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Saraiva MA, Florêncio MH. Burst Phase Analysis of the Aggregation Prone α-synuclein Amyloid Protein. J Fluoresc 2024; 34:381-395. [PMID: 37273030 PMCID: PMC10808200 DOI: 10.1007/s10895-023-03285-1] [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: 04/11/2023] [Accepted: 05/23/2023] [Indexed: 06/06/2023]
Abstract
While some studies inferred that valid information can be retrieved for the refolding of proteins and consequent identification of folding intermediates in the stopped-flow spectrometry collapse phase, other studies report that these burst phase folding intermediates can be questioned, implying a solvent-dependent modification of the still unfolded polypeptide chain. We therefore decided to investigate the burst phase occurring for the α-synuclein (Syn) amyloid protein by stopped-flow spectrometry. Solvent-dependent modification effects indeed occurred for the Nα-acetyl-L-tyrosinamide (NAYA) parent small compound and for the folded monomeric ubiquitin protein. More complex was the burst phase analysis of the disordered Syn amyloid protein. While this amyloid protein was determined to be aggregated at pH 7 and pH 2, in particular, this protein at pH 3 appears to be in a monomeric state in the burst phase analysis performed. In addition, the protein at pH 3 appears to suffer a hydrophobic collapse with the formation of a possible folded intermediate. This folded intermediate seems to result from a fast contraction of the disordered amyloid polypeptide chain, which is proceeded by an expansion of the protein, due to the occurrence of solvent-dependent modification effects in a milliseconds time scale of the burst phase. Generally, it can be argued that both literature criteria of solvent-dependent modifications of the disordered Syn amyloid protein and of the formation of its possible folded intermediate are very likely to occur in the burst phase.
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Affiliation(s)
- Marco A Saraiva
- Centro de Química Estrutural, Institute of Molecular Sciences, Av. Rovisco Pais, Instituto Superior Técnico, University of Lisbon, Campus Alameda, Lisbon, 1049-001, Portugal.
| | - M Helena Florêncio
- Departamento de Química e Bioquímica, Faculdade de Ciências, University of Lisbon, Lisbon, 1749- 016, Portugal
- Laboratório de FTICR e Espectrometria de Massa Estrutural, Faculdade de Ciências, University of Lisbon, Lisbon, 1749-016, Portugal
- MARE - Marine and Environmental Sciences Centre / ARNET - Aquatic Research Network, Faculdade de Ciências, University of Lisbon, Lisbon, 1749-016, Portugal
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2
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Khan S, Naeem A. Bovine serum albumin prevents human hemoglobin aggregation and retains its chaperone-like activity. J Biomol Struct Dyn 2024; 42:346-361. [PMID: 36974939 DOI: 10.1080/07391102.2023.2192802] [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: 02/03/2023] [Accepted: 03/13/2023] [Indexed: 03/29/2023]
Abstract
This study investigates the ability of bovine serum albumin (BSA) to act as an extracellular chaperone (EC) on human hemoglobin (Hb) at a pH of 7.4. The best temperature for studying this behavior was determined by analyzing Hb's aggregation kinetics at multiple temperatures. 55 °C was chosen as the optimal temperature for forming Hb amyloids. BSA was then tested at various concentrations (20-100 μM) to assess its chaperone-like activity on Hb at 55 °C. At a concentration of 100 μM, BSA exhibits chaperone-like activity with a client protein:BSA ratio of 1:10. The high ratio implies that the chaperone activity of BSA is favored by the effects of macromolecular crowding. The results showed that BSA has the potential to inhibit Hb's dissociation into alpha and beta subunits and protein aggregation by inhibiting secondary nucleation. BSA also causes the depolymerization of fibrils over time. The results were validated using molecular docking and all-atom molecular dynamics simulations. MD analysis such as RMSD, RMSF, Rg, SASA, Hydrogen bond, PCA, Free energy landscape (FEL) revealed that the stability of hemoglobin is greater when it is bound to BSA compared to unbound state. The study suggests that BSA can potentially bind to Hb dimers and reduce excitonic interactions, which reduces Hb aggregation. These results are consistent with the aggregation kinetics experiments.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sadaf Khan
- Department of Biochemistry, Aligarh Muslim University, Aligarh, India
| | - Aabgeena Naeem
- Department of Biochemistry, Aligarh Muslim University, Aligarh, India
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3
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Saraiva MA, Florêncio MH. Initial Effect of Temperature Rise on α-Synuclein Aggregation - Entropic Forces Drive the Exposure of Protein Hydrophobic Groups Probed by Fluorescence Spectroscopy. J Fluoresc 2023; 33:1727-1738. [PMID: 36826732 PMCID: PMC10539466 DOI: 10.1007/s10895-023-03192-5] [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: 12/19/2022] [Accepted: 02/17/2023] [Indexed: 02/25/2023]
Abstract
The aberrant formation of α-synuclein (Syn) aggregates, varying in size, structure and morphology, has been linked to the development of Parkinson's disease. In the early stages of Syn aggregation, large protein amyloid aggregates with sizes > 100 nm in hydrodynamic radius have been noticed. These low overall abundant large Syn aggregates are notoriously difficult to study by conventional biophysical methods. Due to the growing importance of studying the early stages of Syn aggregation, we developed a strategy to achieve this purpose, which is the study of the initial effect of the Syn protein aqueous solutions temperature rise. Therefore, the increase of the Syn aqueous solutions entropy by the initial effect of the temperature rise led to the exposure of the protein hydrophobic tyrosyl groups by not interfering with this amyloid protein aggregation. As an attempt to interpret the degree of the referred protein tyrosyl groups exposure, the classic rotameric conformations of the Nα-acetyl-L-tyrosinamide (NAYA) parent compound were used. For both NAYA and Syn, it was determined that the classic rotameric conformations involving the tyrosyl groups indeed accounted for their exposure under steady-state conditions of fluorescence, for lowest molecular species concentrations investigated at least. In this situation, Syn aggregation was observed. For the higher NAYA and Syn concentrations studied, the referred classic rotameric conformation were insufficient in such referred steady-state conditions and, for Syn, in particular, fluorescence anisotropy measurements revealed that less protein aggregation occurs along with its delay. Overall, the developed strategy by focusing on the initial effect of the temperature rise of Syn aqueous solutions in lower concentrations is suitable for informing us about the degree of this protein aggregation in solution.
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Affiliation(s)
- Marco A Saraiva
- Centro de Química Estrutural, Av. Rovisco Pais, Instituto Superior Técnico, University of Lisbon, Campus Alameda, 1049-001, Lisbon, Portugal.
| | - M Helena Florêncio
- Departamento de Química e Bioquímica, Faculdade de Ciências, University of Lisbon, 1749-016, Lisbon, Portugal
- Laboratório de FTICR e Espectrometria de Massa Estrutural, Faculdade de Ciências, University of Lisbon, 1749-016, Lisbon, Portugal
- Faculdade de Ciências, MARE - Marine and Environmental Sciences Centre / ARNET - Aquatic Research Network, University of Lisbon, 1749-016, Lisbon, Portugal
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Saraiva MA, Helena Florêncio M. Identification of a biological excimer involving protein-protein interactions: A case study of the α-synuclein aggregation. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 283:121761. [PMID: 35985235 DOI: 10.1016/j.saa.2022.121761] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 08/03/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Excimer formation based on pyrene derivatives stacking has been used to probe conformational changes associated with a variety of protein interactions. Herein, in search for the nature of the protein interactions involved in amyloid proteins aggregation we studied the spectroscopic features of the Nα-acetyl-l-tyrosinamide (NAYA) parent compound and of a well-known aggregate amyloid protein, the α-synuclein (Syn). The aggregation of this amyloid disordered protein has been implicated in the development of Parkinson's disease, which is an increasingly prevalent and currently incurable neurodegenerative disorder. Also, Syn aggregation has been widely investigated but, information concerning the conformational alterations in the diverse protein aggregated species at the molecular level, is still scarce. Three different molecular configurations of the NAYA parent compound were at least found to exist in its solutions containing 1,4-dioxane. Two of these NAYA molecular configurations were found to produce a more efficient excimer fluorescence. For Syn solutions containing 1,4-dioxane, one molecular configuration involving the intermolecular interaction between the protein tyrosyl group and the protein peptide bond was found to exhibit excimer fluorescence. This study is the first one reporting the formation of a biological excimer exhibiting fluorescence. Although very weak, this can be used as a signature of protein-protein interactions and, ultimately, enabling to access the complex interactions network existing in the amyloid aggregated species.
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Affiliation(s)
- Marco A Saraiva
- Centro de Química Estrutural, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal.
| | - M Helena Florêncio
- Departamento de Química e Bioquímica, Faculdade de Ciências, University of Lisbon, 1749-016 Lisbon, Portugal; Laboratório de FTICR e Espectrometria de Massa Estrutural, Faculdade de Ciências, University of Lisbon, 1749-016 Lisbon, Portugal; MARE - Marine and Environmental Sciences Centre, ARNET - Aquatic Research Network, Faculdade de Ciências, University of Lisbon, Portugal
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Saraiva MA, Florêncio MH. Early α-synuclein aggregation is overall delayed and it can occur by a stepwise mechanism. Biochem Biophys Res Commun 2022; 635:30-36. [DOI: 10.1016/j.bbrc.2022.10.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 09/23/2022] [Accepted: 10/05/2022] [Indexed: 11/02/2022]
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6
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Herrera MG, Amundarain MJ, Nicoletti F, Drechsler M, Costabel M, Gentili PL, Dodero VI. Thin-Plate Superstructures of the Immunogenic 33-mer Gliadin Peptide. Chembiochem 2022; 23:e202200552. [PMID: 36161684 PMCID: PMC9828358 DOI: 10.1002/cbic.202200552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 09/23/2022] [Indexed: 02/03/2023]
Abstract
Gluten related-disorders have a prevalence of 1-5 % worldwide triggered by the ingestion of gluten proteins in wheat, rye, barley, and some oats. In wheat gluten, the most studied protein is gliadin, whose immunodominant 33-mer amino acid fragment remains after digestive proteolysis and accumulates in the gut mucosa. Here, we report the formation of 33-mer thin-plate superstructures using intrinsic tyrosine (Tyr) steady-state fluorescence anisotropy and cryo-TEM in combination with water tension measurements. Furthermore, we showed that fluorescence decay measurements of 33-mer intrinsic fluorophore Tyr provided information on the early stages of the formation of the thin-plate structures. Finally, conformational analysis of Tyr residues using minimalist models by molecular dynamic simulations (MD) demonstrated that changes in Tyr rotamer states depend on the oligomerization stage. Our findings further advance the understanding of the formation of the 33-mer gliadin peptide superstructures and their relation to health and disease.
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Affiliation(s)
- Maria Georgina Herrera
- Faculty of ChemistryOCIIIBielefeld UniversityUniversitätsstr. 2533615BielefeldGermany,Faculty of Exact and Natural SciencesInstitute of BiosciencesBiotechnology and Translational Biology (iB3)University of Buenos AiresIntendente Güiraldes 2160, Ciudad UniversitariaC1428EGABuenos AiresArgentina
| | - Maria Julia Amundarain
- Instituto de Física del Sur (IFISUR)Departamento de FísicaUniversidad Nacional del Sur (UNS)CONICET Av. L. N. Alem1253, B8000CPB -Bahía BlancaArgentina
| | - Franscesco Nicoletti
- Faculty of ChemistryOCIIIBielefeld UniversityUniversitätsstr. 2533615BielefeldGermany,Department of Chemistry, Biology, and BiotechnologyUniversità degli Studi di PerugiaVia Elce di Sotto 806123PerugiaItaly
| | - Marcus Drechsler
- Bavarian Polymer InstituteUniversity BayreuthUniversitaetsstr. 3095447BayreuthGermany
| | - Marcelo Costabel
- Instituto de Física del Sur (IFISUR)Departamento de FísicaUniversidad Nacional del Sur (UNS)CONICET Av. L. N. Alem1253, B8000CPB -Bahía BlancaArgentina
| | - Pier Luigi Gentili
- Department of Chemistry, Biology, and BiotechnologyUniversità degli Studi di PerugiaVia Elce di Sotto 806123PerugiaItaly
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Shear Stress Induces α-Synuclein Aggregation Due to a Less Strained Protein Backbone and Protein Tyrosyl Groups Do Not Intervene in the Aggregation. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12073546] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Parkinson’s disease (PD) is an increasingly prevalent and currently incurable neurodegenerative disorder. The aggregation of the amyloid disordered protein α-synuclein (Syn) has been implicated in the development of PD. In the literature, it has been suggested that tyrosine residues of Syn play an important role in the interactions established during the fibrillation process. Herein, the prevalence of the referred interactions under shear stress conditions of Nα-acetyl-L-tyrosinamide (NAYA) and of Syn solutions by using membrane centrifugal filters with different cut-off of 200 nm, 100 kDa, 50 kDa and 30 kDa, under centrifugation conditions, were investigated. In order to determine the nature of the interactions involving the protein tyrosine residues the NAYA compound, which mimics the peptide bonds in protein and also possesses a tyrosyl group similar to the tyrosyl groups found in the Syn protein molecular structure, was used. It is expected that for a small molecule, such as NAYA, no molecular association occurs, contrary to what exists in the Syn protein solutions, which can more adequately retrieve the type of interactions formed, involving the tyrosyl group. Therefore, sensing the tyrosyl group absorption, spectroscopic techniques, in particular, were used. For NAYA, an intramolecular interaction between the tyrosyl group and the peptide bond was evidenced. For NAYA and Syn, it was observed that decreasing the membrane centrifugal filters pore size, under centrifugation conditions, was concomitant with the minimization of the intramolecular interactions between the tyrosyl group and the peptide bond. With this, it is likely to assume that shear stress conditions in the Syn solutions propel protein aggregation by a less strained protein backbone. Contrary to the centrifugation of NAYA solutions, centrifuging Syn solutions revealed molecular association and a progressive exposure of protein tyrosyl groups to water. Thus, we can also infer that shear stress conditions in the Syn solutions cause the protein tyrosyl groups to not intervene in the protein aggregation.
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Zhang Z, Li M, Zuo Y, Chen S, Zhuo Y, Lu M, Shi G, Gu H. In Vivo Monitoring of pH in Subacute PD Mouse Brains with a Ratiometric Electrochemical Microsensor Based on Poly(melamine) Films. ACS Sens 2022; 7:235-244. [PMID: 34936337 DOI: 10.1021/acssensors.1c02051] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In vivo monitoring of cerebral pH is of great significance because its disturbance is related to some pathological processes such as neurodegenerative diseases, for example, Parkinson's disease (PD). In this study, we developed an electrochemical microsensor based on poly(melamine) (PMel) films for ratiometric monitoring of pH in subacute PD mouse brains. In this microsensor, PMel films were prepared from a simple electropolymerization approach in a melamine-containing solution, serving as the selective pH recognition membrane undergoing a 2H+/2e- process. Meanwhile, electrochemically oxidized graphene oxide (EOGO) produced a built-in correction signal which helped avoid the environmental interference of the complicated brain systems. The potential difference between the peaks generated from EOGO and PMel gradually decreased with the aqueous pH increasing from 4.0 to 9.0, constituting the detection foundation of the ratiometric electrochemical microsensor (REM). The in vitro studies demonstrated that this proposed method exhibited a high sensitivity (a Nernstian response of -61.35 mV/pH) and remarkable selectivity against amino acids, anions, cations, and biochemical and reactive oxygen species coexisting in the brain. Coupled with its excellent stability and reproducibility and good antibiofouling based on short-term detection, the developed REM could serve as a disposable sensor for the determination of cerebral pH in vivo. Its following successful application in the real-time measurement of pH in the striatum, hippocampus, and cortex of rat brains in the events of global cerebral ischemia/reperfusion verified the reliability of this method. Finally, we adopted this robust REM to systematically analyze and compare the average pH in different regions of normal and subacute PD mouse brains.
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Affiliation(s)
- Ziyi Zhang
- A Key Laboratory of Theoretical Organic Chemistry and Functional Molecule of Ministry of Education, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, Hunan 411201, P. R. China
| | - Mengyin Li
- A Key Laboratory of Theoretical Organic Chemistry and Functional Molecule of Ministry of Education, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, Hunan 411201, P. R. China
| | - Yimei Zuo
- A Key Laboratory of Theoretical Organic Chemistry and Functional Molecule of Ministry of Education, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, Hunan 411201, P. R. China
| | - Shu Chen
- A Key Laboratory of Theoretical Organic Chemistry and Functional Molecule of Ministry of Education, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, Hunan 411201, P. R. China
| | - Yi Zhuo
- The National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, Hunan Provincial Key Laboratory of Neurorestoratology, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410006, P.R. China
| | - Ming Lu
- The National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, Hunan Provincial Key Laboratory of Neurorestoratology, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410006, P.R. China
| | - Guoyue Shi
- School of Chemistry and Molecular Engineering, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Hui Gu
- A Key Laboratory of Theoretical Organic Chemistry and Functional Molecule of Ministry of Education, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, Hunan 411201, P. R. China
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Saraiva MA, Florêncio MH. Buffering capacity is determinant for restoring early α-synuclein aggregation. Biophys Chem 2022; 282:106760. [DOI: 10.1016/j.bpc.2022.106760] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/28/2021] [Accepted: 01/10/2022] [Indexed: 11/02/2022]
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Wang Y, Ye Z, Li J, Zhang Y, Guo Y, Cheng JH. Effects of dielectric barrier discharge cold plasma on the activity, structure and conformation of horseradish peroxidase (HRP) and on the activity of litchi peroxidase (POD). Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.111078] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Evidence of the existence of micellar-like aggregates for α-synuclein. Int J Biol Macromol 2021; 177:392-400. [PMID: 33631264 DOI: 10.1016/j.ijbiomac.2021.02.150] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 02/14/2021] [Accepted: 02/20/2021] [Indexed: 11/20/2022]
Abstract
We have been investigating the early stages of α-synuclein (Syn) aggregation, a small presynaptic protein implicated in Parkinson's disease. We previously reported that for pH jumps (1000 s) from pH 7 to pH 2 the variation of the Syn intrinsic fluorescence intensity did not change in the concentration range of ca. 10-50 μM (ref. 16). Additionally, I reported dynamic light scattering (DLS) experiments revealing the formation of early large Syn aggregates (ref. 7). These reported results mean that some molecular entity is being early formed. Herein, it was decided to investigate in detail these early Syn aggregates by using light scattering. By DLS analysis, these aggregates exhibited a hydrodynamic diameter of ca. 420 nm along with a high scattering intensity, characteristic of micellar-like aggregates formation. The critical micelle concentration (CMC) at which the Syn micellar-like aggregates are formed was ca. 10 μM. DLS analysis has also revealed that the micellar-like aggregates for Syn evolved, for protein concentrations >100 μM, to the formation of smaller aggregates (hydrodynamic diameter of ca. 165 nm), possibly Syn oligomers. The Syn micellar-like aggregates formed at pH 7 solutions seem to be active species and to have a role in this protein aggregation mechanism.
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Zeng H, Liu N, Liu XX, Yang YY, Zhou MW. α-Synuclein in traumatic and vascular diseases of the central nervous system. Aging (Albany NY) 2020; 12:22313-22334. [PMID: 33188159 PMCID: PMC7695413 DOI: 10.18632/aging.103675] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 06/29/2020] [Indexed: 12/14/2022]
Abstract
α-Synuclein (α-Syn) is a small, soluble, disordered protein that is widely expressed in the nervous system. Although its physiological functions are not yet fully understood, it is mainly involved in synaptic vesicle transport, neurotransmitter synthesis and release, cell membrane homeostasis, lipid synthesis, mitochondrial and lysosomal activities, and heavy metal removal. The complex and inconsistent pathological manifestations of α-Syn are attributed to its structural instability, mutational complexity, misfolding, and diverse posttranslational modifications. These effects trigger mitochondrial dysfunction, oxidative stress, and neuroinflammatory responses, resulting in neuronal death and neurodegeneration. Several recent studies have discovered the pathogenic roles of α-Syn in traumatic and vascular central nervous system diseases, such as traumatic spinal cord injury, brain injury, and stroke, and in aggravating the processes of neurodegeneration. This review aims to highlight the structural and pathophysiological changes in α-Syn and its mechanism of action in traumatic and vascular diseases of the central nervous system.
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Affiliation(s)
- Hong Zeng
- Department of Rehabilitation Medicine, Peking University Third Hospital, Beijing 100191, China
| | - Nan Liu
- Department of Rehabilitation Medicine, Peking University Third Hospital, Beijing 100191, China
| | - Xiao-Xie Liu
- Department of Rehabilitation Medicine, Peking University Third Hospital, Beijing 100191, China
| | - Yan-Yan Yang
- Department of Rehabilitation Medicine, Peking University Third Hospital, Beijing 100191, China
| | - Mou-Wang Zhou
- Department of Rehabilitation Medicine, Peking University Third Hospital, Beijing 100191, China
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Saraiva MA. Interpretation of α-synuclein UV absorption spectra in the peptide bond and the aromatic regions. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2020; 212:112022. [DOI: 10.1016/j.jphotobiol.2020.112022] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 08/14/2020] [Accepted: 09/05/2020] [Indexed: 10/23/2022]
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Pignataro MF, Herrera MG, Dodero VI. Evaluation of Peptide/Protein Self-Assembly and Aggregation by Spectroscopic Methods. Molecules 2020; 25:E4854. [PMID: 33096797 PMCID: PMC7587993 DOI: 10.3390/molecules25204854] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/17/2020] [Accepted: 10/19/2020] [Indexed: 01/08/2023] Open
Abstract
The self-assembly of proteins is an essential process for a variety of cellular functions including cell respiration, mobility and division. On the other hand, protein or peptide misfolding and aggregation is related to the development of Parkinson's disease and Alzheimer's disease, among other aggregopathies. As a consequence, significant research efforts are directed towards the understanding of this process. In this review, we are focused on the use of UV-Visible Absorption Spectroscopy, Fluorescence Spectroscopy and Circular Dichroism to evaluate the self-organization of proteins and peptides in solution. These spectroscopic techniques are commonly available in most chemistry and biochemistry research laboratories, and together they are a powerful approach for initial as well as routine evaluation of protein and peptide self-assembly and aggregation under different environmental stimulus. Furthermore, these spectroscopic techniques are even suitable for studying complex systems like those in the food industry or pharmaceutical formulations, providing an overall idea of the folding, self-assembly, and aggregation processes, which is challenging to obtain with high-resolution methods. Here, we compiled and discussed selected examples, together with our results and those that helped us better to understand the process of protein and peptide aggregation. We put particular emphasis on the basic description of the methods as well as on the experimental considerations needed to obtain meaningful information, to help those who are just getting into this exciting area of research. Moreover, this review is particularly useful to those out of the field who would like to improve reproducibility in their cellular and biomedical experiments, especially while working with peptide and protein systems as an external stimulus. Our final aim is to show the power of these low-resolution techniques to improve our understanding of the self-assembly of peptides and proteins and translate this fundamental knowledge in biomedical research or food applications.
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Affiliation(s)
- María Florencia Pignataro
- Department of Physiology and Molecular and Cellular Biology, Institute of Biosciences, Biotechnology and Translational Biology (iB3), Faculty of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires C1428EG, Argentina;
- Institute of Biological Chemistry and Physical Chemistry, Dr. Alejandro Paladini, University of Buenos Aires-CONICET, Buenos Aires C1113AAD, Argentina
| | - María Georgina Herrera
- Department of Physiology and Molecular and Cellular Biology, Institute of Biosciences, Biotechnology and Translational Biology (iB3), Faculty of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires C1428EG, Argentina;
- Institute of Biological Chemistry and Physical Chemistry, Dr. Alejandro Paladini, University of Buenos Aires-CONICET, Buenos Aires C1113AAD, Argentina
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
| | - Verónica Isabel Dodero
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
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Rotamer Dynamics: Analysis of Rotamers in Molecular Dynamics Simulations of Proteins. Biophys J 2019; 116:2062-2072. [PMID: 31084902 DOI: 10.1016/j.bpj.2019.04.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 03/28/2019] [Accepted: 04/16/2019] [Indexed: 11/21/2022] Open
Abstract
Given by χ torsional angles, rotamers describe the side-chain conformations of amino acid residues in a protein based on the rotational isomers (hence the word rotamer). Constructed rotamer libraries, based on either protein crystal structures or dynamics studies, are the tools for classifying rotamers (torsional angles) in a way that reflect their frequency in nature. Rotamer libraries are routinely used in structure modeling and evaluation. In this perspective article, we would like to encourage researchers to apply rotamer analyses beyond their traditional use. Molecular dynamics (MD) of proteins highlight the in silico behavior of molecules in solution and thus can identify favorable side-chain conformations. In this article, we used simple computational tools to study rotamer dynamics (RD) in MD simulations. First, we isolated each frame in the MD trajectories in separate Protein Data Bank files via the cpptraj module in AMBER. Then, we extracted torsional angles via the Bio3D module in R language. The classification of torsional angles was also done in R according to the penultimate rotamer library. RD analysis is useful for various applications such as protein folding, study of rotamer-rotamer relationship in protein-protein interaction, real-time correlation between secondary structures and rotamers, study of flexibility of side chains in binding site for molecular docking preparations, use of RD as guide in functional analysis and study of structural changes caused by mutations, providing parameters for improving coarse-grained MD accuracy and speed, and many others. Major challenges facing RD to emerge as a new scientific field involve the validation of results via easy, inexpensive wet-lab methods. This realm is yet to be explored.
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Pérez-Pi I, Evans DA, Horrocks MH, Pham NT, Dolt KS, Koszela J, Kunath T, Auer M. α-Synuclein-Confocal Nanoscanning (ASYN-CONA), a Bead-Based Assay for Detecting Early-Stage α-Synuclein Aggregation. Anal Chem 2019; 91:5582-5590. [PMID: 30964656 PMCID: PMC6534341 DOI: 10.1021/acs.analchem.8b03842] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
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α-Synuclein
fibrils are considered a hallmark of Parkinson’s
disease and other synucleinopathies. However, small oligomers that
formed during the early stages of α-synuclein aggregation are
thought to be the main toxic species causing disease. The formation
of α-synuclein oligomers has proven difficult to follow, because
of the heterogeneity and transient nature of the species formed. Here,
a novel bead-based aggregation assay for monitoring the earliest stages
of α-synuclein oligomerization, α-Synuclein–Confocal
Nanoscanning (ASYN-CONA), is presented. The α-synuclein A91C
single cysteine mutant is modified with a trifunctional chemical tag,
which allows simultaneous fluorescent labeling with a green dye (tetramethylrhodamine,
TMR) and attachment to microbeads. Beads with bound TMR-labeled α-synuclein
are then incubated with a red dye (Cy5)-labeled variant of α-synuclein
A91C, and EtOH (20%) to induce aggregation. Aggregation is detected
by confocal scanning imaging, below the equatorial plane of the beads,
which is known as the CONA technique. On-bead TMR-labeled α-synuclein
and aggregated Cy5-labeled α-synuclein from the solution are
quantitatively monitored in parallel by detection of fluorescent halos
or “rings”. α-Synuclein on-bead oligomerization
results in a linear increase of red bead ring fluorescence intensity
over a period of 5 h. Total internal reflection fluorescence microscopy
was performed on oligomers cleaved from the beads, and it revealed
that (i) oligomers are sufficiently stable in solution to investigate
their composition, consisting of 6 ± 1 monomer units, and (ii)
oligomers containing a mean of 15 monomers bind Thioflavin-T. Various
known inhibitors of α-synuclein aggregation were used to validate
the ASYN-CONA assay for drug screening. Baicalein, curcumin, and rifampicin
showed concentration-dependent inhibition of the α-synuclein
aggregation and the IC50 (the concentration of the compound
at which the maxiumum intensity was reduced by one-half) were calculated.
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Affiliation(s)
- Irene Pérez-Pi
- School of Biological Sciences and Edinburgh Medical School: Biomedical Sciences , University of Edinburgh , The King's Buildings, Edinburgh EH9 3BF , United Kingdom
| | - David A Evans
- School of Biological Sciences and Edinburgh Medical School: Biomedical Sciences , University of Edinburgh , The King's Buildings, Edinburgh EH9 3BF , United Kingdom
| | - Mathew H Horrocks
- EaStCHEM School of Chemistry , University of Edinburgh , Edinburgh EH9 3FJ , United Kingdom.,UK Dementia Research Institute , University of Edinburgh , Chancellor's Building, Edinburgh Medical School , Edinburgh EH16 4SB , United Kingdom
| | - Nhan T Pham
- School of Biological Sciences and Edinburgh Medical School: Biomedical Sciences , University of Edinburgh , The King's Buildings, Edinburgh EH9 3BF , United Kingdom
| | - Karamjit S Dolt
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences , The University of Edinburgh , Edinburgh EH16 4UU , United Kingdom
| | - Joanna Koszela
- School of Biological Sciences and Edinburgh Medical School: Biomedical Sciences , University of Edinburgh , The King's Buildings, Edinburgh EH9 3BF , United Kingdom
| | - Tilo Kunath
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences , The University of Edinburgh , Edinburgh EH16 4UU , United Kingdom
| | - Manfred Auer
- School of Biological Sciences and Edinburgh Medical School: Biomedical Sciences , University of Edinburgh , The King's Buildings, Edinburgh EH9 3BF , United Kingdom
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17
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Dissection of the deep-blue autofluorescence changes accompanying amyloid fibrillation. Arch Biochem Biophys 2018; 651:13-20. [PMID: 29803394 DOI: 10.1016/j.abb.2018.05.019] [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: 12/22/2017] [Revised: 04/02/2018] [Accepted: 05/23/2018] [Indexed: 11/21/2022]
Abstract
Pathogenesis of numerous diseases is associated with the formation of amyloid fibrils. Extrinsic fluorescent dyes, including Thioflavin T (ThT), are used to follow the fibrillation kinetics. It has recently been reported that the so-called deep-blue autofluorescence (dbAF) is changing during the aggregation process. However, the origin of dbAF and the reasons for its change remain debatable. Here, the kinetics of fibril formation in model proteins were comprehensively analyzed using fluorescence lifetime and intensity of ThT, intrinsic fluorescence of proteinaceous fluorophores, and dbAF. For all systems, intensity enhancement of the dbAF band with similar spectral parameters (∼350 nm excitation; ∼450 nm emission) was observed. Although the time course of ThT lifetime (indicative of protofibrils formation) coincided with that of tyrosine residues in insulin, and the kinetic changes in the ThT fluorescence intensity (reflecting formation of mature fibrils) coincided with changes in ThT absorption spectrum, the dbAF band started to increase from the beginning of the incubation process without a lag-phase. Our mass-spectrometry data and model experiments suggested that dbAF could be at least partially related to oxidation of amino acids. This study scrutinizes the dbAF features in the context of the existing hypotheses about the origin of this spectral band.
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18
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Lucato CM, Lupton CJ, Halls ML, Ellisdon AM. Amyloidogenicity at a Distance: How Distal Protein Regions Modulate Aggregation in Disease. J Mol Biol 2017; 429:1289-1304. [PMID: 28342736 DOI: 10.1016/j.jmb.2017.03.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 03/12/2017] [Accepted: 03/14/2017] [Indexed: 12/14/2022]
Abstract
The misfolding of proteins to form amyloid is a key pathological feature of several progressive, and currently incurable, diseases. A mechanistic understanding of the pathway from soluble, native protein to insoluble amyloid is crucial for therapeutic design, and recent efforts have helped to elucidate the key molecular events that trigger protein misfolding. Generally, either global or local structural perturbations occur early in amyloidogenesis to expose aggregation-prone regions of the protein that can then self-associate to form toxic oligomers. Surprisingly, these initiating structural changes are often caused or influenced by protein regions distal to the classically amyloidogenic sequences. Understanding the importance of these distal regions in the pathogenic process has highlighted many remaining knowledge gaps regarding the precise molecular events that occur in classic aggregation pathways. In this review, we discuss how these distal regions can influence aggregation in disease and the recent technical and conceptual advances that have allowed this insight.
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Affiliation(s)
- Christina M Lucato
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Christopher J Lupton
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Michelle L Halls
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Andrew M Ellisdon
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia.
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19
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Yang H, Xu S, Shen L, Liu W, Li G. Changes in aggregation behavior of collagen molecules in solution with varying concentrations of acetic acid. Int J Biol Macromol 2016; 92:581-586. [DOI: 10.1016/j.ijbiomac.2016.07.080] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 07/14/2016] [Accepted: 07/23/2016] [Indexed: 11/27/2022]
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