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Abramov-Harpaz K, Lan-Mark S, Miller Y. Structural packing of the non-amyloid component core domain in α-synuclein plays a role in the stability of the fibrils. Biophys Chem 2024; 310:107239. [PMID: 38663121 DOI: 10.1016/j.bpc.2024.107239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/08/2024] [Accepted: 04/14/2024] [Indexed: 05/23/2024]
Abstract
Parkinson's disease (PD) is one of many neurodegenerative diseases. The protein associated with PD is α-synuclein (AS). Aggregation of AS protein into oligomers, protofilaments, and finally to fibrils yields to the development of PD. The aggregation process of AS leads to the formation of polymorphic AS fibrils. Herein, we compared four polymorphic full-length AS1-140 fibrils, using extensive computational tools. The main conclusion of this study emphasizes the role of the structurally packed non-amyloid component (NAC) core domain in AS fibrils. Polymorphic AS fibrils that presented a packed NAC core domain, exhibited more β-sheets and fewer fluctuations in the NAC domain. Hence, these AS fibrils are more stable and populated than the AS fibrils, by which the NAC domains are more exposed, more fluctuate and less packed in the fibrillary structure. Therefore, this study emphasizes the importance of the NAC domain packing in the morphology of AS fibrils. The results obtained in this study will initiate future studies to develop compounds to prevent and inhibit AS aggregation.
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Affiliation(s)
- Karina Abramov-Harpaz
- Department of Chemistry, Ben-Gurion University of the Negev, P.O. Box 653, Be'er Sheva 8410501, Israel; Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beér-Sheva, 8410501, Israel; The School of Brain Sciences and Cognition, Ben-Gurion University of the Negev, Beér-Sheva, 8410501, Israel
| | - Sapir Lan-Mark
- Department of Chemistry, Ben-Gurion University of the Negev, P.O. Box 653, Be'er Sheva 8410501, Israel; Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beér-Sheva, 8410501, Israel; The School of Brain Sciences and Cognition, Ben-Gurion University of the Negev, Beér-Sheva, 8410501, Israel
| | - Yifat Miller
- Department of Chemistry, Ben-Gurion University of the Negev, P.O. Box 653, Be'er Sheva 8410501, Israel; Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beér-Sheva, 8410501, Israel; The School of Brain Sciences and Cognition, Ben-Gurion University of the Negev, Beér-Sheva, 8410501, Israel.
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2
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Thakkar H, Chatterjee S, Saxena P, Eerla R, Wagh S, Khairnar A, Shah RP. Cell-Engineered Recombinant α-Synuclein: A Gage R&R Validated Protocol. J Proteome Res 2024; 23:16-24. [PMID: 37985371 DOI: 10.1021/acs.jproteome.3c00190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
α-Synuclein (α-Syn) misfolding and its presence in Lewy bodies are observed in almost all Parkinson's disease (PD) patients. Basic biomedical research would benefit from a quick, low-cost approach to purifying α-Syn and developing in vitro and in vivo models for PD. Several research groups utilize PFF-based models, yet the production of α-Syn PFFs is inconsistent, resulting in nonconclusive findings. Some research laboratories prepare recombinant α-Syn (r α-Syn) by molecular cloning to overexpress α-Syn with various purifying techniques. Laboratory-to-laboratory protocols cause considerable variability and sometimes contradictory findings. PD researchers spend more on protein than solving α-Syn's riddles. This article uncovered a novel method for expressing and purifying r α-Syn validated through gage reproducibility and repeatability (Gage R&R). For the production of r α-Syn, we have employed the ability of a high-cell-density-based expression system to overexpress protein in BL21(DE3). A simple, high-throughput, nonchromatographical purification protocol has been devised to facilitate research with higher reproducibility, which was validated through Gage R&R. A crossover experimental design was utilized, and the purified protein was characterized using orthogonal high-end analytical methods, which displayed higher similarity between the isolated r α-Syn. Batch-to-batch variability was the least for produced protein and hence can be utilized for exploring the iceberg of PD.
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Affiliation(s)
- Harsh Thakkar
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research─Ahmedabad (NIPER-A), Opposite Air force Station Palaj, Gandhinagar 382355, Gujarat India
| | - Sayan Chatterjee
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research─Ahmedabad (NIPER-A), Opposite Air force Station Palaj, Gandhinagar 382355, Gujarat India
| | - Purvi Saxena
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research─Ahmedabad (NIPER-A), Opposite Air force Station Palaj, Gandhinagar 382355, Gujarat India
| | - Rameswari Eerla
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research─Ahmedabad (NIPER-A), Opposite Air force Station Palaj, Gandhinagar 382355, Gujarat India
| | - Sachin Wagh
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research─Ahmedabad (NIPER-A), Opposite Air force Station Palaj, Gandhinagar 382355, Gujarat India
| | - Amit Khairnar
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research─Ahmedabad (NIPER-A), Opposite Air force Station Palaj, Gandhinagar 382355, Gujarat India
| | - Ravi P Shah
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research─Ahmedabad (NIPER-A), Opposite Air force Station Palaj, Gandhinagar 382355, Gujarat India
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3
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Rupert J, Monti M, Zacco E, Tartaglia G. RNA sequestration driven by amyloid formation: the alpha synuclein case. Nucleic Acids Res 2023; 51:11466-11478. [PMID: 37870427 PMCID: PMC10681735 DOI: 10.1093/nar/gkad857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/15/2023] [Accepted: 09/26/2023] [Indexed: 10/24/2023] Open
Abstract
Nucleic acids can act as potent modulators of protein aggregation, and RNA has the ability to either hinder or facilitate protein assembly, depending on the molecular context. In this study, we utilized a computational approach to characterize the physico-chemical properties of regions involved in amyloid aggregation. In various experimental datasets, we observed that while the core is hydrophobic and highly ordered, external regions, which are more disordered, display a distinct tendency to interact with nucleic acids. To validate our predictions, we performed aggregation assays with alpha-synuclein (aS140), a non-nucleic acid-binding amyloidogenic protein, and a mutant truncated at the acidic C-terminus (aS103), which is predicted to have a higher tendency to interact with RNA. For both aS140 and aS103, we observed an acceleration of aggregation upon RNA addition, with a significantly stronger effect for aS103. Due to favorable electrostatics, we noted an enhanced nucleic acid sequestration ability for the aggregated aS103, allowing it to entrap a larger amount of RNA compared to the aggregated wild-type counterpart. Overall, our research suggests that RNA sequestration might be a common phenomenon linked to protein aggregation, constituting a gain-of-function mechanism that warrants further investigation.
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Affiliation(s)
- Jakob Rupert
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Via Enrico Melen, 83, 16152, Genova, Italy
- Department of Biology and Biotechnologies ‘Charles Darwin’, Sapienza University of Rome, P.le A. Moro 5, Rome 00185, Italy
| | - Michele Monti
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Via Enrico Melen, 83, 16152, Genova, Italy
| | - Elsa Zacco
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Via Enrico Melen, 83, 16152, Genova, Italy
| | - Gian Gaetano Tartaglia
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Via Enrico Melen, 83, 16152, Genova, Italy
- Department of Biology and Biotechnologies ‘Charles Darwin’, Sapienza University of Rome, P.le A. Moro 5, Rome 00185, Italy
- Catalan Institution for Research and Advanced Studies, ICREA, Passeig Lluís Companys 23, 08010, Barcelona, Spain
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4
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Whitcomb K, Warncke K. Oligomeric and Fibrillar α-Synuclein Display Persistent Dynamics and Compressibility under Controlled Confinement. ACS Chem Neurosci 2023; 14:3905-3912. [PMID: 37861459 PMCID: PMC10623556 DOI: 10.1021/acschemneuro.3c00470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/26/2023] [Indexed: 10/21/2023] Open
Abstract
The roles of α-synuclein in neurotransmitter release in brain neurons and in the Parkinson's disease condition have challenged comprehensive description. To gain insight into molecular mechanistic properties that actuate α-synuclein function and dysfunction, the coupled protein and solvent dynamics of oligomer and fibril forms of human α-synuclein are examined in a low-temperature system that allows control of confinement and localization of a motionally sensitive electron paramagnetic resonance spin probe in the coupled solvent-protein regions. The rotational mobility of the spin probe resolves two distinct α-synuclein-associated solvent components for oligomers and fibrils, as for globular proteins, but with dramatically higher fluidities at each temperature, that are comparable to low-confinement, aqueous-cryosolvent mesophases. In contrast to the temperature-independent volumes of the solvent phases that surround globular and condensate-forming proteins, the higher-fluidity mesophase volume of α-synuclein oligomers and fibrils decreases with decreasing temperature, signaling a compression of this phase. This unique property and thermal hysteresis in the mobilities and component weights, together with previous high-resolution structural characterizations, suggest a model in which the dynamically disordered C-terminal domain of α-synuclein creates a compressible phase that maintains high fluidity under confinement. Robust dynamics and compressibility are fundamental molecular mechanical properties of α-synuclein oligomers and fibrils, which may contribute to dysfunction and inform about function.
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Affiliation(s)
- Katie
Lynn Whitcomb
- Department of Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Kurt Warncke
- Department of Physics, Emory University, Atlanta, Georgia 30322, United States
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5
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Ortigosa-Pascual L, Leiding T, Linse S, Pálmadóttir T. Photo-Induced Cross-Linking of Unmodified α-Synuclein Oligomers. ACS Chem Neurosci 2023; 14:3192-3205. [PMID: 37621159 PMCID: PMC10485903 DOI: 10.1021/acschemneuro.3c00326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023] Open
Abstract
Photo-induced cross-linking of unmodified proteins (PICUP) has been used in the past to study size distributions of protein assemblies. PICUP may, for example, overcome the significant experimental challenges related to the transient nature, heterogeneity, and low concentration of amyloid protein oligomers relative to monomeric and fibrillar species. In the current study, a reaction chamber was designed, produced, and used for PICUP reaction optimization in terms of reaction conditions and lighting time from ms to s. These efforts make the method more reproducible and accessible and enable the use of shorter reaction times compared to previous studies. We applied the optimized method to an α-synuclein aggregation time course to monitor the relative concentration and size distribution of oligomers over time. The data are compared to the time evolution of the fibril mass concentration, as monitored by thioflavin T fluorescence. At all time points, the smaller the oligomer, the higher its concentration observed after PICUP. Moreover, the total oligomer concentration is highest at short aggregation times, and the decline over time follows the disappearance of monomers. We can therefore conclude that these oligomers form from monomers.
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Affiliation(s)
- Lei Ortigosa-Pascual
- Department of Biochemistry and Structural
Biology, Lund University, 221 00 Lund, Sweden
| | - Thom Leiding
- Department of Biochemistry and Structural
Biology, Lund University, 221 00 Lund, Sweden
| | - Sara Linse
- Department of Biochemistry and Structural
Biology, Lund University, 221 00 Lund, Sweden
| | - Tinna Pálmadóttir
- Department of Biochemistry and Structural
Biology, Lund University, 221 00 Lund, Sweden
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6
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Lyubchenko YL. Protein Self-Assembly at the Liquid-Surface Interface. Surface-Mediated Aggregation Catalysis. J Phys Chem B 2023; 127:1880-1889. [PMID: 36812408 DOI: 10.1021/acs.jpcb.2c09029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Protein self-assembly into aggregates of various morphologies is a ubiquitous phenomenon in physical chemistry and biophysics. The critical role of amyloid assemblies in the development of diseases, neurodegenerative diseases especially, highlights the importance of understanding the mechanistic picture of the self-assembly process. The translation of this knowledge to the development of efficient preventions and treatments for diseases requires designing experiments at conditions mimicking those in vivo. This Perspective reviews data satisfying two major requirements: membrane environment and physiologically low concentrations of proteins. Recent progress in experiments and computational modeling resulted in a novel model for the amyloid aggregation process at the membrane-liquid interface. The self-assembly under such conditions has a number of critical features, further understanding of which can lead to the development of efficient preventive means and treatments for Alzheimer's and other devastating neurodegenerative disorders.
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Affiliation(s)
- Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
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7
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Bell R, Castellana-Cruz M, Nene A, Thrush RJ, Xu CK, Kumita JR, Vendruscolo M. Effects of N-terminal Acetylation on the Aggregation of Disease-related α-synuclein Variants. J Mol Biol 2023; 435:167825. [PMID: 36099961 DOI: 10.1016/j.jmb.2022.167825] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 08/31/2022] [Accepted: 09/06/2022] [Indexed: 02/04/2023]
Abstract
Mutations in the SNCA gene, which encodes the protein α-synuclein, have been linked with early onset Parkinson's disease. The exact nature of this association, however, is still poorly understood. To investigate this problem, we started from the observation that α-synuclein is constitutively N-terminally acetylated, a post-translational modification that alters the charge and structure of α-synuclein molecules and affects their interaction with lipid membranes, as well as their aggregation process. We thus studied five N-terminal acetylated familial variants (A30P, E46K, H50Q, G51D and A53T) of α-synuclein through a wide range of biophysical assays to probe the microscopic steps in their aggregation process and the structures of the resulting aggregates. Our results reveal a great complexity in the combined effects of the disease-related mutations with N-terminal acetylation on the aggregation of α-synuclein, which underscores the great sensitivity to even relatively small perturbations of the behaviour of this protein.
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Affiliation(s)
- Rosie Bell
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Marta Castellana-Cruz
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Aishwarya Nene
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Rebecca J Thrush
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Catherine K Xu
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Janet R Kumita
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, UK.
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK.
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8
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Rapid Scan Electron Paramagnetic Resonance Spectroscopy Is a Suitable Tool to Study Intermolecular Interactions of Intrinsically Disordered Protein. BIOLOGY 2023; 12:biology12010079. [PMID: 36671771 PMCID: PMC9856040 DOI: 10.3390/biology12010079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 01/06/2023]
Abstract
Intrinsically disordered proteins (IDPs) are involved in most crucial cellular processes. However, they lack a well-defined fold hampering the investigation of their structural ensemble and interactions. Suitable biophysical methods able to manage their inherent flexibility and broad conformational ensemble are scarce. Here, we used rapid scan (RS) electron paramagnetic resonance (EPR) spectroscopy to study the intermolecular interactions of the IDP α-synuclein (aS). aS aggregation and fibril deposition is the hallmark of Parkinson's disease, and specific point mutations, among them A30P and A53T, were linked to the early onset of the disease. To understand the pathological processes, research intensively investigates aS aggregation kinetics, which was reported to be accelerated in the presence of ethanol. Conventional techniques fail to capture these fast processes due to their limited time resolution and, thus, lose kinetic information. We have demonstrated that RS EPR spectroscopy is suitable for studying aS aggregation by resolving underlying kinetics and highlighting differences in fibrillization behavior. RS EPR spectroscopy outperforms traditional EPR methods in terms of sensitivity by a factor of 5 in our case while significantly reducing data acquisition time. Thus, we were able to sample short time intervals capturing single events taking place during the aggregation process. Further studies will therefore be able to shed light on biological processes proceeding on fast time scales.
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9
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Acquasaliente L, De Filippis V. The Role of Proteolysis in Amyloidosis. Int J Mol Sci 2022; 24:ijms24010699. [PMID: 36614141 PMCID: PMC9820691 DOI: 10.3390/ijms24010699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/23/2022] [Accepted: 12/27/2022] [Indexed: 01/04/2023] Open
Abstract
Amyloidoses are a group of diseases associated with deposits of amyloid fibrils in different tissues. So far, 36 different types of amyloidosis are known, each due to the misfolding and accumulation of a specific protein. Amyloid deposits can be found in several organs, including the heart, brain, kidneys, and spleen, and can affect single or multiple organs. Generally, amyloid-forming proteins become prone to aggregate due to genetic mutations, acquired environmental factors, excessive concentration, or post-translational modifications. Interestingly, amyloid aggregates are often composed of proteolytic fragments, derived from the degradation of precursor proteins by yet unidentified proteases, which display higher amyloidogenic tendency compared to precursor proteins, thus representing an important mechanism in the onset of amyloid-based diseases. In the present review, we summarize the current knowledge on the proteolytic susceptibility of three of the main human amyloidogenic proteins, i.e., transthyretin, β-amyloid precursor protein, and α-synuclein, in the onset of amyloidosis. We also highlight the role that proteolytic enzymes can play in the crosstalk between intestinal inflammation and amyloid-based diseases.
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Affiliation(s)
- Laura Acquasaliente
- Correspondence: (L.A.); (V.D.F.); Tel.: +39-0498275703 (L.A.); +39-0498275698 (V.D.F.)
| | - Vincenzo De Filippis
- Correspondence: (L.A.); (V.D.F.); Tel.: +39-0498275703 (L.A.); +39-0498275698 (V.D.F.)
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10
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Zhang Y, Wang Y, Liu Y, Wei G, Ding F, Sun Y. Molecular Insights into the Misfolding and Dimerization Dynamics of the Full-Length α-Synuclein from Atomistic Discrete Molecular Dynamics Simulations. ACS Chem Neurosci 2022; 13:3126-3137. [PMID: 36278939 PMCID: PMC9797213 DOI: 10.1021/acschemneuro.2c00531] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The misfolding and pathological aggregation of α-synuclein forming insoluble amyloid deposits is associated with Parkinson's disease, the second most common neurodegenerative disease in the world population. Characterizing the self-assembly mechanism of α-synuclein is critical for discovering treatments against synucleinopathies. The intrinsically disordered property, high degrees of freedom, and macroscopic timescales of conformational conversion make its characterization extremely challenging in vitro and in silico. Here, we systematically investigated the dynamics of monomer misfolding and dimerization of the full-length α-synuclein using atomistic discrete molecular dynamics simulations. Our results suggested that both α-synuclein monomers and dimers mainly adopted unstructured formations with partial helices around the N-terminus (residues 8-32) and various β-sheets spanning the residues 35-56 (N-terminal tail) and residues 61-95 (NAC region). The C-terminus mostly assumed an unstructured formation wrapping around the lateral surface and the elongation edge of the β-sheet core formed by an N-terminal tail and NAC regions. Dimerization enhanced the β-sheet formation along with a decrease in the unstructured content. The inter-peptide β-sheets were mainly formed by the N-terminal tail and NACore (residues 68-78) regions, suggesting that these two regions played critical roles in the amyloid aggregation of α-synuclein. Interactions of the C-terminus with the N-terminal tail and the NAC region were significantly suppressed in the α-synuclein dimer, indicating that the interaction of the C-terminus with the N-terminal tail and NAC regions could prevent α-synuclein aggregation. These results on the structural ensembles and early aggregation dynamics of α-synuclein will help understand the nucleation and fibrillization of α-synuclein.
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Affiliation(s)
- Yu Zhang
- Department of Physics, Ningbo University, Ningbo 315211, China
| | - Ying Wang
- Department of Physics, Ningbo University, Ningbo 315211, China
| | - Yuying Liu
- Department of Physics, Ningbo University, Ningbo 315211, China
| | - Guanghong Wei
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai 200433, China
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Yunxiang Sun
- Department of Physics, Ningbo University, Ningbo 315211, China
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai 200433, China
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
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11
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Propagation of Parkinson's disease by extracellular vesicle production and secretion. Biochem Soc Trans 2022; 50:1303-1314. [DOI: 10.1042/bst20220204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/31/2022] [Accepted: 08/31/2022] [Indexed: 11/17/2022]
Abstract
Parkinson's disease (PD) is a common neurodegenerative condition affecting a significant number of individuals globally, resulting in the presentation of debilitating motor and non-motor symptoms, including bradykinesia, resting tremor, as well as mood and sleep disorders. The pathology of PD has been observed to spread through the central nervous system resulting in progressive brain degeneration and a poor prognosis. Aggregated forms of the protein α-synuclein, particularly intermediary aggregates, referred to as oligomers, or preformed fibrils, have been implicated as the causative agent in the degeneration of neuronal processes, including the dysfunction of axonal transport, mitochondrial activity, and ultimately cellular death. Extracellular vesicles (EVs) have been strongly implicated in the propagation of PD pathology. Current observations suggest that aggregated α-synuclein is transported between neurons via small EVs in a series of exocytosis and endocytosis cellular processes leading to the observed spread of neurotoxicity and cellular death. Despite some understanding of the role of EVs in neurodegeneration, the exact mechanism by which these lipidic particles participate in the progression of Parkinson's pathology is not entirely understood. Here we review the current understanding of the role of EVs in the propagation of PD and explore their potential as a therapeutic target.
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12
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The Possible Mechanism of Amyloid Transformation Based on the Geometrical Parameters of Early-Stage Intermediate in Silico Model for Protein Folding. Int J Mol Sci 2022; 23:ijms23169502. [PMID: 36012765 PMCID: PMC9409474 DOI: 10.3390/ijms23169502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/09/2022] [Accepted: 08/19/2022] [Indexed: 12/03/2022] Open
Abstract
The specificity of the available experimentally determined structures of amyloid forms is expressed primarily by the two- and not three-dimensional forms of a single polypeptide chain. Such a flat structure is possible due to the β structure, which occurs predominantly. The stabilization of the fibril in this structure is achieved due to the presence of the numerous hydrogen bonds between the adjacent chains. Together with the different forms of twists created by the single R- or L-handed α-helices, they form the hydrogen bond network. The specificity of the arrangement of these hydrogen bonds lies in their joint orientation in a system perpendicular to the plane formed by the chain and parallel to the fibril axis. The present work proposes the possible mechanism for obtaining such a structure based on the geometric characterization of the polypeptide chain constituting the basis of our early intermediate model for protein folding introduced formerly. This model, being the conformational subspace of Ramachandran plot (the ellipse path), was developed on the basis of the backbone conformation, with the side-chain interactions excluded. Our proposal is also based on the results from molecular dynamics available in the literature leading to the unfolding of α-helical sections, resulting in the β-structural forms. Both techniques used provide a similar suggestion in a search for a mechanism of conformational changes leading to a formation of the amyloid form. The potential mechanism of amyloid transformation is presented here using the fragment of the transthyretin as well as amyloid Aβ.
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13
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Paschold A, Voigt B, Hause G, Kohlmann T, Rothemund S, Binder WH. Modulating the Fibrillization of Parathyroid-Hormone (PTH) Peptides: Azo-Switches as Reversible and Catalytic Entities. Biomedicines 2022; 10:biomedicines10071512. [PMID: 35884817 PMCID: PMC9313110 DOI: 10.3390/biomedicines10071512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/20/2022] [Accepted: 06/23/2022] [Indexed: 11/16/2022] Open
Abstract
We here report a novel strategy to control the bioavailability of the fibrillizing parathyroid hormone (PTH)-derived peptides, where the concentration of the bioactive form is controlled by an reversible, photoswitchable peptide. PTH1–84, a human hormone secreted by the parathyroid glands, is important for the maintenance of extracellular fluid calcium and phosphorus homeostasis. Controlling fibrillization of PTH1–84 represents an important approach for in vivo applications, in view of the pharmaceutical applications for this protein. We embed the azobenzene derivate 3-{[(4-aminomethyl)phenyl]diazenyl}benzoic acid (3,4′-AMPB) into the PTH-derived peptide PTH25–37 to generate the artificial peptide AzoPTH25–37 via solid-phase synthesis. AzoPTH25–37 shows excellent photostability (more than 20 h in the dark) and can be reversibly photoswitched between its cis/trans forms. As investigated by ThT-monitored fibrillization assays, the trans-form of AzoPTH25–37 fibrillizes similar to PTH25–37, while the cis-form of AzoPTH25–37 generates only amorphous aggregates. Additionally, cis-AzoPTH25–37 catalytically inhibits the fibrillization of PTH25–37 in ratios of up to one-fifth. The approach reported here is designed to control the concentration of PTH-peptides, where the bioactive form can be catalytically controlled by an added photoswitchable peptide.
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Affiliation(s)
- André Paschold
- Department of Chemistry, Faculty of Natural Sciences II, Martin-Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany; (A.P.); (T.K.)
| | - Bruno Voigt
- Department of Physics, Faculty of Natural Sciences II, Martin-Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany;
| | - Gerd Hause
- Biozentrum, Martin-Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany;
| | - Tim Kohlmann
- Department of Chemistry, Faculty of Natural Sciences II, Martin-Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany; (A.P.); (T.K.)
| | - Sven Rothemund
- Core Unit Peptide—Technologies, University Leipzig, 04103 Leipzig, Germany;
| | - Wolfgang H. Binder
- Department of Chemistry, Faculty of Natural Sciences II, Martin-Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany; (A.P.); (T.K.)
- Correspondence:
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14
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Roy M, Nath AK, Pal I, Dey SG. Second Sphere Interactions in Amyloidogenic Diseases. Chem Rev 2022; 122:12132-12206. [PMID: 35471949 DOI: 10.1021/acs.chemrev.1c00941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amyloids are protein aggregates bearing a highly ordered cross β structural motif, which may be functional but are mostly pathogenic. Their formation, deposition in tissues and consequent organ dysfunction is the central event in amyloidogenic diseases. Such protein aggregation may be brought about by conformational changes, and much attention has been directed toward factors like metal binding, post-translational modifications, mutations of protein etc., which eventually affect the reactivity and cytotoxicity of the associated proteins. Over the past decade, a global effort from different groups working on these misfolded/unfolded proteins/peptides has revealed that the amino acid residues in the second coordination sphere of the active sites of amyloidogenic proteins/peptides cause changes in H-bonding pattern or protein-protein interactions, which dramatically alter the structure and reactivity of these proteins/peptides. These second sphere effects not only determine the binding of transition metals and cofactors, which define the pathology of some of these diseases, but also change the mechanism of redox reactions catalyzed by these proteins/peptides and form the basis of oxidative damage associated with these amyloidogenic diseases. The present review seeks to discuss such second sphere modifications and their ramifications in the etiopathology of some representative amyloidogenic diseases like Alzheimer's disease (AD), type 2 diabetes mellitus (T2Dm), Parkinson's disease (PD), Huntington's disease (HD), and prion diseases.
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Affiliation(s)
- Madhuparna Roy
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Arnab Kumar Nath
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Ishita Pal
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Somdatta Ghosh Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
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15
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Sorokina SA, Shifrina ZB. Dendrimers as Antiamyloid Agents. Pharmaceutics 2022; 14:pharmaceutics14040760. [PMID: 35456594 PMCID: PMC9031116 DOI: 10.3390/pharmaceutics14040760] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/25/2022] [Accepted: 03/29/2022] [Indexed: 02/07/2023] Open
Abstract
Dendrimer–protein conjugates have significant prospects for biological applications. The complexation changes the biophysical behavior of both proteins and dendrimers. The dendrimers could influence the secondary structure of proteins, zeta-potential, distribution of charged regions on the surface, the protein–protein interactions, etc. These changes offer significant possibilities for the application of these features in nanotheranostics and biomedicine. Based on the dendrimer–protein interactions, several therapeutic applications of dendrimers have emerged. Thus, the formation of stable complexes retains the disordered proteins on the aggregation, which is especially important in neurodegenerative diseases. To clarify the origin of these properties and assess the efficiency of action, the mechanism of protein–dendrimer interaction and the nature and driving force of binding are considered in this review. The review outlines the antiamyloid activity of dendrimers and discusses the effect of dendrimer structures and external factors on their antiamyloid properties.
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16
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Production of Recombinant Alpha-Synuclein: Still No Standardized Protocol in Sight. Biomolecules 2022; 12:biom12020324. [PMID: 35204823 PMCID: PMC8869614 DOI: 10.3390/biom12020324] [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: 12/22/2021] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 01/27/2023] Open
Abstract
Synucleinopathies are a group of neurodegenerative diseases, characterized by the abnormal accumulation of the protein alpha-synuclein (aSyn). aSyn is an intrinsically disordered protein that can adopt different aggregation states, some of which may be associated with disease. Therefore, understanding the transitions between such aggregation states may be essential for deciphering the molecular underpinnings underlying synucleinopathies. Recombinant aSyn is routinely produced and purified from E. coli in many laboratories, and in vitro preparations of aSyn aggregated species became central for modeling neurodegeneration in cell and animal models. Thus, reproducibility and reliability of such studies largely depends on the purity and homogeneity of aSyn preparations across batches and between laboratories. A variety of different methods are in use to produce and purify aSyn, which we review in this commentary. We also show how extraction buffer composition can affect aSyn aggregation, emphasizing the importance of standardizing protocols to ensure reproducibility between different laboratories and studies, which are essential for advancing the field.
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17
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Mohapatra A, Bohara VS, Kumar S, Chaudhary N. Polymyxin B accelerates the α-synuclein aggregation. Biophys Chem 2021; 277:106628. [PMID: 34118773 DOI: 10.1016/j.bpc.2021.106628] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/25/2021] [Accepted: 06/01/2021] [Indexed: 10/21/2022]
Abstract
Parkinson's disease (PD) is a progressive neurodegenerative disorder caused by the loss of dopaminergic neurons. It is characterised by the deposition of insoluble α-synuclein aggregates in the brain. Constipation is a common PD-associated condition, and the treatment of constipation with certain antibiotics seem to improve the PD symptoms. Polymyxin B, a last resort drug in treating the life-threatening Gram-negative bacterial infections, is one such antibiotic. The administration of polymyxin B in PD patients is known to alleviate the movement disorder symptoms; the mechanism of action, however, remains unclear. We, therefore, wondered if polymyxin B could modulate the aggregation of α-synuclein. We find that the polymyxin B catalyses the aggregation of α-synuclein into amyloid fibrils. At equimolar polymyxin B concentration, the lag phase was reduced to around one-third of that in the absence of polymyxin B.
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Affiliation(s)
- Anshuman Mohapatra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, India
| | - Vijay Singh Bohara
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, India
| | - Sachin Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, India
| | - Nitin Chaudhary
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, India.
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18
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Daskalov A, El Mammeri N, Lends A, Shenoy J, Lamon G, Fichou Y, Saad A, Martinez D, Morvan E, Berbon M, Grélard A, Kauffmann B, Ferber M, Bardiaux B, Habenstein B, Saupe SJ, Loquet A. Structures of Pathological and Functional Amyloids and Prions, a Solid-State NMR Perspective. Front Mol Neurosci 2021; 14:670513. [PMID: 34276304 PMCID: PMC8280340 DOI: 10.3389/fnmol.2021.670513] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 05/26/2021] [Indexed: 12/20/2022] Open
Abstract
Infectious proteins or prions are a remarkable class of pathogens, where pathogenicity and infectious state correspond to conformational transition of a protein fold. The conformational change translates into the formation by the protein of insoluble amyloid aggregates, associated in humans with various neurodegenerative disorders and systemic protein-deposition diseases. The prion principle, however, is not limited to pathogenicity. While pathological amyloids (and prions) emerge from protein misfolding, a class of functional amyloids has been defined, consisting of amyloid-forming domains under natural selection and with diverse biological roles. Although of great importance, prion amyloid structures remain challenging for conventional structural biology techniques. Solid-state nuclear magnetic resonance (SSNMR) has been preferentially used to investigate these insoluble, morphologically heterogeneous aggregates with poor crystallinity. SSNMR methods have yielded a wealth of knowledge regarding the fundamentals of prion biology and have helped to solve the structures of several prion and prion-like fibrils. Here, we will review pathological and functional amyloid structures and will discuss some of the obtained structural models. We will finish the review with a perspective on integrative approaches combining solid-state NMR, electron paramagnetic resonance and cryo-electron microscopy, which can complement and extend our toolkit to structurally explore various facets of prion biology.
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Affiliation(s)
- Asen Daskalov
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Nadia El Mammeri
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Alons Lends
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | | | - Gaelle Lamon
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Yann Fichou
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Ahmad Saad
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Denis Martinez
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Estelle Morvan
- CNRS, INSERM, IECB, UMS 3033, University of Bordeaux, Pessac, France
| | - Melanie Berbon
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Axelle Grélard
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Brice Kauffmann
- CNRS, INSERM, IECB, UMS 3033, University of Bordeaux, Pessac, France
| | | | | | | | - Sven J. Saupe
- CNRS, IBGC UMR 5095, University of Bordeaux, Bordeaux, France
| | - Antoine Loquet
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
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19
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Pálmadóttir T, Malmendal A, Leiding T, Lund M, Linse S. Charge Regulation during Amyloid Formation of α-Synuclein. J Am Chem Soc 2021; 143:7777-7791. [PMID: 33998793 PMCID: PMC8161422 DOI: 10.1021/jacs.1c01925] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Indexed: 12/19/2022]
Abstract
Electrostatic interactions play crucial roles in protein function. Measuring pKa value perturbations upon complex formation or self-assembly of e.g. amyloid fibrils gives valuable information about the effect of electrostatic interactions in those processes. Site-specific pKa value determination by solution NMR spectroscopy is challenged by the high molecular weight of amyloid fibrils. Here we report a pH increase during fibril formation of α-synuclein, observed using three complementary experimental methods: pH electrode measurements in water; colorimetric changes of a fluorescent indicator; and chemical shift changes for histidine residues using solution state NMR spectroscopy. A significant pH increase was detected during fibril formation in water, on average by 0.9 pH units from 5.6 to 6.5, showing that protons are taken up during fibril formation. The pH upshift was used to calculate the average change in the apparent pKaave value of the acidic residues, which was found to increase by at least 1.1 unit due to fibril formation. Metropolis Monte Carlo simulations were performed on a comparable system that also showed a proton uptake due to fibril formation. Fibril formation moreover leads to a significant change in proton binding capacitance. Parallel studies of a mutant with five charge deletions in the C-terminal tail revealed a smaller pH increase due to fibril formation, and a smaller change (0.5 units on average) in the apparent pKaave values of the acidic residues. We conclude that the proton uptake during the fibril formation is connected to the high density of acidic residues in the C-terminal tail of α-synuclein.
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Affiliation(s)
- Tinna Pálmadóttir
- Department
of Biochemistry and Structural Biology, Lund University, P.O. Box 124, 221 00, Lund, Sweden
| | - Anders Malmendal
- Department
of Biochemistry and Structural Biology, Lund University, P.O. Box 124, 221 00, Lund, Sweden
- Department
of Science and Environment, Chemistry, Roskilde
University, Roskilde, Denmark
| | - Thom Leiding
- Department
of Biochemistry and Structural Biology, Lund University, P.O. Box 124, 221 00, Lund, Sweden
| | - Mikael Lund
- Department
of Theoretical Chemistry, Lund University, Lund, Sweden
- LINXS
- Lund Institute of Advanced Neutron and X-ray Science, Lund University, Lund, Sweden
| | - Sara Linse
- Department
of Biochemistry and Structural Biology, Lund University, P.O. Box 124, 221 00, Lund, Sweden
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20
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Rumancev C, Vöpel T, Stuhr S, Gundlach AR, Senkbeil T, Osterhoff M, Sprung M, Garamus VM, Ebbinghaus S, Rosenhahn A. In Cellulo Analysis of Huntingtin Inclusion Bodies by Cryogenic Nanoprobe SAXS. CHEMSYSTEMSCHEM 2021. [DOI: 10.1002/syst.202000050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Christoph Rumancev
- Analytical Chemistry – Biointerfaces Ruhr University Bochum Universitätsstr. 150 44780 Bochum Germany
| | - Tobias Vöpel
- Department of Physical Chemistry II Ruhr University Bochum Universitätsstr. 150 44780 Bochum Germany
| | - Susan Stuhr
- Analytical Chemistry – Biointerfaces Ruhr University Bochum Universitätsstr. 150 44780 Bochum Germany
| | - Andreas R. Gundlach
- Analytical Chemistry – Biointerfaces Ruhr University Bochum Universitätsstr. 150 44780 Bochum Germany
| | - Tobias Senkbeil
- Analytical Chemistry – Biointerfaces Ruhr University Bochum Universitätsstr. 150 44780 Bochum Germany
| | - Markus Osterhoff
- Deutsches Elektronen-Synchrotron DESY Notkestr. 85 22607 Hamburg Germany
| | - Michael Sprung
- Deutsches Elektronen-Synchrotron DESY Notkestr. 85 22607 Hamburg Germany
| | - Vasil M. Garamus
- Helmholtz-Zentrum Geesthacht: Centre for Materials and Coast Research Institute of Materials Research Max-Planck-Str. 1 21502 Geesthacht Germany
| | - Simon Ebbinghaus
- Department of Physical Chemistry II Ruhr University Bochum Universitätsstr. 150 44780 Bochum Germany
- Institute of Physical and Theoretical Chemistry TU Braunschweig Rebenring 56 38106 Braunschweig Germany
| | - Axel Rosenhahn
- Analytical Chemistry – Biointerfaces Ruhr University Bochum Universitätsstr. 150 44780 Bochum Germany
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21
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Berland L, Kim L, Abousaway O, Mines A, Mishra S, Clark L, Hofman P, Rashidian M. Nanobodies for Medical Imaging: About Ready for Prime Time? Biomolecules 2021; 11:637. [PMID: 33925941 PMCID: PMC8146371 DOI: 10.3390/biom11050637] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 12/13/2022] Open
Abstract
Recent advances in medical treatments have been revolutionary in shaping the management and treatment landscape of patients, notably cancer patients. Over the last decade, patients with diverse forms of locally advanced or metastatic cancer, such as melanoma, lung cancers, and many blood-borne malignancies, have seen their life expectancies increasing significantly. Notwithstanding these encouraging results, the present-day struggle with these treatments concerns patients who remain largely unresponsive, as well as those who experience severely toxic side effects. Gaining deeper insight into the cellular and molecular mechanisms underlying these variable responses will bring us closer to developing more effective therapeutics. To assess these mechanisms, non-invasive imaging techniques provide valuable whole-body information with precise targeting. An example of such is immuno-PET (Positron Emission Tomography), which employs radiolabeled antibodies to detect specific molecules of interest. Nanobodies, as the smallest derived antibody fragments, boast ideal characteristics for this purpose and have thus been used extensively in preclinical models and, more recently, in clinical early-stage studies as well. Their merit stems from their high affinity and specificity towards a target, among other factors. Furthermore, their small size (~14 kDa) allows them to easily disperse through the bloodstream and reach tissues in a reliable and uniform manner. In this review, we will discuss the powerful imaging potential of nanobodies, primarily through the lens of imaging malignant tumors but also touching upon their capability to image a broader variety of nonmalignant diseases.
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Affiliation(s)
- Léa Berland
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; (L.B.); (L.K.); (O.A.); (A.M.); (S.M.); (L.C.)
- Université Côte d’Azur, CNRS, INSERM, IRCAN, 06100 Nice, France;
| | - Lauren Kim
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; (L.B.); (L.K.); (O.A.); (A.M.); (S.M.); (L.C.)
- Department of Chemistry and Bioengineering, Harvard University, Cambridge, MA 02138, USA
| | - Omar Abousaway
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; (L.B.); (L.K.); (O.A.); (A.M.); (S.M.); (L.C.)
| | - Andrea Mines
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; (L.B.); (L.K.); (O.A.); (A.M.); (S.M.); (L.C.)
| | - Shruti Mishra
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; (L.B.); (L.K.); (O.A.); (A.M.); (S.M.); (L.C.)
| | - Louise Clark
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; (L.B.); (L.K.); (O.A.); (A.M.); (S.M.); (L.C.)
| | - Paul Hofman
- Université Côte d’Azur, CNRS, INSERM, IRCAN, 06100 Nice, France;
- Laboratory of Clinical and Experimental Pathology, FHU OncoAge, Nice Center Hospital, 06100 Nice, France
| | - Mohammad Rashidian
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; (L.B.); (L.K.); (O.A.); (A.M.); (S.M.); (L.C.)
- Department of Radiology, Harvard Medical School, Boston, MA 02115, USA
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22
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Chang J, Hwang HJ, Kim B, Choi YG, Park J, Park Y, Lee BS, Park H, Yoon MJ, Woo JS, Kim C, Park MS, Lee JB, Kim YK. TRIM28 functions as a negative regulator of aggresome formation. Autophagy 2021; 17:4231-4248. [PMID: 33783327 DOI: 10.1080/15548627.2021.1909835] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Selective recognition and elimination of misfolded polypeptides are crucial for protein homeostasis. When the ubiquitin-proteasome system is impaired, misfolded polypeptides tend to form small cytosolic aggregates and are transported to the aggresome and eventually eliminated by the autophagy pathway. Despite the importance of this process, the regulation of aggresome formation remains poorly understood. Here, we identify TRIM28/TIF1β/KAP1 (tripartite motif containing 28) as a negative regulator of aggresome formation. Direct interaction between TRIM28 and CTIF (cap binding complex dependent translation initiation factor) leads to inefficient aggresomal targeting of misfolded polypeptides. We also find that either treatment of cells with poly I:C or infection of the cells by influenza A viruses triggers the phosphorylation of TRIM28 at S473 in a way that depends on double-stranded RNA-activated protein kinase. The phosphorylation promotes association of TRIM28 with CTIF, inhibits aggresome formation, and consequently suppresses viral proliferation. Collectively, our data provide compelling evidence that TRIM28 is a negative regulator of aggresome formation.AbbreviationsBAG3: BCL2-associated athanogene 3; CTIF: CBC-dependent translation initiation factor; CED: CTIF-EEF1A1-DCTN1; DCTN1: dynactin subunit 1; EEF1A1: eukaryotic translation elongation factor 1 alpha 1; EIF2AK2: eukaryotic translation initiation factor 2 alpha kinase 2; HDAC6: histone deacetylase 6; IAV: influenza A virus; IP: immunoprecipitation; PLA: proximity ligation assay; polypeptidyl-puro: polypeptidyl-puromycin; qRT-PCR: quantitative reverse-transcription PCR; siRNA: small interfering RNA.
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Affiliation(s)
- Jeeyoon Chang
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul, Republic of Korea.,Division of Life Sciences, Korea University, Seoul, Republic of Korea
| | - Hyun Jung Hwang
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul, Republic of Korea.,Division of Life Sciences, Korea University, Seoul, Republic of Korea
| | - Byungju Kim
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Yeon-Gil Choi
- Division of Life Sciences, Korea University, Seoul, Republic of Korea
| | - Joori Park
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul, Republic of Korea.,Division of Life Sciences, Korea University, Seoul, Republic of Korea
| | - Yeonkyoung Park
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul, Republic of Korea.,Division of Life Sciences, Korea University, Seoul, Republic of Korea
| | - Ban Seok Lee
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul, Republic of Korea.,Division of Life Sciences, Korea University, Seoul, Republic of Korea
| | - Heedo Park
- Department of Microbiology, Institute for Viral Diseases, College of Medicine, Korea University, Seoul, 02841, Republic of Korea
| | - Min Ji Yoon
- Division of Life Sciences, Korea University, Seoul, Republic of Korea
| | - Jae-Sung Woo
- Division of Life Sciences, Korea University, Seoul, Republic of Korea
| | - Chungho Kim
- Division of Life Sciences, Korea University, Seoul, Republic of Korea
| | - Man-Seong Park
- Department of Microbiology, Institute for Viral Diseases, College of Medicine, Korea University, Seoul, 02841, Republic of Korea
| | - Jong-Bong Lee
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea.,School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, 37673, Republic of Korea
| | - Yoon Ki Kim
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul, Republic of Korea.,Division of Life Sciences, Korea University, Seoul, Republic of Korea
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23
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Liu EN, Park G, Nohara J, Guo Z. Effect of spin labelling on the aggregation kinetics of yeast prion protein Ure2. ROYAL SOCIETY OPEN SCIENCE 2021; 8:201747. [PMID: 33959337 PMCID: PMC8074925 DOI: 10.1098/rsos.201747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 02/10/2021] [Indexed: 06/12/2023]
Abstract
Amyloid formation is involved in a wide range of neurodegenerative diseases including Alzheimer's and prion diseases. Structural understanding of the amyloid is critical to delineate the mechanism of aggregation and its pathological spreading. Site-directed spin labelling has emerged as a powerful structural tool in the studies of amyloid structures and provided structural evidence for the parallel in-register β-sheet structure for a wide range of amyloid proteins. It is generally accepted that spin labelling does not disrupt the structure of the amyloid fibrils, the end product of protein aggregation. The effect on the rate of protein aggregation, however, has not been well characterized. Here, we employed a scanning mutagenesis approach to study the effect of spin labelling on the aggregation rate of 79 spin-labelled variants of the Ure2 prion domain. The aggregation of Ure2 protein is the basis of yeast prion [URE3]. We found that all spin-labelled Ure2 mutants aggregated within the experimental timeframe of 15 to 40 h. Among the 79 spin-labelled positions, only five residue sites (N23, N27, S33, I35 and G42) showed a dramatic delay in the aggregation rate as a result of spin labelling. These positions may be important for fibril nucleation, a rate-limiting step in aggregation. Importantly, spin labelling at most of the sites had a muted effect on Ure2 aggregation kinetics, showing a general tolerance of spin labelling in protein aggregation studies.
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Affiliation(s)
- Emilie N. Liu
- Department of Neurology, Brain Research Institute, Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | - Giovanna Park
- Department of Neurology, Brain Research Institute, Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | - Junsuke Nohara
- Department of Neurology, Brain Research Institute, Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | - Zhefeng Guo
- Department of Neurology, Brain Research Institute, Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
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24
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Lux J, Heyn TR, Kampen I, Schwarz K, Keppler JK, Steffen-Heins A. Amyloid aggregation of spin-labeled β-lactoglobulin. Part I: Influence of spin labeling on amyloid aggregation. Food Hydrocoll 2021. [DOI: 10.1016/j.foodhyd.2020.106178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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25
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Bhak G, Méndez-Ardoy A, Escobedo A, Salvatella X, Montenegro J. An Adhesive Peptide from the C-Terminal Domain of α-Synuclein for Single-Layer Adsorption of Nanoparticles onto Substrates. Bioconjug Chem 2020; 31:2759-2766. [PMID: 33170662 DOI: 10.1021/acs.bioconjchem.0c00544] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The two-dimensional (2D) homogeneous assembly of nanoparticle monolayer arrays onto a broad range of substrates constitutes an important challenge for chemistry, nanotechnology, and material science. α-Synuclein (αS) is an intrinsically disordered protein associated with neuronal protein complexes and has a high degree of structural plasticity and chaperone activity. The C-terminal domain of αS has been linked to the noncovalent interactions of this protein with biological targets and the activity of αS in presynaptic connections. Herein, we have systematically studied peptide fragments of the chaperone-active C-terminal sequence of αS and identified a 17-residue peptide that preserves the versatile binding nature of αS. Attachment of this short peptide to gold nanoparticles afforded colloidally stable nanoparticle suspensions that allowed the homogeneous 2D adhesion of the conjugates onto a wide variety of surfaces, including the formation of crystalline nanoparticle superlattices. The peptide sequence and the strategy reported here describe a new adhesive molecule for the controlled monolayer adhesion of metal nanoparticles and sets a stepping-stone toward the potential application of the adhesive properties of αS.
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Affiliation(s)
- Ghibom Bhak
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Alejandro Méndez-Ardoy
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Albert Escobedo
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain.,Joint BSC-IRB Research Programme in Computational Biology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Xavier Salvatella
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain.,Joint BSC-IRB Research Programme in Computational Biology, Baldiri Reixac 10, 08028 Barcelona, Spain.,ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
| | - Javier Montenegro
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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Anomalous Salt Dependence Reveals an Interplay of Attractive and Repulsive Electrostatic Interactions in α-synuclein Fibril Formation. QRB DISCOVERY 2020. [PMID: 37528959 PMCID: PMC10392692 DOI: 10.1017/qrd.2020.7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Abstractα-Synuclein (α-syn) is an intrinsically disordered protein with a highly asymmetric charge distribution, whose aggregation is linked to Parkinson’s disease. The effect of ionic strength was investigated at mildly acidic pH (5.5) in the presence of catalytic surfaces in the form of α-syn seeds or anionic lipid vesicles using thioflavin T fluorescence measurements. Similar trends were observed with both surfaces: increasing ionic strength reduced the rate of α-syn aggregation although the surfaces as well as α-syn have a net negative charge at pH 5.5. This anomalous salt dependence implies that short-range attractive electrostatic interactions are critical for secondary nucleation as well as heterogeneous primary nucleation. Such interactions were confirmed in Monte Carlo simulations of α-syn monomers interacting with surface-grafted C-terminal tails, and found to be weakened in the presence of salt. Thus, nucleation of α-syn aggregation depends critically on an attractive electrostatic component that is screened by salt to the extent that it outweighs the screening of the long-range repulsion between negatively charged monomers and negative surfaces. Interactions between the positively charged N-termini of α-syn monomers on the one hand, and the negatively C-termini of α-syn on fibrils or vesicles surfaces on the other hand, are thus critical for nucleation.
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Palomino-Hernandez O, Buratti FA, Sacco PS, Rossetti G, Carloni P, Fernandez CO. Role of Tyr-39 for the Structural Features of α-Synuclein and for the Interaction with a Strong Modulator of Its Amyloid Assembly. Int J Mol Sci 2020; 21:ijms21145061. [PMID: 32709107 PMCID: PMC7404028 DOI: 10.3390/ijms21145061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/02/2020] [Accepted: 07/13/2020] [Indexed: 12/03/2022] Open
Abstract
Recent studies suggest that Tyr-39 might play a critical role for both the normal function and the pathological dysfunction of α-synuclein (αS), an intrinsically disordered protein involved in Parkinson’s disease. We perform here a comparative analysis between the structural features of human αS and its Y39A, Y39F, and Y39L variants. By the combined application of site-directed mutagenesis, biophysical techniques, and enhanced sampling molecular simulations, we show that removing aromatic functionality at position 39 of monomeric αS leads to protein variants populating more compact conformations, conserving its disordered nature and secondary structure propensities. Contrasting with the subtle changes induced by mutations on the protein structure, removing aromaticity at position 39 impacts strongly on the interaction of αS with the potent amyloid inhibitor phthalocyanine tetrasulfonate (PcTS). Our findings further support the role of Tyr-39 in forming essential inter and intramolecular contacts that might have important repercussions for the function and the dysfunction of αS.
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Affiliation(s)
- Oscar Palomino-Hernandez
- Computational Biomedicine, Institute for Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations (IAS-5), Forschungszentrum Jülich, 52425 Jülich, Germany; (O.P.-H.); (G.R.)
- Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen, 52425 Aachen, Germany
- Computation-Based Science and Technology Research Center, The Cyprus Institute, 2121 Nicosia, Cyprus
- Institute of Life Science, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Fiamma A. Buratti
- Max Planck Laboratory for Structural Biology, Chemistry and Molecular Biophysics of Rosario (MPLbioR, UNR-MPIbpC) and Instituto de Investigaciones para el Descubrimiento de Fármacos de Rosario (IIDEFAR, UNR-CONICET), Universidad Nacional de Rosario, S2002LRK Rosario, Argentina; (F.A.B.); (P.S.S.)
| | - Pamela S. Sacco
- Max Planck Laboratory for Structural Biology, Chemistry and Molecular Biophysics of Rosario (MPLbioR, UNR-MPIbpC) and Instituto de Investigaciones para el Descubrimiento de Fármacos de Rosario (IIDEFAR, UNR-CONICET), Universidad Nacional de Rosario, S2002LRK Rosario, Argentina; (F.A.B.); (P.S.S.)
| | - Giulia Rossetti
- Computational Biomedicine, Institute for Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations (IAS-5), Forschungszentrum Jülich, 52425 Jülich, Germany; (O.P.-H.); (G.R.)
- Department of Oncology, Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation University Hospital Aachen, RWTH Aachen University, Pauwelsstraße 30, 52074 Aachen, Germany
- Jülich Supercomputing Center (JSC), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Paolo Carloni
- Computational Biomedicine, Institute for Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations (IAS-5), Forschungszentrum Jülich, 52425 Jülich, Germany; (O.P.-H.); (G.R.)
- Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen, 52425 Aachen, Germany
- Institute for Neuroscience and Medicine (INM-11) Forschungszentrum Jülich, 52425 Jülich, Germany
- Correspondence: (P.C.); (C.O.F.); Tel.: +54-341-4237868 (ext. 752) (C.O.F)
| | - Claudio O. Fernandez
- Max Planck Laboratory for Structural Biology, Chemistry and Molecular Biophysics of Rosario (MPLbioR, UNR-MPIbpC) and Instituto de Investigaciones para el Descubrimiento de Fármacos de Rosario (IIDEFAR, UNR-CONICET), Universidad Nacional de Rosario, S2002LRK Rosario, Argentina; (F.A.B.); (P.S.S.)
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
- Correspondence: (P.C.); (C.O.F.); Tel.: +54-341-4237868 (ext. 752) (C.O.F)
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EPR of site-directed spin-labeled proteins: A powerful tool to study structural flexibility. Arch Biochem Biophys 2020; 684:108323. [DOI: 10.1016/j.abb.2020.108323] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 02/17/2020] [Accepted: 02/24/2020] [Indexed: 12/20/2022]
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Sengupta U, Puangmalai N, Bhatt N, Garcia S, Zhao Y, Kayed R. Polymorphic α-Synuclein Strains Modified by Dopamine and Docosahexaenoic Acid Interact Differentially with Tau Protein. Mol Neurobiol 2020; 57:2741-2765. [PMID: 32350746 PMCID: PMC7253398 DOI: 10.1007/s12035-020-01913-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 03/30/2020] [Indexed: 12/22/2022]
Abstract
The pathological hallmark of synucleinopathies, including Parkinson’s disease (PD), is the aggregation of α-synuclein (α-Syn) protein. Even so, tau protein pathology is abundantly found in these diseases. Both α-Syn and tau can exist as polymorphic aggregates, a phenomenon that has been widely studied, mostly in their fibrillar assemblies. We have previously discovered that in addition to α-Syn oligomers, oligomeric tau is also present in the brain tissues of patients with PD and dementia with Lewy bodies (DLB). However, the effect of interaction between polymorphic α-Syn oligomers and tau has not been scrupulously studied. Here, we have explored the structural and functional diversity of distinct α-Syn oligomers, prepared by modifying the protein with dopamine (DA) and docosahexaenoic acid (DHA). The two α-Syn oligomers differed in aggregate size, conformation, sensitivity to proteinase K digestion, tryptic digestion, and toxicity, suggesting them as distinct α-Syn oligomeric strains. We examined their internalization mechanisms in primary neurons and seeding propensity in inducing α-Syn aggregation. Using a combined approach of molecular and cellular techniques, we observed that the tau aggregates cross-seeded with the individual α-Syn oligomeric strains differed in their biochemical and biological properties, suggesting two distinct tau strains. The tau aggregate cross-seeded with the DA-modified α-Syn oligomeric strain possessed a potent intracellular tau seeding propensity. This study provides a comprehensive analysis of unique strain-specific interaction between oligomeric α-Syn and tau. Furthermore, this study allows us to speculate that distinct α-Syn-tau interactions inducing tau aggregation might be an underlying mechanism of neurodegeneration in PD.
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Affiliation(s)
- Urmi Sengupta
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, USA
- Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, USA
| | - Nicha Puangmalai
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, USA
- Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, USA
| | - Nemil Bhatt
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, USA
- Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, USA
| | - Stephanie Garcia
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, USA
- Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, USA
| | - Yingxin Zhao
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, USA
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, USA
| | - Rakez Kayed
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, USA.
- Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, USA.
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New insights on the structure of alpha-synuclein fibrils using cryo-electron microscopy. Curr Opin Neurobiol 2020; 61:89-95. [DOI: 10.1016/j.conb.2020.01.014] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 01/24/2020] [Accepted: 01/27/2020] [Indexed: 01/08/2023]
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Maciążek-Jurczyk M, Janas K, Pożycka J, Szkudlarek A, Rogóż W, Owczarzy A, Kulig K. Human Serum Albumin Aggregation/Fibrillation and its Abilities to Drugs Binding. Molecules 2020; 25:molecules25030618. [PMID: 32023900 PMCID: PMC7038104 DOI: 10.3390/molecules25030618] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 01/23/2020] [Accepted: 01/29/2020] [Indexed: 02/07/2023] Open
Abstract
Human serum albumin (HSA) is a protein that transports neutral and acid ligands in the organism. Depending on the environment's pH conditions, HSA can take one of the five isomeric forms that change its conformation. HSA can form aggregates resembling those in vitro formed from amyloid at physiological pH (neutral and acidic). Not surprisingly, the main goal of the research was aggregation/fibrillation of HSA, the study of the physicochemical properties of formed amyloid fibrils using thioflavin T (ThT) and the analysis of ligand binding to aggregated/fibrillated albumin in the presence of dansyl-l-glutamine (dGlu), dansyl-l-proline (dPro), phenylbutazone (Phb) and ketoprofen (Ket). Solutions of human serum albumin, both non-modified and modified, were examined with the use of fluorescence, absorption and circular dichroism (CD) spectroscopy. The experiments conducted allowed observation of changes in the structure of incubated HSA (HSAINC) in relation to nonmodified HSA (HSAFR). The formed aggregates/fibrillation differed in structure from HSA monomers and dimers. Based on CD spectroscopy, previously absent βstructural constructs have been registered. Whereas, using fluorescence spectroscopy, the association constants differing for fresh and incubated HSA solutions in the presence of dansyl-amino acids and markers for binding sites were calculated and allowed observation of the conformational changes in HSA molecule.
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Affiliation(s)
- Małgorzata Maciążek-Jurczyk
- Department of Physical Pharmacy, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, 40-055 Katowice, Poland; (K.J.); (J.P.); (A.S.); (W.R.); (K.K.)
- Correspondence: ; Tel.: +48-32-364-1582
| | - Kamil Janas
- Department of Physical Pharmacy, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, 40-055 Katowice, Poland; (K.J.); (J.P.); (A.S.); (W.R.); (K.K.)
| | - Jadwiga Pożycka
- Department of Physical Pharmacy, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, 40-055 Katowice, Poland; (K.J.); (J.P.); (A.S.); (W.R.); (K.K.)
| | - Agnieszka Szkudlarek
- Department of Physical Pharmacy, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, 40-055 Katowice, Poland; (K.J.); (J.P.); (A.S.); (W.R.); (K.K.)
| | - Wojciech Rogóż
- Department of Physical Pharmacy, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, 40-055 Katowice, Poland; (K.J.); (J.P.); (A.S.); (W.R.); (K.K.)
| | - Aleksandra Owczarzy
- Independent Public Clinical Hospital No. 1 in Zabrze, Medical University of Silesia, 40-055 Katowice, Poland;
| | - Karolina Kulig
- Department of Physical Pharmacy, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, 40-055 Katowice, Poland; (K.J.); (J.P.); (A.S.); (W.R.); (K.K.)
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Izmailov SA, Rabdano SO, Hasanbasri Z, Podkorytov IS, Saxena S, Skrynnikov NR. Structural and dynamic origins of ESR lineshapes in spin-labeled GB1 domain: the insights from spin dynamics simulations based on long MD trajectories. Sci Rep 2020; 10:957. [PMID: 31969574 PMCID: PMC6976580 DOI: 10.1038/s41598-019-56750-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 12/06/2019] [Indexed: 12/04/2022] Open
Abstract
Site-directed spin labeling (SDSL) ESR is a valuable tool to probe protein systems that are not amenable to characterization by x-ray crystallography, NMR or EM. While general principles that govern the shape of SDSL ESR spectra are known, its precise relationship with protein structure and dynamics is still not fully understood. To address this problem, we designed seven variants of GB1 domain bearing R1 spin label and recorded the corresponding MD trajectories (combined length 180 μs). The MD data were subsequently used to calculate time evolution of the relevant spin density matrix and thus predict the ESR spectra. The simulated spectra proved to be in good agreement with the experiment. Further analysis confirmed that the spectral shape primarily reflects the degree of steric confinement of the R1 tag and, for the well-folded protein such as GB1, offers little information on local backbone dynamics. The rotameric preferences of R1 side chain are determined by the type of the secondary structure at the attachment site. The rotameric jumps involving dihedral angles χ1 and χ2 are sufficiently fast to directly influence the ESR lineshapes. However, the jumps involving multiple dihedral angles tend to occur in (anti)correlated manner, causing smaller-than-expected movements of the R1 proxyl ring. Of interest, ESR spectra of GB1 domain with solvent-exposed spin label can be accurately reproduced by means of Redfield theory. In particular, the asymmetric character of the spectra is attributable to Redfield-type cross-correlations. We envisage that the current MD-based, experimentally validated approach should lead to a more definitive, accurate picture of SDSL ESR experiments.
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Affiliation(s)
- Sergei A Izmailov
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - Sevastyan O Rabdano
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - Zikri Hasanbasri
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Ivan S Podkorytov
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Nikolai R Skrynnikov
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, 199034, Russia.
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA.
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Shinzato T, Sato R, Suzuki K, Tomioka S, Sogawa H, Shulga S, Blume Y, Kurita N. Proposal of therapeutic curcumin derivatives for Alzheimer’s disease based on ab initio molecular simulations. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2019.136883] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Computational prediction and redesign of aberrant protein oligomerization. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 169:43-83. [DOI: 10.1016/bs.pmbts.2019.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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A KLVFFAE-Derived Peptide Probe for Detection of Alpha-Synuclein Fibrils. Appl Biochem Biotechnol 2019; 190:1411-1424. [PMID: 31776941 DOI: 10.1007/s12010-019-03197-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 11/11/2019] [Indexed: 12/27/2022]
Abstract
Aggregation of an amyloid protein, α-synuclein (αS), is a critical step in the neurodegenerative pathway of Parkinson's diseases (PD). Specific detection of amyloid conformers (i.e., monomers, oligomers, and fibrils) produced during αS aggregation is critical in better understanding a molecular basis of PD and developing a diagnostic tool. While various molecular probes are available for detection of αS fibrils, which may serve as a reservoir of toxic αS aggregate forms, these probes suffer from limited conformer-specificity and operational flexibility. In the present study, we explored the potential of non-self-aggregating peptides derived from the highly aggregation-prone KLVFFAE region of an amyloid protein, β-amyloid, as molecular probes for αS aggregates. We show that of the four peptides tested (KLVFWAK, ELVFWAE, and their C-terminal capping variants, all of which were attached with fluorescein isothiocyanate at their respective N-termini), KLVFWAK with C-terminal capping was selectively bound to αS fibrils over monomers and oligomers and readily used for monitoring αS fibrilization. Our analyses suggest that binding of the peptide to αS fibrils is mediated by both electrostatic and hydrophobic interactions. We anticipate that our peptide can readily be optimized for conformer-specificity and operational flexibility. Overall, this study presents the creation of a KLVFFAE-based molecular probe for αS fibrils and demonstrates fine-tuning of its conformer-specificity by terminal mutations and capping.
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Lv G, Kumar A, Huang Y, Eliezer D. A Protofilament-Protofilament Interface in the Structure of Mouse α-Synuclein Fibrils. Biophys J 2019; 114:2811-2819. [PMID: 29925018 DOI: 10.1016/j.bpj.2018.05.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 05/04/2018] [Accepted: 05/07/2018] [Indexed: 12/11/2022] Open
Abstract
Fibrillar α-synuclein (AS) is the major component of Lewy bodies, the pathological hallmark of Parkinson's disease. Using solid-state nuclear magnetic resonance (ssNMR), we previously reported a structural characterization of mouse AS (mAS) fibrils and found that the secondary structure of the mAS fibrils is highly similar to a form of human AS (hAS) fibrils. Recently, a three-dimensional structure of these same hAS fibrils was determined by ssNMR and scanning transmission electron microscopy. Using medium- and long-range distance restraints obtained from ssNMR spectra, we found that the single protofilament structure of mAS fibrils is also similar to that of the hAS fibrils. However, residue-specific water accessibility of mAS fibrils probed by water polarization transfer ssNMR measurements indicates that residues S42-T44 and G84-V95 are largely protected from water even though they are located at the edge of the protofilament. Some of the corresponding resonances also exhibit peak doubling. These observations suggest that these residues may be involved in, to our knowledge, a novel protofilament-protofilament interface. We propose a structural model of mAS fibrils that incorporates this dimer interface.
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Affiliation(s)
- Guohua Lv
- Department of Biochemistry, Weill Cornell Medical College, New York, New York; Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany.
| | - Ashutosh Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Mumbai, India; Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany
| | - Yun Huang
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - David Eliezer
- Department of Biochemistry, Weill Cornell Medical College, New York, New York.
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Iadanza MG, Jackson MP, Hewitt EW, Ranson NA, Radford SE. A new era for understanding amyloid structures and disease. Nat Rev Mol Cell Biol 2019; 19:755-773. [PMID: 30237470 DOI: 10.1038/s41580-018-0060-8] [Citation(s) in RCA: 568] [Impact Index Per Article: 113.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The aggregation of proteins into amyloid fibrils and their deposition into plaques and intracellular inclusions is the hallmark of amyloid disease. The accumulation and deposition of amyloid fibrils, collectively known as amyloidosis, is associated with many pathological conditions that can be associated with ageing, such as Alzheimer disease, Parkinson disease, type II diabetes and dialysis-related amyloidosis. However, elucidation of the atomic structure of amyloid fibrils formed from their intact protein precursors and how fibril formation relates to disease has remained elusive. Recent advances in structural biology techniques, including cryo-electron microscopy and solid-state NMR spectroscopy, have finally broken this impasse. The first near-atomic-resolution structures of amyloid fibrils formed in vitro, seeded from plaque material and analysed directly ex vivo are now available. The results reveal cross-β structures that are far more intricate than anticipated. Here, we describe these structures, highlighting their similarities and differences, and the basis for their toxicity. We discuss how amyloid structure may affect the ability of fibrils to spread to different sites in the cell and between organisms in a prion-like manner, along with their roles in disease. These molecular insights will aid in understanding the development and spread of amyloid diseases and are inspiring new strategies for therapeutic intervention.
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Affiliation(s)
- Matthew G Iadanza
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Matthew P Jackson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Eric W Hewitt
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.
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Abstract
Yeast prions have become important models for the study of the basic mechanisms underlying human amyloid diseases. Yeast prions are pathogenic (unlike the [Het-s] prion of Podospora anserina), and most are amyloid-based with the same in-register parallel β-sheet architecture as most of the disease-causing human amyloids studied. Normal yeast cells eliminate the large majority of prion variants arising, and several anti-prion/anti-amyloid systems that eliminate them have been identified. It is likely that mammalian cells also have anti-amyloid systems, which may be useful in the same way humoral, cellular, and innate immune systems are used to treat or prevent bacterial and viral infections.
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Affiliation(s)
- Reed B Wickner
- Laboratory of Biochemistry and Genetics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892-0830.
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Ningthoujam DS, Mukherjee S, Devi LJ, Singh ES, Tamreihao K, Khunjamayum R, Banerjee S, Mukhopadhyay D. In vitro degradation of β-amyloid fibrils by microbial keratinase. ALZHEIMER'S & DEMENTIA (NEW YORK, N. Y.) 2019; 5:154-163. [PMID: 31193333 PMCID: PMC6527806 DOI: 10.1016/j.trci.2019.03.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
INTRODUCTION Amyloid fibrils are misfolded, protease-resistant forms of normal proteins. They are infectious such as prions or noninfectious such as β-amyloid (Aβ) fibrils causing Alzheimer's disease (AD). Prions and amyloids are structurally similar, possessing cross β-pleated sheet-like structures. As microbial keratinase could degrade prions, we tested keratinase activity on Aβ fibrils. METHODS Lysozyme treated with urea generates Aβ fibrils demonstrated by immunoblotting with anti-Aβ antibody, high-performance liquid chromatography, and Congo red absorption spectroscopy. Two keratinases, Ker1 and Ker2, were purified from an actinomycete Amycolatopsis sp. MBRL 40 and incubated with Aβ fibrils. RESULTS Soluble Ker1 and Ker1 reconstituted on neutral/cationic liposomes degraded Aβ fibrils efficiently. Ker 2 was less potent. DISCUSSION Drugs that target AD inhibit acetylcholinesterase or formation of Aβ fibrils and downstream effects. These drugs have side effects and do not benefit globally in cognition. Keratinases are novel molecules for drug development against AD.
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Affiliation(s)
- Debananda S. Ningthoujam
- Department of Biochemistry, Advanced Level State Biotech Hub, Microbial Biotechnology Research Laboratory, Manipur University, Imphal, Manipur, India
| | - Saikat Mukherjee
- Department of Biochemistry, Advanced Level State Biotech Hub, Microbial Biotechnology Research Laboratory, Manipur University, Imphal, Manipur, India
| | - Laishram Jaya Devi
- Department of Biochemistry, Advanced Level State Biotech Hub, Microbial Biotechnology Research Laboratory, Manipur University, Imphal, Manipur, India
| | - Elangbam Shanta Singh
- Department of Biochemistry, Advanced Level State Biotech Hub, Microbial Biotechnology Research Laboratory, Manipur University, Imphal, Manipur, India
| | - Keishing Tamreihao
- Department of Biochemistry, Advanced Level State Biotech Hub, Microbial Biotechnology Research Laboratory, Manipur University, Imphal, Manipur, India
| | - Rakhi Khunjamayum
- Department of Biochemistry, Advanced Level State Biotech Hub, Microbial Biotechnology Research Laboratory, Manipur University, Imphal, Manipur, India
| | - Sumita Banerjee
- Department of Oral Pathology, Dental College, Regional Institute of Medical Sciences, Imphal, Manipur, India
| | - Debashis Mukhopadhyay
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, West Bengal, India
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Alza NP, Iglesias González PA, Conde MA, Uranga RM, Salvador GA. Lipids at the Crossroad of α-Synuclein Function and Dysfunction: Biological and Pathological Implications. Front Cell Neurosci 2019; 13:175. [PMID: 31118888 PMCID: PMC6504812 DOI: 10.3389/fncel.2019.00175] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/11/2019] [Indexed: 12/15/2022] Open
Abstract
Since its discovery, the study of the biological role of α-synuclein and its pathological implications has been the subject of increasing interest. The propensity to adopt different conformational states governing its aggregation and fibrillation makes this small 14-kDa cytosolic protein one of the main etiologic factors associated with degenerative disorders known as synucleinopathies. The structure, function, and toxicity of α-synuclein and the possibility of different therapeutic approaches to target the protein have been extensively investigated and reviewed. One intriguing characteristic of α-synuclein is the different ways in which it interacts with lipids. Though in-depth studies have been carried out in this field, the information they have produced is puzzling and the precise role of lipids in α-synuclein biology and pathology and vice versa is still largely unknown. Here we provide an overview and discussion of the main findings relating to α-synuclein/lipid interaction and its involvement in the modulation of lipid metabolism and signaling.
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Affiliation(s)
- Natalia P Alza
- Instituto de Investigaciones Bioquímicas de Bahía Blanca, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Sur, Bahía Blanca, Argentina.,Departamento de Química, Universidad Nacional del Sur, Bahía Blanca, Argentina
| | - Pablo A Iglesias González
- Instituto de Investigaciones Bioquímicas de Bahía Blanca, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Sur, Bahía Blanca, Argentina
| | - Melisa A Conde
- Instituto de Investigaciones Bioquímicas de Bahía Blanca, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Sur, Bahía Blanca, Argentina.,Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur, Bahía Blanca, Argentina
| | - Romina M Uranga
- Instituto de Investigaciones Bioquímicas de Bahía Blanca, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Sur, Bahía Blanca, Argentina.,Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur, Bahía Blanca, Argentina
| | - Gabriela A Salvador
- Instituto de Investigaciones Bioquímicas de Bahía Blanca, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Sur, Bahía Blanca, Argentina.,Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur, Bahía Blanca, Argentina
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41
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α-Synuclein misfolding and aggregation: Implications in Parkinson's disease pathogenesis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:890-908. [PMID: 30853581 DOI: 10.1016/j.bbapap.2019.03.001] [Citation(s) in RCA: 232] [Impact Index Per Article: 46.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 03/03/2019] [Accepted: 03/05/2019] [Indexed: 12/21/2022]
Abstract
α-Synuclein (α-Syn) has been extensively studied for its structural and biophysical properties owing to its pathophysiological role in Parkinson's disease (PD). Lewy bodies and Lewy neurites are the pathological hallmarks of PD and contain α-Syn aggregates as their major component. It was therefore hypothesized that α-Syn aggregation is actively associated with PD pathogenesis. The central role of α-Syn aggregation in PD is further supported by the identification of point mutations in α-Syn protein associated with rare familial forms of PD. However, the correlation between aggregation propensities of α-Syn mutants and their association with PD phenotype is not straightforward. Recent evidence suggested that oligomers, formed during the initial stages of aggregation, are the potent neurotoxic species causing cell death in PD. However, the heterogeneous and unstable nature of these oligomers limit their detailed characterization. α-Syn fibrils, on the contrary, are shown to be the infectious agents and propagate in a prion-like manner. Although α-Syn is an intrinsically disordered protein, it exhibits remarkable conformational plasticity by adopting a range of structural conformations under different environmental conditions. In this review, we focus on the structural and functional aspects of α-Syn and role of potential factors that may contribute to the underlying mechanism of synucleinopathies. This information will help to identify novel targets and develop specific therapeutic strategies to combat Parkinson's and other protein aggregation related neurodegenerative diseases.
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Oliveri V. Toward the discovery and development of effective modulators of α-synuclein amyloid aggregation. Eur J Med Chem 2019; 167:10-36. [PMID: 30743095 DOI: 10.1016/j.ejmech.2019.01.045] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 01/21/2019] [Accepted: 01/21/2019] [Indexed: 12/17/2022]
Abstract
A host of human diseases, including Parkinson's disease and Dementia with Lewy bodies, are suspected to be directly linked to protein aggregation. Amyloid protein aggregates and oligomeric intermediates of α-synuclein are observed in synucleinopathies and considered to be mediators of cellular toxicity. Hence, α-synuclein has seen as one of the leading and most compelling targets and is receiving a great deal of attention from researchers. Nevertheless, there is no neuroprotective approach directed toward Parkinson's disease or other synucleinopathies so far. In this review, we summarize the available data concerning inhibitors of α-synuclein aggregation and their advancing towards clinical use. The compounds are grouped according to their chemical structures, providing respective insights into their mechanism of action, pharmacology, and pharmacokinetics. Overall, shared structure-activity elements are emerging, as well as specific binding modes related to the ability of the modulators to establish hydrophobic and hydrogen bonds interactions with the protein. Some molecules with encouraging in vivo data support the possibility of translation to the clinic.
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Affiliation(s)
- Valentina Oliveri
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, viale A. Doria 6, 95125, Catania, Italy.
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43
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Flynn JD, Jiang Z, Lee JC. Segmental 13 C-Labeling and Raman Microspectroscopy of α-Synuclein Amyloid Formation. Angew Chem Int Ed Engl 2018; 57:17069-17072. [PMID: 30371967 PMCID: PMC6688611 DOI: 10.1002/anie.201809865] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/05/2018] [Indexed: 01/05/2023]
Abstract
Mapping conformational changes of α-synuclein (α-syn) from soluble, unstructured monomers to β-sheet- rich aggregates is crucial towards understanding amyloid formation. Raman microspectroscopy is now used to spatially resolve conformational heterogeneity of amyloid aggregates and monitor amyloid formation of segmentally 13 C-labeled α-syn in real-time. As the 13 C-isotope shifts the amide-I stretching frequency to lower energy, the ligated construct, 13 C1-8612 CS87C-140 -α-syn, exhibits two distinct bands allowing for simultaneous detection of secondary structural changes in N-terminal 1-86 and C-terminal 87-140 residues. The disordered-to-β-sheet conformational change is first observed for the N-terminal followed by the C-terminal region. Finally, Raman spectroscopic changes occurred prior to Thioflavin T fluorescence enhancement, indicating that the amide-I band is a superior probe of amyloid formation.
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Affiliation(s)
- Jessica D. Flynn
- National Heart, Lung, and Blood Institute, National
Institutes of Health, Bethesda, MD 20892, United States
| | - Zhiping Jiang
- National Heart, Lung, and Blood Institute, National
Institutes of Health, Bethesda, MD 20892, United States
| | - Jennifer C. Lee
- National Heart, Lung, and Blood Institute, National
Institutes of Health, Bethesda, MD 20892, United States
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Bondarev SA, Bondareva OV, Zhouravleva GA, Kajava AV. BetaSerpentine: a bioinformatics tool for reconstruction of amyloid structures. Bioinformatics 2018; 34:599-608. [PMID: 29444233 DOI: 10.1093/bioinformatics/btx629] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 10/03/2017] [Indexed: 11/12/2022] Open
Abstract
Motivation Numerous experimental studies have suggested that polypeptide chains of large amyloidogenic regions zig-zag in β-serpentine arrangements. These β-serpentines are stacked axially and form the superpleated β-structure. Despite this progress in the understanding of amyloid folds, the determination of their 3D structure at the atomic level is still a problem due to the polymorphism of these fibrils and incompleteness of experimental structural data. Today, the way to get insight into the atomic structure of amyloids is a combination of experimental studies with bioinformatics. Results We developed a computer program BetaSerpentine that reconstructs β-serpentine arrangements from individual β-arches predicted by ArchCandy program and ranks them in order of preference. It was shown that the BetaSerpentine program in combination with the experimental data can be used to gain insight into the detailed 3D structure of amyloids. It opens avenues to the structure-based interpretation and design of the experiments. Availability and implementation BetaSerpentine webserver can be accessed through website: http://bioinfo.montp.cnrs.fr/b-serpentine. Source code is available in git.hub repository (github.com/stanislavspbgu/BetaSerpentine). Contact stanislavspbgu@gmail.com or andrey.kajava@crbm.cnrs.fr. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Stanislav A Bondarev
- Laboratory of Amyloid Biology and Department of Genetics and Biotechnology, St. Petersburg State University, Saint Petersburg 199034, Russia
| | - Olga V Bondareva
- Laboratory of Molecular Systematics, Zoological Institute RAS, Saint Petersburg 199034, Russia
| | - Galina A Zhouravleva
- Laboratory of Amyloid Biology and Department of Genetics and Biotechnology, St. Petersburg State University, Saint Petersburg 199034, Russia
| | - Andrey V Kajava
- Structural Bioinformatics and Molecular Modeling, Centre de Recherche en Biologie Cellulaire de Montpellier, CNRS, Université Montpellier, Montpellier 34293, France.,Institut de Biologie Computationnelle, Montpellier 34095, France.,Bioengineering Department, University ITMO, Saint Petersburg, 197101, Russia
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Flynn JD, Jiang Z, Lee JC. Segmental
13
C‐Labeling and Raman Microspectroscopy of α‐Synuclein Amyloid Formation. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201809865] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jessica D. Flynn
- National Heart, Lung, and Blood Institute National Institutes of Health Bethesda MD 20892 USA
| | - Zhiping Jiang
- National Heart, Lung, and Blood Institute National Institutes of Health Bethesda MD 20892 USA
| | - Jennifer C. Lee
- National Heart, Lung, and Blood Institute National Institutes of Health Bethesda MD 20892 USA
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Bhasne K, Mukhopadhyay S. Formation of Heterotypic Amyloids: α-Synuclein in Co-Aggregation. Proteomics 2018; 18:e1800059. [PMID: 30216674 DOI: 10.1002/pmic.201800059] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/28/2018] [Indexed: 12/13/2022]
Abstract
Protein misfolding resulting in the formation of ordered amyloid aggregates is associated with a number of devastating human diseases. Intrinsically disordered proteins (IDPs) do not autonomously fold up into a unique stable conformation and remain as an ensemble of rapidly fluctuating conformers. Many IDPs are prone to convert into the β-rich amyloid state. One such amyloidogenic IDP is α-synuclein that is involved in Parkinson's disease. Recent studies have indicated that other neuronal proteins, especially IDPs, can co-aggregate with α-synuclein in many pathological ailments. This article describes several such observations highlighting the role of heterotypic protein-protein interactions in the formation of hetero-amyloids. It is believed that the characterizations of molecular cross talks between amyloidogenic proteins as well as the mechanistic studies of heterotypic protein aggregation will allow us to decipher the role of the interacting proteins in amyloid proteomics.
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Affiliation(s)
- Karishma Bhasne
- Centre for Protein Science, Design and Engineering, Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Mohali, Punjab 140306, India.,Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Mohali, Punjab 140306, India
| | - Samrat Mukhopadhyay
- Centre for Protein Science, Design and Engineering, Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Mohali, Punjab 140306, India.,Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Mohali, Punjab 140306, India
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Establishment of Constraints on Amyloid Formation Imposed by Steric Exclusion of Globular Domains. J Mol Biol 2018; 430:3835-3846. [DOI: 10.1016/j.jmb.2018.05.038] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/15/2018] [Accepted: 05/27/2018] [Indexed: 11/18/2022]
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Castillo-Carranza DL, Guerrero-Muñoz MJ, Sengupta U, Gerson JE, Kayed R. α-Synuclein Oligomers Induce a Unique Toxic Tau Strain. Biol Psychiatry 2018; 84:499-508. [PMID: 29478699 PMCID: PMC6201292 DOI: 10.1016/j.biopsych.2017.12.018] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 12/19/2017] [Accepted: 12/22/2017] [Indexed: 12/20/2022]
Abstract
BACKGROUND The coexistence of α-synuclein and tau aggregates in several neurodegenerative disorders, including Parkinson's disease and Alzheimer's disease, raises the possibility that a seeding mechanism is involved in disease progression. METHODS To further investigate the role of α-synuclein in the tau aggregation pathway, we performed a set of experiments using both recombinant and brain-derived tau and α-synuclein oligomers to seed monomeric tau aggregation in vitro and in vivo. Brain-derived tau oligomers were isolated from well-characterized cases of progressive supranuclear palsy (n = 4) and complexes of brain-derived α-synuclein/tau oligomers isolated from patients with Parkinson's disease (n = 4). The isolated structures were purified and characterized by standard biochemical methods, then injected into Htau mice (n = 24) to assess their toxicity and role in tau aggregation. RESULTS We found that α-synuclein induced a distinct toxic tau oligomeric strain that avoids fibril formation. In vivo, Parkinson's disease brain-derived α-synuclein/tau oligomers administered into Htau mouse brains accelerated endogenous tau oligomer formation concurrent with increasing cell loss. CONCLUSIONS Our findings provide evidence, for the first time, that α-synuclein enhances the harmful effects of tau, thus contributing to disease progression.
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Affiliation(s)
| | | | | | | | - Rakez Kayed
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, Texas; Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas.
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49
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Amyloid by Design: Intrinsic Regulation of Microbial Amyloid Assembly. J Mol Biol 2018; 430:3631-3641. [PMID: 30017921 DOI: 10.1016/j.jmb.2018.07.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 07/01/2018] [Accepted: 07/09/2018] [Indexed: 12/14/2022]
Abstract
The term amyloid has historically been used to describe fibrillar aggregates formed as the result of protein misfolding and that are associated with a range of diseases broadly termed amyloidoses. The discovery of "functional amyloids" expanded the amyloid umbrella to encompass aggregates structurally similar to disease-associated amyloids but that engage in a variety of biologically useful tasks without incurring toxicity. The mechanisms by which functional amyloid systems ensure nontoxic assembly has provided insights into potential therapeutic strategies for treating amyloidoses. Some of the most-studied functional amyloids are ones produced by bacteria. Curli amyloids are extracellular fibers made by enteric bacteria that function to encase and protect bacterial communities during biofilm formation. Here we review recent studies highlighting microbial functional amyloid assembly systems that are tailored to enable the assembly of non-toxic amyloid aggregates.
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50
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Guerrero-Ferreira R, Taylor NM, Mona D, Ringler P, Lauer ME, Riek R, Britschgi M, Stahlberg H. Cryo-EM structure of alpha-synuclein fibrils. eLife 2018; 7:36402. [PMID: 29969391 PMCID: PMC6092118 DOI: 10.7554/elife.36402] [Citation(s) in RCA: 386] [Impact Index Per Article: 64.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 07/01/2018] [Indexed: 01/03/2023] Open
Abstract
Parkinson’s disease is a progressive neuropathological disorder that belongs to the class of synucleinopathies, in which the protein alpha-synuclein is found at abnormally high concentrations in affected neurons. Its hallmark are intracellular inclusions called Lewy bodies and Lewy neurites. We here report the structure of cytotoxic alpha-synuclein fibrils (residues 1–121), determined by cryo-electron microscopy at a resolution of 3.4 Å. Two protofilaments form a polar fibril composed of staggered β-strands. The backbone of residues 38 to 95, including the fibril core and the non-amyloid component region, are well resolved in the EM map. Residues 50–57, containing three of the mutation sites associated with familial synucleinopathies, form the interface between the two protofilaments and contribute to fibril stability. A hydrophobic cleft at one end of the fibril may have implications for fibril elongation, and invites for the design of molecules for diagnosis and treatment of synucleinopathies. People with Parkinson’s disease have damaged cells in a part of the brain involved in movement, learning and reward-seeking behaviors. These cells contain blob-like aggregates that contain abnormally high amounts of a protein called alpha-synuclein. It is generally believed that, within these blobs, this protein clusters together into small needles called fibrils. Discerning the structure of a fibril could help researchers to understand both how alpha-synuclein damages brain cells and how diseases like Parkinson’s spread. Biophysicists have attempted to reveal the fibril structure previously. But many of these efforts only looked at short segments of the alpha-synuclein protein. Researchers still need more detailed imagery of the fibrils to confirm previous findings regarding their architecture and ultimately to identify ways to counteract the damage they cause. Guerrero-Ferreira et al. used a technique called cryo-electron microscopy to capture images of frozen fibrils made from a version of human alpha-synuclein that readily aggregates and that is only slightly shorter than the full-length protein. Processing these high-resolution images with computer software then revealed a three-dimensional model of the fibril structure, in which fine details are clearly visible. In the fibril, the proteins cluster to form a helix, similar to a flight of stairs. Each turn of the helix is formed by two alpha-synuclein molecules, facing each other but rotated by almost 180 degrees from one another. The three-dimensional model displays which parts of the protein lie at the core of the helix and thereby stabilize the fibril structure. Guerrero-Ferreira et al. speculate that fibrils may also take alternative forms because common alpha-synuclein mutations, which correlate with disease, would destabilize the observed helical structure. In the future, researchers may be able to use the features of this three-dimensional model to help design molecules that would make the fibrils detectable via medical imaging. This could help doctors to diagnose people with Parkinson’s disease at an earlier stage. Further research is also needed to understand where and how fibrils form, if differences in fibril structures exist within or between patients, possibly leading to different sub-classes of the disease, and how such fibrils interact with and possibly damage human brain cells.
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Affiliation(s)
| | - Nicholas Mi Taylor
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Basel, Switzerland
| | - Daniel Mona
- Roche Pharma Research and Early Development, Neuroscience, Ophthalmology and Rare Diseases Discovery and Translational Area/Neuroscience Discovery, Roche Innovation Center Basel, Basel, Switzerland
| | - Philippe Ringler
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Basel, Switzerland
| | - Matthias E Lauer
- Roche Pharma Research and Early Development, Chemical Biology, Roche Innovation Center Basel, Basel, Switzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland
| | - Markus Britschgi
- Roche Pharma Research and Early Development, Neuroscience, Ophthalmology and Rare Diseases Discovery and Translational Area/Neuroscience Discovery, Roche Innovation Center Basel, Basel, Switzerland
| | - Henning Stahlberg
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Basel, Switzerland
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