1
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Andretto V, Rosso A, Zilio S, Sidi-Boumedine J, Boschetti G, Sankar S, Buffier M, Miele AE, Denis M, Choffour PA, Briançon S, Nancey S, Kryza D, Lollo G. Peptide-Based Hydrogel for Nanosystems Encapsulation: the Next Generation of Localized Delivery Systems for the Treatment of Intestinal Inflammations. Adv Healthc Mater 2024:e2303280. [PMID: 38445812 DOI: 10.1002/adhm.202303280] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 02/10/2024] [Indexed: 03/07/2024]
Abstract
Conventional therapies for inflammatory bowel diseases are mainly based on systemic treatments which cause side effects and toxicity over long-term administration. Nanoparticles appear as a valid alternative to allow a preferential accumulation in inflamed tissues following oral administration while reducing systemic drug exposure. To increase their residence time in the inflamed intestine, the nanoparticles are here associated with a hydrogel matrix. A bioadhesive peptide-based hydrogel is mixed with nanoemulsions, creating a hybrid lipid-polymer nanocomposite. Mucopenetrating nanoemulsions of 100 nm are embedded in a scaffold constituted of the self-assembling peptide hydrogel product PuraStat. The nanocomposite is fully characterized to study the impact of lipid particles in the hydrogel structure. Rheological measurements and circular dichroism analyses are performed to investigate the system's microstructure and physical properties. Biodistribution studies demonstrate that the nanocomposite acts as a depot in the stomach and facilitates the slow release of the nanoemulsions in the intestine. Efficacy studies upon oral administration of the drug-loaded system show the improvement of the disease score in a mouse model of intestinal inflammation.
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Affiliation(s)
- Valentina Andretto
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, LAGEPP UMR 5007, 43 Boulevard du 11 Novembre 1918, Villeurbanne, F-69622, France
| | - Annalisa Rosso
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, LAGEPP UMR 5007, 43 Boulevard du 11 Novembre 1918, Villeurbanne, F-69622, France
| | - Serena Zilio
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, LAGEPP UMR 5007, 43 Boulevard du 11 Novembre 1918, Villeurbanne, F-69622, France
- SATT, Ouest Valorisation, 14C Rue du Patis Tatelin, Renne, 35708, France
| | - Jacqueline Sidi-Boumedine
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, LAGEPP UMR 5007, 43 Boulevard du 11 Novembre 1918, Villeurbanne, F-69622, France
| | - Gilles Boschetti
- Department of Gastroenterology, Lyon Sud Hospital, Hospices Civil de Lyon and CIRI, Lyon, 69495, France
| | - Sharanya Sankar
- 3-D Matrix Europe SAS, Medical Technology, Caluire-et-Cuire, 69300, France
| | - Marie Buffier
- 3-D Matrix Europe SAS, Medical Technology, Caluire-et-Cuire, 69300, France
| | - Adriana Erica Miele
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ISA UMR 5280, 5 rue de la Doua, Villeurbanne, F-69100, France
- Dept Biochemical Sciences, Sapienza University of Rome, P.le Aldo Moro 5, Rome, I-00185, Italy
| | - Morgane Denis
- Univ Lyon, Université Claude Bernard Lyon, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, 69008, France
- Antineo, R&D Department, Lyon, 69008, France
| | | | - Stéphanie Briançon
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, LAGEPP UMR 5007, 43 Boulevard du 11 Novembre 1918, Villeurbanne, F-69622, France
| | - Stéphane Nancey
- Department of Gastroenterology, Lyon Sud Hospital, Hospices Civil de Lyon and CIRI, Lyon, 69495, France
| | - David Kryza
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, LAGEPP UMR 5007, 43 Boulevard du 11 Novembre 1918, Villeurbanne, F-69622, France
- Hospices Civils de Lyon, Lyon, 69437, France
| | - Giovanna Lollo
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, LAGEPP UMR 5007, 43 Boulevard du 11 Novembre 1918, Villeurbanne, F-69622, France
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2
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Nedvědová Š, De Stefano D, Walker O, Hologne M, Miele AE. Revisiting Schistosoma mansoni Micro-Exon Gene (MEG) Protein Family: A Tour into Conserved Motifs and Annotation. Biomolecules 2023; 13:1275. [PMID: 37759676 PMCID: PMC10526429 DOI: 10.3390/biom13091275] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/15/2023] [Accepted: 08/18/2023] [Indexed: 09/29/2023] Open
Abstract
Genome sequencing of the human parasite Schistosoma mansoni revealed an interesting gene superfamily, called micro-exon gene (meg), that encodes secreted MEG proteins. The genes are composed of short exons (3-81 base pairs) regularly interspersed with long introns (up to 5 kbp). This article recollects 35 S. mansoni specific meg genes that are distributed over 7 autosomes and one pair of sex chromosomes and that code for at least 87 verified MEG proteins. We used various bioinformatics tools to produce an optimal alignment and propose a phylogenetic analysis. This work highlighted intriguing conserved patterns/motifs in the sequences of the highly variable MEG proteins. Based on the analyses, we were able to classify the verified MEG proteins into two subfamilies and to hypothesize their duplication and colonization of all the chromosomes. Together with motif identification, we also proposed to revisit MEGs' common names and annotation in order to avoid duplication, to help the reproducibility of research results and to avoid possible misunderstandings.
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Affiliation(s)
- Štěpánka Nedvědová
- UMR 5280 Institute of Analytical Sciences, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, 69100 Villeurbanne, France; (Š.N.); (O.W.); (M.H.)
- Department of Chemistry, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, 16500 Prague, Czech Republic
- Department of Zoology and Fisheries, Center of Infectious Animal Diseases, Czech University of Life Sciences, 16500 Prague, Czech Republic
| | - Davide De Stefano
- UMR 5280 Institute of Analytical Sciences, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, 69100 Villeurbanne, France; (Š.N.); (O.W.); (M.H.)
| | - Olivier Walker
- UMR 5280 Institute of Analytical Sciences, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, 69100 Villeurbanne, France; (Š.N.); (O.W.); (M.H.)
| | - Maggy Hologne
- UMR 5280 Institute of Analytical Sciences, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, 69100 Villeurbanne, France; (Š.N.); (O.W.); (M.H.)
| | - Adriana Erica Miele
- UMR 5280 Institute of Analytical Sciences, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, 69100 Villeurbanne, France; (Š.N.); (O.W.); (M.H.)
- Department of Biochemical Sciences, Sapienza University of Rome, 00185 Rome, Italy
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3
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Nedvedova S, Guillière F, Miele AE, Cantrelle FX, Dvorak J, Walker O, Hologne M. Divide, conquer and reconstruct: How to solve the 3D structure of recalcitrant Micro-Exon Gene (MEG) protein from Schistosoma mansoni. PLoS One 2023; 18:e0289444. [PMID: 37535563 PMCID: PMC10399815 DOI: 10.1371/journal.pone.0289444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 07/19/2023] [Indexed: 08/05/2023] Open
Abstract
Micro-Exon Genes are a widespread class of genes known for their high variability, widespread in the genome of parasitic trematodes such as Schistosoma mansoni. In this study, we present a strategy that allowed us to solve the structures of three alternatively spliced isoforms from the Schistoma mansoni MEG 2.1 family for the first time. All isoforms are hydrophobic, intrinsically disordered, and recalcitrant to be expressed in high yield in heterologous hosts. We resorted to the chemical synthesis of shorter pieces, before reconstructing the entire sequence. Here, we show that isoform 1 partially folds in a-helix in the presence of trifluoroethanol while isoform 2 features two rigid elbows, that maintain the peptide as disordered, preventing any structuring. Finally, isoform 3 is dominated by the signal peptide, which folds into a-helix. We demonstrated that combining biophysical techniques, like circular dichroism and nuclear magnetic resonance at natural abundance, with in silico molecular dynamics simulation for isoform 1 only, was the key to solve the structure of MEG 2.1. Our results provide a crucial piece to the puzzle of this elusive and highly variable class of proteins.
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Affiliation(s)
- Stepanka Nedvedova
- Université de Lyon, CNRS, UCB Lyon1, Institut des Sciences Analytiques, UMR5280, 5 rue de la Doua, Villeurbanne, France
- Department of Chemistry, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
- Department of Zoology and Fisheries, Center of Infectious Animal Diseases, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Florence Guillière
- Université de Lyon, CNRS, UCB Lyon1, Institut des Sciences Analytiques, UMR5280, 5 rue de la Doua, Villeurbanne, France
| | - Adriana Erica Miele
- Université de Lyon, CNRS, UCB Lyon1, Institut des Sciences Analytiques, UMR5280, 5 rue de la Doua, Villeurbanne, France
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - François-Xavier Cantrelle
- Université de Lille, CNRS, UMR8576 -UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Jan Dvorak
- Department of Zoology and Fisheries, Center of Infectious Animal Diseases, Czech University of Life Sciences Prague, Prague, Czech Republic
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czechia
- Faculty of Environmental Sciences, Center of Infectious Animal Diseases, Czech University of Life Sciences in Prague, Prague, Czech Republic
| | - Olivier Walker
- Université de Lyon, CNRS, UCB Lyon1, Institut des Sciences Analytiques, UMR5280, 5 rue de la Doua, Villeurbanne, France
| | - Maggy Hologne
- Université de Lyon, CNRS, UCB Lyon1, Institut des Sciences Analytiques, UMR5280, 5 rue de la Doua, Villeurbanne, France
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4
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Brunori M, Miele AE. Modulation of Allosteric Control and Evolution of Hemoglobin. Biomolecules 2023; 13:biom13030572. [PMID: 36979507 PMCID: PMC10046315 DOI: 10.3390/biom13030572] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/17/2023] [Accepted: 03/18/2023] [Indexed: 03/30/2023] Open
Abstract
Allostery arises when a ligand-induced change in shape of a binding site of a protein is coupled to a tertiary/quaternary conformational change with a consequent modulation of functional properties. The two-state allosteric model of Monod, Wyman and Changeux [J. Mol. Biol. 1965; 12, 88-118] is an elegant and effective theory to account for protein regulation and control. Tetrameric hemoglobin (Hb), the oxygen transporter of all vertebrates, has been for decades the ideal system to test for the validity of the MWC theory. The small ligands affecting Hb's behavior (organic phosphates, protons, bicarbonate) are produced by the red blood cell during metabolism. By binding to specific sites, these messengers make Hb sensing the environment and reacting consequently. HbI and HbIV from trout and human HbA are classical cooperative models, being similar yet different. They share many fundamental features, starting with the globin fold and the quaternary assembly, and reversible cooperative O2 binding. Nevertheless, they differ in ligand affinity, binding of allosteric effectors, and stability of the quaternary assembly. Here, we recollect essential functional properties and correlate them to the tertiary and quaternary structures available in the protein databank to infer on the molecular basis of the evolution of oxygen transporters.
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Affiliation(s)
- Maurizio Brunori
- Accademia Nazionale dei Lincei, via della Lungara, 00165 Rome, Italy
- Department of Biochemical Sciences, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Adriana Erica Miele
- Department of Biochemical Sciences, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
- Institute of Analytical Sciences, UMR 5280 ISA CNRS UCBL, Université Claude Bernard Lyon 1, 5 Rue de la Doua, 69100 Villeurbanne, France
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5
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Rocchi C, Louvat C, Miele AE, Batisse J, Guillon C, Ballut L, Lener D, Negroni M, Ruff M, Gouet P, Fiorini F. The HIV-1 Integrase C-Terminal Domain Induces TAR RNA Structural Changes Promoting Tat Binding. Int J Mol Sci 2022; 23:13742. [PMID: 36430221 PMCID: PMC9692563 DOI: 10.3390/ijms232213742] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 10/28/2022] [Accepted: 11/03/2022] [Indexed: 11/10/2022] Open
Abstract
Recent evidence indicates that the HIV-1 Integrase (IN) binds the viral genomic RNA (gRNA), playing a critical role in the morphogenesis of the viral particle and in the stability of the gRNA once in the host cell. By combining biophysical, molecular biology, and biochemical approaches, we found that the 18-residues flexible C-terminal tail of IN acts as a sensor of the peculiar apical structure of the trans-activation response element RNA (TAR), interacting with its hexaloop. We show that the binding of the whole IN C-terminal domain modifies TAR structure, exposing critical nucleotides. These modifications favour the subsequent binding of the HIV transcriptional trans-activator Tat to TAR, finally displacing IN from TAR. Based on these results, we propose that IN assists the binding of Tat to TAR RNA. This working model provides a mechanistic sketch accounting for the emerging role of IN in the early stages of proviral transcription and could help in the design of anti-HIV-1 therapeutics against this new target of the viral infectious cycle.
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Affiliation(s)
- Cecilia Rocchi
- Molecular Microbiology and Structural Biochemistry, MMSB-IBCP, UMR 5086, CNRS, University of Lyon, 7 Passage du Vercors, CEDEX 07, 69367 Lyon, France
| | - Camille Louvat
- Molecular Microbiology and Structural Biochemistry, MMSB-IBCP, UMR 5086, CNRS, University of Lyon, 7 Passage du Vercors, CEDEX 07, 69367 Lyon, France
| | - Adriana Erica Miele
- Institute of Analytical Sciences, UMR 5280 CNRS UCBL University of Lyon, 5 Rue de la Doua, 69100 Villeurbanne, France
- Department of Biochemical Sciences, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Julien Batisse
- Chromatin Stability and DNA Mobility, Department of Integrated Structural Biology, IGBMC, CNRS, UMR 7104—Inserm U 158, University of Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Christophe Guillon
- Molecular Microbiology and Structural Biochemistry, MMSB-IBCP, UMR 5086, CNRS, University of Lyon, 7 Passage du Vercors, CEDEX 07, 69367 Lyon, France
| | - Lionel Ballut
- Molecular Microbiology and Structural Biochemistry, MMSB-IBCP, UMR 5086, CNRS, University of Lyon, 7 Passage du Vercors, CEDEX 07, 69367 Lyon, France
| | - Daniela Lener
- RNA Architecture and Reactivity, IBMC, CNRS, UPR 9002, University of Strasbourg, 2, Allée Konrad Roentgen, 67084 Strasbourg, France
| | - Matteo Negroni
- RNA Architecture and Reactivity, IBMC, CNRS, UPR 9002, University of Strasbourg, 2, Allée Konrad Roentgen, 67084 Strasbourg, France
| | - Marc Ruff
- Chromatin Stability and DNA Mobility, Department of Integrated Structural Biology, IGBMC, CNRS, UMR 7104—Inserm U 158, University of Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Patrice Gouet
- Molecular Microbiology and Structural Biochemistry, MMSB-IBCP, UMR 5086, CNRS, University of Lyon, 7 Passage du Vercors, CEDEX 07, 69367 Lyon, France
| | - Francesca Fiorini
- Molecular Microbiology and Structural Biochemistry, MMSB-IBCP, UMR 5086, CNRS, University of Lyon, 7 Passage du Vercors, CEDEX 07, 69367 Lyon, France
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6
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Cardarelli S, Miele AE, Campolo F, Massimi M, Mancini P, Biagioni S, Naro F, Giorgi M, Saliola M. Cellular Redox Metabolism Is Modulated by the Distinct Localization of Cyclic Nucleotide Phosphodiesterase 5A Isoforms. Int J Mol Sci 2022; 23:ijms23158587. [PMID: 35955722 PMCID: PMC9368758 DOI: 10.3390/ijms23158587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/18/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022] Open
Abstract
3′-5′ cyclic nucleotide phosphodiesterases (PDEs) are a family of evolutionarily conserved cAMP and/or cGMP hydrolyzing enzymes, components of transduction pathways regulating crucial aspects of cell life. Among them, cGMP-specific PDE5—being a regulator of vascular smooth muscle contraction—is the molecular target of several drugs used to treat erectile dysfunction and pulmonary hypertension. Production of full-length murine PDE5A isoforms in the milk-yeast Kluyveromyces lactis showed that the quaternary assembly of MmPDE5A1 is a mixture of dimers and tetramers, while MmPDE5A2 and MmPDE5A3 only assembled as dimers. We showed that the N-terminal peptide is responsible for the tetramer assembly of MmPDE5A1, while that of the MmPDE5A2 is responsible for its mitochondrial localization. Overexpression of the three isoforms alters at different levels the cAMP/cGMP equilibrium as well as the NAD(P)+/NAD(P)H balance and induces a metabolic switch from oxidative to fermentative. In particular, the mitochondrial localization of MmPDE5A2 unveiled the existence of a cAMP-cGMP signaling cascade in this organelle, for which we propose a metabolic model that could explain the role of PDE5 in some cardiomyopathies and some of the side effects of its inhibitors.
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Affiliation(s)
- Silvia Cardarelli
- Department of Biology and Biotechnology “C. Darwin”, Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy; (S.C.); (S.B.); (M.S.)
| | - Adriana Erica Miele
- Department of Biochemical Sciences, Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy
- UMR 5280 ISA-CNRS-UCBL, Université de Lyon, 5 Rue de La Doua, 69100 Villeurbanne, France
- Correspondence: (A.E.M.); (M.G.)
| | - Federica Campolo
- Department of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Rome, Italy; (F.C.); (P.M.)
| | - Mara Massimi
- Department of Life, Health and Environmental Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy;
| | - Patrizia Mancini
- Department of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Rome, Italy; (F.C.); (P.M.)
| | - Stefano Biagioni
- Department of Biology and Biotechnology “C. Darwin”, Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy; (S.C.); (S.B.); (M.S.)
| | - Fabio Naro
- Department of Anatomical, Histological, Forensic, and Orthopaedic Sciences, Sapienza University of Rome, Via A. Borelli 50, 00161 Rome, Italy;
| | - Mauro Giorgi
- Department of Biology and Biotechnology “C. Darwin”, Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy; (S.C.); (S.B.); (M.S.)
- Correspondence: (A.E.M.); (M.G.)
| | - Michele Saliola
- Department of Biology and Biotechnology “C. Darwin”, Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy; (S.C.); (S.B.); (M.S.)
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7
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Ardini M, Baiocco P, Di Matteo A, Giardina G, Miele AE. Editorial: Tailored Modulation of Interactions Between Biomolecules: Fundamentals and Applications. Front Mol Biosci 2022; 9:961452. [PMID: 35911973 PMCID: PMC9332331 DOI: 10.3389/fmolb.2022.961452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 06/24/2022] [Indexed: 12/05/2022] Open
Affiliation(s)
- Matteo Ardini
- Department of Public Health, Life and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
- *Correspondence: Matteo Ardini,
| | - Paola Baiocco
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Adele Di Matteo
- CNR Institute of Molecular Biology and Pathology, Roma, Italy
| | - Giorgio Giardina
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Adriana Erica Miele
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
- Institut des Sciences Analytiques, UMR 5280 CNRS UCBL, University of Lyon, Villeurbanne, France
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8
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Gondelaud F, Bouakil M, Le Fèvre A, Miele AE, Chirot F, Duclos B, Liwo A, Ricard-Blum S. Extended disorder at the cell surface: The conformational landscape of the ectodomains of syndecans. Matrix Biol Plus 2021; 12:100081. [PMID: 34505054 PMCID: PMC8416954 DOI: 10.1016/j.mbplus.2021.100081] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 07/11/2021] [Accepted: 07/12/2021] [Indexed: 10/26/2022] Open
Abstract
Syndecans are membrane proteoglycans regulating extracellular matrix assembly, cell adhesion and signaling. Their ectodomains can be shed from the cell surface, and act as paracrine and autocrine effectors or as competitors of full-length syndecans. We report the first biophysical characterization of the recombinant ectodomains of the four human syndecans using biophysical techniques, and show that they behave like flexible random-coil intrinsically disordered proteins, and adopt several conformation ensembles in solution. We have characterized their conformational landscapes using native mass spectrometry (MS) and ion-mobility MS, and demonstrated that the syndecan ectodomains explore the majority of their conformational landscape, from minor compact, globular-like, conformations to extended ones. We also report that the ectodomain of syndecan-4, corresponding to a natural isoform, is able to dimerize via a disulfide bond. We have generated a three-dimensional model of the C-terminus of this dimer, which supports the dimerization via a disulfide bond. Furthermore, we have mapped the NXIP adhesion motif of syndecans and their sequences involved in the formation of ternary complexes with integrins and growth factor receptors on the major conformations of their ectodomains, and shown that these sequences are not accessible in all the conformations, suggesting that only some of them are biologically active. Lastly, although the syndecan ectodomains have a far lower number of amino acid residues than their membrane partners, their intrinsic disorder and flexibility allow them to adopt extended conformations, which have roughly the same size as the cell surface receptors (e.g., integrins and growth factor receptors) they bind to.
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Key Words
- CCS, collision cross section
- CD, circular dichroism
- CSD, charge state distribution
- Cell-matrix interactions
- Conformations
- DLS, dynamic light scattering
- DTT, dithiothreitol
- ED, ectodomain
- ESI-IM-MS, electrospray ionization - ion mobility - mass spectrometry
- ESI-MS, electrospray ionization - mass spectrometry
- GAG, glycosaminoglycan
- IDP, intrinsically disordered protein
- Intrinsically disordered proteins
- MoRF, molecular recognition feature
- PAGE, polyacrylamide gel electrophoresis
- PMG, pre-molten globule
- RC, random-coil
- SASA, solvent accessible surface area
- SAXS, small angle X-ray scattering
- SDC, syndecan
- SDS, sodium dodecyl sulfate
- SEC, size exclusion chromatography
- Syndecans
- TFE, trifluoroethanol
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Affiliation(s)
- Frank Gondelaud
- Univ Lyon, University Claude Bernard Lyon 1, CNRS, INSA Lyon, CPE, Institute of Molecular and Supramolecular Chemistry and Biochemistry (ICBMS), UMR 5246, F-69622 Villeurbanne cedex, France
| | - Mathilde Bouakil
- Univ Lyon, University Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, UMR 5306, Cité Lyonnaise de l'Environnement et de l'Analyse, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Aurélien Le Fèvre
- Univ Lyon, University Claude Bernard Lyon 1, CNRS, Institut des Sciences Analytiques, UMR 5280, 5 Rue de la Doua, 69100 Villeurbanne, France
| | - Adriana Erica Miele
- Univ Lyon, University Claude Bernard Lyon 1, CNRS, INSA Lyon, CPE, Institute of Molecular and Supramolecular Chemistry and Biochemistry (ICBMS), UMR 5246, F-69622 Villeurbanne cedex, France
| | - Fabien Chirot
- Univ Lyon, University Claude Bernard Lyon 1, CNRS, Institut des Sciences Analytiques, UMR 5280, 5 Rue de la Doua, 69100 Villeurbanne, France
| | - Bertrand Duclos
- Univ Lyon, University Claude Bernard Lyon 1, CNRS, INSA Lyon, CPE, Institute of Molecular and Supramolecular Chemistry and Biochemistry (ICBMS), UMR 5246, F-69622 Villeurbanne cedex, France
| | - Adam Liwo
- Laboratory of Molecular Modeling, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Sylvie Ricard-Blum
- Univ Lyon, University Claude Bernard Lyon 1, CNRS, INSA Lyon, CPE, Institute of Molecular and Supramolecular Chemistry and Biochemistry (ICBMS), UMR 5246, F-69622 Villeurbanne cedex, France
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9
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Buttinelli M, Panetta G, Bucci A, Frascaria D, Morea V, Miele AE. Protein Engineering of Multi-Modular Transcription Factor Alcohol Dehydrogenase Repressor 1 (Adr1p), a Tool for Dissecting In Vitro Transcription Activation. Biomolecules 2019; 9:biom9090497. [PMID: 31533362 PMCID: PMC6769490 DOI: 10.3390/biom9090497] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 09/03/2019] [Accepted: 09/11/2019] [Indexed: 11/17/2022] Open
Abstract
Studying transcription machinery assembly in vitro is challenging because of long intrinsically disordered regions present within the multi-modular transcription factors. One example is alcohol dehydrogenase repressor 1 (Adr1p) from fermenting yeast, responsible for the metabolic switch from glucose to ethanol. The role of each individual transcription activation domain (TAD) has been previously studied, but their interplay and their roles in enhancing the stability of the protein is not known. In this work, we designed five unique miniAdr1 constructs containing either TADs I-II-III or TAD I and III, connected by linkers of different sizes and compositions. We demonstrated that miniAdr1-BL, containing only PAR-TAD I+III with a basic linker (BL), binds the cognate DNA sequence, located in the promoter of the ADH2 (alcohol dehydrogenase 2) gene, and is necessary to stabilize the heterologous expression. In fact, we found that the sequence of the linker between TAD I and III affected the solubility of free miniAdr1 proteins, as well as the stability of their complexes with DNA. miniAdr1-BL is the stable unit able to recognize ADH2 in vitro, and hence it is a promising tool for future studies on nucleosomal DNA binding and transcription machinery assembly in vitro.
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Affiliation(s)
- Memmo Buttinelli
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy; (M.B.); (A.B.); (D.F.)
| | - Gianna Panetta
- Department of Biochemical Sciences, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy;
| | - Ambra Bucci
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy; (M.B.); (A.B.); (D.F.)
- Department of Biochemical Sciences, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy;
| | - Daniele Frascaria
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy; (M.B.); (A.B.); (D.F.)
| | - Veronica Morea
- National Research Council of Italy (CNR), Institute of Molecular Biology and Pathology, P.le Aldo Moro 5, 00185 Rome, Italy;
| | - Adriana Erica Miele
- Department of Biochemical Sciences, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy;
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS), UMR 5246 CNRS–UCBL-Université de Lyon, 43 boulevard du 11 Novembre 1918, 69622 Villeurbanne, France
- Correspondence: ; Tel.: +39-06-4991-0556
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Cardarelli S, Miele AE, Zamparelli C, Biagioni S, Naro F, Malatesta F, Giorgi M, Saliola M. The oligomeric assembly of the phosphodiesterase-5 is a mixture of dimers and tetramers: A putative role in the regulation of function. Biochim Biophys Acta Gen Subj 2018; 1862:2183-2190. [PMID: 30025857 DOI: 10.1016/j.bbagen.2018.07.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 06/25/2018] [Accepted: 07/11/2018] [Indexed: 12/28/2022]
Abstract
BACKGROUND Phosphodiesterases (PDEs) are a superfamily of evolutionary conserved cyclic nucleotides (cAMP/cGMP) hydrolysing enzymes, components of transduction pathways regulating crucial aspects of cell life. PDE5, one of these families, is the molecular target of several drugs used to treat erectile dysfunction and pulmonary hypertension. Despite its medical relevance, PDE5 macromolecular structure has only been solved for the isolated regulatory and catalytic domains. The definition of the quaternary structure of the full length PDE5 (MmPDE5A1), produced in large amounts in the yeast Kluyveromyces lactis, could greatly enhance the knowledge on its assembly/allosteric regulation and the development of new inhibitors for clinical-therapeutic applications. METHODS Small-angle X-ray scattering (SAXS), analytical ultracentrifugation (AUC), size exclusion chromatography (SEC), native polyacrylamide gel electrophoresis (PAGE) and western blot (WB) were used to assess the assembly of PDE5A1. RESULTS The full length MmPDE5A1 isoform is a mixture of dimers and tetramers in solution. We also report data showing that dimers and tetramers also coexist in vivo in platelets, blood components naturally containing high levels of PDE5. CONCLUSIONS This is the first time that structural studies on the full length protein evidenced the assembly of PDE5 in tetramers in addition to the expected dimers. GENERAL SIGNIFICANCE The assembly of PDE5 in tetramers in platelets, beside the dimers, opens the possibility to alternative assembly/allosteric regulation of this enzyme, as component of large signaling complexes, in all cellular districts in which PDE5 is present.
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Affiliation(s)
- Silvia Cardarelli
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy.
| | - Adriana Erica Miele
- Department of Biochemical Sciences 'Rossi Fanelli', Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy; UMR 5246 ICBMS - CNRS - UCBL, Université de Lyon, Campus La Doua, 43 bd 11 Novembre 1918, 69622 Villeurbanne, Cedex, France.
| | - Carlotta Zamparelli
- Department of Biochemical Sciences 'Rossi Fanelli', Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy.
| | - Stefano Biagioni
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy.
| | - Fabio Naro
- Department of Anatomical, Histological, Forensic, and Orthopaedic Sciences, Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy.
| | - Francesco Malatesta
- Department of Biochemical Sciences 'Rossi Fanelli', Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy.
| | - Mauro Giorgi
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy.
| | - Michele Saliola
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy.
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Angelucci F, Miele AE, Ardini M, Boumis G, Saccoccia F, Bellelli A. Typical 2-Cys peroxiredoxins in human parasites: Several physiological roles for a potential chemotherapy target. Mol Biochem Parasitol 2016; 206:2-12. [PMID: 27002228 DOI: 10.1016/j.molbiopara.2016.03.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 03/16/2016] [Accepted: 03/17/2016] [Indexed: 01/07/2023]
Abstract
Peroxiredoxins (Prxs) are ubiquitary proteins able to play multiple physiological roles, that include thiol-dependent peroxidase, chaperone holdase, sensor of H2O2, regulator of H2O2-dependent signal cascades, and modulator of the immune response. Prxs have been found in a great number of human pathogens, both eukaryotes and prokaryotes. Gene knock-out studies demonstrated that Prxs are essential for the survival and virulence of at least some of the pathogens tested, making these proteins potential drug targets. However, the multiplicity of roles played by Prxs constitutes an unexpected obstacle to drug development. Indeed, selective inhibitors of some of the functions of Prxs are known (namely of the peroxidase and holdase functions) and are here reported. However, it is often unclear which function is the most relevant in each pathogen, hence which one is most desirable to inhibit. Indeed there are evidences that the main physiological role of Prxs may not be the same in different parasites. We here review which functions of Prxs have been demonstrated to be relevant in different human parasites, finding that the peroxidase and chaperone activities figure prominently, whereas other known functions of Prxs have rarely, if ever, been observed in parasites, or have largely escaped detection thus far.
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Affiliation(s)
- Francesco Angelucci
- Department of Health, Life and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Adriana Erica Miele
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | - Matteo Ardini
- Department of Health, Life and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Giovanna Boumis
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | - Fulvio Saccoccia
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | - Andrea Bellelli
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy.
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Miele AE, Bellelli A, Brunori M. Hemoglobin Allostery: New Views on Old Players. J Mol Biol 2013; 425:1515-26. [DOI: 10.1016/j.jmb.2012.12.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 12/18/2012] [Accepted: 12/20/2012] [Indexed: 11/30/2022]
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Angelucci F, Miele AE, Boumis G, Brunori M, Dimastrogiovanni D, Bellelli A. Macromolecular bases of antischistosomal therapy. Curr Top Med Chem 2011; 11:2012-28. [PMID: 21619508 DOI: 10.2174/156802611796575939] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Accepted: 07/31/2010] [Indexed: 11/22/2022]
Abstract
Schistosomiasis is a widespread tropical parasitic disease, currently treated with Praziquantel, whose precise molecular target is actually unknown. Several other drugs are known to kill the schistosomes in vivo and in vitro, but these are seldom employed because of toxicity, high cost, complex administration or other reasons. The improvement of known drugs or the development of entirely new ones is a desirable goal, in view of the fact that strains of Schistosoma mansoni with reduced sensitivity to Praziquantel have appeared. In this review, we tried to collect the information available on known or putative macromolecular targets of schistosomicidal drugs; thus we focused on the biochemistry of the parasite, rather than the clinical properties of the drugs. The rationale of this approach is that drug design may become realistic if the mechanism of action of each known drug were known at atomic detail, ideally as the 3D structure of each drug in complex with its target. Important macromolecular targets of known drugs reviewed below are: Thioredoxin Glutathione Reductase; Cyclophilin; Acetyl Cholinesterase; Proteases and Purine Nucleoside Phosphorylase. Moreover, a few enzymes of the parasite are known, or thought, to be "druggable", and therefore interesting, even though no specific drugs are available as yet: examples of such enzymes are Glutathione Peroxidase and Peroxiredoxins.
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Affiliation(s)
- Francesco Angelucci
- Department of Biochemical Sciences "A. Rossi Fanelli", "Sapienza" University of Rome, Italy
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Dimastrogiovanni D, Anselmi M, Miele AE, Boumis G, Petersson L, Angelucci F, Nola AD, Brunori M, Bellelli A. Combining crystallography and molecular dynamics: The case ofSchistosoma mansoniphospholipid glutathione peroxidase. Proteins 2010; 78:259-70. [DOI: 10.1002/prot.22536] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Abstract
MOTIVATION We investigate the relationship between the quality of models of protein structure and their usefulness as search models in molecular replacement, a widely used method to experimentally determine protein structures by X-ray crystallography. RESULTS We used the available models submitted to the Critical Assessment of Techniques for Protein Structure Prediction to verify in which cases they can be automatically used as search templates for molecular replacement. Our results show that there is a correlation between the quality of the models and their suitability for molecular replacement but that the traditional method of relying on sequence identity between the model and the template used to build it is not diagnostic for the success of the procedure. AVAILABILITY Additional data are available at http://cassandra.bio.uniroma1.it/mr-results-casp.html
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Affiliation(s)
- Alejandro Giorgetti
- Department of Biochemical Sciences, University of Rome La Sapienza, Rome, Italy
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Bellelli A, Brunori M, Miele AE, Panetta G, Vallone B. The Allosteric Properties of Hemoglobin: Insights from Natural and Site Directed Mutants. Curr Protein Pept Sci 2006; 7:17-45. [PMID: 16472167 DOI: 10.2174/138920306775474121] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
After over a century of extensive research, hemoglobin has become the prototype of allosteric and cooperative proteins. Its molecular structure, known in great detail, has allowed the design of hundreds of site directed mutations, aimed at interfering with its function, and thus at testing our hypotheses on the molecular mechanisms of allostery. The wealth of information thus obtained is difficult to read except for specialists, not only because it makes use of many different technical approaches, but also because of its intrinsically patchy nature. Moreover, several researchers have tried to assign specific roles to segments of the polypeptide chains, rather than to single residues, and have tested their hypotheses by multiple point mutations or by complete replacement with the homologous segment from a different hemoglobin to produce chimeric macromolecules. This approach is in great need of a revision since putative functionally relevant segments partially overlap. This review briefly describes the structure and function of hemoglobin, and analyzes the effect of point mutations, multiple mutations and segment replacement, with special attention to possible biotechnological applications, ranging from pharmacology (Hb solutions as resuscitating fluids and sources of the protein found in hemoglobinopathies for biochemical studies) to bioreactors. Occasional reference is made to site directed mutants of myoglobin, whenever this helps clarifying perplexing results obtained on hemoglobin.
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Affiliation(s)
- Andrea Bellelli
- Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Universita degli Studi di Roma La Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy.
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Draghi F, Miele AE, Travaglini-Allocatelli C, Vallone B, Brunori M, Gibson QH, Olson JS. Controlling ligand binding in myoglobin by mutagenesis. J Biol Chem 2002; 277:7509-19. [PMID: 11744723 DOI: 10.1074/jbc.m109206200] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A quadruple mutant of sperm whale myoglobin was constructed to mimic the structure found in Ascaris suum hemoglobin. The replacements include His(E7)-->Gln, Leu(B10)-->Tyr, Thr(E10)--> Arg, and Ile(G8)-->Phe. Single, double, and triple mutants were characterized to dissect out the effects of the individual substitutions. The crystal structures of the deoxy and oxy forms of the quadruple mutant were determined and compared with that of native Ascaris hemoglobin. Tyr(B10) myoglobin displays low O(2) affinity, high dissociation rate constants, and heterogeneous kinetic behavior, suggesting unfavorable steric interactions between the B10 phenol side chain and His(E7). In contrast, all mutants containing the Tyr(B10)/Gln(E7) pair show high O(2) affinity, low dissociation rate constants, and simple, monophasic kinetic behavior. Replacement of Ile(107) with Phe enhances nanosecond geminate recombination singly and in combination with the Tyr(B10)/Gln(E7)/Arg(E10) mutation by limiting access to the Xe4 site. These kinetic results and comparisons with native Ascaris hemoglobin demonstrate the importance of distal pocket cavities in governing the kinetics of ligand binding. The approximately 150-fold higher O(2) affinity of Ascaris hemoglobin compared with that for Tyr(B10)/Gln(E7)-containing myoglobin mutants appears to be the result of favorable proximal effects in the Ascaris protein, due to a staggered orientation of His(F8), the lack of a hydrogen bonding lattice between the F4, F7, and F8 residues, and the presence of a large polar Trp(G5) residue in the interior portion of the proximal heme pocket.
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Affiliation(s)
- Federica Draghi
- A. Rossi Fanelli Department of Biochemical Sciences, CNR Center of Molecular Biology, University of Rome La Sapienza, P. le. A. Moro 5, 00185 Rome, Italy
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Miele AE, Draghi F, Arcovito A, Bellelli A, Brunori M, Travaglini-Allocatelli C, Vallone B. Control of heme reactivity by diffusion: structural basis and functional characterization in hemoglobin mutants. Biochemistry 2001; 40:14449-58. [PMID: 11724557 DOI: 10.1021/bi011602d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The effect of mutagenesis on O(2), CO, and NO binding to mutants of human hemoglobin, designed to modify some features of the reactivity that hinder use of hemoglobin solutions as blood substitute, has been extensively investigated. The kinetics may be interpreted in the framework of the Monod-Wyman-Changeux two-state allosteric model, based on the high-resolution crystallographic structures of the mutants and taking into account the control of heme reactivity by the distal side mutations. The mutations involve residues at topological position B10 and E7, i.e., Leu (B10) to Tyr and His (E7) to Gln, on either the alpha chains alone (yielding the hybrid tetramer Hbalpha(YQ)), the beta chains alone (hybrid tetramer Hbbeta(YQ)), or both types of chains (Hb(YQ)). Our data indicate that the two mutations affect ligand diffusion into the pocket, leading to proteins with low affinity for O(2) and CO, and especially with reduced reactivity toward NO, a difficult goal to achieve. The observed kinetic heterogeneity between the alpha(YQ) and beta(YQ) chains in Hb(YQ) has been rationalized on the basis of the three-dimensional structure of the active site. Furthermore, we report for the first time an experiment of partial CO binding, selective for the beta chains, to high salt crystals of the mutant Hb(YQ) in the T-state; these crystallographic data may be interpreted as "snapshots" of the initial events possibly occurring on ligand binding to the T-allosteric state of this peculiar mutant Hb.
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Affiliation(s)
- A E Miele
- Department of Biochemical Sciences "A. Rossi Fanelli" and CNR Centre for Molecular Biology, University of Rome "La Sapienza", P.le A. Moro 5, 00185 Rome, Italy
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Miele AE, Santanché S, Travaglini-Allocatelli C, Vallone B, Brunori M, Bellelli A. Modulation of ligand binding in engineered human hemoglobin distal pocket. J Mol Biol 1999; 290:515-24. [PMID: 10390349 DOI: 10.1006/jmbi.1999.2869] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Functional and structural studies on hemoglobin and myoglobin from different animals and engineered variants have enlightened the great importance of the physico-chemical properties of the side-chains at topological position B10 and E7. These residues proved to be crucial to the discrimination and stabilisation of gaseous ligands. In view of the data obtained on the high oxygen affinity hemoglobin from Ascaris worms and a new mutant of sperm whale myoglobin, we selected the two mutations Leu B10-->Tyr and His E7-->Gln as potentially relevant to control ligand binding parameters in the alpha and beta-chains of human hemoglobin. Here, we present an investigation of three new mutants: HbalphaYQ (alpha2YQbeta2A), HbbetaYQ (alpha2Abeta2YQ) and HbalphabetaYQ (alpha2YQbeta2YQ). They are characterised by a very low reactivity for NO, O2 and CO, and a reduced cooperativity. Their functional properties are not inconsistent with the behaviour expected for a two-state allosteric model. Proteins with these substitutions may be considered as candidates for the synthesis of a possible "blood substitute", which should yield an O2 adduct stable to autoxidation and slowly reacting with NO. The mutant HbalphabetaYQ is particularly interesting because the rate of reaction of NO with the oxy and deoxy derivatives is reduced. A structural interpretation of our data is presented based on the 3D structure of deoxy HbalphabetaYQ determined by crystallography at 1.8 A resolution.
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Affiliation(s)
- A E Miele
- Department of Biochemical Sciences and C.N.R. Centre of Molecular Biology, University of Rome "La Sapienza", P.le A. Moro, 5, Rome, 00185, Italy
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Vallone B, Miele AE, Vecchini P, Chiancone E, Brunori M. Free energy of burying hydrophobic residues in the interface between protein subunits. Proc Natl Acad Sci U S A 1998; 95:6103-7. [PMID: 9600924 PMCID: PMC27592 DOI: 10.1073/pnas.95.11.6103] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/1998] [Accepted: 03/05/1998] [Indexed: 02/07/2023] Open
Abstract
We have obtained an experimental estimate of the free energy change associated with variations at the interface between protein subunits, a subject that has raised considerable interest since the concept of accessible surface area was introduced by Lee and Richards [Lee, B. & Richards, F. M. (1971) J. Mol. Biol. 55, 379-400]. We determined by analytical ultracentrifugation the dimer-tetramer equilibrium constant of five single and three double mutants of human Hb. One mutation is at the stationary alpha1 beta1 interface, and all of the others are at the sliding alpha1 beta2 interface where cleavage of the tetramer into dimers and ligand-linked allosteric changes are known to occur. A surprisingly good linear correlation between the change in the free energy of association of the mutants and the change in buried hydrophobic surface area was obtained, after corrections for the energetic cost of losing steric complementarity at the alphabeta dimer interface. The slope yields an interface stabilization free energy of -15 +/- 1.2 cal/mol upon burial of 1 A2 of hydrophobic surface, in very good agreement with the theoretical estimate given by Eisenberg and McLachlan [Eisenberg, D. & McLachlan, A. D. (1986) Nature (London) 319, 199-203].
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Affiliation(s)
- B Vallone
- Istituto Pasteur-Fondazione Cenci Bolognetti e Centro di Biologia Molecolare del Consiglio Nazionale delle Ricerche, c/o Dipartimento di Scienze Biochimiche, Università di Roma "La Sapienza," P.le A. Moro 5, 00185 Rome, Italy
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Vallone B, Bellelli A, Miele AE, Brunori M, Fermi G. Probing the alpha 1 beta 2 interface of human hemoglobin by mutagenesis. Role of the FG-C contact regions. J Biol Chem 1996; 271:12472-80. [PMID: 8647854 DOI: 10.1074/jbc.271.21.12472] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The allosteric transition of hemoglobin involves an extensive reorganization of the alpha 1 beta 2 interface, in which two contact regions have been identified. This paper concerns at the effect of two mutations located in the "switch" (alpha C3 Thr --> Trp) and the "flexible joint" (beta C3 Trp --> Thr). We have expressed and characterized one double and two single mutants: Hb alpha T38W/beta W37T, Hb beta W37T, and Hb alpha T38W, whose structure has been determined by crystallography. We present data on: (i) the interface structure in the contact regions, (ii) oxygen and CO binding kinetics and cooperativity, (iii) dissociation rates of deoxy tetramers and association rates of deoxy dimers, and (iv) the effect of NaI on deoxy tetramer dissociation rate constant. All the mutants are tetrameric and T-state in the deoxygenated derivative. Reassociation of deoxygenated dimers is not modified by interface mutations. DeoxyHb alpha T38W/beta W37T dissociate much faster. We propose a binding site for I- at the switch region. The single mutants binds O2 cooperatively; the double one is almost non-cooperative, a feature confirmed by CO binding. The functional data, analyzed with the two-state model, indicate that these mutations reduce the value of the allosteric constant LO.
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Affiliation(s)
- B Vallone
- Department of Biochemical Sciences A. Rossi Fanelli, University of Rome La Sapienza, Italy
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