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Toledo PL, Gianotti AR, Vazquez DS, Ermácora MR. Protein nanocondensates: the next frontier. Biophys Rev 2023; 15:515-530. [PMID: 37681092 PMCID: PMC10480383 DOI: 10.1007/s12551-023-01105-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 07/21/2023] [Indexed: 09/09/2023] Open
Abstract
Over the past decade, myriads of studies have highlighted the central role of protein condensation in subcellular compartmentalization and spatiotemporal organization of biological processes. Conceptually, protein condensation stands at the highest level in protein structure hierarchy, accounting for the assembly of bodies ranging from thousands to billions of molecules and for densities ranging from dense liquids to solid materials. In size, protein condensates range from nanocondensates of hundreds of nanometers (mesoscopic clusters) to phase-separated micron-sized condensates. In this review, we focus on protein nanocondensation, a process that can occur in subsaturated solutions and can nucleate dense liquid phases, crystals, amorphous aggregates, and fibers. We discuss the nanocondensation of proteins in the light of general physical principles and examine the biophysical properties of several outstanding examples of nanocondensation. We conclude that protein nanocondensation cannot be fully explained by the conceptual framework of micron-scale biomolecular condensation. The evolution of nanocondensates through changes in density and order is currently under intense investigation, and this should lead to the development of a general theoretical framework, capable of encompassing the full range of sizes and densities found in protein condensates.
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Affiliation(s)
- Pamela L. Toledo
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876, Bernal, Buenos Aires, Argentina
- Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Alejo R. Gianotti
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876, Bernal, Buenos Aires, Argentina
- Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Diego S. Vazquez
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876, Bernal, Buenos Aires, Argentina
- Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Mario R. Ermácora
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876, Bernal, Buenos Aires, Argentina
- Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Bernal, Argentina
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Hendriks WJAJ, van Cruchten RTP, Pulido R. Hereditable variants of classical protein tyrosine phosphatase genes: Will they prove innocent or guilty? Front Cell Dev Biol 2023; 10:1051311. [PMID: 36755664 PMCID: PMC9900141 DOI: 10.3389/fcell.2022.1051311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/28/2022] [Indexed: 01/24/2023] Open
Abstract
Protein tyrosine phosphatases, together with protein tyrosine kinases, control many molecular signaling steps that control life at cellular and organismal levels. Impairing alterations in the genes encoding the involved proteins is expected to profoundly affect the quality of life-if compatible with life at all. Here, we review the current knowledge on the effects of germline variants that have been reported for genes encoding a subset of the protein tyrosine phosphatase superfamily; that of the thirty seven classical members. The conclusion must be that the newest genome research tools produced an avalanche of data that suggest 'guilt by association' for individual genes to specific disorders. Future research should face the challenge to investigate these accusations thoroughly and convincingly, to reach a mature genotype-phenotype map for this intriguing protein family.
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Affiliation(s)
- Wiljan J. A. J. Hendriks
- Department of Cell Biology, Radboud University Medical Centre, Nijmegen, The Netherlands,*Correspondence: Wiljan J. A. J. Hendriks,
| | | | - Rafael Pulido
- Biomarkers in Cancer Unit, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
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Vazquez DS, Toledo PL, Gianotti AR, Ermácora MR. Protein conformation and biomolecular condensates. Curr Res Struct Biol 2022; 4:285-307. [PMID: 36164646 PMCID: PMC9508354 DOI: 10.1016/j.crstbi.2022.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/08/2022] [Accepted: 09/13/2022] [Indexed: 10/27/2022] Open
Abstract
Protein conformation and cell compartmentalization are fundamental concepts and subjects of vast scientific endeavors. In the last two decades, we have witnessed exciting advances that unveiled the conjunction of these concepts. An avalanche of studies highlighted the central role of biomolecular condensates in membraneless subcellular compartmentalization that permits the spatiotemporal organization and regulation of myriads of simultaneous biochemical reactions and macromolecular interactions. These studies have also shown that biomolecular condensation, driven by multivalent intermolecular interactions, is mediated by order-disorder transitions of protein conformation and by protein domain architecture. Conceptually, protein condensation is a distinct level in protein conformational landscape in which collective folding of large collections of molecules takes place. Biomolecular condensates arise by the physical process of phase separation and comprise a variety of bodies ranging from membraneless organelles to liquid condensates to solid-like conglomerates, spanning lengths from mesoscopic clusters (nanometers) to micrometer-sized objects. In this review, we summarize and discuss recent work on the assembly, composition, conformation, material properties, thermodynamics, regulation, and functions of these bodies. We also review the conceptual framework for future studies on the conformational dynamics of condensed proteins in the regulation of cellular processes.
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Affiliation(s)
- Diego S. Vazquez
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes and Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Argentina
| | - Pamela L. Toledo
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes and Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Argentina
| | - Alejo R. Gianotti
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes and Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Argentina
| | - Mario R. Ermácora
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes and Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Argentina
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Ashraf UM, Mell B, Jose PA, Kumarasamy S. Deep transcriptomic profiling of Dahl salt-sensitive rat kidneys with mutant form of Resp18. Biochem Biophys Res Commun 2021; 572:35-40. [PMID: 34340197 DOI: 10.1016/j.bbrc.2021.07.071] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/15/2021] [Accepted: 07/20/2021] [Indexed: 01/26/2023]
Abstract
Expression of Regulated endocrine specific protein 18 (Resp18) is localized in numerous tissues and cell types; however, its exact cellular function is unknown. We previously showed that targeted disruption of the Resp18 locus in the Dahl SS (SS) rat (Resp18mutant) results in higher blood pressure (BP), increased renal fibrosis, increased urinary protein excretion, and decreased mean survival time following a chronic (6 weeks) 2% high salt (HS) diet compared with the SS rat. Based on this prominent renal injury phenotype, we hypothesized that targeted disruption of Resp18 in the SS rat promotes an early onset hypertensive-signaling event through altered signatures of the renal transcriptome in response to HS. To test this hypothesis, both SS and Resp18mutant rats were exposed to a 7-day 2% HS diet and BP was recorded by radiotelemetry. After a 7-day exposure to the HS diet, systolic BP was significantly increased in the Resp18mutant rat compared with the SS rat throughout the circadian cycle. Therefore, we sought to investigate the renal transcriptomic response to HS in the Resp18mutant rat. Using RNA sequencing, Resp18mutant rats showed a differential expression of 25 renal genes, including upregulation of Ren. Upregulation of renal Ren and other differentially expressed genes were confirmed via qRT-PCR. Moreover, circulating renin activity was significantly higher in the Resp18mutant rat compared with the WT SS rat after 7 days on HS. Collectively, these observations demonstrate that disruption of the Resp18 gene in the SS rat is associated with an altered renal transcriptomics signature as an early response to salt load.
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Affiliation(s)
- Usman M Ashraf
- Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, 43614, USA
| | - Blair Mell
- Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, 43614, USA
| | - Pedro A Jose
- Department of Medicine, Division of Kidney Diseases & Hypertension, The George Washington University School of Medicine & Health Sciences, Washington, DC, 20052, USA; Department of Pharmacology and Physiology, The George Washington University School of Medicine & Health Sciences, Washington, DC, 20052, USA
| | - Sivarajan Kumarasamy
- Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, 43614, USA; Department of Biomedical Sciences, Ohio University, Athens, OH, 45701, USA; Diabetes Institute, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, 45701, USA.
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Bolandi V, Azghadi SK, Shahami M, Fereidouni M. Prevalence of IA-2 antibody in patients suffering from diabetes and their first-degree relatives. Int J Diabetes Dev Ctries 2020. [DOI: 10.1007/s13410-020-00882-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Atari E, Perry MC, Jose PA, Kumarasamy S. Regulated Endocrine-Specific Protein-18, an Emerging Endocrine Protein in Physiology: A Literature Review. Endocrinology 2019; 160:2093-2100. [PMID: 31294787 DOI: 10.1210/en.2019-00397] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 07/04/2019] [Indexed: 01/10/2023]
Abstract
Regulated endocrine-specific protein-18 (RESP18), a novel 18-kDa protein, was first identified in neuroendocrine tissue. Subsequent studies showed that Resp18 is expressed in the adrenal medulla, brain, pancreas, pituitary, retina, stomach, superior cervical ganglion, testis, and thyroid and also circulates in the plasma. Resp18 has partial homology with the islet cell antigen 512, also known as protein tyrosine phosphatase, receptor type N (PTPRN), but does not have phosphatase activity. Resp18 might serve as an intracellular signal; however, its function is unclear. It is regulated by dopamine, glucocorticoids, and insulin. We recently reported that the targeted disruption of the Resp18 locus in Dahl salt-sensitive rats increased their blood pressure and caused renal injury. The aim of the present review was to provide a comprehensive summary of the reported data currently available, especially the expression and proposed organ-specific function of Resp18.
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Affiliation(s)
- Ealla Atari
- Center for Hypertension and Precision Medicine, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
- Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - Mitchel C Perry
- Center for Hypertension and Precision Medicine, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
- Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - Pedro A Jose
- Division of Kidney Diseases and Hypertension, Department of Medicine, The George Washington University School of Medicine & Health Sciences, Washington, DC
- Department of Pharmacology and Physiology, The George Washington University School of Medicine & Health Sciences, Washington, DC
| | - Sivarajan Kumarasamy
- Center for Hypertension and Precision Medicine, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
- Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
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Toledo PL, Torkko JM, Müller A, Wegbrod C, Sönmez A, Solimena M, Ermácora MR. ICA512 RESP18 homology domain is a protein-condensing factor and insulin fibrillation inhibitor. J Biol Chem 2019; 294:8564-8576. [PMID: 30979722 DOI: 10.1074/jbc.ra119.007607] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/09/2019] [Indexed: 12/19/2022] Open
Abstract
Type 1 diabetes islet cell autoantigen 512 (ICA512/IA-2) is a tyrosine phosphatase-like intrinsic membrane protein involved in the biogenesis and turnover of insulin secretory granules (SGs) in pancreatic islet β-cells. Whereas its membrane-proximal and cytoplasmic domains have been functionally and structurally characterized, the role of the ICA512 N-terminal segment named "regulated endocrine-specific protein 18 homology domain" (RESP18HD), which encompasses residues 35-131, remains largely unknown. Here, we show that ICA512 RESP18HD residues 91-131 encode for an intrinsically disordered region (IDR), which in vitro acts as a condensing factor for the reversible aggregation of insulin and other β-cell proteins in a pH and Zn2+-regulated fashion. At variance with what has been shown for other granule cargoes with aggregating properties, the condensing activity of ICA512 RESP18HD is displayed at a pH close to neutral, i.e. in the pH range found in the early secretory pathway, whereas it is resolved at acidic pH and Zn2+ concentrations resembling those present in mature SGs. Moreover, we show that ICA512 RESP18HD residues 35-90, preceding the IDR, inhibit insulin fibrillation in vitro Finally, we found that glucose-stimulated secretion of RESP18HD upon exocytosis of SGs from insulinoma INS-1 cells is associated with cleavage of its IDR, conceivably to prevent its aggregation upon exposure to neutral pH in the extracellular milieu. Taken together, these findings point to ICA512 RESP18HD being a condensing factor for protein sorting and granulogenesis early in the secretory pathway and for prevention of amyloidogenesis.
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Affiliation(s)
- Pamela L Toledo
- Grupo de Biología Estructural y Biotecnología, Universidad Nacional de Quilmes, 1876 Bernal, Buenos Aires, Argentina; IMBICE, CONICET-CIC-Universidad Nacional de La Plata, B1906APO La Plata, Buenos Aires, Argentina
| | - Juha M Torkko
- Grupo de Biología Estructural y Biotecnología, Universidad Nacional de Quilmes, 1876 Bernal, Buenos Aires, Argentina; IMBICE, CONICET-CIC-Universidad Nacional de La Plata, B1906APO La Plata, Buenos Aires, Argentina; Department of Molecular Diabetology, University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany; Paul Langerhans Institute Dresden of the Helmholtz Center Munich at the University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD e.V.), 85764 Neuherberg, Germany
| | - Andreas Müller
- Department of Molecular Diabetology, University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany; Paul Langerhans Institute Dresden of the Helmholtz Center Munich at the University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD e.V.), 85764 Neuherberg, Germany
| | - Carolin Wegbrod
- Department of Molecular Diabetology, University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany; Paul Langerhans Institute Dresden of the Helmholtz Center Munich at the University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD e.V.), 85764 Neuherberg, Germany
| | - Anke Sönmez
- Department of Molecular Diabetology, University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany; Paul Langerhans Institute Dresden of the Helmholtz Center Munich at the University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD e.V.), 85764 Neuherberg, Germany
| | - Michele Solimena
- Department of Molecular Diabetology, University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany; Paul Langerhans Institute Dresden of the Helmholtz Center Munich at the University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD e.V.), 85764 Neuherberg, Germany; Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.
| | - Mario R Ermácora
- Grupo de Biología Estructural y Biotecnología, Universidad Nacional de Quilmes, 1876 Bernal, Buenos Aires, Argentina; IMBICE, CONICET-CIC-Universidad Nacional de La Plata, B1906APO La Plata, Buenos Aires, Argentina.
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