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Cozzi M, Failla M, Gianquinto E, Kovachka S, Buoli Comani V, Compari C, De Bei O, Giaccari R, Marchesani F, Marchetti M, Ronda L, Rolando B, Baroni M, Cruciani G, Campanini B, Bettati S, Faggiano S, Lazzarato L, Spyrakis F. Identification of small molecules affecting the interaction between human hemoglobin and Staphylococcus aureus IsdB hemophore. Sci Rep 2024; 14:8272. [PMID: 38594253 PMCID: PMC11003968 DOI: 10.1038/s41598-024-55931-8] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 02/29/2024] [Indexed: 04/11/2024] Open
Abstract
Human hemoglobin (Hb) is the preferred iron source of Staphylococcus aureus. This pathogenic bacterium exploits a sophisticated protein machinery called Iron-regulated surface determinant (Isd) system to bind Hb, extract and internalize heme, and finally degrade it to complete iron acquisition. IsdB, the surface exposed Hb receptor, is a proven virulence factor of S. aureus and the inhibition of its interaction with Hb can be pursued as a strategy to develop new classes of antimicrobials. To identify small molecules able to disrupt IsdB:Hb protein-protein interactions (PPIs), we carried out a structure-based virtual screening campaign and developed an ad hoc immunoassay to screen the retrieved set of commercially available compounds. Saturation-transfer difference (STD) NMR was applied to verify specific interactions of a sub-set of molecules, chosen based on their efficacy in reducing the amount of Hb bound to IsdB. Among molecules for which direct binding was verified, the best hit was submitted to ITC analysis to measure the binding affinity to Hb, which was found to be in the low micromolar range. The results demonstrate the viability of the proposed in silico/in vitro experimental pipeline to discover and test IsdB:Hb PPI inhibitors. The identified lead compound will be the starting point for future SAR and molecule optimization campaigns.
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Affiliation(s)
- Monica Cozzi
- Department of Food and Drug, University of Parma, Parma, Italy
| | | | - Eleonora Gianquinto
- Department of Drug Science and Technology, University of Turin, Turin, Italy
| | - Sandra Kovachka
- Department of Drug Science and Technology, University of Turin, Turin, Italy
- The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | | | | | - Omar De Bei
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | | | | | | | - Luca Ronda
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Institute of Biophysics, National Research Council, Pisa, Italy
| | - Barbara Rolando
- Department of Drug Science and Technology, University of Turin, Turin, Italy
| | - Massimo Baroni
- Molecular Discovery Ltd, Kisnetic Business Centre, Elstree, Borehamwood, Hertfordshire, UK
| | - Gabriele Cruciani
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | | | - Stefano Bettati
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Institute of Biophysics, National Research Council, Pisa, Italy
| | - Serena Faggiano
- Department of Food and Drug, University of Parma, Parma, Italy.
- Institute of Biophysics, National Research Council, Pisa, Italy.
| | - Loretta Lazzarato
- Department of Drug Science and Technology, University of Turin, Turin, Italy
| | - Francesca Spyrakis
- Department of Drug Science and Technology, University of Turin, Turin, Italy.
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2
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Toma L, Mattarozzi M, Ronda L, Marassi V, Zattoni A, Fortunati S, Giannetto M, Careri M. Are Aptamers Really Promising as Receptors for Analytical Purposes? Insights into Anti-Lysozyme DNA Aptamers through a Multitechnique Study. Anal Chem 2024; 96:2719-2726. [PMID: 38294352 DOI: 10.1021/acs.analchem.3c05883] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Aptamers are recognition elements increasingly used for the development of biosensing strategies, especially in the detection of proteins or small molecule targets. Lysozyme, which is recognized as an important biomarker for various diseases and a major allergenic protein found in egg whites, is one of the main analytical targets of aptamer-based biosensors. However, since aptamer-based strategies can be prone to artifacts and data misinterpretation, rigorous strategies for multifaceted characterization of the aptamer-target interaction are needed. In this work, a multitechnique approach has been devised to get further insights into the binding performance of the anti-lysozyme DNA aptamers commonly used in the literature. To study molecular interactions between lysozyme and different anti-lysozyme DNA aptamers, measurements based on a magneto-electrochemical apta-assay, circular dichroism spectroscopy, fluorescence spectroscopy, and asymmetrical flow field-flow fractionation were performed. The reliability and versatility of the approach were proved by investigating a SELEX-selected RNA aptamer reported in the literature, that acts as a positive control. The results confirmed that an interaction in the low micromolar range is present in the investigated binding buffers, and the binding is not associated with a conformational change of either the protein or the DNA aptamer. The similar behavior of the anti-lysozyme DNA aptamers compared to that of randomized sequences and polythymine, used as negative controls, showed nonsequence-specific interactions. This study demonstrates that severe testing of aptamers resulting from SELEX selection is the unique way to push these biorecognition elements toward reliable and reproducible results in the analytical field.
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Affiliation(s)
- Lorenzo Toma
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43124, Italy
| | - Monica Mattarozzi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43124, Italy
- Interdepartmental Center SITEIA.PARMA, University of Parma, Parma 43124, Italy
| | - Luca Ronda
- Department of Medicine and Surgery, University of Parma, Parma 43124, Italy
- CNR, Institute of Biophysics, Pisa 56124, Italy
| | - Valentina Marassi
- Department of Chemistry, University of Bologna, Via Selmi 2, Bologna 40126, Italy
- byFlow srl, Bologna 40126, Italy
- INBB, National Institute for Biostructures and Biosystems, Rome 00136 , Italy
| | - Andrea Zattoni
- Department of Chemistry, University of Bologna, Via Selmi 2, Bologna 40126, Italy
- byFlow srl, Bologna 40126, Italy
- INBB, National Institute for Biostructures and Biosystems, Rome 00136 , Italy
| | - Simone Fortunati
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43124, Italy
- INBB, National Institute for Biostructures and Biosystems, Rome 00136 , Italy
| | - Marco Giannetto
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43124, Italy
- Interdepartmental Center SITEIA.PARMA, University of Parma, Parma 43124, Italy
- INBB, National Institute for Biostructures and Biosystems, Rome 00136 , Italy
| | - Maria Careri
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43124, Italy
- Interdepartmental Center SITEIA.PARMA, University of Parma, Parma 43124, Italy
- INBB, National Institute for Biostructures and Biosystems, Rome 00136 , Italy
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3
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Marchetti M, Ronda L, Cozzi M, Bettati S, Bruno S. Genetically Encoded Biosensors for the Fluorescence Detection of O 2 and Reactive O 2 Species. Sensors (Basel) 2023; 23:8517. [PMID: 37896609 PMCID: PMC10611200 DOI: 10.3390/s23208517] [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] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/07/2023] [Accepted: 10/14/2023] [Indexed: 10/29/2023]
Abstract
The intracellular concentrations of oxygen and reactive oxygen species (ROS) in living cells represent critical information for investigating physiological and pathological conditions. Real-time measurement often relies on genetically encoded proteins that are responsive to fluctuations in either oxygen or ROS concentrations. The direct binding or chemical reactions that occur in their presence either directly alter the fluorescence properties of the binding protein or alter the fluorescence properties of fusion partners, mostly consisting of variants of the green fluorescent protein. Oxygen sensing takes advantage of several mechanisms, including (i) the oxygen-dependent hydroxylation of a domain of the hypoxia-inducible factor-1, which, in turn, promotes its cellular degradation along with fluorescent fusion partners; (ii) the naturally oxygen-dependent maturation of the fluorophore of green fluorescent protein variants; and (iii) direct oxygen binding by proteins, including heme proteins, expressed in fusion with fluorescent partners, resulting in changes in fluorescence due to conformational alterations or fluorescence resonance energy transfer. ROS encompass a group of highly reactive chemicals that can interconvert through various chemical reactions within biological systems, posing challenges for their selective detection through genetically encoded sensors. However, their general reactivity, and particularly that of the relatively stable oxygen peroxide, can be exploited for ROS sensing through different mechanisms, including (i) the ROS-induced formation of disulfide bonds in engineered fluorescent proteins or fusion partners of fluorescent proteins, ultimately leading to fluorescence changes; and (ii) conformational changes of naturally occurring ROS-sensing domains, affecting the fluorescence properties of fusion partners. In this review, we will offer an overview of these genetically encoded biosensors.
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Affiliation(s)
- Marialaura Marchetti
- Department of Medicine and Surgery, University of Parma, 43125 Parma, Italy; (M.M.); (L.R.); (M.C.)
| | - Luca Ronda
- Department of Medicine and Surgery, University of Parma, 43125 Parma, Italy; (M.M.); (L.R.); (M.C.)
- Institute of Biophysics, Italian National Research Council (CNR), 56124 Pisa, Italy
| | - Monica Cozzi
- Department of Medicine and Surgery, University of Parma, 43125 Parma, Italy; (M.M.); (L.R.); (M.C.)
| | - Stefano Bettati
- Department of Medicine and Surgery, University of Parma, 43125 Parma, Italy; (M.M.); (L.R.); (M.C.)
- Institute of Biophysics, Italian National Research Council (CNR), 56124 Pisa, Italy
| | - Stefano Bruno
- Department of Food and Drug, University of Parma, 43124 Parma, Italy;
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Mori G, Liuzzi A, Ronda L, Di Palma M, Chegkazi MS, Bui S, Garcia-Maya M, Ragazzini J, Malatesta M, Della Monica E, Rivetti C, Antin PB, Bettati S, Steiner RA, Percudani R. Cysteine Enrichment Mediates Co-Option of Uricase in Reptilian Skin and Transition to Uricotelism. Mol Biol Evol 2023; 40:msad200. [PMID: 37695804 PMCID: PMC10517255 DOI: 10.1093/molbev/msad200] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 08/07/2023] [Accepted: 08/16/2023] [Indexed: 09/13/2023] Open
Abstract
Uric acid is the main means of nitrogen excretion in uricotelic vertebrates (birds and reptiles) and the end product of purine catabolism in humans and a few other mammals. While uricase is inactivated in mammals unable to degrade urate, the presence of orthologous genes without inactivating mutations in avian and reptilian genomes is unexplained. Here we show that the Gallus gallus gene we name cysteine-rich urate oxidase (CRUOX) encodes a functional protein representing a unique case of cysteine enrichment in the evolution of vertebrate orthologous genes. CRUOX retains the ability to catalyze urate oxidation to hydrogen peroxide and 5-hydroxyisourate (HIU), albeit with a 100-fold reduced efficiency. However, differently from all uricases hitherto characterized, it can also facilitate urate regeneration from HIU, a catalytic property that we propose depends on its enrichment in cysteine residues. X-ray structural analysis highlights differences in the active site compared to known orthologs and suggests a mechanism for cysteine-mediated self-aggregation under H2O2-oxidative conditions. Cysteine enrichment was concurrent with the transition to uricotelism and a shift in gene expression from the liver to the skin where CRUOX is co-expressed with β-keratins. Therefore, the loss of urate degradation in amniotes has followed opposite evolutionary trajectories: while uricase has been eliminated by pseudogenization in some mammals, it has been repurposed as a redox-sensitive enzyme in the reptilian skin.
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Affiliation(s)
- Giulia Mori
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Anastasia Liuzzi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Luca Ronda
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Michele Di Palma
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Magda S Chegkazi
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Soi Bui
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Mitla Garcia-Maya
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Jasmine Ragazzini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Marco Malatesta
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Emanuele Della Monica
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Claudio Rivetti
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Parker B Antin
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, USA
| | - Stefano Bettati
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Roberto A Steiner
- Department of Biomedical Sciences, University of Padova, Padova, Italy
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Riccardo Percudani
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
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5
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Pellegrino S, Ronda L. Editorial: Chemically modified proteins and oligopeptides: A toolbox for therapeutics, diagnostics, and analytics. Front Chem 2022; 10:1054229. [DOI: 10.3389/fchem.2022.1054229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 09/30/2022] [Indexed: 11/13/2022] Open
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De Bei O, Marchetti M, Ronda L, Gianquinto E, Lazzarato L, Chirgadze DY, Hardwick SW, Cooper LR, Spyrakis F, Luisi BF, Campanini B, Bettati S. Cryo-EM structures of staphylococcal IsdB bound to human hemoglobin reveal the process of heme extraction. Proc Natl Acad Sci U S A 2022; 119:e2116708119. [PMID: 35357971 PMCID: PMC9168843 DOI: 10.1073/pnas.2116708119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 02/11/2022] [Indexed: 12/02/2022] Open
Abstract
Iron surface determinant B (IsdB) is a hemoglobin (Hb) receptor essential for hemic iron acquisition by Staphylococcus aureus. Heme transfer to IsdB is possible from oxidized Hb (metHb), but inefficient from Hb either bound to oxygen (oxyHb) or bound to carbon monoxide (HbCO), and encompasses a sequence of structural events that are currently poorly understood. By single-particle cryo-electron microscopy, we determined the structure of two IsdB:Hb complexes, representing key species along the heme extraction pathway. The IsdB:HbCO structure, at 2.9-Å resolution, provides a snapshot of the preextraction complex. In this early stage of IsdB:Hb interaction, the hemophore binds to the β-subunits of the Hb tetramer, exploiting a folding-upon-binding mechanism that is likely triggered by a cis/trans isomerization of Pro173. Binding of IsdB to α-subunits occurs upon dissociation of the Hb tetramer into α/β dimers. The structure of the IsdB:metHb complex reveals the final step of the extraction process, where heme transfer to IsdB is completed. The stability of the complex, both before and after heme transfer from Hb to IsdB, is influenced by isomerization of Pro173. These results greatly enhance current understanding of structural and dynamic aspects of the heme extraction mechanism by IsdB and provide insight into the interactions that stabilize the complex before the heme transfer event. This information will support future efforts to identify inhibitors of heme acquisition by S. aureus by interfering with IsdB:Hb complex formation.
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Affiliation(s)
- Omar De Bei
- Interdepartmental Center Biopharmanet-TEC, University of Parma, Parma 43124, Italy
| | - Marialaura Marchetti
- Interdepartmental Center Biopharmanet-TEC, University of Parma, Parma 43124, Italy
- Department of Medicine and Surgery, University of Parma, Parma 43126, Italy
| | - Luca Ronda
- Interdepartmental Center Biopharmanet-TEC, University of Parma, Parma 43124, Italy
- Department of Medicine and Surgery, University of Parma, Parma 43126, Italy
- Institute of Biophysics, National Research Council, Pisa 56124, Italy
| | - Eleonora Gianquinto
- Department of Drug Science and Technology, University of Turin, Turin 10125, Italy
| | - Loretta Lazzarato
- Department of Drug Science and Technology, University of Turin, Turin 10125, Italy
| | - Dimitri Y. Chirgadze
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Steven W. Hardwick
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Lee R. Cooper
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Francesca Spyrakis
- Department of Drug Science and Technology, University of Turin, Turin 10125, Italy
| | - Ben F. Luisi
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Barbara Campanini
- Interdepartmental Center Biopharmanet-TEC, University of Parma, Parma 43124, Italy
- Department of Food and Drug, University of Parma, Parma 43124, Italy
| | - Stefano Bettati
- Interdepartmental Center Biopharmanet-TEC, University of Parma, Parma 43124, Italy
- Department of Medicine and Surgery, University of Parma, Parma 43126, Italy
- Institute of Biophysics, National Research Council, Pisa 56124, Italy
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7
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Marassi V, Mattarozzi M, Toma L, Giordani S, Ronda L, Roda B, Zattoni A, Reschiglian P, Careri M. FFF-based high-throughput sequence shortlisting to support the development of aptamer-based analytical strategies. Anal Bioanal Chem 2022; 414:5519-5527. [PMID: 35182166 PMCID: PMC9242963 DOI: 10.1007/s00216-022-03971-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 12/11/2021] [Revised: 02/05/2022] [Accepted: 02/08/2022] [Indexed: 01/13/2023]
Abstract
Aptamers are biomimetic receptors that are increasingly exploited for the development of optical and electrochemical aptasensors. They are selected in vitro by the SELEX (Systematic Evolution of Ligands by Exponential Enrichment) procedure, but although they are promising recognition elements, for their reliable applicability for analytical purposes, one cannot ignore sample components that cause matrix effects. This particularly applies when different SELEX-selected aptamers and related truncated sequences are available for a certain target, and the choice of the aptamer should be driven by the specific downstream application. In this context, the present work aimed at investigating the potentialities of asymmetrical flow field-flow fractionation (AF4) with UV detection for the development of a screening method of a large number of anti-lysozyme aptamers towards lysozyme, including randomized sequences and an interfering agent (serum albumin). The possibility to work in native conditions and selectively monitor the evolution of untagged aptamer signal as a result of aptamer-protein binding makes the devised method effective as a strategy for shortlisting the most promising aptamers both in terms of affinity and in terms of selectivity, to support subsequent development of aptamer-based analytical devices.
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Affiliation(s)
- Valentina Marassi
- Department of Chemistry, University of Bologna, Via Selmi 2, Bologna, Italy. .,byFlow Srl, Bologna, Italy.
| | - Monica Mattarozzi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy.
| | - Lorenzo Toma
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy
| | - Stefano Giordani
- Department of Chemistry, University of Bologna, Via Selmi 2, Bologna, Italy
| | - Luca Ronda
- Department of Medicine and Surgery, University of Parma, Parco Area delle Scienze, 23/A, 43124, Parma, Italy.,Institute of Biophysics, CNR, 56124, Pisa, Italy
| | - Barbara Roda
- Department of Chemistry, University of Bologna, Via Selmi 2, Bologna, Italy.,byFlow Srl, Bologna, Italy
| | - Andrea Zattoni
- Department of Chemistry, University of Bologna, Via Selmi 2, Bologna, Italy.,byFlow Srl, Bologna, Italy
| | - Pierluigi Reschiglian
- Department of Chemistry, University of Bologna, Via Selmi 2, Bologna, Italy.,byFlow Srl, Bologna, Italy
| | - Maria Careri
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy
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8
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Cooper CE, Bird M, Sheng X, Simons M, Ronda L, Mozzarelli A, Reeder BJ. Stability of a Novel PEGylation Site on a Putative Haemoglobin-Based Oxygen Carrier. Adv Exp Med Biol 2022; 1395:295-299. [PMID: 36527652 DOI: 10.1007/978-3-031-14190-4_48] [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] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
PEGylation of protein sulfhydryl residues is a common method used to create a stable drug conjugate to enhance vascular retention times. We recently created a putative haemoglobin-based oxygen carrier using maleimide-PEG to selectively modify a single engineered cysteine residue in the α subunit (αAla19Cys). However, maleimide-PEG adducts are subject to deconjugation via retro-Michael reactions, with consequent cross-conjugation to endogenous plasma thiols such as those found on human serum albumin or glutathione. In previous studies mono-sulfone-PEG adducts have been shown to be less susceptible to deconjugation. We therefore compared the stability of our maleimide-PEG Hb adduct with one created using a mono-sulfone PEG. The corresponding mono-sulfone-PEG adduct was significantly more stable when incubated at 37 °C for 7 days in the presence of 1 mM reduced glutathione, 20 mg/mL human serum albumin, or human serum. In all cases haemoglobin treated with mono-sulfone-PEG retained >90% of its conjugation whereas maleimide-PEG showed significant deconjugation, especially in the presence of 1 mM reduced glutathione where <70% of the maleimide-PEG conjugate remained intact. Although maleimide-PEGylation of Hb seems adequate for an oxygen therapeutic intended for acute use, if longer vascular retention is required reagents such as mono-sulfone-PEG may be more appropriate.
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Affiliation(s)
- C E Cooper
- School of Life Sciences, University of Essex, Colchester, UK.
| | - M Bird
- Abzena Ltd., Babraham, Cambridge, UK
| | - X Sheng
- Abzena Ltd., Babraham, Cambridge, UK
| | - M Simons
- School of Life Sciences, University of Essex, Colchester, UK
| | - L Ronda
- University of Parma, Parma, Italy
- Institute of Biophysics, Pisa, Italy
| | - A Mozzarelli
- University of Parma, Parma, Italy
- Institute of Biophysics, Pisa, Italy
| | - B J Reeder
- School of Life Sciences, University of Essex, Colchester, UK
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9
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Faggiano S, Ronda L, Bruno S, Abbruzzetti S, Viappiani C, Bettati S, Mozzarelli A. From hemoglobin allostery to hemoglobin-based oxygen carriers. Mol Aspects Med 2021; 84:101050. [PMID: 34776270 DOI: 10.1016/j.mam.2021.101050] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 07/28/2021] [Revised: 11/05/2021] [Accepted: 11/05/2021] [Indexed: 12/18/2022]
Abstract
Hemoglobin (Hb) plays its vital role through structural and functional properties evolutionarily optimized to work within red blood cells, i.e., the tetrameric assembly, well-defined oxygen affinity, positive cooperativity, and heterotropic allosteric regulation by protons, chloride and 2,3-diphosphoglycerate. Outside red blood cells, the Hb tetramer dissociates into dimers, which exhibit high oxygen affinity and neither cooperativity nor allosteric regulation. They are prone to extravasate, thus scavenging endothelial NO and causing hypertension, and cause nephrotoxicity. In addition, they are more prone to autoxidation, generating radicals. The need to overcome the adverse effects associated with cell-free Hb has always been a major hurdle in the development of substitutes of allogeneic blood transfusions for all clinical situations where blood is unavailable or cannot be used due to, for example, religious objections. This class of therapeutics, indicated as hemoglobin-based oxygen carriers (HBOCs), is formed by genetically and/or chemically modified Hbs. Many efforts were devoted to the exploitation of the wealth of biochemical and biophysical information available on Hb structure, function, and dynamics to design safe HBOCs, overcoming the negative effects of free plasma Hb. Unfortunately, so far, no HBOC has been approved by FDA and EMA, except for compassionate use. However, the unmet clinical needs that triggered intensive investigations more than fifty years ago are still awaiting an answer. Recently, HBOCs "repositioning" has led to their successful application in organ perfusion fluids.
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Affiliation(s)
- Serena Faggiano
- Department of Food and Drug, University of Parma, Parma, Italy; Institute of Biophysics, National Research Council, Pisa, Italy
| | - Luca Ronda
- Institute of Biophysics, National Research Council, Pisa, Italy; Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Stefano Bruno
- Department of Food and Drug, University of Parma, Parma, Italy
| | - Stefania Abbruzzetti
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parma, Italy
| | - Cristiano Viappiani
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parma, Italy
| | - Stefano Bettati
- Institute of Biophysics, National Research Council, Pisa, Italy; Department of Medicine and Surgery, University of Parma, Parma, Italy; National Institute of Biostructures and Biosystems, Rome, Italy
| | - Andrea Mozzarelli
- Department of Food and Drug, University of Parma, Parma, Italy; Institute of Biophysics, National Research Council, Pisa, Italy.
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10
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Cooper CE, Bird M, Sheng X, Choi JW, Silkstone GGA, Simons M, Syrett N, Piano R, Ronda L, Bettati S, Paredi G, Mozzarelli A, Reeder BJ. Stability of Maleimide-PEG and Mono-Sulfone-PEG Conjugation to a Novel Engineered Cysteine in the Human Hemoglobin Alpha Subunit. Front Chem 2021; 9:707797. [PMID: 34381760 PMCID: PMC8350135 DOI: 10.3389/fchem.2021.707797] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 05/10/2021] [Accepted: 07/07/2021] [Indexed: 12/14/2022] Open
Abstract
In order to use a Hemoglobin Based Oxygen Carrier as an oxygen therapeutic or blood substitute, it is necessary to increase the size of the hemoglobin molecule to prevent rapid renal clearance. A common method uses maleimide PEGylation of sulfhydryls created by the reaction of 2-iminothiolane at surface lysines. However, this creates highly heterogenous mixtures of molecules. We recently engineered a hemoglobin with a single novel, reactive cysteine residue on the surface of the alpha subunit creating a single PEGylation site (βCys93Ala/αAla19Cys). This enabled homogenous PEGylation by maleimide-PEG with >80% efficiency and no discernible effect on protein function. However, maleimide-PEG adducts are subject to deconjugation via retro-Michael reactions and cross-conjugation to endogenous thiol species in vivo. We therefore compared our maleimide-PEG adduct with one created using a mono-sulfone-PEG less susceptible to deconjugation. Mono-sulfone-PEG underwent reaction at αAla19Cys hemoglobin with > 80% efficiency, although some side reactions were observed at higher PEG:hemoglobin ratios; the adduct bound oxygen with similar affinity and cooperativity as wild type hemoglobin. When directly compared to maleimide-PEG, the mono-sulfone-PEG adduct was significantly more stable when incubated at 37°C for seven days in the presence of 1 mM reduced glutathione. Hemoglobin treated with mono-sulfone-PEG retained > 90% of its conjugation, whereas for maleimide-PEG < 70% of the maleimide-PEG conjugate remained intact. Although maleimide-PEGylation is certainly stable enough for acute therapeutic use as an oxygen therapeutic, for pharmaceuticals intended for longer vascular retention (weeks-months), reagents such as mono-sulfone-PEG may be more appropriate.
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Affiliation(s)
- Chris E Cooper
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | | | | | | | - Gary G A Silkstone
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Michelle Simons
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Natalie Syrett
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Riccardo Piano
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Luca Ronda
- Department of Medicine and Surgery, University of Parma, Parma, Italy.,Institute of Biophysics, National Research Council, Pisa, Italy
| | - Stefano Bettati
- Department of Medicine and Surgery, University of Parma, Parma, Italy.,Institute of Biophysics, National Research Council, Pisa, Italy
| | | | - Andrea Mozzarelli
- Institute of Biophysics, National Research Council, Pisa, Italy.,Department of Food and Drug, University of Parma, Parma, Italy
| | - Brandon J Reeder
- School of Life Sciences, University of Essex, Colchester, United Kingdom
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11
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Portörő I, Mukli P, Kocsis L, Hermán P, Caccia D, Perrella M, Mozzarelli A, Ronda L, Mathe D, Eke A. Model-based evaluation of the microhemodynamic effects of PEGylated HBOC molecules in the rat brain cortex: a laser speckle imaging study. Biomed Opt Express 2020; 11:4150-4175. [PMID: 32923034 PMCID: PMC7449705 DOI: 10.1364/boe.388089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 04/24/2020] [Accepted: 05/04/2020] [Indexed: 06/11/2023]
Abstract
Hemoglobin-based oxygen carriers (HBOCs) were developed with the aim of substituting transfusions in emergency events. However, they exhibit adverse events, such as nitric oxide (NO) scavenging, vasoactivity, enhanced platelet aggregation, presently hampering their clinical application. The impact of two prototypical PEGylated HBOCs, Euro-PEG-Hb and PEG-HbO2, endowed by different oxygen affinities and hydrodynamic volumes, was assessed on the cerebrocortical parenchymal microhemodynamics, and extravasation through the blood-brain-barrier (BBB) by laser speckle contrast imaging (LSCI) method and near-infrared (NIR) imaging, respectively. By evaluating voxel-wise cerebrocortical red blood cell velocity, non-invasively for its mean kernel-wise value ( v ¯ RBC ), and model-derived kernel-wise predictions for microregional tissue hematocrit, THt, and fractional change in hematocrit-corrected vascular resistance, R', as measures of potential adverse effects (enhanced platelet aggregation and vasoactivity, respectively) we found i) no significant difference between tested HBOCs in the systemic and microregional parameters, and in the relative spatial dispersion of THt, and R' as additional measures of HBOC-related adverse effects, and ii) no extravasation through BBB by Euro-PEG-Hb. We conclude that Euro-PEG-Hb does not exhibit adverse effects in the brain microcirculation that could be directly attributed to NO scavenging.
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Affiliation(s)
- István Portörő
- Institute of Translational Medicine, Semmelweis University, Hungary
- These authors contributed equally to this work
| | - Péter Mukli
- Institute of Translational Medicine, Semmelweis University, Hungary
- Department of Physiology, Semmelweis University, Hungary
- These authors contributed equally to this work
| | - László Kocsis
- Institute of Translational Medicine, Semmelweis University, Hungary
| | - Péter Hermán
- Department of Radiology and Biomedical Imaging, Yale University, New Haven, CT 06520, USA
| | - Dario Caccia
- Department of Biomedical Science and Technology, University of Milan, Italy
- Department of Food and Drug, University of Parma, Italy
| | - Michele Perrella
- Department of Biomedical Science and Technology, University of Milan, Italy
| | - Andrea Mozzarelli
- Department of Food and Drug, University of Parma, Italy
- Institute of Biophysics, National Research Council, Pisa, Italy
- Biopharmanet-TEC, University of Parma, Italy
| | - Luca Ronda
- Institute of Biophysics, National Research Council, Pisa, Italy
- Biopharmanet-TEC, University of Parma, Italy
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Domokos Mathe
- CROmed Research and Service Centers Ltd., Budapest, Hungary
| | - Andras Eke
- Institute of Translational Medicine, Semmelweis University, Hungary
- Department of Physiology, Semmelweis University, Hungary
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12
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Cooper CE, Silkstone GGA, Simons M, Gretton S, Rajagopal BS, Allen-Baume V, Syrett N, Shaik T, Popa G, Sheng X, Bird M, Choi JW, Piano R, Ronda L, Bettati S, Paredi G, Mozzarelli A, Reeder BJ. Engineering hemoglobin to enable homogenous PEGylation without modifying protein functionality. Biomater Sci 2020; 8:3896-3906. [PMID: 32539053 DOI: 10.1039/c9bm01773a] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In order to infuse hemoglobin into the vasculature as an oxygen therapeutic or blood substitute, it is necessary to increase the size of the molecule to enhance vascular retention. This aim can be achieved by PEGylation. However, using non-specific conjugation methods creates heterogenous mixtures and alters protein function. Site-specific PEGylation at the naturally reactive thiol on human hemoglobin (βCys93) alters hemoglobin oxygen binding affinity and increases its autooxidation rate. In order to avoid this issue, new reactive thiol residues were therefore engineered at sites distant to the heme group and the α/β dimer/dimer interface. The two mutants were βCys93Ala/αAla19Cys and βCys93Ala/βAla13Cys. Gel electrophoresis, size exclusion chromatography and mass spectrometry revealed efficient PEGylation at both αAla19Cys and βAla13Cys, with over 80% of the thiols PEGylated in the case of αAla19Cys. For both mutants there was no significant effect on the oxygen affinity or the cooperativity of oxygen binding. PEGylation at αAla19Cys had the additional benefit of decreasing the rates of autoxidation and heme release, properties that have been considered contributory factors to the adverse clinical side effects exhibited by previous hemoglobin based oxygen carriers. PEGylation at αAla19Cys may therefore be a useful component of future clinical products.
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Affiliation(s)
- Chris E Cooper
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK.
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13
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Marchetti M, De Bei O, Bettati S, Campanini B, Kovachka S, Gianquinto E, Spyrakis F, Ronda L. Iron Metabolism at the Interface between Host and Pathogen: From Nutritional Immunity to Antibacterial Development. Int J Mol Sci 2020; 21:E2145. [PMID: 32245010 PMCID: PMC7139808 DOI: 10.3390/ijms21062145] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [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] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/16/2020] [Accepted: 03/17/2020] [Indexed: 02/08/2023] Open
Abstract
Nutritional immunity is a form of innate immunity widespread in both vertebrates and invertebrates. The term refers to a rich repertoire of mechanisms set up by the host to inhibit bacterial proliferation by sequestering trace minerals (mainly iron, but also zinc and manganese). This strategy, selected by evolution, represents an effective front-line defense against pathogens and has thus inspired the exploitation of iron restriction in the development of innovative antimicrobials or enhancers of antimicrobial therapy. This review focuses on the mechanisms of nutritional immunity, the strategies adopted by opportunistic human pathogen Staphylococcus aureus to circumvent it, and the impact of deletion mutants on the fitness, infectivity, and persistence inside the host. This information finally converges in an overview of the current development of inhibitors targeting the different stages of iron uptake, an as-yet unexploited target in the field of antistaphylococcal drug discovery.
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Affiliation(s)
- Marialaura Marchetti
- Interdepartmental Center Biopharmanet-TEC, University of Parma, 43124 Parma, Italy; (M.M.); (S.B.)
| | - Omar De Bei
- Department of Food and Drug, University of Parma, 43124 Parma, Italy; (O.D.B.); (B.C.)
| | - Stefano Bettati
- Interdepartmental Center Biopharmanet-TEC, University of Parma, 43124 Parma, Italy; (M.M.); (S.B.)
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
- Institute of Biophysics, National Research Council, 56124 Pisa, Italy
- National Institute of Biostructures and Biosystems, 00136 Rome, Italy
| | - Barbara Campanini
- Department of Food and Drug, University of Parma, 43124 Parma, Italy; (O.D.B.); (B.C.)
| | - Sandra Kovachka
- Department of Drug Science and Technology, University of Turin, 10125 Turin, Italy; (S.K.); (E.G.); (F.S.)
| | - Eleonora Gianquinto
- Department of Drug Science and Technology, University of Turin, 10125 Turin, Italy; (S.K.); (E.G.); (F.S.)
| | - Francesca Spyrakis
- Department of Drug Science and Technology, University of Turin, 10125 Turin, Italy; (S.K.); (E.G.); (F.S.)
| | - Luca Ronda
- Interdepartmental Center Biopharmanet-TEC, University of Parma, 43124 Parma, Italy; (M.M.); (S.B.)
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
- Institute of Biophysics, National Research Council, 56124 Pisa, Italy
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14
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Zangelmi E, Ronda L, Castagna C, Campanini B, Veiga-da-Cunha M, Van Schaftingen E, Peracchi A. Off to a slow start: Analyzing lag phases and accelerating rates in steady-state enzyme kinetics. Anal Biochem 2020; 593:113595. [PMID: 31987861 DOI: 10.1016/j.ab.2020.113595] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 08/13/2019] [Revised: 01/10/2020] [Accepted: 01/20/2020] [Indexed: 10/25/2022]
Abstract
Steady-state enzyme kinetics typically relies on the measurement of 'initial rates', obtained when the substrate is not significantly consumed and the amount of product formed is negligible. Although initial rates are usually faster than those measured later in the reaction time-course, sometimes the speed of the reaction appears instead to increase with time, reaching a steady level only after an initial delay or 'lag phase'. This behavior needs to be interpreted by the experimentalists. To assist interpretation, this article analyzes the many reasons why, during an enzyme assay, the observed rate can be slow in the beginning and then progressively accelerate. The possible causes range from trivial artifacts to instances in which deeper mechanistic or biophysical factors are at play. We provide practical examples for most of these causes, based firstly on experiments conducted with ornithine δ-aminotransferase and with other pyridoxal-phosphate dependent enzymes that have been studied in our laboratory. On the side to this survey, we provide evidence that the product of the ornithine δ-aminotransferase reaction, glutamate 5-semialdehyde, cyclizes spontaneously to pyrroline 5-carboxylate with a rate constant greater than 3 s-1.
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Affiliation(s)
- Erika Zangelmi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124, Parma, Italy
| | - Luca Ronda
- Department of Medicine and Surgery, University of Parma, 43126, Parma, Italy
| | - Camilla Castagna
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124, Parma, Italy
| | - Barbara Campanini
- Department of Food and Drug, University of Parma, 43124, Parma, Italy
| | - Maria Veiga-da-Cunha
- De Duve Institute and WELBIO, UCLouvain, Avenue Hippocrate 75, 1200, Bruxelles, Belgium
| | - Emile Van Schaftingen
- De Duve Institute and WELBIO, UCLouvain, Avenue Hippocrate 75, 1200, Bruxelles, Belgium
| | - Alessio Peracchi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124, Parma, Italy.
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15
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Marchetti M, Ronda L, Percudani R, Bettati S. Immobilization of Allantoinase for the Development of an Optical Biosensor of Oxidative Stress States. Sensors (Basel) 2019; 20:s20010196. [PMID: 31905788 PMCID: PMC6983136 DOI: 10.3390/s20010196] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 12/23/2019] [Accepted: 12/27/2019] [Indexed: 02/04/2023]
Abstract
Allantoin, the natural end product of purine catabolism in mammals, is non-enzymatically produced from the scavenging of reactive oxygen species through the degradation of uric acid. Levels of allantoin in biological fluids are sensitively influenced by the presence of free radicals, making this molecule a candidate marker of acute oxidative stress in clinical analyses. With this aim, we exploited allantoinase—the enzyme responsible for allantoin hydrolization in plants and lower organisms—for the development of a biosensor exploiting a fast enzymatic-chemical assay for allantoin quantification. Recombinant allantoinase was entrapped in a wet nanoporous silica gel matrix and its structural properties, function, and stability were characterized through fluorescence spectroscopy and circular dichroism measurements, and compared to the soluble enzyme. Physical immobilization in silica gel minimally influences the structure and the catalytic efficiency of entrapped allantoinase, which can be reused several times and stored for several months with good activity retention. These results, together with the relative ease of the sol-gel preparation and handling, make the encapsulated allantoinase a good candidate for the development of an allantoin biosensor.
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Affiliation(s)
- Marialaura Marchetti
- Centro Interdipartimentale Biopharmanet-TEC, Università di Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy; (M.M.); (S.B.)
| | - Luca Ronda
- Centro Interdipartimentale Biopharmanet-TEC, Università di Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy; (M.M.); (S.B.)
- Dipartimento di Medicina e Chirurgia, Università di Parma, Via Gramsci 14, 43126 Parma, Italy
- Correspondence: ; Tel.: +39-0521-905502
| | - Riccardo Percudani
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Via Parco Area delle Scienze 11/A, 43124 Parma, Italy;
| | - Stefano Bettati
- Centro Interdipartimentale Biopharmanet-TEC, Università di Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy; (M.M.); (S.B.)
- Dipartimento di Medicina e Chirurgia, Università di Parma, Via Gramsci 14, 43126 Parma, Italy
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16
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Gianquinto E, Moscetti I, De Bei O, Campanini B, Marchetti M, Luque FJ, Cannistraro S, Ronda L, Bizzarri AR, Spyrakis F, Bettati S. Interaction of human hemoglobin and semi-hemoglobins with the Staphylococcus aureus hemophore IsdB: a kinetic and mechanistic insight. Sci Rep 2019; 9:18629. [PMID: 31819099 PMCID: PMC6901573 DOI: 10.1038/s41598-019-54970-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 11/21/2019] [Indexed: 12/21/2022] Open
Abstract
Among multidrug-resistant bacteria, methicillin-resistant Staphylococcus aureus is emerging as one of the most threatening pathogens. S. aureus exploits different mechanisms for its iron supply, but the preferred one is acquisition of organic iron through the expression of hemoglobin (Hb) receptors. One of these, IsdB, belonging to the Isd (Iron-Regulated Surface Determinant) system, was shown to be essential for bacterial growth and virulence. Therefore, interaction of IsdB with Hb represents a promising target for the rational design of a new class of antibacterial molecules. However, despite recent investigations, many structural and mechanistic details of complex formation and heme extraction process are still elusive. By combining site-directed mutagenesis, absorption spectroscopy, surface plasmon resonance and molecular dynamics simulations, we tackled most of the so far unanswered questions: (i) the exact complex stoichiometry, (ii) the microscopic kinetic rates of complex formation, (iii) the IsdB selectivity for binding to, and extracting heme from, α and β subunits of Hb, iv) the role of specific amino acid residues and structural regions in driving complex formation and heme transfer, and (v) the structural/dynamic effect played by the hemophore on Hb.
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Affiliation(s)
- Eleonora Gianquinto
- Department of Drug Science and Technology, University of Turin, Turin, 10125, Italy
| | - Ilaria Moscetti
- Department of Environmental and Biological Sciences, University of Tuscia, Viterbo, 01100, Italy
| | - Omar De Bei
- Department of Food and Drug, University of Parma, Parma, 43124, Italy
| | - Barbara Campanini
- Department of Food and Drug, University of Parma, Parma, 43124, Italy.,Interdepartment Center Biopharmanet-TEC, University of Parma, Parma, 43124, Italy
| | - Marialaura Marchetti
- Department of Drug Science and Technology, University of Turin, Turin, 10125, Italy.,Interdepartment Center Biopharmanet-TEC, University of Parma, Parma, 43124, Italy
| | - F Javier Luque
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Sciences, Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, Santa Coloma de Gramenet, 08921, Spain
| | - Salvatore Cannistraro
- Department of Environmental and Biological Sciences, University of Tuscia, Viterbo, 01100, Italy
| | - Luca Ronda
- Interdepartment Center Biopharmanet-TEC, University of Parma, Parma, 43124, Italy.,Department of Medicine and Surgery, University of Parma, Parma, 43126, Italy.,Institute of Biophysics, National Research Council, Pisa, 56124, Italy
| | - Anna Rita Bizzarri
- Department of Environmental and Biological Sciences, University of Tuscia, Viterbo, 01100, Italy.
| | - Francesca Spyrakis
- Department of Drug Science and Technology, University of Turin, Turin, 10125, Italy.
| | - Stefano Bettati
- Interdepartment Center Biopharmanet-TEC, University of Parma, Parma, 43124, Italy. .,Department of Medicine and Surgery, University of Parma, Parma, 43126, Italy. .,Institute of Biophysics, National Research Council, Pisa, 56124, Italy.
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17
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Cooper CE, Silkstone GGA, Simons M, Rajagopal B, Syrett N, Shaik T, Gretton S, Welbourn E, Bülow L, Eriksson NL, Ronda L, Mozzarelli A, Eke A, Mathe D, Reeder BJ. Engineering tyrosine residues into hemoglobin enhances heme reduction, decreases oxidative stress and increases vascular retention of a hemoglobin based blood substitute. Free Radic Biol Med 2019; 134:106-118. [PMID: 30594736 PMCID: PMC6597946 DOI: 10.1016/j.freeradbiomed.2018.12.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 11/22/2018] [Accepted: 12/24/2018] [Indexed: 01/29/2023]
Abstract
Hemoglobin (Hb)-based oxygen carriers (HBOC) are modified extracellular proteins, designed to replace or augment the oxygen-carrying capacity of erythrocytes. However, clinical results have generally been disappointing due to adverse side effects, in part linked to the intrinsic oxidative toxicity of Hb. Previously a redox-active tyrosine residue was engineered into the Hb β subunit (βF41Y) to facilitate electron transfer between endogenous antioxidants such as ascorbate and the oxidative ferryl heme species, converting the highly oxidizing ferryl species into the less reactive ferric (met) form. We inserted different single tyrosine mutations into the α and β subunits of Hb to determine if this effect of βF41Y was unique. Every mutation that was inserted within electron transfer range of the protein surface and the heme increased the rate of ferryl reduction. However, surprisingly, three of the mutations (βT84Y, αL91Y and βF85Y) also increased the rate of ascorbate reduction of ferric(met) Hb to ferrous(oxy) Hb. The rate enhancement was most evident at ascorbate concentrations equivalent to that found in plasma (< 100 μM), suggesting that it might be of benefit in decreasing oxidative stress in vivo. The most promising mutant (βT84Y) was stable with no increase in autoxidation or heme loss. A decrease in membrane damage following Hb addition to HEK cells correlated with the ability of βT84Y to maintain the protein in its oxygenated form. When PEGylated and injected into mice, βT84Y was shown to have an increased vascular half time compared to wild type PEGylated Hb. βT84Y represents a new class of mutations with the ability to enhance reduction of both ferryl and ferric Hb, and thus has potential to decrease adverse side effects as one component of a final HBOC product.
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Affiliation(s)
- Chris E Cooper
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom.
| | - Gary G A Silkstone
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom
| | - Michelle Simons
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom
| | - Badri Rajagopal
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom
| | - Natalie Syrett
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom
| | - Thoufieq Shaik
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom
| | - Svetlana Gretton
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom
| | - Elizabeth Welbourn
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom
| | - Leif Bülow
- Pure and Applied Biochemistry, Department of Chemistry, Lund University, Box 124, 221 00 Lund, Sweden
| | - Nélida Leiva Eriksson
- Pure and Applied Biochemistry, Department of Chemistry, Lund University, Box 124, 221 00 Lund, Sweden
| | - Luca Ronda
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Andrea Mozzarelli
- Department of Food and Drug, University of Parma, Parma, Italy; Institute of Biophysics, National Research Council (CNR), Pisa, Italy
| | - Andras Eke
- Department of Physiology, Semmelweis University, Budapest, Hungary
| | - Domokos Mathe
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Brandon J Reeder
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom.
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18
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Faggiano S, Ronda L, Raboni S, Sartor F, Cavatorta V, Sgarbi E, Caivano G, Pertile M, Mozzarelli A. Phospholipid components of the synthetic pulmonary surfactant CHF5633 probed by fluorescence spectroscopy. Int J Pharm 2018; 553:290-297. [PMID: 30366070 DOI: 10.1016/j.ijpharm.2018.10.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 07/25/2018] [Revised: 10/15/2018] [Accepted: 10/17/2018] [Indexed: 11/19/2022]
Abstract
CHF5633 (Chiesi Farmaceutici, Italy) is a synthetic pulmonary surfactant currently under clinical development for the treatment of Respiratory Distress Syndrome in premature infants. The product is composed of phospholipids in liposomal organization, together with two peptide analogues of human surfactant proteins B and C. Phospholipids in liposomes can undergo oxidation of unsaturated lipids and hydrolysis, with formation of fatty acids and lysolipids, both affecting the physico-chemical properties of the formulation. We exploited two fluorescence probes, Prodan and ADIFAB, to evaluate the stability of the phospholipid components of CHF5633. While Prodan enters the phospholipid bilayer and probes the polarity of this environment, ADIFAB binds free fatty acids in the aqueous phase, allowing to determine their concentration. Changes of Prodan fluorescence emission indicated an increase in the polarity of the phospholipid bilayer as a function of time. This behavior is coupled with an increase in fatty acids concentration in the aqueous phase, as determined by ADIFAB, and an increase in lysolipids concentration, as determined by HPLC-MS. Prodan and ADIFAB resulted efficient probes to monitor phospholipids hydrolysis in liposomes, reporting an increased stability of CHF5633 at pH values higher than 6.5.
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Affiliation(s)
- Serena Faggiano
- Department of Food and Drug, University of Parma, Parma, Italy; Institute of Biophysics, CNR, Pisa, Italy
| | - Luca Ronda
- Department of Medicine and Surgery, University of Parma, Parma, Italy; Interdepartmental Center Biopharmanet-TEC, University of Parma, Parma, Italy.
| | - Samanta Raboni
- Department of Food and Drug, University of Parma, Parma, Italy; Institute of Biophysics, CNR, Pisa, Italy
| | - Franco Sartor
- CMC Department R&D, Chiesi Farmaceutici, Parma, Italy
| | | | - Elisa Sgarbi
- CMC Department R&D, Chiesi Farmaceutici, Parma, Italy
| | | | | | - Andrea Mozzarelli
- Department of Food and Drug, University of Parma, Parma, Italy; Institute of Biophysics, CNR, Pisa, Italy; Interdepartmental Center Biopharmanet-TEC, University of Parma, Parma, Italy; National Institute of Biostructures and Biomolecules, Rome, Italy
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19
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Lolli G, Raboni S, Pasqualetto E, Benoni R, Campanini B, Ronda L, Mozzarelli A, Bettati S, Battistutta R. Insight into GFPmut2 pH Dependence by Single Crystal Microspectrophotometry and X-ray Crystallography. J Phys Chem B 2018; 122:11326-11337. [PMID: 30179482 DOI: 10.1021/acs.jpcb.8b07260] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The fluorescence of Green Fluorescent Protein (wtGFP) and variants has been exploited in distinct applications in cellular and analytical biology. GFPs emission depends on the population of the protonated (A-state) and deprotonated (B-state) forms of the chromophore. Whereas wtGFP is pH-independent, mutants in which Ser65 is replaced by either threonine or alanine (as in GFPmut2) are pH-dependent, with a p Ka around 6. Given the wtGFP pH-independence, only the structure of the protonated form was determined. The deprotonated form was deduced on the basis of the crystal structure of the Ser65Thr mutant at basic pH, assuming that it corresponds to the conformation populated in solution. Here, we present an investigation where structures of the protonated and deprotonated forms of GFPmut2 were determined from crystals grown in either MPD at pH 6 or PEG at pH 8.5, and moved to either higher or lower pH. Both crystal forms of GFPmut2 were titrated monitoring the process via polarized absorption microspectrophotometry in order to precisely correlate the protonation process with the structures. We found that (i) in solution, chromophore titration is not thermodynamically coupled with any residue and Glu222 is always protonated independent of the protonation state of the chromophore; (ii) the lack of coupling is reflected in the structural behavior of the chromophore and Glu222 environments, with only the former showing variations with pH; (iii) titrations of low-pH and high-pH grown crystals exhibit a Hill coefficient of about 0.75, indicating an anticooperative behavior not observed in solution; (iv) structures where pH was changed in the crystal point to Glu222 as the ionizable group responsible for the outset of the anticooperative behavior; and (v) in GFPmut2 the canonical GFP proton wire involving the chromophore is not interrupted at the level of Ser205 and Glu222 at basic pH as in the Ser65Thr mutant. This allows proposing the structure of the deprotonated state of GFPmut2 as an alternative model for the analogous state of wtGFP.
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Affiliation(s)
- Graziano Lolli
- Centro di Biologia Integrata - CIBIO , Università di Trento , 38123 Povo , Trento , Italy
| | - Samanta Raboni
- Dipartimento di Scienze degli Alimenti e del Farmaco , Università di Parma , 43124 Parma , Italy
| | - Elisa Pasqualetto
- Dipartimento di Scienze Chimiche , Università degli Studi di Padova and Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche , 35131 Padua , Italy
| | - Roberto Benoni
- Dipartimento di Medicina e Chirurgia , Università di Parma , 43125 Parma , Italy
| | - Barbara Campanini
- Dipartimento di Scienze degli Alimenti e del Farmaco , Università di Parma , 43124 Parma , Italy
| | - Luca Ronda
- Dipartimento di Medicina e Chirurgia , Università di Parma , 43125 Parma , Italy
| | - Andrea Mozzarelli
- Dipartimento di Scienze degli Alimenti e del Farmaco , Università di Parma , 43124 Parma , Italy.,Istituto di Biofisica , Consiglio Nazionale delle Ricerche , 56124 Pisa , Italy.,Istituto Nazionale Biostrutture e Biosistemi , 00136 Rome , Italy
| | - Stefano Bettati
- Dipartimento di Medicina e Chirurgia , Università di Parma , 43125 Parma , Italy.,Istituto Nazionale Biostrutture e Biosistemi , 00136 Rome , Italy
| | - Roberto Battistutta
- Dipartimento di Scienze Chimiche , Università degli Studi di Padova and Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche , 35131 Padua , Italy
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20
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Alomari E, Ronda L, Bruno S, Paredi G, Marchetti M, Bettati S, Olivari D, Fumagalli F, Novelli D, Ristagno G, Latini R, Cooper CE, Reeder BJ, Mozzarelli A. High- and low-affinity PEGylated hemoglobin-based oxygen carriers: Differential oxidative stress in a Guinea pig transfusion model. Free Radic Biol Med 2018; 124:299-310. [PMID: 29920341 PMCID: PMC6191936 DOI: 10.1016/j.freeradbiomed.2018.06.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 06/11/2018] [Accepted: 06/15/2018] [Indexed: 12/26/2022]
Abstract
Hemoglobin-based oxygen carriers (HBOCs) are an investigational replacement for blood transfusions and are known to cause oxidative damage to tissues. To investigate the correlation between their oxygen binding properties and these detrimental effects, we investigated two PEGylated HBOCs endowed with different oxygen binding properties - but otherwise chemically identical - in a Guinea pig transfusion model. Plasma samples were analyzed for biochemical markers of inflammation, tissue damage and organ dysfunction; proteins and lipids of heart and kidney extracts were analyzed for markers of oxidative damage. Overall, both HBOCs produced higher oxidative stress in comparison to an auto-transfusion control group. Particularly, tissue 4-hydroxynonenal adducts, tissue malondialdehyde adducts and plasma 8-oxo-2'-deoxyguanosine exhibited significantly higher levels in comparison with the control group. For malondialdehyde adducts, a higher level in the renal tissue was observed for animals treated with the high-affinity HBOC, hinting at a correlation between the HBOCs oxygen binding properties and the oxidative stress they produce. Moreover, we found that the high-affinity HBOC produced greater tissue oxygenation in comparison with the low affinity one, possibly correlating with the higher oxidative stress it induced.
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Affiliation(s)
- Esra'a Alomari
- Department of Food and Drug, University of Parma, Parma, Italy
| | - Luca Ronda
- Department of Medicine and Surgery, University of Parma, Parma, Italy; Biopharmanet-TEC, University of Parma, Parma, Italy
| | - Stefano Bruno
- Department of Food and Drug, University of Parma, Parma, Italy; Biopharmanet-TEC, University of Parma, Parma, Italy.
| | - Gianluca Paredi
- Department of Food and Drug, University of Parma, Parma, Italy; Interdepartmental Center SITEIA.PARMA, University of Parma, Parma 43121, Italy
| | - Marialaura Marchetti
- Department of Medicine and Surgery, University of Parma, Parma, Italy; Biopharmanet-TEC, University of Parma, Parma, Italy
| | - Stefano Bettati
- Department of Medicine and Surgery, University of Parma, Parma, Italy; Biopharmanet-TEC, University of Parma, Parma, Italy; Istituto Nazionale Biostrutture e Biosistemi, Rome, Italy
| | - Davide Olivari
- Istituto di Ricerche Farmacologiche 'Mario Negri', Milan, Italy
| | | | - Deborah Novelli
- Istituto di Ricerche Farmacologiche 'Mario Negri', Milan, Italy
| | | | - Roberto Latini
- Istituto di Ricerche Farmacologiche 'Mario Negri', Milan, Italy
| | - Chris E Cooper
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
| | - Brandon J Reeder
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
| | - Andrea Mozzarelli
- Department of Food and Drug, University of Parma, Parma, Italy; Biopharmanet-TEC, University of Parma, Parma, Italy; Istituto Nazionale Biostrutture e Biosistemi, Rome, Italy; Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Pisa, Italy
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21
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Oh J, Liuzzi A, Ronda L, Marchetti M, Corsini R, Folli C, Bettati S, Rhee S, Percudani R. Diatom Allantoin Synthase Provides Structural Insights into Natural Fusion Protein Therapeutics. ACS Chem Biol 2018; 13:2237-2246. [PMID: 29874034 DOI: 10.1021/acschembio.8b00404] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Humans have lost the ability to convert urate into the more soluble allantoin with the evolutionary inactivation of three enzymes of the uricolytic pathway. Restoration of this function through enzyme replacement therapy can treat severe hyperuricemia and Lesch-Nyhan disease. Through a genomic exploration of natural gene fusions, we found that plants and diatoms independently evolved a fusion protein (allantoin synthase) complementing two human pseudogenes. The 1.85-Å-resolution crystal structure of allantoin synthase from the diatom Phaeodactylum tricornutum provides a rationale for the domain combinations observed in the metabolic pathway, suggesting that quaternary structure is key to the evolutionary success of protein domain fusions. Polyethylene glycol (PEG) conjugation experiments indicate that a PEG-modified form of the natural fusion protein provides advantages over separate enzymes in terms of activity maintenance and manufacturing of the bioconjugate. These results suggest that the combination of different activities in a single molecular unit can simplify the production and chemical modification of recombinant proteins for multifunctional enzyme therapy.
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Affiliation(s)
- Juntaek Oh
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Anastasia Liuzzi
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124, Parma, Italy
| | - Luca Ronda
- Department of Medicine and Surgery, University of Parma, 43124, Parma, Italy
- Biopharmanet-TEC Interdepartmental Center, University of Parma, 43124, Parma, Italy
| | - Marialaura Marchetti
- Biopharmanet-TEC Interdepartmental Center, University of Parma, 43124, Parma, Italy
| | - Romina Corsini
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124, Parma, Italy
| | - Claudia Folli
- Department of Food and Drug, University of Parma, 43124, Parma, Italy
| | - Stefano Bettati
- Department of Medicine and Surgery, University of Parma, 43124, Parma, Italy
- Biopharmanet-TEC Interdepartmental Center, University of Parma, 43124, Parma, Italy
- National Institute of Biostructures and Biosystems, 00136, Rome, Italy
| | - Sangkee Rhee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Riccardo Percudani
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124, Parma, Italy
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22
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Ronda L, Pioselli B, Catinella S, Salomone F, Marchetti M, Bettati S. Quenching of tryptophan fluorescence in a highly scattering solution: Insights on protein localization in a lung surfactant formulation. PLoS One 2018; 13:e0201926. [PMID: 30075031 PMCID: PMC6075776 DOI: 10.1371/journal.pone.0201926] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 07/24/2018] [Indexed: 11/18/2022] Open
Abstract
CHF5633 (Chiesi Farmaceutici, Italy) is a synthetic surfactant developed for respiratory distress syndrome replacement therapy in pre-term newborn infants. CHF5633 contains two phospholipids (dipalmitoylphosphatidylcholine and 1-palmitoyl-2oleoyl-sn-glycero-3-phosphoglycerol sodium salt), and peptide analogues of surfactant protein C (SP-C analogue) and surfactant protein B (SP-B analogue). Both proteins are fundamental for an optimal surfactant activity in vivo and SP-B genetic deficiency causes lethal respiratory failure after birth. Fluorescence emission of the only tryptophan residue present in SP-B analogue (SP-C analogue has none) could in principle be exploited to probe SP-B analogue conformation, localization and interaction with other components of the pharmaceutical formulation. However, the high light scattering activity of the multi-lamellar vesicles suspension characterizing the pharmaceutical surfactant formulation represents a challenge for such studies. We show here that quenching of tryptophan fluorescence and Singular Value Decomposition analysis can be used to accurately calculate and subtract background scattering. The results indicate, with respect to Trp microenvironment, a conformationally homogeneous population of SP-B. Trp is highly accessible to the water phase, suggesting a surficial localization on the membrane of phospholipid vesicles, similarly to what observed for full length SP-B in natural lung surfactant, and supporting an analogous role in protein anchoring to the lipid phase.
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Affiliation(s)
- Luca Ronda
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Biopharmanet-TEC, University of Parma, Parma, Italy
- * E-mail: (LR); (SB)
| | | | | | | | | | - Stefano Bettati
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Biopharmanet-TEC, University of Parma, Parma, Italy
- Italian National Institute of Biostructures and Biosystems, Rome, Italy
- * E-mail: (LR); (SB)
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23
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Alomari E, Bruno S, Ronda L, Paredi G, Bettati S, Mozzarelli A. Protein carbonylation detection methods: A comparison. Data Brief 2018; 19:2215-2220. [PMID: 30229098 PMCID: PMC6141388 DOI: 10.1016/j.dib.2018.06.088] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 06/27/2018] [Indexed: 01/30/2023] Open
Abstract
The data reported here are a comparison among four different methods for the detection of carbonylated proteins, a validated biomarker of oxidative stress. The reference samples were heart and kidney extracts of Guinea pigs transfused with hemoglobin-based oxygen carriers (Alomari et al. FRBM, [11]). We measured the carbonyl content of organ extracts by using i) the Levine spectrophotometric method, which takes advantage of the chromogenic reaction of carbonyl groups with 2,4-dinitrophenylhydrazine (DNPH), ii) a commercially available ELISA assay based on an anti-DNPH antibodies, iii) a commercially available Western blot method based on anti-DNPH antibodies and iv) an in-gel detection approach with the fluorophoric reagent fluorescein-5-thiosemicarbazide. The former two methods measure total protein carbonylation of a sample, whereas the latter two require an electrophoretic separation and therefore potentially allow for the identification of specific carbonylated proteins.
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Affiliation(s)
- Esra'a Alomari
- Department of Food and Drug, University of Parma, Parma, Italy
| | - Stefano Bruno
- Department of Food and Drug, University of Parma, Parma, Italy.,Biopharmanet-TEC, University of Parma, Parma, Italy
| | - Luca Ronda
- Department of Medicine and Surgery, University of Parma, Parma, Italy.,Biopharmanet-TEC, University of Parma, Parma, Italy
| | - Gianluca Paredi
- Department of Food and Drug, University of Parma, Parma, Italy
| | - Stefano Bettati
- Department of Medicine and Surgery, University of Parma, Parma, Italy.,Biopharmanet-TEC, University of Parma, Parma, Italy.,Istituto Nazionale Biostrutture e Biosistemi, Rome, Italy
| | - Andrea Mozzarelli
- Department of Food and Drug, University of Parma, Parma, Italy.,Biopharmanet-TEC, University of Parma, Parma, Italy.,Istituto Nazionale Biostrutture e Biosistemi, Rome, Italy.,Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Pisa, Italy
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24
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Paredi G, Benoni R, Pighini G, Ronda L, Dowle A, Ashford D, Thomas J, Saccani G, Virgili R, Mozzarelli A. Proteomics of Parma Dry-Cured Ham: Analysis of Salting Exudates. J Agric Food Chem 2017; 65:6307-6316. [PMID: 28662581 DOI: 10.1021/acs.jafc.7b01293] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The production of Parma dry-cured ham involves the steps of salting, drying, and ripening. Although sea salt is the only preserving agent, there are strategies being developed with the goal of reducing salt content in order to decrease its negative impact on consumer health. A 24 h pressure treatment was applied before salting to reduce thickness and inequalities in shape. To evaluate the potential impact of the pressure step on the process outcome, differential proteomic analyses by complementary 2D-PAGE and LC-MS/MS were carried out on exudates collected at day 1, 5, and 18 of the salting phase for hams treated or untreated with pressure. Specific proteins were found differentially abundant in exudates from pressed vs unpressed hams and as a function of time. These changes include glycolytic enzymes and several myofibrillar proteins. These findings indicate that pressure causes a faster loosening of the myofibrillar structure with the release of specific groups of proteins.
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Affiliation(s)
| | | | | | | | - Adam Dowle
- Bioscience Technology Facility, Department of Biology, University of York , York YO10 5DD, United Kingdom
| | - David Ashford
- Bioscience Technology Facility, Department of Biology, University of York , York YO10 5DD, United Kingdom
| | - Jerry Thomas
- Bioscience Technology Facility, Department of Biology, University of York , York YO10 5DD, United Kingdom
| | - Giovanna Saccani
- Stazione Sperimentale per l'Industria delle Conserve Alimentari (SSICA) , Parma 43100, Italy
| | - Roberta Virgili
- Stazione Sperimentale per l'Industria delle Conserve Alimentari (SSICA) , Parma 43100, Italy
| | - Andrea Mozzarelli
- Institute of Biophysics, National Research Council , Pisa 56124, Italy
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25
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Ronda L, Marchetti M, Piano R, Liuzzi A, Corsini R, Percudani R, Bettati S. A Trivalent Enzymatic System for Uricolytic Therapy of HPRT Deficiency and Lesch-Nyhan Disease. Pharm Res 2017; 34:1477-1490. [PMID: 28508122 PMCID: PMC5445154 DOI: 10.1007/s11095-017-2167-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [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: 02/28/2017] [Accepted: 04/25/2017] [Indexed: 12/21/2022]
Abstract
PURPOSE Because of the evolutionary loss of the uricolytic pathway, humans accumulate poorly soluble urate as the final product of purine catabolism. Restoration of uricolysis through enzyme therapy is a promising treatment for severe hyperuricemia caused by deficiency of hypoxanthine-guanine phosphoribosyltransferase (HPRT). To this end, we studied the effect of PEG conjugation on the activity and stability of the enzymatic complement required for conversion of urate into the more soluble (S)-allantoin. METHODS We produced in recombinant form three zebrafish enzymes required in the uricolytic pathway. We carried out a systematic study of the effect of PEGylation on the function and stability of the three enzymes by varying PEG length, chemistry and degree of conjugation. We assayed in vitro the uricolytic activity of the PEGylated enzymatic triad. RESULTS We defined conditions that allow PEGylated enzymes to retain native-like enzymatic activity even after lyophilization or prolonged storage. A combination of the three enzymes in an appropriate ratio allowed efficient conversion of urate to (S)-allantoin with no accumulation of intermediate metabolites. CONCLUSIONS Pharmaceutical restoration of the uricolytic pathway is a viable approach for the treatment of severe hyperuricemia.
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Affiliation(s)
- Luca Ronda
- Department of Medicine and Surgery,, University of Parma, Parco Area delle Scienze 23/A, 43124, Parma, Italy
| | - Marialaura Marchetti
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma,, Parco Area delle Scienze 23/A, 43124, Parma, Italy
| | - Riccardo Piano
- Department of Medicine and Surgery,, University of Parma, Parco Area delle Scienze 23/A, 43124, Parma, Italy
| | - Anastasia Liuzzi
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma,, Parco Area delle Scienze 23/A, 43124, Parma, Italy
| | - Romina Corsini
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma,, Parco Area delle Scienze 23/A, 43124, Parma, Italy
| | - Riccardo Percudani
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma,, Parco Area delle Scienze 23/A, 43124, Parma, Italy.
| | - Stefano Bettati
- Department of Medicine and Surgery,, University of Parma, Parco Area delle Scienze 23/A, 43124, Parma, Italy. .,National Institute of Biostructures and Biosystems, Viale Medaglie d'Oro 305, 00136, Rome, Italy.
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26
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Zennaro C, Tonon F, Zarattini P, Clai M, Corbelli A, Carraro M, Marchetti M, Ronda L, Paredi G, Rastaldi MP, Percudani R. The renal phenotype of allopurinol-treated HPRT-deficient mouse. PLoS One 2017; 12:e0173512. [PMID: 28282408 PMCID: PMC5345830 DOI: 10.1371/journal.pone.0173512] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 02/21/2017] [Indexed: 12/02/2022] Open
Abstract
Excess of uric acid is mainly treated with xanthine oxidase (XO) inhibitors, also called uricostatics because they block the conversion of hypoxanthine and xanthine into urate. Normally, accumulation of upstream metabolites is prevented by the hypoxanthine-guanine phosphoribosyltransferase (HPRT) enzyme. The recycling pathway, however, is impaired in the presence of HPRT deficiency, as observed in Lesch-Nyhan disease. To gain insights into the consequences of purine accumulation with HPRT deficiency, we investigated the effects of the XO inhibitor allopurinol in Hprt-lacking (HPRT-/-) mice. Allopurinol was administered in the drinking water of E12-E14 pregnant mothers at dosages of 150 or 75 μg/ml, and mice sacrificed after weaning. The drug was well tolerated by wild-type animals and heterozygous HPRT+/- mice. Instead, a profound alteration of the renal function was observed in the HPRT-/- model. Increased hypoxanthine and xanthine concentrations were found in the blood. The kidneys showed a yellowish appearance, diffuse interstitial nephritis, with dilated tubules, inflammatory and fibrotic changes of the interstitium. There were numerous xanthine tubular crystals, as determined by HPLC analysis. Oil red O staining demonstrated lipid accumulation in the same location of xanthine deposits. mRNA analysis showed increased expression of adipogenesis-related molecules as well as profibrotic and proinflammatory pathways. Immunostaining showed numerous monocyte-macrophages and overexpression of alpha-smooth muscle actin in the tubulointerstitium. In vitro, addition of xanthine to tubular cells caused diffuse oil red O positivity and modification of the cell phenotype, with loss of epithelial features and appearance of mesenchymal characteristics, similarly to what was observed in vivo. Our results indicate that in the absence of HPRT, blockade of XO by allopurinol causes rapidly developing renal failure due to xanthine deposition within the mouse kidney. Xanthine seems to be directly involved in promoting lipid accumulation and subsequent phenotype changes of tubular cells, with activation of inflammation and fibrosis.
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Affiliation(s)
- Cristina Zennaro
- Department of Medical, Surgery and Health Sciences, Università degli Studi di Trieste, Trieste, Italy
| | - Federica Tonon
- Department of Medical, Surgery and Health Sciences, Università degli Studi di Trieste, Trieste, Italy
| | - Paola Zarattini
- Department of Life Sciences, Università degli Studi di Trieste, Trieste, Trieste, Italy
| | - Milan Clai
- Department of Pathology and Legal Medicine, Azienda Sanitaria Universitaria Integrata di Trieste, Trieste, Italy
| | - Alessandro Corbelli
- Unit of Bio-imaging, Department of Cardiovascular Research, IRCCS Mario Negri Institute for Pharmacological Research, Milano, Italy
| | - Michele Carraro
- Department of Medical, Surgery and Health Sciences, Università degli Studi di Trieste, Trieste, Italy
| | | | - Luca Ronda
- Department of Neurosciences, University of Parma, Parma, Italy
| | - Gianluca Paredi
- Department of Pharmacy and SITEIA, PARMA Interdepartmental Center, University of Parma, Parma, Italy
| | - Maria Pia Rastaldi
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
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27
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Bruno S, Margiotta M, Marchesani F, Paredi G, Orlandi V, Faggiano S, Ronda L, Campanini B, Mozzarelli A. Magnesium and calcium ions differentially affect human serine racemase activity and modulate its quaternary equilibrium toward a tetrameric form. Biochim Biophys Acta Proteins Proteom 2017; 1865:381-387. [PMID: 28089597 DOI: 10.1016/j.bbapap.2017.01.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 12/21/2016] [Accepted: 01/05/2017] [Indexed: 11/18/2022]
Abstract
Serine racemase is the pyridoxal 5'-phosphate dependent enzyme that catalyzes both production and catabolism of d-serine, a co-agonist of the NMDA glutamate receptors. Mg2+, or, alternatively, Ca2+, activate human serine racemase by binding both at a specific site and - as ATP-metal complexes - at a distinct ATP binding site. We show that Mg2+ and Ca2+ bind at the metal binding site with a 4.5-fold difference in affinity, producing a similar thermal stabilization and partially shifting the dimer-tetramer equilibrium in favour of the latter. The ATP-Ca2+ complex produces a 2-fold lower maximal activation in comparison to the ATP-Mg2+ complex and exhibits a 3-fold higher EC50. The co-presence of ATP and metals further stabilizes the tetramer. In consideration of the cellular concentrations of Mg2+ and Ca2+, even taking into account the fluctuations of the latter, these results point to Mg2+ as the sole physiologically relevant ligand both at the metal binding site and at the ATP binding site. The stabilization of the tetramer by both metals and ATP-metal complexes suggests a quaternary activation mechanism mediated by 5'-phosphonucleotides similar to that observed in the distantly related prokaryotic threonine deaminases. This allosteric mechanism has never been observed before in mammalian fold type II pyridoxal 5'-phosphate dependent enzymes.
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Affiliation(s)
| | | | | | - Gianluca Paredi
- Interdepartment Center SITEIA.PARMA, University of Parma, Italy
| | | | | | - Luca Ronda
- Department of Neurosciences, University of Parma, Italy
| | | | - Andrea Mozzarelli
- Department of Pharmacy, University of Parma, Italy; Institute of Biophysics, CNR, Pisa, Italy; National Institute of Biostructures and Biomolecules, Rome, Italy
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28
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Marchetti M, Liuzzi A, Fermi B, Corsini R, Folli C, Speranzini V, Gandolfi F, Bettati S, Ronda L, Cendron L, Berni R, Zanotti G, Percudani R. Catalysis and Structure of Zebrafish Urate Oxidase Provide Insights into the Origin of Hyperuricemia in Hominoids. Sci Rep 2016; 6:38302. [PMID: 27922051 PMCID: PMC5138847 DOI: 10.1038/srep38302] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 11/03/2016] [Indexed: 01/24/2023] Open
Abstract
Urate oxidase (Uox) catalyses the first reaction of oxidative uricolysis, a three-step enzymatic pathway that allows some animals to eliminate purine nitrogen through a water-soluble compound. Inactivation of the pathway in hominoids leads to elevated levels of sparingly soluble urate and puts humans at risk of hyperuricemia and gout. The uricolytic activities lost during evolution can be replaced by enzyme therapy. Here we report on the functional and structural characterization of Uox from zebrafish and the effects on the enzyme of the missense mutation (F216S) that preceded Uox pseudogenization in hominoids. Using a kinetic assay based on the enzymatic suppression of the spectroscopic interference of the Uox reaction product, we found that the F216S mutant has the same turnover number of the wild-type enzyme but a much-reduced affinity for the urate substrate and xanthine inhibitor. Our results indicate that the last functioning Uox in hominoid evolution had an increased Michaelis constant, possibly near to upper end of the normal range of urate in the human serum (~300 μM). Changes in the renal handling of urate during primate evolution can explain the genetic modification of uricolytic activities in the hominoid lineage without the need of assuming fixation of deleterious mutations.
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Affiliation(s)
| | - Anastasia Liuzzi
- Department of Life Sciences, University of Parma, 43124, Parma, Italy
| | - Beatrice Fermi
- Department of Life Sciences, University of Parma, 43124, Parma, Italy
| | - Romina Corsini
- Department of Life Sciences, University of Parma, 43124, Parma, Italy
| | - Claudia Folli
- Department of Food Science University of Parma, 43124, Parma, Italy
| | | | | | - Stefano Bettati
- Department of Neurosciences, University of Parma, 43124, Parma, Italy
| | - Luca Ronda
- Department of Neurosciences, University of Parma, 43124, Parma, Italy
| | - Laura Cendron
- Department of Biology, University of Padova, 35121, Padova, Italy
| | - Rodolfo Berni
- Department of Life Sciences, University of Parma, 43124, Parma, Italy
| | - Giuseppe Zanotti
- Department of Biology, University of Padova, 35121, Padova, Italy
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Dell'Acqua M, Ronda L, Piano R, Pellegrino S, Clerici F, Rossi E, Mozzarelli A, Gelmi ML, Abbiati G. MediaChrom: Discovering a Class of Pyrimidoindolone-Based Polarity-Sensitive Dyes. J Org Chem 2015; 80:10939-54. [PMID: 26473465 DOI: 10.1021/acs.joc.5b02066] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
A small library of six polarity-sensitive fluorescent dyes, nicknamed MediaChrom, was prepared. This class of dyes is characterized by a pyrimidoindolone core fitted out with a conjugated push-pull system and a carboxy linker for a conceivable coupling with biomolecules. The optimized eight-step synthetic strategy involves a highly chemo- and regioselective gold-catalyzed cycloisomerization reaction. The photophysical properties of MediaChrom dyes have been evaluated in-depth. In particular, the MediaChrom bearing a diethylamino as an electron-donating group and a trifluoromethyl as an electron-withdrawing group displays the most interesting and advantageous spectroscopic features (e.g., absorption and emission in the visible range and a good quantum yield). Promising results in terms of sensitivity have been obtained in vitro on this dye as a membrane/lipophilic probe and as a peptide fluorescent label.
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Affiliation(s)
- Monica Dell'Acqua
- Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica "A. Marchesini", Università degli Studi di Milano , Via Venezian, 21, 20133 Milano, Italy
| | | | | | - Sara Pellegrino
- Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica "A. Marchesini", Università degli Studi di Milano , Via Venezian, 21, 20133 Milano, Italy
| | - Francesca Clerici
- Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica "A. Marchesini", Università degli Studi di Milano , Via Venezian, 21, 20133 Milano, Italy
| | - Elisabetta Rossi
- Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica "A. Marchesini", Università degli Studi di Milano , Via Venezian, 21, 20133 Milano, Italy
| | | | - Maria Luisa Gelmi
- Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica "A. Marchesini", Università degli Studi di Milano , Via Venezian, 21, 20133 Milano, Italy
| | - Giorgio Abbiati
- Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica "A. Marchesini", Università degli Studi di Milano , Via Venezian, 21, 20133 Milano, Italy
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Ronda L, Bruno S, Campanini B, Mozzarelli A, Abbruzzetti S, Viappiani C, Cupane A, Levantino M, Bettati S. Immobilization of Proteins in Silica Gel: Biochemical and Biophysical Properties. CURR ORG CHEM 2015. [DOI: 10.2174/1385272819666150601211349] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Ronda L, Bruno S, Bettati S, Storici P, Mozzarelli A. From protein structure to function via single crystal optical spectroscopy. Front Mol Biosci 2015; 2:12. [PMID: 25988179 PMCID: PMC4428442 DOI: 10.3389/fmolb.2015.00012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [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: 01/12/2015] [Accepted: 03/31/2015] [Indexed: 11/23/2022] Open
Abstract
The more than 100,000 protein structures determined by X-ray crystallography provide a wealth of information for the characterization of biological processes at the molecular level. However, several crystallographic “artifacts,” including conformational selection, crystallization conditions and radiation damages, may affect the quality and the interpretation of the electron density maps, thus limiting the relevance of structure determinations. Moreover, for most of these structures, no functional data have been obtained in the crystalline state, thus posing serious questions on their validity in infereing protein mechanisms. In order to solve these issues, spectroscopic methods have been applied for the determination of equilibrium and kinetic properties of proteins in the crystalline state. These methods are UV-vis spectrophotometry, spectrofluorimetry, IR, EPR, Raman, and resonance Raman spectroscopy. Some of these approaches have been implemented with on-line instruments at X-ray synchrotron beamlines. Here, we provide an overview of investigations predominantly carried out in our laboratory by single crystal polarized absorption UV-vis microspectrophotometry, the most applied technique for the functional characterization of proteins in the crystalline state. Studies on hemoglobins, pyridoxal 5′-phosphate dependent enzymes and green fluorescent protein in the crystalline state have addressed key biological issues, leading to either straightforward structure-function correlations or limitations to structure-based mechanisms.
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Affiliation(s)
- Luca Ronda
- Department of Neurosciences, University of Parma Parma, Italy
| | - Stefano Bruno
- Department of Pharmacy, University of Parma Parma, Italy
| | - Stefano Bettati
- Department of Neurosciences, University of Parma Parma, Italy ; National Institute of Biostructures and Biosystems Rome, Italy
| | | | - Andrea Mozzarelli
- Department of Pharmacy, University of Parma Parma, Italy ; National Institute of Biostructures and Biosystems Rome, Italy ; Institute of Biophysics, Consiglio Nazionale delle Ricerche Pisa, Italy
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Schiroli D, Ronda L, Peracchi A. Kinetic characterization of the human O-phosphoethanolamine phospho-lyase reveals unconventional features of this specialized pyridoxal phosphate-dependent lyase. FEBS J 2014; 282:183-99. [PMID: 25327712 DOI: 10.1111/febs.13122] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [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: 08/15/2014] [Revised: 10/14/2014] [Accepted: 10/17/2014] [Indexed: 11/28/2022]
Abstract
Human O-phosphoethanolamine (PEA) phospho-lyase is a pyridoxal 5'-phosphate (PLP) dependent enzyme that catalyzes the degradation of PEA to acetaldehyde, phosphate and ammonia. Physiologically, the enzyme is involved in phospholipid metabolism and is expressed mainly in the brain, where its expression becomes dysregulated in the course of neuropsychiatric diseases. Mechanistically, PEA phospho-lyase shows a remarkable substrate selectivity, strongly discriminating against other amino compounds structurally similar to PEA. Herein, we studied the enzyme under steady-state and pre-steady-state conditions, analyzing its kinetic features and getting insights into the factors that contribute to its specificity. The pH dependence of the catalytic parameters and the pattern of inhibition by the product phosphate and by other anionic compounds suggest that the active site of PEA phospho-lyase is optimized to bind dianionic groups and that this is a prime determinant of the enzyme specificity towards PEA. Single- and multiple-wavelength stopped-flow studies show that upon reaction with PEA the main absorption band of PLP (λmax = 412 nm) rapidly blue-shifts to ~ 400 nm. Further experiments suggest that the newly formed and rather stable 400-nm species most probably represents a Michaelis (noncovalent) complex of PEA with the enzyme. Accumulation of such an early intermediate during turnover is unusual for PLP-dependent enzymes and appears counterproductive for absolute catalytic performance, but it can contribute to optimize substrate specificity. PEA phospho-lyase may hence represent a case of selectivity-efficiency tradeoff. In turn, the strict specificity of the enzyme seems important to prevent inactivation by other amines, structurally resembling PEA, that occur in the brain.
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Affiliation(s)
- Davide Schiroli
- Department of Life Sciences, Laboratory of Biochemistry, Molecular Biology and Bioinformatics, University of Parma, Italy
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Nakagawa A, Lui FE, Wassaf D, Yefidoff-Freedman R, Casalena D, Palmer MA, Meadows J, Mozzarelli A, Ronda L, Abdulmalik O, Bloch KD, Safo MK, Zapol WM. Identification of a small molecule that increases hemoglobin oxygen affinity and reduces SS erythrocyte sickling. ACS Chem Biol 2014; 9:2318-25. [PMID: 25061917 PMCID: PMC4205001 DOI: 10.1021/cb500230b] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Small
molecules that increase the oxygen affinity of human hemoglobin
may reduce sickling of red blood cells in patients with sickle cell
disease. We screened 38 700 compounds using small molecule
microarrays and identified 427 molecules that bind to hemoglobin.
We developed a high-throughput assay for evaluating the ability of
the 427 small molecules to modulate the oxygen affinity of hemoglobin.
We identified a novel allosteric effector of hemoglobin, di(5-(2,3-dihydro-1,4-benzodioxin-2-yl)-4H-1,2,4-triazol-3-yl)disulfide
(TD-1). TD-1 induced a greater increase in oxygen affinity of human
hemoglobin in solution and in red blood cells than did 5-hydroxymethyl-2-furfural
(5-HMF), N-ethylmaleimide (NEM), or diformamidine disulfide. The three-dimensional
structure of hemoglobin complexed with TD-1 revealed that monomeric
units of TD-1 bound covalently to β-Cys93 and β-Cys112,
as well as noncovalently to the central water cavity of the hemoglobin
tetramer. The binding of TD-1 to hemoglobin stabilized the relaxed
state (R3-state) of hemoglobin. TD-1 increased the oxygen affinity
of sickle hemoglobin and inhibited in vitro hypoxia-induced
sickling of red blood cells in patients with sickle cell disease without
causing hemolysis. Our study indicates that TD-1 represents a novel
lead molecule for the treatment of patients with sickle cell disease.
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Affiliation(s)
- Akito Nakagawa
- Anesthesia Center
for Critical Care Research, Department of Anesthesia, Critical Care,
and Pain Medicine, Massachusetts General Hospital and Harvard Medical
School, 55 Fruit Street, Boston, Massachusetts 02114, United States
| | - Francine E. Lui
- Anesthesia Center
for Critical Care Research, Department of Anesthesia, Critical Care,
and Pain Medicine, Massachusetts General Hospital and Harvard Medical
School, 55 Fruit Street, Boston, Massachusetts 02114, United States
| | - Dina Wassaf
- The Broad Institute
of MIT and Harvard, Chemical Biology Platform, 7 Cambridge Center, Cambridge, Massachusetts 02142, United States
| | - Revital Yefidoff-Freedman
- Anesthesia Center
for Critical Care Research, Department of Anesthesia, Critical Care,
and Pain Medicine, Massachusetts General Hospital and Harvard Medical
School, 55 Fruit Street, Boston, Massachusetts 02114, United States
| | - Dominick Casalena
- The Broad Institute
of MIT and Harvard, Chemical Biology Platform, 7 Cambridge Center, Cambridge, Massachusetts 02142, United States
| | - Michelle A. Palmer
- The Broad Institute
of MIT and Harvard, Chemical Biology Platform, 7 Cambridge Center, Cambridge, Massachusetts 02142, United States
| | - Jacqueline Meadows
- Department
of Medicinal Chemistry, Institute for Structural Biology and Drug
Discovery, School of Pharmacy, Virginia Commonwealth University, 800 East Leigh Street, Richmond, Virginia 23219, United States
| | - Andrea Mozzarelli
- Department
of Pharmacy, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy
| | - Luca Ronda
- Department
of Neuroscience, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy
| | - Osheiza Abdulmalik
- Division of Hematology,
The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States
| | - Kenneth D. Bloch
- Anesthesia Center
for Critical Care Research, Department of Anesthesia, Critical Care,
and Pain Medicine, Massachusetts General Hospital and Harvard Medical
School, 55 Fruit Street, Boston, Massachusetts 02114, United States
| | - Martin K. Safo
- Department
of Medicinal Chemistry, Institute for Structural Biology and Drug
Discovery, School of Pharmacy, Virginia Commonwealth University, 800 East Leigh Street, Richmond, Virginia 23219, United States
| | - Warren M. Zapol
- Anesthesia Center
for Critical Care Research, Department of Anesthesia, Critical Care,
and Pain Medicine, Massachusetts General Hospital and Harvard Medical
School, 55 Fruit Street, Boston, Massachusetts 02114, United States
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Pellegrino S, Ronda L, Annoni C, Contini A, Erba E, Gelmi ML, Piano R, Paredi G, Mozzarelli A, Bettati S. Molecular insights into dimerization inhibition of c-Maf transcription factor. Biochim Biophys Acta 2014; 1844:2108-15. [PMID: 25220806 DOI: 10.1016/j.bbapap.2014.09.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 08/01/2014] [Accepted: 09/02/2014] [Indexed: 01/01/2023]
Abstract
The Maf protein family belongs to the activator protein 1 (AP-1) superfamily of transcription factors that bind specific DNA target sequences through a basic region and exploit a leucine zipper (LZ) motif for protein-protein interactions leading to homo- or hetero-dimerization. Mafs unique DNA-binding domain contains a highly conserved extended homology region (EHR) that allows to recognize longer DNA sequences than other basic leucine zipper (bZIP) transcription factors. Inspired by the fact that overexpression of Mafs is observed in about 50% of cases of multiple myeloma, a hematological malignant disorder, we undertook a peptide inhibitor approach. The LZ domain of c-Maf, one of large Mafs, was produced by solid phase peptide synthesis. We characterized its secondary structure and dimerization properties, and found that dimerization and folding events are strictly coupled. Moreover, potential peptidic c-Maf dimerization inhibitors were computationally designed and synthesized. These compounds were demonstrated by circular dichroism (CD) spectroscopy and MALDI-TOF mass spectrometry to bind to c-Maf LZ monomers, to drive folding of their partially disordered structure and to efficiently compete with dimerization, suggesting a way for interfering with the function of c-Maf and, more generally, of intrinsically disordered proteins, till now considered undruggable targets.
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Affiliation(s)
- Sara Pellegrino
- DISFARM - Section of General and Organic Chemistry "A. Marchesini", University of Milan, Via Venezian 21, 20133 Milan, Italy
| | - Luca Ronda
- Department of Neurosciences, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy
| | - Chiara Annoni
- DISFARM - Section of General and Organic Chemistry "A. Marchesini", University of Milan, Via Venezian 21, 20133 Milan, Italy
| | - Alessandro Contini
- DISFARM - Section of General and Organic Chemistry "A. Marchesini", University of Milan, Via Venezian 21, 20133 Milan, Italy
| | - Emanuela Erba
- DISFARM - Section of General and Organic Chemistry "A. Marchesini", University of Milan, Via Venezian 21, 20133 Milan, Italy
| | - Maria Luisa Gelmi
- DISFARM - Section of General and Organic Chemistry "A. Marchesini", University of Milan, Via Venezian 21, 20133 Milan, Italy
| | - Riccardo Piano
- Department of Neurosciences, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy
| | - Gianluca Paredi
- Department of Pharmacy, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy; SITEIA.PARMA Interdepartmental Center, University of Parma, Parco Area delle Scienze 181/A, 43124 Parma, Italy
| | - Andrea Mozzarelli
- Department of Pharmacy, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy; National Institute of Biostructures and Biosystems, Viale Medaglie d'Oro 305, 00136 Rome, Italy
| | - Stefano Bettati
- Department of Neurosciences, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy; National Institute of Biostructures and Biosystems, Viale Medaglie d'Oro 305, 00136 Rome, Italy.
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Ronda L, Bettati S, Henry ER, Kashav T, Sanders JM, Royer WE, Mozzarelli A. Tertiary and quaternary allostery in tetrameric hemoglobin from Scapharca inaequivalvis. Biochemistry 2013; 52:2108-17. [PMID: 23458680 DOI: 10.1021/bi301620x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The clam Scapharca inaequivalvis possesses two cooperative oxygen binding hemoglobins in its red cells: a homodimeric HbI and a heterotetrameric A2B2 HbII. Each AB dimeric half of HbII is assembled in a manner very similar to that of the well-studied HbI. This study presents crystal structures of HbII along with oxygen binding data both in the crystalline state and in wet nanoporous silica gels. Despite very similar ligand-linked structural transitions observed in HbI and HbII crystals, HbII in the crystal or encapsulated in silica gels apparently exhibits minimal cooperativity in oxygen binding, in contrast with the full cooperativity exhibited by HbI crystals. However, oxygen binding curves in the crystal indicate the presence of a significant functional inequivalence of A and B chains. When this inequivalence is taken into account, both crystal and R state gel functional data are consistent with the conservation of a tertiary contribution to cooperative oxygen binding, quantitatively similar to that measured for HbI, and are in keeping with the structural information. Furthermore, our results indicate that to fully express cooperative ligand binding, HbII requires quaternary transitions hampered by crystal lattice and gel encapsulation, revealing greater complexity in cooperative function than the direct communication across a dimeric interface observed in HbI.
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Affiliation(s)
- Luca Ronda
- Department of Pharmacy, University of Parma , Parco Area delle Scienze, 23/A, 43124 Parma, Italy
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Ronda L, Merlino A, Bettati S, Verde C, Balsamo A, Mazzarella L, Mozzarelli A, Vergara A. Role of tertiary structures on the Root effect in fish hemoglobins. Biochim Biophys Acta 2013; 1834:1885-93. [PMID: 23376186 DOI: 10.1016/j.bbapap.2013.01.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Revised: 01/21/2013] [Accepted: 01/23/2013] [Indexed: 10/27/2022]
Abstract
Many fish hemoglobins exhibit a marked dependence of oxygen affinity and cooperativity on proton concentration, called Root effect. Both tertiary and quaternary effects have been evoked to explain the allosteric regulation brought about by protons in fish hemoglobins. However, no general rules have emerged so far. We carried out a complementary crystallographic and microspectroscopic characterization of ligand binding to crystals of deoxy-hemoglobin from the Antarctic fish Trematomus bernacchii (HbTb) at pH6.2 and pH8.4. At low pH ligation has negligible structural effects, correlating with low affinity and absence of cooperativity in oxygen binding. At high pH, ligation causes significant changes at the tertiary structural level, while preserving structural markers of the T state. These changes mainly consist in a marked displacement of the position of the switch region CD corner towards an R-like position. The functional data on T-state crystals validate the relevance of the crystallographic observations, revealing that, differently from mammalian Hbs, in HbTb a significant degree of cooperativity in oxygen binding is due to tertiary conformational changes, in the absence of the T-R quaternary transition. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.
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Affiliation(s)
- Luca Ronda
- Department of Pharmacy, University of Parma, Parma, Italy
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Ronda L, Mozzarelli A, Aloe R, Lippi G. Development of a novel, hemolysis-resistant reagent for assessment of α-amylase in biological fluids. Clin Chem Lab Med 2013; 51:1409-15. [DOI: 10.1515/cclm-2012-0376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 01/29/2013] [Indexed: 01/26/2023]
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Coppola D, Bruno S, Ronda L, Viappiani C, Abbruzzetti S, di Prisco G, Verde C, Mozzarelli A. Low affinity PEGylated hemoglobin from Trematomus bernacchii, a model for hemoglobin-based blood substitutes. BMC Biochem 2011; 12:66. [PMID: 22185675 PMCID: PMC3268738 DOI: 10.1186/1471-2091-12-66] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 12/20/2011] [Indexed: 01/03/2023]
Abstract
Background Conjugation of human and animal hemoglobins with polyethylene glycol has been widely explored as a means to develop blood substitutes, a novel pharmaceutical class to be used in surgery or emergency medicine. However, PEGylation of human hemoglobin led to products with significantly different oxygen binding properties with respect to the unmodified tetramer and high NO dioxygenase reactivity, known causes of toxicity. These recent findings call for the biotechnological development of stable, low-affinity PEGylated hemoglobins with low NO dioxygenase reactivity. Results To investigate the effects of PEGylation on protein structure and function, we compared the PEGylation products of human hemoglobin and Trematomus bernacchii hemoglobin, a natural variant endowed with a remarkably low oxygen affinity and high tetramer stability. We show that extension arm facilitated PEGylation chemistry based on the reaction of T. bernacchii hemoglobin with 2-iminothiolane and maleimido-functionalyzed polyethylene glycol (MW 5000 Da) leads to a tetraPEGylated product, more homogeneous than the corresponding derivative of human hemoglobin. PEGylated T. bernacchii hemoglobin largely retains the low affinity of the unmodified tetramer, with a p50 50 times higher than PEGylated human hemoglobin. Moreover, it is still sensitive to protons and the allosteric effector ATP, indicating the retention of allosteric regulation. It is also 10-fold less reactive towards nitrogen monoxide than PEGylated human hemoglobin. Conclusions These results indicate that PEGylated hemoglobins, provided that a suitable starting hemoglobin variant is chosen, can cover a wide range of oxygen-binding properties, potentially meeting the functional requirements of blood substitutes in terms of oxygen affinity, tetramer stability and NO dioxygenase reactivity.
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Affiliation(s)
- Daniela Coppola
- Department of Biochemistry and Molecular Biology, University of Parma, Parma, Italy
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Faggiano S, Bruno S, Ronda L, Pizzonia P, Pioselli B, Mozzarelli A. Modulation of expression and polymerization of hemoglobin Polytaur, a potential blood substitute. Arch Biochem Biophys 2011; 505:42-7. [DOI: 10.1016/j.abb.2010.09.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Revised: 09/27/2010] [Accepted: 09/27/2010] [Indexed: 11/25/2022]
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Ronda L, Bruno S, Bettati S, Mozzarelli A. Protein crystal microspectrophotometry. Biochim Biophys Acta 2010; 1814:734-41. [PMID: 21184848 DOI: 10.1016/j.bbapap.2010.12.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Revised: 12/10/2010] [Accepted: 12/11/2010] [Indexed: 11/16/2022]
Abstract
Single crystal microspectrophotometry has emerged as a valuable technique for monitoring molecular events that take place within protein crystals, thus tightly coupling structure to function. Absorption and fluorescence spectra, ligand binding affinities and kinetic constants can be determined, allowing i) the definition of the experimental conditions for X-ray crystallography experiments and their interpretation, ii) the assessment of whether crystal lattice forces have altered conformational equilibria, iii) the comparison with data obtained in solution. Microspectrophotometric measurements using oriented crystals and linearly polarized light are carried out usually off-line with respect to X-ray data collection and are aimed at an in- depth characterization of protein function in the crystal, leading to robust structure-function relationships. The power of this approach is highlighted by reporting a few case studies, including hemoglobins, pyridoxal 5'-phosphate-dependent enzymes and acetylcholinesterases. This article is part of a Special Issue entitled: Protein Structure and Function in the Crystalline State.
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Affiliation(s)
- Luca Ronda
- Department of Biochemistry and Molecular Biology, University of Parma, Parma, Italy
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42
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Ronda L, Bazhulina NP, Morozova EA, Revtovich SV, Chekhov VO, Nikulin AD, Demidkina TV, Mozzarelli A. Exploring methionine γ-lyase structure-function relationship via microspectrophotometry and X-ray crystallography. Biochim Biophys Acta 2010; 1814:834-42. [PMID: 20601224 DOI: 10.1016/j.bbapap.2010.06.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Revised: 06/17/2010] [Accepted: 06/18/2010] [Indexed: 11/26/2022]
Abstract
Pyridoxal 5'-phosphate (PLP) dependent methionine γ-lyase catalyzes the breakdown of L-methionine to α-ketobutyric acid, methanethiol and ammonia. This enzyme, present in anaerobic microorganisms, has biomedical interest both for its activity as antitumor agent, depleting methionine supply in methionine-dependent cancers, and as target in the treatment of human pathogen infections, activating the pro-drug trifluoromethionine. To validate the structure of the enzyme from Citrobacter freundii, crystallized from monomethyl ether polyethylene glycol 2000, for the development of lead compounds, the reactivity of the crystalline enzyme towards L-methionine, substrate analogs and inhibitors was determined by polarized absorption microspectrophotometry. Spectral data were also collected for enzyme crystals, grown in monomethyl ether polyethylene glycol 2000 in the presence of ammonium sulfate. The three-dimensional structure of these enzyme crystals, solved at 1.65Å resolution with R(free) 23.2%, revealed the surprising absence of the aldimine bond between the active site Lys210 and PLP. Different hypothesis are proposed and discussed in the light of spectral and structural data, pointing out to the relevance of the complementarity between X-ray crystallography and single crystal spectroscopy for the understanding of biological mechanisms at molecular level. This article is part of a Special Issue entitled: Protein Structure and Function in the Crystalline State.
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Affiliation(s)
- Luca Ronda
- Department of Biochemistry and Molecular Biology, University of Parma, Parma, Italy
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Faggiano S, Ronda L, Bruno S, Jankevics H, Mozzarelli A. Polymerized and polyethylene glycol-conjugated hemoglobins: a globin-based calibration curve for dynamic light scattering analysis. Anal Biochem 2010; 401:266-70. [PMID: 20184856 DOI: 10.1016/j.ab.2010.02.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2010] [Revised: 02/19/2010] [Accepted: 02/19/2010] [Indexed: 11/26/2022]
Abstract
Dynamic light scattering (DLS) is a technique capable of determining the hydrodynamic radius of proteins. From this parameter, a molecular weight can be assessed provided that an appropriate calibration curve is available. To this goal, a globin-based calibration curve was used to determine the polymerization state of a recombinant hemoglobin-based oxygen carrier and to assess the equivalent molecular weight of hemoglobins conjugated with polyethylene glycol molecules. The good agreement between DLS values and those obtained from gel filtration chromatography is a consequence of the high similarity in structure, shape, and density within the globin superfamily. Moreover, globins and heme proteins in general share similar spectroscopic properties, thereby reducing possible systematic errors associated with the absorption of the probe radiation by the chromophore.
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Affiliation(s)
- Serena Faggiano
- Department of Biochemistry and Molecular Biology, University of Parma, 43124 Parma, Italy
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Bruno S, Ronda L, Bettati S, Mozzarelli A. Trapping Hemoglobin in Rigid Matrices: Fine Tuning of Oxygen Binding Properties by Modulation of Encapsulation Protocols. ACTA ACUST UNITED AC 2009; 35:69-79. [PMID: 17364472 DOI: 10.1080/10731190600974541] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [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: 10/23/2022]
Abstract
Encapsulation of hemoglobin in a biocompatible matrix is a potential strategy for obtaining blood substitutes. Such a system would retain most of the immunogenic and functional properties of the physiologically relevant oxygen carrier but would prevent protein extravasation and dimer/dimer dissociation. We applied this approach by entrapping hemoglobin in wet nanoporous silica gel, in the presence and absence of allosteric effectors. Silica gels, although not suitable for intravenous perfusion, are inert and optically transparent, thus allowing a full characterization of the functional and structural properties of encapsulated hemoglobin by spectroscopic techniques. Results indicate that hemoglobin molecules, entrapped using different protocols, exhibit an oxygen affinity that can be modulated between 12 and 140 torr. This tunability could be exploited to meet distinct clinical needs.
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Affiliation(s)
- Stefano Bruno
- Department of Biochemistry and Molecular Biology, University of Parma, Parma, Italy
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Caccia D, Ronda L, Frassi R, Perrella M, Del Favero E, Bruno S, Pioselli B, Abbruzzetti S, Viappiani C, Mozzarelli A. PEGylation Promotes Hemoglobin Tetramer Dissociation. Bioconjug Chem 2009; 20:1356-66. [DOI: 10.1021/bc900130f] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dario Caccia
- Dipartimento di Scienze e Tecnologie Biomediche, Dipartimento di Chimica, Biochimica e Biotecnologie per la Medicina, Università degli Studi di Milano, and LITA (Laboratorio Interdisciplinare di Tecnologie Avanzate), 20090 Segrate, Milano, Italy, and Dipartimento di Biochimica e Biologia Molecolare, Dipartimento di Fisica, Università di Parma, and NEST CNR-INFM, Istituto Nazionale di Biostrutture e Biosistemi, 43100 Parma, Italy
| | - Luca Ronda
- Dipartimento di Scienze e Tecnologie Biomediche, Dipartimento di Chimica, Biochimica e Biotecnologie per la Medicina, Università degli Studi di Milano, and LITA (Laboratorio Interdisciplinare di Tecnologie Avanzate), 20090 Segrate, Milano, Italy, and Dipartimento di Biochimica e Biologia Molecolare, Dipartimento di Fisica, Università di Parma, and NEST CNR-INFM, Istituto Nazionale di Biostrutture e Biosistemi, 43100 Parma, Italy
| | - Raffaella Frassi
- Dipartimento di Scienze e Tecnologie Biomediche, Dipartimento di Chimica, Biochimica e Biotecnologie per la Medicina, Università degli Studi di Milano, and LITA (Laboratorio Interdisciplinare di Tecnologie Avanzate), 20090 Segrate, Milano, Italy, and Dipartimento di Biochimica e Biologia Molecolare, Dipartimento di Fisica, Università di Parma, and NEST CNR-INFM, Istituto Nazionale di Biostrutture e Biosistemi, 43100 Parma, Italy
| | - Michele Perrella
- Dipartimento di Scienze e Tecnologie Biomediche, Dipartimento di Chimica, Biochimica e Biotecnologie per la Medicina, Università degli Studi di Milano, and LITA (Laboratorio Interdisciplinare di Tecnologie Avanzate), 20090 Segrate, Milano, Italy, and Dipartimento di Biochimica e Biologia Molecolare, Dipartimento di Fisica, Università di Parma, and NEST CNR-INFM, Istituto Nazionale di Biostrutture e Biosistemi, 43100 Parma, Italy
| | - Elena Del Favero
- Dipartimento di Scienze e Tecnologie Biomediche, Dipartimento di Chimica, Biochimica e Biotecnologie per la Medicina, Università degli Studi di Milano, and LITA (Laboratorio Interdisciplinare di Tecnologie Avanzate), 20090 Segrate, Milano, Italy, and Dipartimento di Biochimica e Biologia Molecolare, Dipartimento di Fisica, Università di Parma, and NEST CNR-INFM, Istituto Nazionale di Biostrutture e Biosistemi, 43100 Parma, Italy
| | - Stefano Bruno
- Dipartimento di Scienze e Tecnologie Biomediche, Dipartimento di Chimica, Biochimica e Biotecnologie per la Medicina, Università degli Studi di Milano, and LITA (Laboratorio Interdisciplinare di Tecnologie Avanzate), 20090 Segrate, Milano, Italy, and Dipartimento di Biochimica e Biologia Molecolare, Dipartimento di Fisica, Università di Parma, and NEST CNR-INFM, Istituto Nazionale di Biostrutture e Biosistemi, 43100 Parma, Italy
| | - Barbara Pioselli
- Dipartimento di Scienze e Tecnologie Biomediche, Dipartimento di Chimica, Biochimica e Biotecnologie per la Medicina, Università degli Studi di Milano, and LITA (Laboratorio Interdisciplinare di Tecnologie Avanzate), 20090 Segrate, Milano, Italy, and Dipartimento di Biochimica e Biologia Molecolare, Dipartimento di Fisica, Università di Parma, and NEST CNR-INFM, Istituto Nazionale di Biostrutture e Biosistemi, 43100 Parma, Italy
| | - Stefania Abbruzzetti
- Dipartimento di Scienze e Tecnologie Biomediche, Dipartimento di Chimica, Biochimica e Biotecnologie per la Medicina, Università degli Studi di Milano, and LITA (Laboratorio Interdisciplinare di Tecnologie Avanzate), 20090 Segrate, Milano, Italy, and Dipartimento di Biochimica e Biologia Molecolare, Dipartimento di Fisica, Università di Parma, and NEST CNR-INFM, Istituto Nazionale di Biostrutture e Biosistemi, 43100 Parma, Italy
| | - Cristiano Viappiani
- Dipartimento di Scienze e Tecnologie Biomediche, Dipartimento di Chimica, Biochimica e Biotecnologie per la Medicina, Università degli Studi di Milano, and LITA (Laboratorio Interdisciplinare di Tecnologie Avanzate), 20090 Segrate, Milano, Italy, and Dipartimento di Biochimica e Biologia Molecolare, Dipartimento di Fisica, Università di Parma, and NEST CNR-INFM, Istituto Nazionale di Biostrutture e Biosistemi, 43100 Parma, Italy
| | - Andrea Mozzarelli
- Dipartimento di Scienze e Tecnologie Biomediche, Dipartimento di Chimica, Biochimica e Biotecnologie per la Medicina, Università degli Studi di Milano, and LITA (Laboratorio Interdisciplinare di Tecnologie Avanzate), 20090 Segrate, Milano, Italy, and Dipartimento di Biochimica e Biologia Molecolare, Dipartimento di Fisica, Università di Parma, and NEST CNR-INFM, Istituto Nazionale di Biostrutture e Biosistemi, 43100 Parma, Italy
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Ronda L, Bruno S, Abbruzzetti S, Viappiani C, Bettati S. Ligand reactivity and allosteric regulation of hemoglobin-based oxygen carriers. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 2008; 1784:1365-77. [DOI: 10.1016/j.bbapap.2008.04.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2008] [Revised: 04/21/2008] [Accepted: 04/24/2008] [Indexed: 01/05/2023]
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Ronda L, Abbruzzetti S, Bruno S, Bettati S, Mozzarelli A, Viappiani C. Ligand-Induced Tertiary Relaxations During the T-to-R Quaternary Transition in Hemoglobin. J Phys Chem B 2008; 112:12790-4. [DOI: 10.1021/jp803040j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Luca Ronda
- Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Parma, CNISM, and Dipartimento di Fisica, Università degli Studi di Parma, CNISM, and NEST CNR-INFM
| | - Stefania Abbruzzetti
- Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Parma, CNISM, and Dipartimento di Fisica, Università degli Studi di Parma, CNISM, and NEST CNR-INFM
| | - Stefano Bruno
- Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Parma, CNISM, and Dipartimento di Fisica, Università degli Studi di Parma, CNISM, and NEST CNR-INFM
| | - Stefano Bettati
- Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Parma, CNISM, and Dipartimento di Fisica, Università degli Studi di Parma, CNISM, and NEST CNR-INFM
| | - Andrea Mozzarelli
- Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Parma, CNISM, and Dipartimento di Fisica, Università degli Studi di Parma, CNISM, and NEST CNR-INFM
| | - Cristiano Viappiani
- Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Parma, CNISM, and Dipartimento di Fisica, Università degli Studi di Parma, CNISM, and NEST CNR-INFM
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Abbruzzetti S, Bruno S, Faggiano S, Ronda L, Grandi E, Mozzarelli A, Viappiani C. Characterization of ligand migration mechanisms inside hemoglobins from the analysis of geminate rebinding kinetics. Methods Enzymol 2008; 437:329-45. [PMID: 18433636 DOI: 10.1016/s0076-6879(07)37017-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
The presence of internal hydrophobic cavities and packing defects has been demonstrated for several small globular proteins, including hemoglobins. The reduced thermodynamic stability appears to be compensated for by the capability of controlling ligand diffusion through the protein matrix to the active site, possibly by stocking more than one reactant molecule in selected sites. Photolysis of carbon monoxide complexes of hemoglobins encapsulated in silica gels leads to multiphasic geminate rebinding kinetics at room temperature, reflecting rebinding also from different temporary docking sites inside the protein matrix. A careful analysis of the ligand rebinding kinetics allows the determination of the microscopic rates for the underlying reactions, including those governing the migration to and from the docking sites. This chapter describes the experimental approach used to characterize the ligand rebinding kinetics for heme proteins in silica gels after nanosecond laser flash photolysis and the computational methods necessary to retrieve the kinetic parameters.
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Woods A, Rutter K, Gardner L, Lewis V, Saxena S, George S, Chalmers R, Griffiths C, Speight E, Anstey A, Ronda L, McGibbon D, Barker J, Smith C. Inpatient management of psoriasis: a multicentre service review to establish national admission standards. Br J Dermatol 2007; 158:266-72. [DOI: 10.1111/j.1365-2133.2007.08338.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Ronda L, Faggiano S, Bettati S, Hellmann N, Decker H, Weidenbach T, Mozzarelli A. Hemocyanin from E. californicum encapsulated in silica gels: Oxygen binding and conformational states. Gene 2007; 398:202-7. [PMID: 17512140 DOI: 10.1016/j.gene.2007.02.036] [Citation(s) in RCA: 7] [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] [Received: 12/11/2006] [Revised: 02/24/2007] [Accepted: 02/26/2007] [Indexed: 11/30/2022]
Abstract
Cooperativity depends on the existence of equilibria among functionally distinct conformational states that are affected by homo and heterotropic effectors. In order to isolate the quaternary conformations of hemocyanin from E. californicum, the 24-meric giant protein was encapsulated in wet, nanoporous silica gels, either in the absence or presence of oxygen. The deoxy- and oxy-hemocyanin gels exhibit a p50 for oxygen of 11 and 2.5 torr, respectively, values in close agreement with those for hemocyanin in solution. The observed Hill coefficients are lower than unity, indicating a conformational heterogeneity within each locked conformational state, a finding in agreement with the assumption that at least four conformational states are required to explain the oxygen binding properties of E. californicum hemocyanin in solution.
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Affiliation(s)
- Luca Ronda
- Department of Biochemistry and Molecular Biology, University of Parma, Parma, Italy
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