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Freiberger MI, Ruiz-Serra V, Pontes C, Romero-Durana M, Galaz-Davison P, Ramírez-Sarmiento CA, Schuster CD, Marti MA, Wolynes PG, Ferreiro DU, Parra RG, Valencia A. Local energetic frustration conservation in protein families and superfamilies. Nat Commun 2023; 14:8379. [PMID: 38104123 PMCID: PMC10725452 DOI: 10.1038/s41467-023-43801-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 11/20/2023] [Indexed: 12/19/2023] Open
Abstract
Energetic local frustration offers a biophysical perspective to interpret the effects of sequence variability on protein families. Here we present a methodology to analyze local frustration patterns within protein families and superfamilies that allows us to uncover constraints related to stability and function, and identify differential frustration patterns in families with a common ancestry. We analyze these signals in very well studied protein families such as PDZ, SH3, ɑ and β globins and RAS families. Recent advances in protein structure prediction make it possible to analyze a vast majority of the protein space. An automatic and unsupervised proteome-wide analysis on the SARS-CoV-2 virus demonstrates the potential of our approach to enhance our understanding of the natural phenotypic diversity of protein families beyond single protein instances. We apply our method to modify biophysical properties of natural proteins based on their family properties, as well as perform unsupervised analysis of large datasets to shed light on the physicochemical signatures of poorly characterized proteins such as the ones belonging to emergent pathogens.
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Affiliation(s)
- Maria I Freiberger
- Laboratorio de Fisiología de Proteínas, Departamento de Química Biológica - IQUIBICEN/CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, C1428EGA, Argentina
| | - Victoria Ruiz-Serra
- Computational Biology Group, Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain
| | - Camila Pontes
- Computational Biology Group, Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain
| | - Miguel Romero-Durana
- Computational Biology Group, Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain
| | - Pablo Galaz-Davison
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine, and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, 7820436, Chile
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, 8331150, Chile
| | - Cesar A Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine, and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, 7820436, Chile
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, 8331150, Chile
| | - Claudio D Schuster
- Laboratorio de Bioinformática, Departamento de Química Biológica - IQUIBICEN/CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina
| | - Marcelo A Marti
- Laboratorio de Bioinformática, Departamento de Química Biológica - IQUIBICEN/CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina
| | - Peter G Wolynes
- Center for Theoretical Biological Physics and Department of Chemistry, Rice University, Houston, TX, 77005, USA
| | - Diego U Ferreiro
- Laboratorio de Fisiología de Proteínas, Departamento de Química Biológica - IQUIBICEN/CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, C1428EGA, Argentina
| | - R Gonzalo Parra
- Computational Biology Group, Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain.
| | - Alfonso Valencia
- Computational Biology Group, Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
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Martin A, Fernandez MC, Cattaneo ER, Schuster CD, Venara M, Clément F, Berenstein A, Lombardi MG, Bergadá I, Gutierrez M, Martí MA, Gonzalez-Baro MR, Pennisi PA. Type 1 Insulin-Like Growth Factor Receptor Nuclear Localization in High-Grade Glioma Cells Enhances Motility, Metabolism, and In Vivo Tumorigenesis. Front Endocrinol (Lausanne) 2022; 13:849279. [PMID: 35574033 PMCID: PMC9094447 DOI: 10.3389/fendo.2022.849279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/11/2022] [Indexed: 11/16/2022] Open
Abstract
Gliomas are the most frequent solid tumors in children. Among these, high-grade gliomas are less common in children than in adults, though they are similar in their aggressive clinical behavior. In adults, glioblastoma is the most lethal tumor of the central nervous system. Insulin-like growth factor 1 receptor (IGF1R) plays an important role in cancer biology, and its nuclear localization has been described as an adverse prognostic factor in different tumors. Previously, we have demonstrated that, in pediatric gliomas, IGF1R nuclear localization is significantly associated with high-grade tumors, worst clinical outcome, and increased risk of death. Herein we explore the role of IGF1R intracellular localization by comparing two glioblastoma cell lines that differ only in their IGF1R capacity to translocate to the nucleus. In vitro, IGF1R nuclear localization enhances glioblastoma cell motility and metabolism without affecting their proliferation. In vivo, IGF1R has the capacity to translocate to the nucleus and allows not only a higher proliferation rate and the earlier development of tumors but also renders the cells sensitive to OSI906 therapy. With this work, we provide evidence supporting the implications of the presence of IGF1R in the nucleus of glioma cells and a potential therapeutic opportunity for patients harboring gliomas with IGF1R nuclear localization.
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Affiliation(s)
- Ayelen Martin
- Centro de Investigaciones Endocrinológicas “Dr. César Bergadá” CONICET—FEI—División de Endocrinología, Hospital de Niños R. Gutierrez, Buenos Aires, Argentina
| | - María Celia Fernandez
- Centro de Investigaciones Endocrinológicas “Dr. César Bergadá” CONICET—FEI—División de Endocrinología, Hospital de Niños R. Gutierrez, Buenos Aires, Argentina
| | - Elizabeth R. Cattaneo
- Instituto de Investigaciones Bioquímicas de La Plata, CONICET, Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Claudio D. Schuster
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires, Argentina
| | - Marcela Venara
- Centro de Investigaciones Endocrinológicas “Dr. César Bergadá” CONICET—FEI—División de Endocrinología, Hospital de Niños R. Gutierrez, Buenos Aires, Argentina
| | - Florencia Clément
- Centro de Investigaciones Endocrinológicas “Dr. César Bergadá” CONICET—FEI—División de Endocrinología, Hospital de Niños R. Gutierrez, Buenos Aires, Argentina
| | - Ariel Berenstein
- Centro de Investigaciones Endocrinológicas “Dr. César Bergadá” CONICET—FEI—División de Endocrinología, Hospital de Niños R. Gutierrez, Buenos Aires, Argentina
- Instituto Multidisciplinario de Investigaciones en Patologías Pediátricas, CONICET, Hospital de Niños R. Gutierrez, Buenos Aires, Argentina
| | | | - Ignacio Bergadá
- Centro de Investigaciones Endocrinológicas “Dr. César Bergadá” CONICET—FEI—División de Endocrinología, Hospital de Niños R. Gutierrez, Buenos Aires, Argentina
| | - Mariana Gutierrez
- Centro de Investigaciones Endocrinológicas “Dr. César Bergadá” CONICET—FEI—División de Endocrinología, Hospital de Niños R. Gutierrez, Buenos Aires, Argentina
| | - Marcelo A. Martí
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires, Argentina
| | - María R. Gonzalez-Baro
- Instituto de Investigaciones Bioquímicas de La Plata, CONICET, Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Patricia A. Pennisi
- Centro de Investigaciones Endocrinológicas “Dr. César Bergadá” CONICET—FEI—División de Endocrinología, Hospital de Niños R. Gutierrez, Buenos Aires, Argentina
- *Correspondence: Patricia A. Pennisi,
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Hammerschmid D, Germani F, Drusin SI, Fagnen C, Schuster CD, Hoogewijs D, Marti MA, Venien-Bryan C, Moens L, Van Doorslaer S, Sobott F, Dewilde S. Structural modeling of a novel membrane-bound globin-coupled sensor in Geobacter sulfurreducens. Comput Struct Biotechnol J 2021; 19:1874-1888. [PMID: 33995893 PMCID: PMC8076648 DOI: 10.1016/j.csbj.2021.03.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 03/24/2021] [Accepted: 03/24/2021] [Indexed: 12/12/2022] Open
Abstract
Globin-coupled sensors (GCS) usually consist of three domains: a sensor/globin, a linker, and a transmitter domain. The globin domain (GD), activated by ligand binding and/or redox change, induces an intramolecular signal transduction resulting in a response of the transmitter domain. Depending on the nature of the transmitter domain, GCSs can have different activities and functions, including adenylate and di-guanylate cyclase, histidine kinase activity, aerotaxis and/or oxygen sensing function. The gram-negative delta-proteobacterium Geobacter sulfurreducens expresses a protein with a GD covalently linked to a four transmembrane domain, classified, by sequence similarity, as GCS (GsGCS). While its GD is fully characterized, not so its transmembrane domain, which is rarely found in the globin superfamily. In the present work, GsGCS was characterized spectroscopically and by native ion mobility-mass spectrometry in combination with cryo-electron microscopy. Although lacking high resolution, the oligomeric state and the electron density map were valuable for further rational modeling of the full-length GsGCS structure. This model demonstrates that GsGCS forms a transmembrane domain-driven tetramer with minimal contact between the GDs and with the heme groups oriented outward. This organization makes an intramolecular signal transduction less likely. Our results, including the auto-oxidation rate and redox potential, suggest a potential role for GsGCS as redox sensor or in a membrane-bound e-/H+ transfer. As such, GsGCS might act as a player in connecting energy production to the oxidation of organic compounds and metal reduction. Database searches indicate that GDs linked to a four or seven helices transmembrane domain occur more frequently than expected.
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Key Words
- AfGcHK, Anaeromyxobacter sp. Fw109-5 GcHK
- AsFRMF, Ascaris suum FRMF-amide receptor
- AvGReg, Azotobacter vinilandii Greg
- BpGReg, Bordetella pertussis Greg
- BsHemAT, Bacillus subtilis HemAT
- CCS, collision cross section
- CIU, collision-induced unfolding
- CMC, critical micelle concentration
- CV, cyclic voltammetry
- CeGLB26, Caenorhabditis elegans globin 26
- CeGLB33, Caenorhabditis elegans globin 33
- CeGLB6, Caenorhabditis elegans globin 6
- DDM, n-dodecyl-β-d-maltoside
- DPV, differential pulse voltammetry
- EcDosC, Escherichia coli Dos with DGC activity
- FMRF, H-Phe-Met-Arg-Phe-NH2 neuropeptide
- GCS, globin-coupled sensor
- GD, globin domain
- GGDEF, Gly-Gly-Asp-Glu-Phe motive
- Gb, globin
- Geobacter sulfurreducens
- GintHb, hemoglobin from Gasterophilus intestinalis
- Globin-coupled sensor
- GsGCS, Geobacter sulfurreducens GCS
- GsGCS162, GD of GsGCS
- IM-MS, ion mobility-mass spectrometry
- LmHemAC, Leishmania major HemAC
- MaPgb, Methanosarcina acetivorans protoglobin
- MtTrHbO, Mycobacterium tuberculosis truncated hemoglobin O
- NH4OAc, ammonium acetate
- OG, n-octyl-β-d-glucopyranoside
- PDE, phosphodiesterase
- PcMb, Physether catodon myoglobin
- PccGCS, Pectobacterium carotivorum GCS
- PsiE, phosphate-starvation-inducible E
- RR, resonance Raman
- SCE, saturated calomel electrode
- SHE, standard hydrogen electrode
- SaktrHb, Streptomyces avermitilis truncated hemoglobin-antibiotic monooxygenase
- SwMb, myoglobin from sperm whale
- TD, Transmitter domain
- TmD, Transmembrane domain
- Transmembrane domain
- Transmembrane-coupled globins
- mNgb, mouse neuroglobin
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Affiliation(s)
- Dietmar Hammerschmid
- Proteinchemistry, Proteomics and Epigenetic Signalling, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
- Biomolecular & Analytical Mass Spectrometry, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Francesca Germani
- Proteinchemistry, Proteomics and Epigenetic Signalling, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Salvador I. Drusin
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - Charline Fagnen
- Sorbonne Université, UMR 7590, CNRS, Muséum National d’Histoire Naturelle, Institut de Minéralogie, Physique des Matériaux et Cosmochimie, IMPMC, 75005 Paris, France
| | - Claudio D. Schuster
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - David Hoogewijs
- Section of Medicine, Department of Endocrinology, Metabolism and Cardiovascular System, University of Fribourg, Switzerland
| | - Marcelo A. Marti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - Catherine Venien-Bryan
- Sorbonne Université, UMR 7590, CNRS, Muséum National d’Histoire Naturelle, Institut de Minéralogie, Physique des Matériaux et Cosmochimie, IMPMC, 75005 Paris, France
| | - Luc Moens
- Proteinchemistry, Proteomics and Epigenetic Signalling, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Sabine Van Doorslaer
- Biophysics and Biomedical Physics, Department of Chemistry, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
- School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, United Kingdom
| | - Sylvia Dewilde
- Proteinchemistry, Proteomics and Epigenetic Signalling, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
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