstrated a degree of structural complexity approaching that of PrP. Even these larger fragments did not adopt the prion structure itself with detailed fidelity, and in some cases their structures were radically different from that of pathogenic PrP(Sc).
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Affiliation(s)
- William Wan
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee
| | - Holger Wille
- Institute for Neurodegenerative Diseases and Department of Neurology, University of California, San Francisco, San Francisco, California
| | - Jan Stöhr
- Institute for Neurodegenerative Diseases and Department of Neurology, University of California, San Francisco, San Francisco, California
| | - Amy Kendall
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee
| | - Wen Bian
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee
| | - Michele McDonald
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee
| | - Sarah Tiggelaar
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee
| | - Joel C Watts
- Institute for Neurodegenerative Diseases and Department of Neurology, University of California, San Francisco, San Francisco, California
| | - Stanley B Prusiner
- Institute for Neurodegenerative Diseases and Department of Neurology, University of California, San Francisco, San Francisco, California
| | - Gerald Stubbs
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee.
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26
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Galant NJ, Bugyei-Twum A, Rakhit R, Walsh P, Sharpe S, Arslan PE, Westermark P, Higaki JN, Torres R, Tapia J, Chakrabartty A. Substoichiometric inhibition of transthyretin misfolding by immune-targeting sparsely populated misfolding intermediates: a potential diagnostic and therapeutic for TTR amyloidoses. Sci Rep 2016; 6:25080. [PMID: 27122057 PMCID: PMC4848561 DOI: 10.1038/srep25080] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 04/08/2016] [Indexed: 12/22/2022] Open
Abstract
Wild-type and mutant transthyretin (TTR) can misfold and deposit in the heart, peripheral nerves, and other sites causing amyloid disease. Pharmacological chaperones, Tafamidis(®) and diflunisal, inhibit TTR misfolding by stabilizing native tetrameric TTR; however, their minimal effective concentration is in the micromolar range. By immune-targeting sparsely populated TTR misfolding intermediates (i.e. monomers), we achieved fibril inhibition at substoichiometric concentrations. We developed an antibody (misTTR) that targets TTR residues 89-97, an epitope buried in the tetramer but exposed in the monomer. Nanomolar misTTR inhibits fibrillogenesis of misfolded TTR under micromolar concentrations. Pan-specific TTR antibodies do not possess such fibril inhibiting properties. We show that selective targeting of misfolding intermediates is an alternative to native state stabilization and requires substoichiometric concentrations. MisTTR or its derivative may have both diagnostic and therapeutic potential.
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Affiliation(s)
- Natalie J. Galant
- Princess Margaret Cancer Centre, University Health Network, Departments of Medical Biophysics and Biochemistry, University of Toronto, TMDT 4-305, 101 College Street, Toronto, Ontario, Canada M5G 1L7
| | - Antoinette Bugyei-Twum
- Princess Margaret Cancer Centre, University Health Network, Departments of Medical Biophysics and Biochemistry, University of Toronto, TMDT 4-305, 101 College Street, Toronto, Ontario, Canada M5G 1L7
| | - Rishi Rakhit
- Department of Chemical and Systems Biology, Stanford University, CA 94305, USA
| | - Patrick Walsh
- Molecular Structure and Function Program, the Hospital for Sick Children, Department of Biochemistry, University of Toronto, 1 King’s College Circle, Toronto, Ontario, Canada M5S 1A8
| | - Simon Sharpe
- Molecular Structure and Function Program, the Hospital for Sick Children, Department of Biochemistry, University of Toronto, 1 King’s College Circle, Toronto, Ontario, Canada M5S 1A8
| | - Pharhad Eli Arslan
- Princess Margaret Cancer Centre, University Health Network, Departments of Medical Biophysics and Biochemistry, University of Toronto, TMDT 4-305, 101 College Street, Toronto, Ontario, Canada M5G 1L7
| | - Per Westermark
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Jeffrey N. Higaki
- Departments of Biochemistry and Histopathology, Prothena Biosciences Inc., South San Francisco, CA 94080
| | - Ronald Torres
- Departments of Biochemistry and Histopathology, Prothena Biosciences Inc., South San Francisco, CA 94080
| | - José Tapia
- Departments of Biochemistry and Histopathology, Prothena Biosciences Inc., South San Francisco, CA 94080
| | - Avijit Chakrabartty
- Princess Margaret Cancer Centre, University Health Network, Departments of Medical Biophysics and Biochemistry, University of Toronto, TMDT 4-305, 101 College Street, Toronto, Ontario, Canada M5G 1L7
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27
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Nagel-Steger L, Owen MC, Strodel B. An Account of Amyloid Oligomers: Facts and Figures Obtained from Experiments and Simulations. Chembiochem 2016; 17:657-76. [PMID: 26910367 DOI: 10.1002/cbic.201500623] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Indexed: 12/27/2022]
Abstract
The deposition of amyloid in brain tissue in the context of neurodegenerative diseases involves the formation of intermediate species-termed oligomers-of lower molecular mass and with structures that deviate from those of mature amyloid fibrils. Because these oligomers are thought to be primarily responsible for the subsequent disease pathogenesis, the elucidation of their structure is of enormous interest. Nevertheless, because of the high aggregation propensity and the polydispersity of oligomeric species formed by the proteins or peptides in question, the preparation of appropriate samples for high-resolution structural methods has proven to be rather difficult. This is why theoretical approaches have been of particular importance in gaining insights into possible oligomeric structures for some time. Only recently has it been possible to achieve some progress with regard to the experimentally based structural characterization of defined oligomeric species. Here we discuss how theory and experiment are used to determine oligomer structures and what can be done to improve the integration of the two disciplines.
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Affiliation(s)
- Luitgard Nagel-Steger
- Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätstrasse 1, 40225, Düsseldorf, Germany
| | - Michael C Owen
- Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany. .,Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Universitätstrasse 1, 40225, Düsseldorf, Germany.
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28
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Zhang B, Zhu D, Wang W, Gong G, Du W. Influence of oxodiperoxovanadate complexes on prion neuropeptide fibril formation. RSC Adv 2016. [DOI: 10.1039/c5ra25849a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Different oxodiperoxovanadate complexes inhibit the fibril formation of prion neuropeptides by different action modes.
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Affiliation(s)
- Baohong Zhang
- Department of Chemistry
- Renmin University of China
- Beijing
- China
- College of Materials Science and Engineering
| | - Dengsen Zhu
- Department of Chemistry
- Renmin University of China
- Beijing
- China
| | - Wenji Wang
- Department of Chemistry
- Renmin University of China
- Beijing
- China
| | - Gehui Gong
- Department of Chemistry
- Renmin University of China
- Beijing
- China
| | - Weihong Du
- Department of Chemistry
- Renmin University of China
- Beijing
- China
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29
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Zhu D, Zhao C, Wang X, Wang W, Wang B, Du W. Roles of DMSO-type ruthenium complexes in disaggregation of prion neuropeptide PrP106–126. RSC Adv 2016. [DOI: 10.1039/c5ra21523d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
DMSO-type ruthenium complexes with aromatic ligands disaggregate the mature PrP106–126 fibrilsviametal coordination and hydrophobic interaction.
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Affiliation(s)
- Dengsen Zhu
- Department of Chemistry
- Renmin University of China
- Beijing
- China
| | - Cong Zhao
- Department of Chemistry
- Renmin University of China
- Beijing
- China
| | - Xuesong Wang
- Department of Chemistry
- Renmin University of China
- Beijing
- China
| | - Wenji Wang
- Department of Chemistry
- Renmin University of China
- Beijing
- China
| | - Baohuai Wang
- College of Chemistry and Molecular Engineering
- Peking University
- China
| | - Weihong Du
- Department of Chemistry
- Renmin University of China
- Beijing
- China
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30
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Li B. The pathogenesis of soluble PrP fragments containing Aβ binding sites. Virus Res 2015; 211:194-8. [PMID: 26528810 DOI: 10.1016/j.virusres.2015.10.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 10/19/2015] [Accepted: 10/23/2015] [Indexed: 12/28/2022]
Abstract
Prion protein (PrP) has proven to bind amyloid beta (Aβ) oligomers with high affinity, changing our understanding of both prion diseases (PD) and Alzheimer's disease (AD) at the molecular and phenotypic levels, although the latter currently lacks sufficient attentions. Transgenic mice expressing anchorless PrP developed unusual diseases reminiscent of AD with tremendous amyloid plaque formation. In this review, we described two interesting observations at the phenotypic level. First, common pathogenic mutations of the PRNP gene in Gerstmann-Sträussler-Scheinker (GSS) syndrome were clustered at PrP95-105. Meanwhile, all nonsense PRNP mutations that generated soluble PrP 95-105 exhibited phenotypes with abundant amyloid formations. We speculate that PrP-Aβ oligomers binding might be the underlying mechanism of the predominant amyloid phenotypes. Second, soluble PrP-Aβ oligomer complexes might exist in the extracellular space at the beginning of both PD and AD and subserve an initial neuroprotective function. Thus, the diseases would only present after long-term accumulation. This might be the central common pathogenic event of both PD and AD.
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Affiliation(s)
- Baiya Li
- Department of Otorhinolaryngology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, PR China.
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31
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Lin K, Yu Z, Yu Y, Liao X, Huang P, Guo C, Lin D. Distinct effects of Cu2+-binding on oligomerization of human and rabbit prion proteins. Acta Biochim Biophys Sin (Shanghai) 2015; 47:842-50. [PMID: 26350098 DOI: 10.1093/abbs/gmv081] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 06/12/2015] [Indexed: 11/13/2022] Open
Abstract
The cellular prion protein (PrP(C)) is a kind of cell-surface Cu(2+)-binding glycoprotein. The oligomerization of PrP(C) is highly related to transmissible spongiform encephalopathies (TSEs). Cu(2+) plays a vital role in the oligomerization of PrP(C), and participates in the pathogenic process of TSE diseases. It is expected that Cu(2+)-binding has different effects on the oligomerization of TSE-sensitive human PrP(C) (HuPrP(C)) and TSE-resistant rabbit PrP(C) (RaPrP(C)). However, the details of the distinct effects remain unclear. In the present study, we measured the interactions of Cu(2+) with HuPrP(C) (91-230) and RaPrP(C) (91-228) by isothermal titration calorimetry, and compared the effects of Cu(2+)-binding on the oligomerization of both PrPs. The measured dissociation constants (Kd) of Cu(2+) were 11.1 ± 2.1 μM for HuPrP(C) and 21.1 ± 3.1 μM for RaPrP(C). Cu(2+)-binding promoted the oligomerization of HuPrP(C) more significantly than that of RaPrP(C). The far-ultraviolet circular dichroism spectroscopy experiments showed that Cu(2+)-binding induced more significant secondary structure change and increased more β-sheet content for HuPrP(C) compared with RaPrP(C). Moreover, the urea-induced unfolding transition experiments indicated that Cu(2+)-binding decreased the conformational stability of HuPrP(C) more distinctly than that of RaPrP(C). These results suggest that RaPrP(C) possesses a low susceptibility to Cu(2+), potentially weakening the risk of Cu(2+)-induced TSE diseases. Our work sheds light on the Cu(2+)-promoted oligomerization of PrP(C), and may be helpful for further understanding the TSE-resistance of rabbits.
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Affiliation(s)
- Kejiang Lin
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 21009, China
| | - Ziyao Yu
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 21009, China
| | - Yuanhui Yu
- High-field NMR Research Center, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xinli Liao
- High-field NMR Research Center, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Pei Huang
- High-field NMR Research Center, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Chenyun Guo
- High-field NMR Research Center, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Donghai Lin
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 21009, China High-field NMR Research Center, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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32
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Wan W, Stöhr J, Kendall A, Stubbs G. Truncated forms of the prion protein PrP demonstrate the need for complexity in prion structure. Prion 2015; 9:333-8. [PMID: 26325658 DOI: 10.1080/19336896.2015.1084464] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Self-propagation of aberrant protein folds is the defining characteristic of prions. Knowing the structural basis of self-propagation is essential to understanding prions and their related diseases. Prion rods are amyloid fibrils, but not all amyloids are prions. Prions have been remarkably intractable to structural studies, so many investigators have preferred to work with peptide fragments, particularly in the case of the mammalian prion protein PrP. We compared the structures of a number of fragments of PrP by X-ray fiber diffraction, and found that although all of the peptides adopted amyloid conformations, only the larger fragments adopted conformations that modeled the complexity of self-propagating prions, and even these fragments did not always adopt the PrP structure. It appears that the relatively complex structure of the prion form of PrP is not accessible to short model peptides, and that self-propagation may be tied to a level of structural complexity unobtainable in simple model systems. The larger fragments of PrP, however, are useful to illustrate the phenomenon of deformed templating (heterogeneous seeding), which has important biological consequences.
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Affiliation(s)
- William Wan
- a Department of Biological Sciences and Center for Structural Biology ; Vanderbilt University ; Nashville , TN USA
| | - Jan Stöhr
- b Institute for Neurodegenerative Diseases and Department of Neurology ; University of California, San Francisco ; San Francisco , CA USA
| | - Amy Kendall
- a Department of Biological Sciences and Center for Structural Biology ; Vanderbilt University ; Nashville , TN USA
| | - Gerald Stubbs
- a Department of Biological Sciences and Center for Structural Biology ; Vanderbilt University ; Nashville , TN USA
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33
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Ning L, Pan D, Zhang Y, Wang S, Liu H, Yao X. Effects of the Pathogenic Mutation A117V and the Protective Mutation H111S on the Folding and Aggregation of PrP106-126: Insights from Replica Exchange Molecular Dynamics Simulations. PLoS One 2015; 10:e0125899. [PMID: 25993001 PMCID: PMC4439087 DOI: 10.1371/journal.pone.0125899] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 03/24/2015] [Indexed: 11/19/2022] Open
Abstract
The fragment 106-126 of prion protein exhibits similar properties to full-length prion. Experiments have shown that the A117V mutation enhances the aggregation of PrP106-126, while the H111S mutation abolishes the assembly. However, the mechanism of the change in the aggregation behavior of PrP106-126 upon the two mutations is not fully understood. In this study, replica exchange molecular dynamics simulations were performed to investigate the conformational ensemble of the WT PrP106-126 and its two mutants A117V and H111S. The obtained results indicate that the three species are all intrinsically disordered but they have distinct morphological differences. The A117V mutant has a higher propensity to form β-hairpin structures than the WT, while the H111S mutant has a higher population of helical structures. Furthermore, the A117V mutation increases the hydrophobic solvent accessible surface areas of PrP106-126 and the H111S mutation reduces the exposure of hydrophobic residues. It can be concluded that the difference in populations of β-hairpin structures and the change of hydrophobic solvent accessible areas may induce the different aggregation behaviors of the A117V and the H111S mutated PrP106-126. Understanding why the two mutations have contrary effects on the aggregation of PrP106-126 is very meaningful for further elucidation of the mechanism underlying aggregation and design of inhibitor against aggregation process.
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Affiliation(s)
- Lulu Ning
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
| | - Dabo Pan
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
- School of pharmaceutical technology, Qiandongnan National Polytechnic, Kaili, China
| | - Yan Zhang
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Shaopeng Wang
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
| | - Huanxiang Liu
- School of Pharmacy, Lanzhou University, Lanzhou, China
- * E-mail: (HL); (XY)
| | - Xiaojun Yao
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China
- * E-mail: (HL); (XY)
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34
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Ning L, Wang Q, Zheng Y, Liu H, Yao X. Effects of the A117V mutation on the folding and aggregation of palindromic sequences (PrP113–120) in prion: insights from replica exchange molecular dynamics simulations. MOLECULAR BIOSYSTEMS 2015; 11:647-55. [DOI: 10.1039/c4mb00546e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The A117V mutation enhances the aggregation propensity of the palindromic sequences in prion protein.
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Affiliation(s)
- Lulu Ning
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry
- Lanzhou University
- Lanzhou 730000
- China
| | - Qianqian Wang
- School of Pharmacy
- Lanzhou University
- Lanzhou 730000
- China
| | - Yang Zheng
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry
- Lanzhou University
- Lanzhou 730000
- China
| | - Huanxiang Liu
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry
- Lanzhou University
- Lanzhou 730000
- China
- School of Pharmacy
| | - Xiaojun Yao
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry
- Lanzhou University
- Lanzhou 730000
- China
- State Key Laboratory of Quality Research in Chinese Medicine
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35
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He L, Wang X, Zhu D, Zhao C, Du W. Methionine oxidation of amyloid peptides by peroxovanadium complexes: inhibition of fibril formation through a distinct mechanism. Metallomics 2015; 7:1562-72. [DOI: 10.1039/c5mt00133a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Peroxovanadium complexes inhibit the fibril formation of neurodegenerative amyloid peptides by oxidizing methionine residues.
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Affiliation(s)
- Lei He
- Department of Chemistry
- Renmin University of China
- Beijing, China
| | - Xuesong Wang
- Department of Chemistry
- Renmin University of China
- Beijing, China
| | - Dengsen Zhu
- Department of Chemistry
- Renmin University of China
- Beijing, China
| | - Cong Zhao
- Department of Chemistry
- Renmin University of China
- Beijing, China
| | - Weihong Du
- Department of Chemistry
- Renmin University of China
- Beijing, China
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36
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Tycko R. Physical and structural basis for polymorphism in amyloid fibrils. Protein Sci 2014; 23:1528-39. [PMID: 25179159 DOI: 10.1002/pro.2544] [Citation(s) in RCA: 176] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 08/28/2014] [Accepted: 08/29/2014] [Indexed: 12/24/2022]
Abstract
As our understanding of the molecular structures of amyloid fibrils has matured over the past 15 years, it has become clear that, while amyloid fibrils do have well-defined molecular structures, their molecular structures are not uniquely determined by the amino acid sequences of their constituent peptides and proteins. Self-propagating molecular-level polymorphism is a common phenomenon. This article reviews current information about amyloid fibril structures, variations in molecular structures that underlie amyloid polymorphism, and physical considerations that explain the development and persistence of amyloid polymorphism. Much of this information has been obtained through solid state nuclear magnetic resonance measurements. The biological significance of amyloid polymorphism is also discussed briefly. Although this article focuses primarily on studies of fibrils formed by amyloid-β peptides, the same principles apply to many amyloid-forming peptides and proteins.
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Affiliation(s)
- Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892-0520
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37
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Rehbein P, Saxena K, Schlepckow K, Schwalbe H. Protocol for aerosol-free recombinant production and NMR analysis of prion proteins. JOURNAL OF BIOMOLECULAR NMR 2014; 59:111-117. [PMID: 24771297 DOI: 10.1007/s10858-014-9831-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 04/17/2014] [Indexed: 06/03/2023]
Abstract
The central hallmark of prion diseases is the misfolding of cellular prion protein (PrP(C)) into a disease-associated aggregated isoform known as scrapie prion protein (PrP(Sc)). NMR spectroscopy has made many essential contributions to the characterization of recombinant PrP in its folded, unfolded and aggregated states. Recent studies reporting on de novo generation of prions from recombinant PrP and infection of animals using prion aerosols suggest that adjustment of current biosafety measures may be necessary, particularly given the relatively high protein concentrations required for NMR applications that favor aggregation. We here present a protocol for the production of recombinant PrP under biosafety level 2 conditions that avoids entirely exposure of the experimenter to aerosols that might contain harmful PrP aggregates. In addition, we introduce an NMR sample tube setup that allows for safe handling of PrP samples at the spectrometer that usually is not part of a dedicated biosafety level 2 laboratory.
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Affiliation(s)
- Peter Rehbein
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
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38
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Wang X, Cui M, Zhao C, He L, Zhu D, Wang B, Du W. Regulation of aggregation behavior and neurotoxicity of prion neuropeptides by platinum complexes. Inorg Chem 2014; 53:5044-54. [PMID: 24787240 DOI: 10.1021/ic500092t] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Prion diseases belong to a group of infectious, fatal neurodegenerative disorders. The conformational conversion of a cellular prion protein (PrP(C)) into an abnormal misfolded isoform (PrP(Sc)) is the key event in prion disease pathology. PrP106-126 resembles PrP(Sc) in some physicochemical and biological characteristics, such as apoptosis induction in neurons, fibrillar formation, and mediation of the conversion of native cellular PrP(C) to PrP(Sc). Numerous studies have been conducted to explore the inhibiting methods on the aggregation and neurotoxicity of prion neuropeptide PrP106-126. We showed that PrP106-126 aggregation, as assessed by fluorescence assay and atomic force microscopy, is inhibited by platinum complexes cisplatin, carboplatin, and Pt(bpy)Cl2. ESI-MS and NMR assessments of PrP106-126 and its mutant peptides demonstrate that platinum complexes bind to the peptides in coordination and nonbonded interactions, which rely on the ligand properties and the peptide sequence. In peptides, methionine residue is preferred as a potent binding site over histidine residue for the studied platinum complexes, implying a typical thiophile characteristic of platinum. The neurotoxicity induced by PrP106-126 is better inhibited by Pt(bpy)Cl2 and cisplatin. Furthermore, the ligand configuration contributes to both the binding affinity and the inhibition of peptide aggregation. The pursuit of novel platinum candidates that selectively target prion neuropeptide is noteworthy for medicinal inorganic chemistry and chemical biology.
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Affiliation(s)
- Xuesong Wang
- Department of Chemistry, Renmin University of China , Beijing 100872, People's Republic of China
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39
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Walsh P, Vanderlee G, Yau J, Campeau J, Sim VL, Yip CM, Sharpe S. The mechanism of membrane disruption by cytotoxic amyloid oligomers formed by prion protein(106-126) is dependent on bilayer composition. J Biol Chem 2014; 289:10419-10430. [PMID: 24554723 PMCID: PMC4036164 DOI: 10.1074/jbc.m113.515866] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 02/01/2014] [Indexed: 11/06/2022] Open
Abstract
The formation of fibrillar aggregates has long been associated with neurodegenerative disorders such as Alzheimer and Parkinson diseases. Although fibrils are still considered important to the pathology of these disorders, it is now widely understood that smaller amyloid oligomers are the toxic entities along the misfolding pathway. One characteristic shared by the majority of amyloid oligomers is the ability to disrupt membranes, a commonality proposed to be responsible for their toxicity, although the mechanisms linking this to cell death are poorly understood. Here, we describe the physical basis for the cytotoxicity of oligomers formed by the prion protein (PrP)-derived amyloid peptide PrP(106-126). We show that oligomers of this peptide kill several mammalian cells lines, as well as mouse cerebellar organotypic cultures, and we also show that they exhibit antimicrobial activity. Physical perturbation of model membranes mimicking bacterial or mammalian cells was investigated using atomic force microscopy, polarized total internal reflection fluorescence microscopy, and NMR spectroscopy. Disruption of anionic membranes proceeds through a carpet or detergent model as proposed for other antimicrobial peptides. By contrast, when added to zwitterionic membranes containing cholesterol-rich ordered domains, PrP(106-126) oligomers induce a loss of domain separation and decreased membrane disorder. Loss of raft-like domains may lead to activation of apoptotic pathways, resulting in cell death. This work sheds new light on the physical mechanisms of amyloid cytotoxicity and is the first to clearly show membrane type-specific modes of action for a cytotoxic peptide.
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Affiliation(s)
- Patrick Walsh
- Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, Ontario M5G 1X8; Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8
| | - Gillian Vanderlee
- Institute of Biomaterials and Biomedical Engineering, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1
| | - Jason Yau
- Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, Ontario M5G 1X8; Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8
| | - Jody Campeau
- Department of Medicine, Division of Neurology, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Valerie L Sim
- Department of Medicine, Division of Neurology, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Christopher M Yip
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8; Institute of Biomaterials and Biomedical Engineering, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1
| | - Simon Sharpe
- Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, Ontario M5G 1X8; Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8.
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Han J, Song QQ, Sun P, Zhang J, Wang X, Song J, Li GQ, Liu YH, Mei GY, Shi Q, Tian C, Chen C, Gao C, Zhao B, Dong XP. Interaction between 14-3-3β and PrP influences the dimerization of 14-3-3 and fibrillization of PrP106–126. Int J Biochem Cell Biol 2014; 47:20-8. [DOI: 10.1016/j.biocel.2013.10.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 10/24/2013] [Accepted: 10/28/2013] [Indexed: 11/15/2022]
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41
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Gill AC. β-hairpin-mediated formation of structurally distinct multimers of neurotoxic prion peptides. PLoS One 2014; 9:e87354. [PMID: 24498083 PMCID: PMC3909104 DOI: 10.1371/journal.pone.0087354] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 12/19/2013] [Indexed: 01/09/2023] Open
Abstract
Protein misfolding disorders are associated with conformational changes in specific proteins, leading to the formation of potentially neurotoxic amyloid fibrils. During pathogenesis of prion disease, the prion protein misfolds into β-sheet rich, protease-resistant isoforms. A key, hydrophobic domain within the prion protein, comprising residues 109-122, recapitulates many properties of the full protein, such as helix-to-sheet structural transition, formation of fibrils and cytotoxicity of the misfolded isoform. Using all-atom, molecular simulations, it is demonstrated that the monomeric 109-122 peptide has a preference for α-helical conformations, but that this peptide can also form β-hairpin structures resulting from turns around specific glycine residues of the peptide. Altering a single amino acid within the 109-122 peptide (A117V, associated with familial prion disease) increases the prevalence of β-hairpin formation and these observations are replicated in a longer peptide, comprising residues 106-126. Multi-molecule simulations of aggregation yield different assemblies of peptide molecules composed of conformationally-distinct monomer units. Small molecular assemblies, consistent with oligomers, comprise peptide monomers in a β-hairpin-like conformation and in many simulations appear to exist only transiently. Conversely, larger assemblies are comprised of extended peptides in predominately antiparallel β-sheets and are stable relative to the length of the simulations. These larger assemblies are consistent with amyloid fibrils, show cross-β structure and can form through elongation of monomer units within pre-existing oligomers. In some simulations, assemblies containing both β-hairpin and linear peptides are evident. Thus, in this work oligomers are on pathway to fibril formation and a preference for β-hairpin structure should enhance oligomer formation whilst inhibiting maturation into fibrils. These simulations provide an important new atomic-level model for the formation of oligomers and fibrils of the prion protein and suggest that stabilization of β-hairpin structure may enhance cellular toxicity by altering the balance between oligomeric and fibrillar protein assemblies.
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Affiliation(s)
- Andrew C. Gill
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Easter Bush Campus, University of Edinburgh, Roslin, Edinburgh, United Kingdom
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42
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Zhao C, Wang X, He L, Zhu D, Wang B, Du W. Influence of gold–bipyridyl derivants on aggregation and disaggregation of the prion neuropeptide PrP106–126. Metallomics 2014; 6:2117-25. [DOI: 10.1039/c4mt00219a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Gold–bipyridyl derivants affect aggregation and disaggregation of a prion neuropeptide PrP106–126.
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Affiliation(s)
- Cong Zhao
- Department of Chemistry
- Renmin University of China
- Beijing, China
| | - Xuesong Wang
- Department of Chemistry
- Renmin University of China
- Beijing, China
| | - Lei He
- Department of Chemistry
- Renmin University of China
- Beijing, China
| | - Dengsen Zhu
- Department of Chemistry
- Renmin University of China
- Beijing, China
| | - Baohuai Wang
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing, China
| | - Weihong Du
- Department of Chemistry
- Renmin University of China
- Beijing, China
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43
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Baral PK, Swayampakula M, Rout MK, Kav NNV, Spyracopoulos L, Aguzzi A, James MNG. Structural basis of prion inhibition by phenothiazine compounds. Structure 2013; 22:291-303. [PMID: 24373770 DOI: 10.1016/j.str.2013.11.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 11/19/2013] [Accepted: 11/20/2013] [Indexed: 01/10/2023]
Abstract
Conformational transitions of the cellular form of the prion protein, PrP(C), into an infectious isoform, PrP(Sc), are considered to be central events in the progression of fatal neurodegenerative diseases known as transmissible spongiform encephalopathies. Tricyclic phenothiazine compounds exhibit antiprion activity; however, the underlying molecular mechanism of PrP(Sc) inhibition remains elusive. We report the molecular structures of two phenothiazine compounds, promazine and chlorpromazine bound to a binding pocket formed at the intersection of the structured and the unstructured domains of the mouse prion protein. Promazine binding induces structural rearrangement of the unstructured region proximal to β1, through the formation of a "hydrophobic anchor." We demonstrate that these molecules, promazine in particular, allosterically stabilize the misfolding initiator-motifs such as the C terminus of α2, the α2-α3 loop, as well as the polymorphic β2-α2 loop. Hence, the stabilization effects of the phenothiazine derivatives on initiator-motifs induce a PrP(C) isoform that potentially resists oligomerization.
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Affiliation(s)
- Pravas Kumar Baral
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Mridula Swayampakula
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Manoj Kumar Rout
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Nat N V Kav
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Leo Spyracopoulos
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Adriano Aguzzi
- Department of Pathology, Institute of Neuropathology, University Hospital Zurich, Zurich 8091, Switzerland
| | - Michael N G James
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.
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Wang X, He L, Zhao C, Du W, Lin J. Gold complexes inhibit the aggregation of prion neuropeptides. J Biol Inorg Chem 2013; 18:767-78. [DOI: 10.1007/s00775-013-1030-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 08/05/2013] [Indexed: 12/19/2022]
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45
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Vilches S, Vergara C, Nicolás O, Sanclimens G, Merino S, Varón S, Acosta GA, Albericio F, Royo M, Río JAD, Gavín R. Neurotoxicity of prion peptides mimicking the central domain of the cellular prion protein. PLoS One 2013; 8:e70881. [PMID: 23940658 PMCID: PMC3733940 DOI: 10.1371/journal.pone.0070881] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 06/25/2013] [Indexed: 12/20/2022] Open
Abstract
The physiological functions of PrP(C) remain enigmatic, but the central domain, comprising highly conserved regions of the protein may play an important role. Indeed, a large number of studies indicate that synthetic peptides containing residues 106-126 (CR) located in the central domain (CD, 95-133) of PrP(C) are neurotoxic. The central domain comprises two chemically distinct subdomains, the charge cluster (CC, 95-110) and a hydrophobic region (HR, 112-133). The aim of the present study was to establish the individual cytotoxicity of CC, HR and CD. Our results show that only the CD peptide is neurotoxic. Biochemical, Transmission Electron Microscopy and Atomic Force Microscopy experiments demonstrated that the CD peptide is able to activate caspase-3 and disrupt the cell membrane, leading to cell death.
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Affiliation(s)
- Silvia Vilches
- Molecular and Cellular Neurobiotechnology, Institute for Bioengineering of Catalonia (IBEC), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain
| | - Cristina Vergara
- Molecular and Cellular Neurobiotechnology, Institute for Bioengineering of Catalonia (IBEC), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain
| | - Oriol Nicolás
- Molecular and Cellular Neurobiotechnology, Institute for Bioengineering of Catalonia (IBEC), Barcelona, Spain
- Department of Cell Biology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Gloria Sanclimens
- Combinatorial Chemistry Unit, Scientific Park of Barcelona, Barcelona, Spain
| | - Sandra Merino
- Department of Physicochemistry, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Sonia Varón
- Combinatorial Chemistry Unit, Scientific Park of Barcelona, Barcelona, Spain
| | - Gerardo A. Acosta
- Institute for Research in Biomedicine (IRB), Barcelona, Spain
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona, Spain
| | - Fernando Albericio
- Institute for Research in Biomedicine (IRB), Barcelona, Spain
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona, Spain
- Department of Organic Chemistry, Faculty of Chemistry, University of Barcelona, Barcelona, Spain
| | - Miriam Royo
- Combinatorial Chemistry Unit, Scientific Park of Barcelona, Barcelona, Spain
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona, Spain
| | - José A. Del Río
- Molecular and Cellular Neurobiotechnology, Institute for Bioengineering of Catalonia (IBEC), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain
- Department of Cell Biology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Rosalina Gavín
- Molecular and Cellular Neurobiotechnology, Institute for Bioengineering of Catalonia (IBEC), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain
- Department of Cell Biology, Faculty of Biology, University of Barcelona, Barcelona, Spain
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46
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Chatterjee B, Lee CY, Lin C, Chen EHL, Huang CL, Yang CC, Chen RPY. Amyloid core formed of full-length recombinant mouse prion protein involves sequence 127-143 but not sequence 107-126. PLoS One 2013; 8:e67967. [PMID: 23844138 PMCID: PMC3700907 DOI: 10.1371/journal.pone.0067967] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 05/23/2013] [Indexed: 12/23/2022] Open
Abstract
The principal event underlying the development of prion disease is the conversion of soluble cellular prion protein (PrP(C)) into its disease-causing isoform, PrP(Sc). This conversion is associated with a marked change in secondary structure from predominantly α-helical to a high β-sheet content, ultimately leading to the formation of aggregates consisting of ordered fibrillar assemblies referred to as amyloid. In vitro, recombinant prion proteins and short prion peptides from various species have been shown to form amyloid under various conditions and it has been proposed that, theoretically, any protein and peptide could form amyloid under appropriate conditions. To identify the peptide segment involved in the amyloid core formed from recombinant full-length mouse prion protein mPrP(23-230), we carried out seed-induced amyloid formation from recombinant prion protein in the presence of seeds generated from the short prion peptides mPrP(107-143), mPrP(107-126), and mPrP(127-143). Our results showed that the amyloid fibrils formed from mPrP(107-143) and mPrP(127-143), but not those formed from mPrP(107-126), were able to seed the amyloidogenesis of mPrP(23-230), showing that the segment residing in sequence 127-143 was used to form the amyloid core in the fibrillization of mPrP(23-230).
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Affiliation(s)
| | - Chung-Yu Lee
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Chen Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Eric H.-L. Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chao-Li Huang
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Chien-Chih Yang
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Rita P.-Y. Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- * E-mail:
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47
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Cheng H, Huang WYC, Tsai TWT, Mou Y, Chao JCH, Chan JCC. Depletion of Water Molecules Near the End Stage of Steric Zipper Formation. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.201300073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Hsin‐Mei Cheng
- Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - William Y. C. Huang
- Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - Tim W. T. Tsai
- Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - Yun Mou
- Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - John Chin Hao Chao
- Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - Jerry C. C. Chan
- Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
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48
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Chuang CC, Liao TY, Chen EHL, Chen RPY. How do amino acid substitutions affect the amyloidogenic properties and seeding efficiency of prion peptides. Amino Acids 2013; 45:785-96. [PMID: 23736988 PMCID: PMC3776267 DOI: 10.1007/s00726-013-1522-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Accepted: 05/22/2013] [Indexed: 11/28/2022]
Abstract
The amino acid sequences in the amyloidogenic region (amino acids 108–144) of several mammalian prion proteins were compared and variations were found to occur at residues 109 (M or L), 112 (M or V), 129 (M, V, or L), 135 (N or S), 138 (M, L, or I), 139 (M or I), and 143 (N or S). Using the bovine PrP peptide (residues 108–144 based on the numbering of the human prion protein sequence) as a control peptide, several peptides with one amino acid differing from that of the bovine PrP peptide at residues 109, 112, 135, 138, 139, or 143 and several mammalian PrP peptides were synthesized, and the effects of these amino acid substitutions on the amyloidogenic properties of these peptides were compared and discussed on the basis of the chemical and structural properties of amino acids. Our results showed that the V112M substitution accelerated nucleation of amyloidogenesis, while the N143S and I139M substitutions retarded nucleation. These effects tended to cancel each other out when two substitutions with opposite effects were present on the same peptide. Moreover, acceleration or inhibition of nucleation was not necessarily correlated with effect on seeding efficiency. Using amyloid fibrils prepared from the bovine PrP peptide as seeds, the seeding efficiency for the monomer peptides with the M129L, S135N, N143S, or I139M substitution was decreased compared to that for bPrP peptide. Of all the mammalian peptides used in this study, the dog, mule deer, and pig PrP peptides had the lowest seeding efficiencies.
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Affiliation(s)
- Chi-Chen Chuang
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, 106, Taiwan, ROC
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49
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Huang P, Lian F, Wen Y, Guo C, Lin D. Prion protein oligomer and its neurotoxicity. Acta Biochim Biophys Sin (Shanghai) 2013; 45:442-51. [PMID: 23557632 DOI: 10.1093/abbs/gmt037] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The prion diseases, also known as transmissible spongiform encephalopathies, are fatal neurodegenerative disorders. According to the 'protein only' hypothesis, the key molecular event in the pathogenesis of prion disease is the conformational conversion of the host-derived cellular prion protein (PrP(C)) into a misfolded form (scrapie PrP, PrP(Sc)). Increasing evidence has shown that the most infectious factor is the smaller subfibrillar oligomers formed by prion proteins. Both the prion oligomer and PrP(Sc) are rich in β-sheet structure and resistant to the proteolysis of proteinase K. The prion oligomer is soluble in physiologic environments whereas PrP(Sc) is insoluble. Various prion oligomers are formed in different conditions. Prion oligomers exhibited more neurotoxicity both in vitro and in vivo than the fibrillar forms of PrP(Sc), implying that prion oligomers could be potential drug targets for attacking prion diseases. In this article, we describe recent experimental evidence regarding prion oligomers, with a special focus on prion oligomer formation and its neurotoxicity.
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Affiliation(s)
- Pei Huang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 21009, China
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50
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Li J, van der Wel PCA. Spinning-rate encoded chemical shift correlations from rotational resonance solid-state NMR experiments. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 230:117-24. [PMID: 23475055 PMCID: PMC3635064 DOI: 10.1016/j.jmr.2013.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 01/22/2013] [Accepted: 02/04/2013] [Indexed: 05/23/2023]
Abstract
Structural measurements in magic-angle-spinning (MAS) solid-state NMR rely heavily on (13)C-(13)C distance measurements. Broadbanded recoupling methods are used to generate many cross-peaks, but have complex polarization transfer mechanisms that limit the precision of distance constraints and can suffer from weak intensities for distant peaks due to relaxation, the broad distribution of polarization, as well as dipolar truncation. Frequency-selective methods that feature narrow-banded recoupling can reduce these effects. Indeed, rotational resonance (R(2)) experiments have found application in many different biological systems, where they have afforded improved precision and accuracy. Unfortunately, a highly selective transfer mechanism also leads to few cross-peaks in the resulting spectra, which complicates the extraction of multiple constraints. R(2)-width (R(2)W) measurements that scan a range of MAS rates to probe the R(2) matching conditions of one or more sites can improve precision, and also permit multiple simultaneous distance measurements. However, multidimensional R(2)W can be very time-consuming. Here, we present an approach that facilitates the acquisition of 2D-like spectra based on a series of 1D R(2)W experiments, by taking advantage of the chemical shift information encoded in the MAS rates where matching occurs. This yields a more time-efficient experiment with many of the benefits of more conventional multidimensional R(2)W measurements. The obtained spectra reveal long-distance (13)C-(13)C cross-peaks resulting from R(2)-mediated polarization transfer. This experiment also enables the efficient setup and targeted implementation of traditional R(2) or R(2)W experiments. Analogous applications may extend to other variable-MAS and frequency-selective solid-state NMR experiments.
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Affiliation(s)
- Jun Li
- Department of Structural Biology, University of Pittsburgh School of Medicine, Biomedical Science Tower 3, 3501 Fifth Ave, Pittsburgh, Pennsylvania 15260, USA
| | - Patrick C. A. van der Wel
- Department of Structural Biology, University of Pittsburgh School of Medicine, Biomedical Science Tower 3, 3501 Fifth Ave, Pittsburgh, Pennsylvania 15260, USA
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