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Sárkány Z, Figueiredo F, Macedo-Ribeiro S, Martins PM. NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation. Mol Biol Cell 2024; 35:mr1. [PMID: 38117593 PMCID: PMC10916857 DOI: 10.1091/mbc.e23-07-0289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 11/27/2023] [Accepted: 12/13/2023] [Indexed: 12/22/2023] Open
Abstract
The assembly of biomolecular condensate in eukaryotic cells and the accumulation of amyloid deposits in neurons are processes involving the nucleation and growth (NAG) of new protein phases. To therapeutically target protein phase separation, drug candidates are tested in in vitro assays that monitor the increase in the mass or size of the new phase. Limited mechanistic insight is, however, provided if empirical or untestable kinetic models are fitted to these progress curves. Here we present the web server NAGPKin that quantifies NAG rates using mass-based or size-based progress curves as the input data. A report is generated containing the fitted NAG parameters and elucidating the phase separation mechanisms at play. The NAG parameters can be used to predict particle size distributions of, for example, protein droplets formed by liquid-liquid phase separation (LLPS) or amyloid fibrils formed by protein aggregation. Because minimal intervention is required from the user, NAGPKin is a good platform for standardized reporting of LLPS and protein self-assembly data. NAGPKin is useful for drug discovery as well as for fundamental studies on protein phase separation. NAGPKin is freely available (no login required) at https://nagpkin.i3s.up.pt.
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Affiliation(s)
- Zsuzsa Sárkány
- Biomolecular Structure and Function Group, IBMC – Instituto de Biologia Molecular e Celular, Porto 4200-135, Portugal
- i3S – Instituto de Investigação e Inovação em Saúde da Universidade do Porto, Porto 4200-135, Portugal
| | - Francisco Figueiredo
- Biomolecular Structure and Function Group, IBMC – Instituto de Biologia Molecular e Celular, Porto 4200-135, Portugal
- i3S – Instituto de Investigação e Inovação em Saúde da Universidade do Porto, Porto 4200-135, Portugal
| | - Sandra Macedo-Ribeiro
- Biomolecular Structure and Function Group, IBMC – Instituto de Biologia Molecular e Celular, Porto 4200-135, Portugal
- i3S – Instituto de Investigação e Inovação em Saúde da Universidade do Porto, Porto 4200-135, Portugal
| | - Pedro M. Martins
- Biomolecular Structure and Function Group, IBMC – Instituto de Biologia Molecular e Celular, Porto 4200-135, Portugal
- i3S – Instituto de Investigação e Inovação em Saúde da Universidade do Porto, Porto 4200-135, Portugal
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2
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Abstract
Amyloids are organized suprastructural polypeptide arrangements. The prevalence of amyloid-related processes of pathophysiological relevance has been linked to aging-related degenerative diseases. Besides the role of genetic polymorphisms on the relative risk of amyloid diseases, the contributions of nongenetic ontogenic cluster of factors remain elusive. In recent decades, mounting evidences have been suggesting the role of essential micronutrients, in particular transition metals, in the regulation of amyloidogenic processes, both directly (such as binding to amyloid proteins) or indirectly (such as regulating regulatory partners, processing enzymes, and membrane transporters). The features of transition metals as regulatory cofactors of amyloid proteins and the consequences of metal dyshomeostasis in triggering amyloidogenic processes, as well as the evidences showing amelioration of symptoms by dietary supplementation, suggest an exaptative role of metals in regulating amyloid pathways. The self- and cross-talk replicative nature of these amyloid processes along with their systemic distribution support the concept of their metastatic nature. The role of amyloidosis as nutrient sensors would act as intra- and transgenerational epigenetic metabolic programming factors determining health span and life span, viability, which could participate as an evolutive selective pressure.
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Affiliation(s)
- Luís Maurício T R Lima
- Laboratory for Pharmaceutical Biotechnology - pbiotech, Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratory for Macromolecules (LAMAC-DIMAV), National Institute of Metrology, Quality and Technology - INMETRO, Duque de Caxias, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Tháyna Sisnande
- Laboratory for Pharmaceutical Biotechnology - pbiotech, Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
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Vaillard AS, El Haitami A, Fontaine P, Cousin F, Gutfreund P, Goldmann M, Cantin S. Surface Pressure-Induced Interdiffused Structure Evidenced by Neutron Reflectometry in Cellulose Acetate/Polybutadiene Langmuir Films. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:5717-5730. [PMID: 33905653 DOI: 10.1021/acs.langmuir.1c00745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Binary blends of water-insoluble polymers are a versatile strategy to obtain nanostructured films at the air-water interface. However, there are few reported structural studies of such systems in the literature. Depending on the compatibility of the polymers and the role of the air-water interface, one can expect various morphologies. In that context, we probed Langmuir monolayers of cellulose acetate (CA), of deuterated and postoxidized polybutadiene (PBd) and three mixtures of CA/PBd at various concentrations by coupling surface pressure-area isotherms, Brewster angle microscopy (BAM), and neutron reflectometry at the air-water interface to determine their thermodynamic and structural properties. The homogeneity of the films in the vertical direction, averaged laterally over the spatial coherence length of the neutron beam (∼5 μm), was assessed by neutron reflectometry measurements using D2O/H2O subphases contrast-matched to the mixed films. At 5 mN/m, the whole mixed films can be described by a single slightly hydrated thin layer. However, at 15 mN/m, the fit of the reflectivity curves requires a two-layer model consisting of a CA/PBd blend layer in contact with the water, interdiffused with a PBd layer at the interface with air. At intermediate surface pressure (10 mN/m), the determined structure was between those obtained at 5 and 15 mN/m depending on film composition. This PBd enrichment at the air-film interface at high surface pressure, which leads to the PBd depletion in the blend monolayer at the water surface, is attributed to the hydrophobic character of this polymer compared with the predominantly hydrophilic CA.
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Affiliation(s)
| | | | - Philippe Fontaine
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin, BP48, 91192 Gif sur Yvette Cedex, France
| | - Fabrice Cousin
- Laboratoire Léon Brillouin, Université Paris-Saclay, CEA-CNRS UMR 12, F-91191 Gif-sur-Yvette, France
| | - Philipp Gutfreund
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Michel Goldmann
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin, BP48, 91192 Gif sur Yvette Cedex, France
- Institut des NanoSciences de Paris, Sorbonne Université, 4 Place Jussieu, 75252 Paris Cedex 05, France
- Faculté des Sciences Fondamentales et Biomédicales, Université de Paris, 45 rue des Sts-Pères, 75006 Paris, France
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Lehman SE, Karageorgos I, Filteau JR, Vreeland WN. Effect of Azide Preservative on Thermomechanical Aggregation of Purified Reference Protein Materials. J Pharm Sci 2021; 110:1948-1957. [PMID: 33453208 DOI: 10.1016/j.xphs.2021.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 10/22/2022]
Abstract
Protein aggregation can affect the quality of protein-based therapeutics. Attempting to unravel factors influencing protein aggregation involves systematic studies. These studies often include sodium azide or similar preservatives in the aggregation buffer. This work shows effects of azide on aggregation of two highly purified reference proteins, both a bovine serum albumin (BSA) as well as a monoclonal antibody (NISTmAb). The proteins were aggregated by thermomechanical stress, consisting of simultaneous heating of the solution with gentle agitation. Protein aggregates were characterized by asymmetric flow field flow fractionation (AF4) with light scattering measurements along with quantification by UV spectroscopy, revealing strong time-dependent generation of aggregated protein and an increase in aggregate molar mass. Gel electrophoresis was used to probe the reversibility of the aggregation and demonstrated complete reversibility for the NISTmAb, but not so for the BSA. Kinetic fitting to a commonly implemented nucleated polymerization model was also employed to provide mechanistic details into the kinetic process. The model suggests that the aggregation of the NISTmAb proceeds via nucleated growth and aggregate-aggregate condensation in a way that is dependent on the concentration (and presence) of the azide anion. This work overall implicates azide preservatives as having demonstrable effects on thermomechanical stress and aggregation of proteins undergoing systematic aggregation and stability studies.
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Affiliation(s)
- Sean E Lehman
- Biomolecular Measurement Division, Bioprocess Measurements Group, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Ioannis Karageorgos
- Biomolecular Measurement Division, Bioprocess Measurements Group, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Jeremy R Filteau
- Biomolecular Measurement Division, Bioprocess Measurements Group, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA; Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
| | - Wyatt N Vreeland
- Biomolecular Measurement Division, Bioprocess Measurements Group, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
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Ferreira C, Pinto MF, Macedo-Ribeiro S, Pereira PJB, Rocha FA, Martins PM. Protein crystals as a key for deciphering macromolecular crowding effects on biological reactions. Phys Chem Chem Phys 2020; 22:16143-16149. [PMID: 32638771 DOI: 10.1039/d0cp02469d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
When placed in the same environment, biochemically unrelated macromolecules influence each other's biological function through macromolecular crowding (MC) effects. This has been illustrated in vitro by the effects of inert polymers on protein stability, protein structure, enzyme kinetics and protein aggregation kinetics. While a unified way to quantitatively characterize MC is still lacking, we show that the crystal solubility of lysozyme can be used to predict the influence of crowding agents on the catalytic efficiency of this enzyme. In order to capture general enthalpic effects, as well as hard entropic effects that are specific of large molecules, we tested sucrose and its cross-linked polymer Ficoll-70 as additives. Despite the different conditions of pH and ionic strength adopted, both the crystallization and the enzymatic assays point to an entropic contribution of approximately -1 kcal mol-1 caused by MC. Our results demonstrate that the thermodynamic activity of proteins is markedly increased by the reduction of accessible volume caused by the presence of macromolecular cosolutes. Unlike what is observed in protein folding studies, this MC effect cannot be reproduced using equivalent concentrations of monomeric crowding units. Applicable to any crystallizable protein, the thermodynamic interpretation of MC based on crystal solubility is expected to help in elucidating the full extent and importance of hard-type interactions in the crowded environment of the cell.
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Affiliation(s)
- Cecília Ferreira
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Maria Filipa Pinto
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal and ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal and IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal. and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Sandra Macedo-Ribeiro
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal. and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Pedro José Barbosa Pereira
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal. and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Fernando Alberto Rocha
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Pedro Miguel Martins
- ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal and IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal. and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
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Collagen hydrogel confinement of Amyloid-β (Aβ) accelerates aggregation and reduces cytotoxic effects. Acta Biomater 2020; 112:164-173. [PMID: 32464268 DOI: 10.1016/j.actbio.2020.05.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 01/09/2023]
Abstract
Alzheimer's disease (AD) is the most common form of dementia and is associated with the accumulation of amyloid-β (Aβ), a peptide whose aggregation has been associated with neurotoxicity. Drugs targeting Aβ have shown great promise in 2D in vitro models and mouse models, yet preclinical and clinical trials for AD have been highly disappointing. We propose that current in vitro culture systems for discovering and developing AD drugs have significant limitations; specifically, that Aβ aggregation is vastly different in these 2D cultures carried out on flat plastic or glass substrates vs. in a 3D environment, such as brain tissue, where Aβ confinement alters aggregation kinetics and thermodynamics. In this work, we identified attenuation of Aβ cytotoxicity in 3D hydrogel culture compared to 2D cell culture. We investigated Aβ structure and aggregation in solution vs. hydrogel using Transmission Electron Microscopy (TEM), Fluorescence Correlation Spectroscopy (FCS), and Thioflavin T (ThT) assays. Our results reveal that the equilibrium is shifted to stable extended β-sheet (ThT positive) aggregates in hydrogels and away from the relatively unstable/unstructured presumed toxic oligomeric Aβ species in solution. Volume exclusion imparted by hydrogel confinement stabilizes unfolded, presumably toxic species, promoting stable extended β-sheet fibrils. STATEMENT OF SIGNIFICANCE: Alzheimer's disease (AD) is a devastating disease and has been studied for over 100 years. Yet, no cure exists and only 5 prescription drugs are FDA-approved to temporarily treat the AD symptoms of declining brain functions related to thinking and memory. Why don't we have more effective treatments to cure AD or relieve AD symptoms? We propose that current culture methods based upon cells cultured on flat, stiff substrates have significant limitations for discovering and developing AD drugs. This study provides strong evidence that AD drugs should be tested in 3D culture systems as a step along the development pathway towards new, more effective drugs to treat AD.
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Zhao G, Dong X, Sun Y. Self-Assembled Curcumin-Poly(carboxybetaine methacrylate) Conjugates: Potent Nano-Inhibitors against Amyloid β-Protein Fibrillogenesis and Cytotoxicity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:1846-1857. [PMID: 30134656 DOI: 10.1021/acs.langmuir.8b01921] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Fibrillogenesis of amyloid β-protein (Aβ) is a pathological hallmark of Alzheimer's disease, so inhibition of Aβ aggregation is considered as an important strategy for the precaution and treatment of AD. Curcumin (Cur) has been recognized as an effective inhibitor of Aβ fibrillogenesis, but its potential application is limited by its poor bioavailability. Herein, we proposed to conjugate Cur to a zwitterionic polymer, poly(carboxybetaine methacrylate) (pCB), and synthesized three Cur@pCB conjugates of different degrees of substitution (DS, 1.9-2.9). Cur@pCB conjugates self-assembled into nanogels of 120-190 nm. The inhibition effects of Cur@pCB conjugates on the fibrillation and cytotoxicity of Aβ42 was investigated by extensive biophysical and biological analyses. Thioflavin T fluorescence assays and atomic force microscopic observations revealed that the Cur@pCB conjugates were much more efficient than molecular curcumin on inhibiting Aβ42 fibrillation, and cytotoxicity assays also indicated the same tendency. Of the three conjugates, Cur1@pCB of the lowest DS (1.97) exhibited the best performance; 5 μM Cur1@pCB functioned similarly with 25 μM free curcumin. Moreover, 5 μM Cur1@pCB increased the cell viability by 43% but free curcumin at the same concentration showed little effect. It is considered that the highly hydrated state of the zwitterionic polymers resulted in the superiority of Cur@pCB over free curcumin. Namely, the dense hydration layer on the conjugates strongly stabilized the bound Aβ on curcumin anchored on the polymer, suppressing the conformational transition of the protein to β-sheet-rich structures. This was demonstrated by circular dichroism spectroscopy, in which Cur1@pCB was proven to be the strongest in the three conjugates. The research has thus revealed a new function of zwitterionic polymer pCBMA and provided new insights into the development of more potent nanoinhibitors for suppressing Aβ fibrillogenesis and cytotoxicity.
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Affiliation(s)
- Guangfu Zhao
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology , Tianjin University , Tianjin 300072 , China
| | - Xiaoyan Dong
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology , Tianjin University , Tianjin 300072 , China
| | - Yan Sun
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology , Tianjin University , Tianjin 300072 , China
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8
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Sárkány Z, Rocha F, Damas AM, Macedo-Ribeiro S, Martins PM. Chemical Kinetic Strategies for High-Throughput Screening of Protein Aggregation Modulators. Chem Asian J 2019; 14:500-508. [DOI: 10.1002/asia.201801703] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/11/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Zsuzsa Sárkány
- LEPABE-Departamento de Engenharia Química; Faculdade de Engenharia da Universidade do Porto; Rua Dr. Roberto Frias 4200-465 Porto Portugal
| | - Fernando Rocha
- LEPABE-Departamento de Engenharia Química; Faculdade de Engenharia da Universidade do Porto; Rua Dr. Roberto Frias 4200-465 Porto Portugal
| | - Ana M. Damas
- ICBAS-Instituto de Ciências Biomédicas Abel Salazar; Universidade do Porto; 4050-313 Porto Portugal
| | - Sandra Macedo-Ribeiro
- IBMC-Instituto de Biologia Molecular e Celular; Universidade do Porto; 4200-135 Porto Portugal
- Instituto de Investigação e Inovação em Saúde; Universidade do Porto; 4200-135 Porto Portugal
| | - Pedro M. Martins
- IBMC-Instituto de Biologia Molecular e Celular; Universidade do Porto; 4200-135 Porto Portugal
- Instituto de Investigação e Inovação em Saúde; Universidade do Porto; 4200-135 Porto Portugal
- ICBAS-Instituto de Ciências Biomédicas Abel Salazar; Universidade do Porto; 4050-313 Porto Portugal
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9
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Silva A, Almeida B, Fraga JS, Taboada P, Martins PM, Macedo-Ribeiro S. Distribution of Amyloid-Like and Oligomeric Species from Protein Aggregation Kinetics. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Alexandra Silva
- IBMC-Instituto de Biologia Molecular e Celular and I3s-Instituto de Investigação e Inovação em Saúde Portugal; Universidade do Porto; 4150-180 Porto Portugal
| | - Bruno Almeida
- IBMC-Instituto de Biologia Molecular e Celular and I3s-Instituto de Investigação e Inovação em Saúde Portugal; Universidade do Porto; 4150-180 Porto Portugal
- Present address: Life and Health Sciences Research Institute (ICVS); School of Medicine; University of Minho; 4710-057 Braga Portugal
- ICVS/3B's-PT Government Associate Laboratory; University of Minho; Braga/Guimarães Portugal
| | - Joana S. Fraga
- IBMC-Instituto de Biologia Molecular e Celular and I3s-Instituto de Investigação e Inovação em Saúde Portugal; Universidade do Porto; 4150-180 Porto Portugal
| | - Pablo Taboada
- Área de Física de la Materia Condensada; Facultad de Física; Universidad de Santiago de Compostela; Instituto de Investigación Sanitaria (IDIS) de Santiago de Compostela; Spain
| | - Pedro M. Martins
- IBMC-Instituto de Biologia Molecular e Celular and I3s-Instituto de Investigação e Inovação em Saúde Portugal; Universidade do Porto; 4150-180 Porto Portugal
- LEPABE-Departamento de Engenharia Química; Faculdade de Engenharia da Universidade do Porto; Rua Dr. Roberto Frias 4200-465 Porto Portugal
- ICBAS-Instituto de Ciências Biomédicas Abel Salazar; Universidade do Porto; Portugal
| | - Sandra Macedo-Ribeiro
- IBMC-Instituto de Biologia Molecular e Celular and I3s-Instituto de Investigação e Inovação em Saúde Portugal; Universidade do Porto; 4150-180 Porto Portugal
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10
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Silva A, Almeida B, Fraga JS, Taboada P, Martins PM, Macedo-Ribeiro S. Distribution of Amyloid-Like and Oligomeric Species from Protein Aggregation Kinetics. Angew Chem Int Ed Engl 2017; 56:14042-14045. [PMID: 28906069 DOI: 10.1002/anie.201707345] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Indexed: 12/13/2022]
Abstract
Amyloid fibrils and soluble oligomers are two types of protein aggregates associated with neurodegeneration. Classic therapeutic strategies try to prevent the nucleation and spread of amyloid fibrils, whilst diffusible oligomers have emerged as promising drug targets affecting downstream pathogenic processes. We developed a generic protein aggregation model and validate it against measured compositions of fibrillar and non-fibrillar assemblies of ataxin-3, a protein implicated in Machado-Joseph disease. The derived analytic rate-law equations can be used to 1) identify the presence of parallel aggregation pathways and 2) estimate the critical sizes of amyloid fibrils. The discretized population balance supporting our model is the first to quantitatively fit time-resolved measurements of size and composition of both amyloid-like and oligomeric species. The new theoretical framework can be used to screen a new class of drugs specifically targeting toxic oligomers.
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Affiliation(s)
- Alexandra Silva
- IBMC-Instituto de Biologia Molecular e Celular and I3s-Instituto de Investigação e Inovação em Saúde Portugal, Universidade do Porto, 4150-180, Porto, Portugal
| | - Bruno Almeida
- IBMC-Instituto de Biologia Molecular e Celular and I3s-Instituto de Investigação e Inovação em Saúde Portugal, Universidade do Porto, 4150-180, Porto, Portugal.,Present address: Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory, University of Minho, Braga/Guimarães, Portugal
| | - Joana S Fraga
- IBMC-Instituto de Biologia Molecular e Celular and I3s-Instituto de Investigação e Inovação em Saúde Portugal, Universidade do Porto, 4150-180, Porto, Portugal
| | - Pablo Taboada
- Área de Física de la Materia Condensada, Facultad de Física, Universidad de Santiago de Compostela, Instituto de Investigación Sanitaria (IDIS) de Santiago de Compostela, Spain
| | - Pedro M Martins
- IBMC-Instituto de Biologia Molecular e Celular and I3s-Instituto de Investigação e Inovação em Saúde Portugal, Universidade do Porto, 4150-180, Porto, Portugal.,LEPABE-Departamento de Engenharia Química, Faculdade de Engenharia da Universidade do Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal.,ICBAS-Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Portugal
| | - Sandra Macedo-Ribeiro
- IBMC-Instituto de Biologia Molecular e Celular and I3s-Instituto de Investigação e Inovação em Saúde Portugal, Universidade do Porto, 4150-180, Porto, Portugal
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11
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Ferreira C, Barbosa S, Taboada P, Rocha FA, Damas AM, Martins PM. The nucleation of protein crystals as a race against time with on- and off-pathways. J Appl Crystallogr 2017. [DOI: 10.1107/s1600576717007312] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
High supersaturation levels are a necessary but insufficient condition for the crystallization of purified proteins. Unlike most small molecules, proteins can take diverse aggregation pathways that make the outcome of crystallization assays quite unpredictable. Here, dynamic light scattering and optical microscopy were used to show that the nucleation of lysozyme crystals is preceded by an initial step of protein oligomerization and by the progressive formation of metastable clusters. Because these steps deplete the concentration of soluble monomers, the probability of obtaining protein crystals decreases as time progresses. Stochastic variations of the induction time are thus amplified to a point where fast crystallization can coexist with unyielding regimes in the same conditions. With an initial hydrodynamic radius of ∼100 nm, the metastable clusters also promote the formation of protein crystals through a mechanism of heterogeneous nucleation. Crystal growth (on-pathway) takes place in parallel with cluster growth (off-pathway). The Janus-faced influence of the mesoscopic clusters is beneficial when it accelerates the formation of the first precrystalline nuclei and is detrimental as it depletes the solution of protein ready to crystallize. Choosing the right balance between the two effects is critical for determining the success of protein crystallization trials. The results presented here suggest that a mild oligomerization degree promotes the formation of a small number of metastable clusters which then catalyze the nucleation of well differentiated crystals.
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