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do Amaral MJ, Passos YM, Almeida MS, Pinheiro AS, Cordeiro Y. In Vitro Characterization of Protein:Nucleic Acid Liquid-Liquid Phase Separation by Microscopy Methods and Nanoparticle Tracking Analysis. Methods Mol Biol 2023; 2551:605-631. [PMID: 36310228 DOI: 10.1007/978-1-0716-2597-2_37] [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: 06/16/2023]
Abstract
Uncontrolled assembly/disassembly of physiologically formed liquid condensates is linked to irreversible aggregation. Hence, the quest for understanding protein-misfolding disease mechanism might lie in the studies of protein:nucleic acid coacervation. Several proteins with intrinsically disordered regions as well as nucleic acids undergo phase separation in the cellular context, and this process is key to physiological signaling and is related to pathologies. Phase separation is reproducible in vitro by mixing the target recombinant protein with specific nucleic acids at various stoichiometric ratios and then examined by microscopy and nanotracking methods presented herein. We describe protocols to qualitatively assess hallmarks of protein-rich condensates, characterize their structure using intrinsic and extrinsic dyes, quantify them, and analyze their morphology over time. Analysis by nanoparticle tracking provides information on the concentration and diameter of high-order protein oligomers formed in the presence of nucleic acid. Using the model protein (globular domain of recombinant murine PrP) and DNA aptamers (high-affinity oligonucleotides with 25 nucleotides in length), we provide examples of a systematic screening of liquid-liquid phase separation in vitro.
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Affiliation(s)
- Mariana J do Amaral
- Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Yulli M Passos
- Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcius S Almeida
- Protein Advanced Biochemistry, Institute of Medical Biochemistry Leopoldo de Meis and National Center for Structural Biology and Bioimaging, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Anderson S Pinheiro
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Yraima Cordeiro
- Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
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Kovachev PS, Gomes MPB, Cordeiro Y, Ferreira NC, Valadão LPF, Ascari LM, Rangel LP, Silva JL, Sanyal S. RNA modulates aggregation of the recombinant mammalian prion protein by direct interaction. Sci Rep 2019; 9:12406. [PMID: 31455808 PMCID: PMC6712051 DOI: 10.1038/s41598-019-48883-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 08/12/2019] [Indexed: 12/22/2022] Open
Abstract
Recent studies have proposed that nucleic acids act as potential cofactors for protein aggregation and prionogenesis. By means of sedimentation, transmission electron microscopy, circular dichroism, static and dynamic light scattering, we have studied how RNA can influence the aggregation of the murine recombinant prion protein (rPrP). We find that RNA, independent of its sequence, source and size, modulates rPrP aggregation in a bimodal fashion, affecting both the extent and the rate of rPrP aggregation in a concentration dependent manner. Analogous to RNA-induced liquid-liquid phase transitions observed for other proteins implicated in neurodegenerative diseases, high protein to RNA ratios stimulate rPrP aggregation, while low ratios suppress it. However, the latter scenario also promotes formation of soluble oligomeric aggregates capable of seeding de novo rPrP aggregation. Furthermore, RNA co-aggregates with rPrP and thereby gains partial protection from RNase digestion. Our results also indicate that rPrP interacts with the RNAs with its N-terminus. In summary, this study elucidates the proposed adjuvant role of RNA in prion protein aggregation and propagation, and thus advocates an auxiliary role of the nucleic acids in protein aggregation in general.
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Affiliation(s)
- Petar Stefanov Kovachev
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Box-596, 75124, Sweden
| | - Mariana P B Gomes
- Instituto de Tecnologia em Imunobiológicos, Bio-Manguinhos, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Yraima Cordeiro
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Natália C Ferreira
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil.,Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States of America
| | - Leticia P Felix Valadão
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Lucas M Ascari
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Luciana P Rangel
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Jerson L Silva
- Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Ciência Tecnologia de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil.
| | - Suparna Sanyal
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Box-596, 75124, Sweden.
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Bera A, Nandi PK. Nucleic acid induced unfolding of recombinant prion protein globular fragment is pH dependent. Protein Sci 2014; 23:1780-8. [PMID: 25271002 DOI: 10.1002/pro.2573] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 09/29/2014] [Indexed: 01/18/2023]
Abstract
Nucleic acid can catalyze the conversion of α-helical cellular prion protein to β-sheet rich Proteinase K resistant prion protein oligomers and amyloid polymers in vitro and in solution. Because unfolding of a protein molecule from its ordered α-helical structure is considered to be a necessary step for the structural conversion to its β-sheet rich isoform, we have studied the unfolding of the α-helical globular 121-231 fragment of mouse recombinant prion protein in the presence of different nucleic acids at neutral and acid pH. Nucleic acids, either single or double stranded, do not have any significant effect on the secondary structure of the protein fragment at neutral pH; however the protein secondary structure is modified by the nucleic acids at pH 5. Nucleic acids do not show any significant effect on the temperature induced unfolding of the globular prion protein domain at neutral pH which, however, undergoes a gross conformational change at pH 5 as evidenced from the lowering of the midpoint of thermal denaturation temperatures, Tm, of the protein. The extent of Tm decrease shows a dependence on the nature of nucleic acid. The interaction of nucleic acid with the nonpolar groups exposed from the protein interior at pH 5 probably contributes substantially to the unfolding process of the protein.
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Affiliation(s)
- Alakesh Bera
- Infectiologie Animale et Santé Publique, Institut National de la Recherche Agronomique, 37380, Nouzilly, France
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Biophysical and morphological studies on the dual interaction of non-octarepeat prion protein peptides with copper and nucleic acids. J Biol Inorg Chem 2014; 19:839-51. [DOI: 10.1007/s00775-014-1115-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Accepted: 01/28/2014] [Indexed: 12/21/2022]
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Macedo B, Millen TA, Braga CACA, Gomes MPB, Ferreira PS, Kraineva J, Winter R, Silva JL, Cordeiro Y. Nonspecific Prion Protein–Nucleic Acid Interactions Lead to Different Aggregates and Cytotoxic Species. Biochemistry 2012; 51:5402-13. [DOI: 10.1021/bi300440e] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bruno Macedo
- Faculdade de Farmacia, Universidade Federal do Rio de Janeiro, RJ 21941-590,
Rio de Janeiro, Brazil
| | - Thiago A. Millen
- Instituto de Bioquimica Medica, Universidade Federal do Rio de Janeiro, Rio de Janeiro,
Brazil
| | - Carolina A. C. A. Braga
- Instituto de Bioquimica Medica, Universidade Federal do Rio de Janeiro, Rio de Janeiro,
Brazil
| | - Mariana P. B. Gomes
- Faculdade de Farmacia, Universidade Federal do Rio de Janeiro, RJ 21941-590,
Rio de Janeiro, Brazil
| | - Priscila S. Ferreira
- Instituto de Bioquimica Medica, Universidade Federal do Rio de Janeiro, Rio de Janeiro,
Brazil
| | - Julia Kraineva
- Faculty of Chemistry,
Physical
Chemistry I, Dortmund University, Dortmund,
Germany
| | - Roland Winter
- Faculty of Chemistry,
Physical
Chemistry I, Dortmund University, Dortmund,
Germany
| | - Jerson L. Silva
- Instituto de Bioquimica Medica, Universidade Federal do Rio de Janeiro, Rio de Janeiro,
Brazil
| | - Yraima Cordeiro
- Faculdade de Farmacia, Universidade Federal do Rio de Janeiro, RJ 21941-590,
Rio de Janeiro, Brazil
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Linden R, Cordeiro Y, Lima LMTR. Allosteric function and dysfunction of the prion protein. Cell Mol Life Sci 2012; 69:1105-24. [PMID: 21984610 PMCID: PMC11114699 DOI: 10.1007/s00018-011-0847-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Revised: 09/16/2011] [Accepted: 09/20/2011] [Indexed: 12/30/2022]
Abstract
Transmissible spongiform encephalopathies (TSEs) are neurodegenerative diseases associated with progressive oligo- and multimerization of the prion protein (PrP(C)), its conformational conversion, aggregation and precipitation. We recently proposed that PrP(C) serves as a cell surface scaffold protein for a variety of signaling modules, the effects of which translate into wide-range functional consequences. Here we review evidence for allosteric functions of PrP(C), which constitute a common property of scaffold proteins. The available data suggest that allosteric effects among PrP(C) and its partners are involved in the assembly of multi-component signaling modules at the cell surface, impose upon both physiological and pathological conformational responses of PrP(C), and that allosteric dysfunction of PrP(C) has the potential to entail progressive signal corruption. These properties may be germane both to physiological roles of PrP(C), as well as to the pathogenesis of the TSEs and other degenerative/non-communicable diseases.
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Affiliation(s)
- Rafael Linden
- Instituto de Biofísica Carlos Chagas Filho, UFRJ, CCS, Cidade Universitária, Rio de Janeiro, Brazil.
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Cellular prion protein localizes to the nucleus of endocrine and neuronal cells and interacts with structural chromatin components. Eur J Cell Biol 2011; 90:414-9. [DOI: 10.1016/j.ejcb.2010.11.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Revised: 11/25/2010] [Accepted: 11/25/2010] [Indexed: 11/18/2022] Open
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Attri P, Venkatesu P, Kumar A, Byrne N. A protic ionic liquid attenuates the deleterious actions of urea on α-chymotrypsin. Phys Chem Chem Phys 2011; 13:17023-6. [DOI: 10.1039/c1cp22195g] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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9
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Silva JL, Vieira TCRG, Gomes MPB, Rangel LP, Scapin SMN, Cordeiro Y. Experimental approaches to the interaction of the prion protein with nucleic acids and glycosaminoglycans: Modulators of the pathogenic conversion. Methods 2010; 53:306-17. [PMID: 21145399 DOI: 10.1016/j.ymeth.2010.12.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Accepted: 12/02/2010] [Indexed: 11/17/2022] Open
Abstract
The concept that transmissible spongiform encephalopathies (TSEs) are caused only by proteins has changed the traditional paradigm that disease transmission is due solely to an agent that carries genetic information. The central hypothesis for prion diseases proposes that the conversion of a cellular prion protein (PrP(C)) into a misfolded, β-sheet-rich isoform (PrP(Sc)) accounts for the development of (TSE). There is substantial evidence that the infectious material consists chiefly of a protein, PrP(Sc), with no genomic coding material, unlike a virus particle, which has both. However, prions seem to have other partners that chaperone their activities in converting the PrP(C) into the disease-causing isoform. Nucleic acids (NAs) and glycosaminoglycans (GAGs) are the most probable accomplices of prion conversion. Here, we review the recent experimental approaches that have been employed to characterize the interaction of prion proteins with nucleic acids and glycosaminoglycans. A PrP recognizes many nucleic acids and GAGs with high affinities, and this seems to be related to a pathophysiological role for this interaction. A PrP binds nucleic acids and GAGs with structural selectivity, and some PrP:NA complexes can become proteinase K-resistant, undergoing amyloid oligomerization and conversion to a β-sheet-rich structure. These results are consistent with the hypothesis that endogenous polyanions (such as NAs and GAGs) may accelerate the rate of prion disease progression by acting as scaffolds or lattices that mediate the interaction between PrP(C) and PrP(Sc) molecules. In addition to a still-possible hypothesis that nucleic acids and GAGs, especially those from the host, may modulate the conversion, the recent structural characterization of the complexes has raised the possibility of developing new diagnostic and therapeutic strategies.
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Affiliation(s)
- Jerson L Silva
- Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Instituto de Bioquímica Médica, Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Brazil.
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