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Samal S, Nelson S, Du Z, Wang D, Wang T, Yang C, Deng Q, Parkinson EI, Mei J. Blood-Catalyzed Polymerization Creates Conductive Polymer in Live Zebrafish. RESEARCH SQUARE 2024:rs.3.rs-3602290. [PMID: 38978602 PMCID: PMC11230466 DOI: 10.21203/rs.3.rs-3602290/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Conducting polymers are of great interest in bioimaging, bio-interfaces, and bioelectronics for their biocompatibility and the unique combination of optical, electrical, and mechanical properties. They are typically prepared outside through traditional organic synthesis and delivered into the biological systems. The ability to call for the polymerization ingredients available inside the living systems to generate conducting polymers in vivo will offer new venues in future biomedical applications. This study is the first report of in vivo synthesis of an n-doped conducting polymer (n-PBDF) within live zebrafish embryos, achieved through whole blood catalyzed polymerization of 3,7-dihydrobenzo[1,2-b:4,5-b']difuran-2,6-dione (BDF). Prior to this, the efficacy of such a polymerization was rigorously established through a sequence of in vitro experiments involving Hemin, Hemoproteins (Hemoglobin, Myoglobin, and Cytochrome C), red blood cells, and the whole blood. Ultimately, in cellulo formed n-PBDF within cultured primary neurons demonstrated enhanced bio-interfaces and led to more effective light-induced neural activation than the prefabricated polymer. This underscores the potential advantages of synthesizing conducting polymers directly in living systems for biomedical applications.
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Affiliation(s)
- Sanket Samal
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Samantha Nelson
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Zhiyi Du
- Department of Chemistry, Boston University, Boston, MA, USA
| | - Decheng Wang
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Tianqi Wang
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Chen Yang
- Department of Chemistry, Boston University, Boston, MA, USA
| | - Qing Deng
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Purdue Institute for Inflammation, Immunology & Infectious Diseases, Purdue University, West Lafayette, IN, USA
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, USA
| | - Elizabeth I. Parkinson
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Jianguo Mei
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
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2
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Moura RT, Quintano M, Antonio JJ, Freindorf M, Kraka E. Automatic Generation of Local Vibrational Mode Parameters: From Small to Large Molecules and QM/MM Systems. J Phys Chem A 2022; 126:9313-9331. [DOI: 10.1021/acs.jpca.2c07871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Renaldo T. Moura
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas75275-0314, United States
- Department of Chemistry and Physics Center of Agrarian Sciences, Federal University of Paraiba, Areia, PB58397-000, Brazil
| | - Mateus Quintano
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas75275-0314, United States
| | - Juliana J. Antonio
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas75275-0314, United States
| | - Marek Freindorf
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas75275-0314, United States
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas75275-0314, United States
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3
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Exertier C, Sebastiani F, Freda I, Gugole E, Cerutti G, Parisi G, Montemiglio LC, Becucci M, Viappiani C, Bruno S, Savino C, Zamparelli C, Anselmi M, Abbruzzetti S, Smulevich G, Vallone B. Probing the Role of Murine Neuroglobin CDloop-D-Helix Unit in CO Ligand Binding and Structural Dynamics. ACS Chem Biol 2022; 17:2099-2108. [PMID: 35797699 PMCID: PMC9396615 DOI: 10.1021/acschembio.2c00172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
We produced a neuroglobin variant, namely, Ngb CDless,
with the
excised CDloop- and D-helix, directly joining the C- and E-helices.
The CDless variant retained bis-His hexacoordination, and we investigated
the role of the CDloop–D-helix unit in controlling the CO binding
and structural dynamics by an integrative approach based on X-ray
crystallography, rapid mixing, laser flash photolysis, resonance Raman
spectroscopy, and molecular dynamics simulations. Rapid mixing and
laser flash photolysis showed that ligand affinity was unchanged with
respect to the wild-type protein, albeit with increased on and off
constants for rate-limiting heme iron hexacoordination by the distal
His64. Accordingly, resonance Raman spectroscopy highlighted a more
open distal pocket in the CO complex that, in agreement with MD simulations,
likely involves His64 swinging inward and outward of the distal heme
pocket. Ngb CDless displays a more rigid overall structure with respect
to the wild type, abolishing the structural dynamics of the CDloop–D-helix
hypothesized to mediate its signaling role, and it retains ligand
binding control by distal His64. In conclusion, this mutant may represent
a tool to investigate the involvement of CDloop–D-helix in
neuroprotective signaling in a cellular or animal model.
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Affiliation(s)
- Cécile Exertier
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza, Università di Roma, Piazzale A. Moro 5, I-00185 Rome, Italy
| | - Federico Sebastiani
- Dipartimento di Chimica ″Ugo Schiff″, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino, Italy
| | - Ida Freda
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza, Università di Roma, Piazzale A. Moro 5, I-00185 Rome, Italy
| | - Elena Gugole
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza, Università di Roma, Piazzale A. Moro 5, I-00185 Rome, Italy
| | - Gabriele Cerutti
- Zuckerman Mind Brain Behavior Institute, Columbia University, 3227 Broadway, New York, New York 10027, United States
| | - Giacomo Parisi
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Viale Regina Elena, 291, I-00161 Rome, Italy
| | - Linda Celeste Montemiglio
- Institute of Molecular Biology and Pathology, National Research Council, Piazzale A. Moro 5, 00185 Rome, Italy
| | - Maurizio Becucci
- Dipartimento di Chimica ″Ugo Schiff″, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino, Italy
| | - Cristiano Viappiani
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parco Area delle Scienze, 7/A, I-43124 Parma, Italy
| | - Stefano Bruno
- Department of Food and Drugs, University of Parma, Parco Area delle Scienze 27/A, I-43124 Parma, Italy
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology, National Research Council, Piazzale A. Moro 5, 00185 Rome, Italy
| | - Carlotta Zamparelli
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza, Università di Roma, Piazzale A. Moro 5, I-00185 Rome, Italy
| | - Massimiliano Anselmi
- Theoretical Physics and Center for Biophysics, Saarland University, Campus E2 6, 66123 Saarbrücken, Germany
| | - Stefania Abbruzzetti
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parco Area delle Scienze, 7/A, I-43124 Parma, Italy
| | - Giulietta Smulevich
- Dipartimento di Chimica ″Ugo Schiff″, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino, Italy
| | - Beatrice Vallone
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza, Università di Roma, Piazzale A. Moro 5, I-00185 Rome, Italy
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4
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Giordano D, Verde C, Corti P. Nitric Oxide Production and Regulation in the Teleost Cardiovascular System. Antioxidants (Basel) 2022; 11:antiox11050957. [PMID: 35624821 PMCID: PMC9137985 DOI: 10.3390/antiox11050957] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/06/2022] [Accepted: 05/09/2022] [Indexed: 01/08/2023] Open
Abstract
Nitric Oxide (NO) is a free radical with numerous critical signaling roles in vertebrate physiology. Similar to mammals, in the teleost system the generation of sufficient amounts of NO is critical for the physiological function of the cardiovascular system. At the same time, NO amounts are strictly controlled and kept within basal levels to protect cells from NO toxicity. Changes in oxygen tension highly influence NO bioavailability and can modulate the mechanisms involved in maintaining the NO balance. While NO production and signaling appears to have general similarities with mammalian systems, the wide range of environmental adaptations made by fish, particularly with regards to differing oxygen availabilities in aquatic habitats, creates a foundation for a variety of in vivo models characterized by different implications of NO production and signaling. In this review, we present the biology of NO in the teleost cardiovascular system and summarize the mechanisms of NO production and signaling with a special emphasis on the role of globin proteins in NO metabolism.
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Affiliation(s)
- Daniela Giordano
- Institute of Biosciences and BioResources (IBBR), National Research Council (CNR), Via Pietro Castellino 111, 80131 Napoli, Italy; (D.G.); (C.V.)
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn (SZN), Villa Comunale, 80121 Napoli, Italy
| | - Cinzia Verde
- Institute of Biosciences and BioResources (IBBR), National Research Council (CNR), Via Pietro Castellino 111, 80131 Napoli, Italy; (D.G.); (C.V.)
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn (SZN), Villa Comunale, 80121 Napoli, Italy
| | - Paola Corti
- Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Division of Cardiology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Correspondence:
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5
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Giordano D, Verde C. Expression of Recombinant Cold-Adapted (Hemo)Globins from Marine Bacteria. Methods Mol Biol 2022; 2498:283-292. [PMID: 35727550 DOI: 10.1007/978-1-0716-2313-8_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The production of recombinant proteins in bacteria made possible to obtain large quantities of proteins essential for basic and applied research. Escherichia coli remains one of the organisms of choice for recombinant proteins because of its ability to grow at high density and availability of a vast catalog of cloning vectors and mutant host strains. Here, we describe the protocols for the expression of cold-adapted (hemo)globins in Escherichia coli.
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Affiliation(s)
- Daniela Giordano
- Institute of Biosciences and BioResources (IBBR), CNR, Naples, Italy.
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn (SZN), Villa Comunale, Naples, Italy.
| | - Cinzia Verde
- Institute of Biosciences and BioResources (IBBR), CNR, Naples, Italy
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn (SZN), Villa Comunale, Naples, Italy
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6
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Exertier C, Montemiglio LC, Freda I, Gugole E, Parisi G, Savino C, Vallone B. Neuroglobin, clues to function and mechanism. Mol Aspects Med 2021; 84:101055. [PMID: 34876274 DOI: 10.1016/j.mam.2021.101055] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 12/19/2022]
Abstract
Neuroglobin is expressed in vertebrate brain and belongs to a branch of the globin family that diverged early in evolution. Sequence conservation and presence in nervous cells of several taxa suggests a relevant role in the nervous system, with tight structural restraints. Twenty years after its discovery, a rich scientific literature provides convincing evidence of the involvement of neuroglobin in sustaining neuron viability in physiological and pathological conditions however, a full and conclusive picture of its specific function, or set of functions is still lacking. The difficulty of unambiguously assigning a precise mechanism and biochemical role to neuroglobin might arise from the participation to one or more cell mechanism that redundantly guarantee the functioning of the highly specialized and metabolically demanding central nervous system of vertebrates. Here we collect findings and hypotheses arising from recent biochemical, biophysical, structural, in cell and in vivo experimental work on neuroglobin, aiming at providing an overview of the most recent literature. Proteins are said to have jobs and hobbies, it is possible that, in the case of neuroglobin, evolution has selected for it more than one job, and support to cover for its occasional failings. Disentangling the mechanisms and roles of neuroglobin is thus a challenging task that might be achieved by considering data from different disciplines and experimental approaches.
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Affiliation(s)
- Cécile Exertier
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza, Università di Roma, P.le A. Moro 5, 00185, Rome, Italy
| | - Linda Celeste Montemiglio
- Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro 5, 00185, Rome, Italy
| | - Ida Freda
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza, Università di Roma, P.le A. Moro 5, 00185, Rome, Italy
| | - Elena Gugole
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza, Università di Roma, P.le A. Moro 5, 00185, Rome, Italy
| | - Giacomo Parisi
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, 00161, Rome, Italy
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro 5, 00185, Rome, Italy.
| | - Beatrice Vallone
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza, Università di Roma, P.le A. Moro 5, 00185, Rome, Italy.
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7
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Fry HC, Peters BL, Ferguson AL. Pushing and Pulling: A Dual pH Trigger Controlled by Varying the Alkyl Tail Length in Heme Coordinating Peptide Amphiphiles. J Phys Chem B 2021; 125:1317-1330. [PMID: 33529038 DOI: 10.1021/acs.jpcb.0c07713] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Some organisms in nature that undergo anaerobic respiration utilize 1D nanoscale arrays of densely packed cytochromes containing the molecule heme. The assemblies can be mimicked with 1D nanoscale fibrils composed of peptide amphiphiles designed to coordinate heme in dense arrays. To create such materials and assemblies, it is critical to understand the assembly process and what controls the various aspects of hierarchical assembly. MD simulations suggest that shorter alkyl chains on the peptide lead to more dynamic structures than the peptides with longer chains that yield kinetically trapped states. The hydration parameters manifest themselves experimentally through the observation of a dual pH trigger, which controls the peptide assembly rate, the heme binding affinity, and heme organization kinetics. Great strides in understanding the relative complexity of the self-assembly process in relation to incorporating a functional moiety like heme opens up many possibilities in developing abiotic assemblies for bioelectronic devices and assemblies.
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Affiliation(s)
- H Christopher Fry
- Center for Nansocale Materials, Argonne National Laboratory, 9700 S. Cass Ave. Lemont, Argonne, Illinois 60712, United States
| | - Brandon L Peters
- Materials Science Division, Argonne National Laboratory, 9700 S. Cass Ave. Lemont, Argonne, Illinois 60712, United States
| | - Andrew L Ferguson
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, United States
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8
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Giordano D, Corti P, Coppola D, Altomonte G, Xue J, Russo R, di Prisco G, Verde C. Regulation of globin expression in Antarctic fish under thermal and hypoxic stress. Mar Genomics 2020; 57:100831. [PMID: 33250437 DOI: 10.1016/j.margen.2020.100831] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/18/2020] [Accepted: 11/18/2020] [Indexed: 01/27/2023]
Abstract
In the freezing waters of the Southern Ocean, Antarctic teleost fish, the Notothenioidei, have developed unique adaptations to cope with cold, including, at the extreme, the loss of hemoglobin in icefish. As a consequence, icefish are thought to be the most vulnerable of the Antarctic fish species to ongoing ocean warming. Some icefish also fail to express myoglobin but all appear to retain neuroglobin, cytoglobin-1, cytoglobin-2, and globin-X. Despite the lack of the inducible heat shock response, Antarctic notothenioid fish are endowed with physiological plasticity to partially compensate for environmental changes, as shown by numerous physiological and genomic/transcriptomic studies over the last decade. However, the regulatory mechanisms that determine temperature/oxygen-induced changes in gene expression remain largely unexplored in these species. Proteins such as globins are susceptible to environmental changes in oxygen levels and temperature, thus playing important roles in mediating Antarctic fish adaptations. In this study, we sequenced the full-length transcripts of myoglobin, neuroglobin, cytoglobin-1, cytoglobin-2, and globin-X from the Antarctic red-blooded notothenioid Trematomus bernacchii and the white-blooded icefish Chionodraco hamatus and evaluated transcripts levels after exposure to high temperature and low oxygen levels. Basal levels of globins are similar in the two species and both stressors affect the expression of Antarctic fish globins in brain, retina and gills. Temperature up-regulates globin expression more effectively in white-blooded than in red-blooded fish while hypoxia strongly up-regulates globins in red-blooded fish, particularly in the gills. These results suggest globins function as regulators of temperature and hypoxia tolerance. This study provides the first insights into globin transcriptional changes in Antarctic fish.
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Affiliation(s)
- Daniela Giordano
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111, Napoli 80131, Italy; Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn (SZN), Villa Comunale, Napoli 80121, Italy.
| | - Paola Corti
- Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15213, USA; Division of Cardiology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Daniela Coppola
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111, Napoli 80131, Italy; Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn (SZN), Villa Comunale, Napoli 80121, Italy
| | - Giovanna Altomonte
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111, Napoli 80131, Italy; Department of Science, Roma Tre University, Viale Guglielmo Marconi 446, Roma I-00146, Italy
| | - Jianmin Xue
- Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Roberta Russo
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111, Napoli 80131, Italy
| | - Guido di Prisco
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111, Napoli 80131, Italy
| | - Cinzia Verde
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111, Napoli 80131, Italy; Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn (SZN), Villa Comunale, Napoli 80121, Italy
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9
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Giordano D, Pesce A, Vermeylen S, Abbruzzetti S, Nardini M, Marchesani F, Berghmans H, Seira C, Bruno S, Javier Luque F, di Prisco G, Ascenzi P, Dewilde S, Bolognesi M, Viappiani C, Verde C. Structural and functional properties of Antarctic fish cytoglobins-1: Cold-reactivity in multi-ligand reactions. Comput Struct Biotechnol J 2020; 18:2132-2144. [PMID: 32913582 PMCID: PMC7451756 DOI: 10.1016/j.csbj.2020.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 07/10/2020] [Accepted: 08/05/2020] [Indexed: 12/11/2022] Open
Abstract
While the functions of the recently discovered cytoglobin, ubiquitously expressed in vertebrate tissues, remain uncertain, Antarctic fish provide unparalleled models to study novel protein traits that may arise from cold adaptation. We report here the spectral, ligand-binding and enzymatic properties (peroxynitrite isomerization, nitrite-reductase activity) of cytoglobin-1 from two Antarctic fish, Chaenocephalus aceratus and Dissostichus mawsoni, and present the crystal structure of D. mawsoni cytoglobin-1. The Antarctic cytoglobins-1 display high O2 affinity, scarcely compatible with an O2-supply role, a slow rate constant for nitrite-reductase activity, and do not catalyze peroxynitrite isomerization. Compared with mesophilic orthologues, the cold-adapted cytoglobins favor binding of exogenous ligands to the hexa-coordinated bis-histidyl species, a trait related to their higher rate constant for distal-His/heme-Fe dissociation relative to human cytoglobin. At the light of a remarkable 3D-structure conservation, the observed differences in ligand-binding kinetics may reflect Antarctic fish cytoglobin-1 specific features in the dynamics of the heme distal region and of protein matrix cavities, suggesting adaptation to functional requirements posed by the cold environment. Taken together, the biochemical and biophysical data presented suggest that in Antarctic fish, as in humans, cytoglobin-1 unlikely plays a role in O2 transport, rather it may be involved in processes such as NO detoxification.
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Key Words
- C.aceCygb-1*, Mutant of C.aceCygb-1
- C.aceCygb-1, Cytoglobin-1 of C. aceratus
- CO, Carbon monoxide
- CYGB, Human Cygb
- Cold-adaptation
- Cygb, Cytoglobin
- Cygb-1, Cytoglobin 1
- Cygb-2, Cytoglobin 2
- Cygbh, Hexa-coordinated bis-histidyl species
- Cygbp, Penta-coordinated Cygb
- Cytoglobin
- D.mawCygb-1*, Mutant of D.mawCygb-1
- D.mawCygb-1, Cytoglobin-1 of D. mawsoni
- DTT, Dithiothreitol
- Hb, Hemoglobin
- Ligand properties
- MD, Molecular Dynamics
- Mb, Myoglobin
- NGB, Human neuroglobin
- NO dioxygenase
- NO, Nitric oxide
- RNS, Reactive Nitrogen Species
- ROS, Reactive Oxygen Species
- X-ray structure
- p50, O2 partial pressure required to achieve half saturation
- rms, Root-mean square
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Affiliation(s)
- Daniela Giordano
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111 80131 Napoli, Italy.,Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Alessandra Pesce
- Department of Physics, University of Genova, Via Dodecaneso 33, I-16121 Genova, Italy
| | - Stijn Vermeylen
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Stefania Abbruzzetti
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parco Area delle Scienze 7A, 43124 Parma, Italy
| | - Marco Nardini
- Department of Biosciences, University of Milano, Via Celoria 26, I-20133 Milano, Italy
| | - Francesco Marchesani
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 23A, 43124, Parma, Italy
| | - Herald Berghmans
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Constantí Seira
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Science, Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, Av. Prat de la Riba 171, Santa Coloma de Gramenet E-08921, Spain
| | - Stefano Bruno
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 23A, 43124, Parma, Italy
| | - F Javier Luque
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Science, Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, Av. Prat de la Riba 171, Santa Coloma de Gramenet E-08921, Spain
| | - Guido di Prisco
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111 80131 Napoli, Italy
| | - Paolo Ascenzi
- Interdepartmental Laboratory for Electron Microscopy, Roma Tre University, Via della Vasca Navale 79, I-00146 Roma, Italy
| | - Sylvia Dewilde
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Martino Bolognesi
- Department of Biosciences, University of Milano, Via Celoria 26, I-20133 Milano, Italy
| | - Cristiano Viappiani
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parco Area delle Scienze 7A, 43124 Parma, Italy
| | - Cinzia Verde
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111 80131 Napoli, Italy.,Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
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10
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Milazzo L, Exertier C, Becucci M, Freda I, Montemiglio LC, Savino C, Vallone B, Smulevich G. Lack of orientation selectivity of the heme insertion in murine neuroglobin revealed by resonance Raman spectroscopy. FEBS J 2020; 287:4082-4097. [PMID: 32034988 DOI: 10.1111/febs.15241] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/30/2020] [Accepted: 02/05/2020] [Indexed: 01/17/2023]
Abstract
Different murine neuroglobin variants showing structural and dynamic alterations that are associated with perturbation of ligand binding have been studied: the CD loop mutants characterized by an enhanced flexibility (Gly-loop40-48 and Gly-loop44-47 ), the F106A mutant, and the double Gly-loop44-47 /F106A mutant. Their ferric resonance Raman spectra in solution and in crystals are almost identical. In the high-frequency region, the identification of a double set of core size marker bands indicates the presence of two 6-coordinate low spin species. The resonance Raman data, together with the corresponding crystal structures, indicate the presence of two neuroglobin conformers with a reversed (A conformer) or a canonical (B conformer) heme insertion orientation. With the identification of the marker bands corresponding to each conformer, the data indicate that the B conformer increases at the expense of the A form, predominantly in the Gly-loop44-47 /F106A double mutant, as confirmed by X-ray crystallography. This is the first time that a reversed heme insertion has been identified by resonance Raman in a native 6-coordinate low-spin heme protein. This diagnostic tool could be extended to other heme proteins in order to detect heme orientational disorder, which are likely to be correlated to functionally relevant heme dynamics. DATABASE: Crystallographic structure: structural data are deposited in the Protein Data Bank under the 6RA6 PDB entry.
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Affiliation(s)
- Lisa Milazzo
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Florence, Italy
| | - Cécile Exertier
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Italy.,Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza, Università di Roma, Italy
| | - Maurizio Becucci
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Florence, Italy.,European Laboratory for Non-Linear Spectroscopy - LENS, Florence, Italy
| | - Ida Freda
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Italy.,Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza, Università di Roma, Italy
| | - Linda Celeste Montemiglio
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Italy.,Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza, Università di Roma, Italy.,CNR Institute of Molecular Biology and Pathology, Rome, Italy
| | | | - Beatrice Vallone
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Italy.,Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza, Università di Roma, Italy.,CNR Institute of Molecular Biology and Pathology, Rome, Italy
| | - Giulietta Smulevich
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Florence, Italy
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11
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Giordano D, Boubeta FM, di Prisco G, Estrin DA, Smulevich G, Viappiani C, Verde C. Conformational Flexibility Drives Cold Adaptation in Pseudoalteromonas haloplanktis TAC125 Globins. Antioxid Redox Signal 2020; 32:396-411. [PMID: 31578873 DOI: 10.1089/ars.2019.7887] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Significance: Temperature is one of the most important drivers in shaping protein adaptations. Many biochemical and physiological processes are influenced by temperature. Proteins and enzymes from organisms living at low temperature are less stable in comparison to high-temperature adapted proteins. The lower stability is generally due to greater conformational flexibility. Recent Advances: Adaptive changes in the structure of cold-adapted proteins may occur at subunit interfaces, distant from the active site, thus producing energy changes associated with conformational transitions transmitted to the active site by allosteric modulation, valid also for monomeric proteins in which tertiary structural changes may play an essential role. Critical Issues: Despite efforts, the current experimental and computational methods still fail to produce general principles on protein evolution, since many changes are protein and species dependent. Environmental constraints or other biological cellular signals may override the ancestral information included in the structure of the protein, thus introducing inaccuracy in estimates and predictions on the evolutionary adaptations of proteins in response to cold adaptation. Future Directions: In this review, we describe the studies and approaches used to investigate stability and flexibility in the cold-adapted globins of the Antarctic marine bacterium Pseudoalteromonas haloplanktis TAC125. In fact, future research directions will be prescient on more detailed investigation of cold-adapted proteins and the role of fluctuations between different conformational states.
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Affiliation(s)
- Daniela Giordano
- Institute of Biosciences and BioResources (IBBR), CNR, Napoli, Italy.,Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Fernando Martín Boubeta
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Guido di Prisco
- Institute of Biosciences and BioResources (IBBR), CNR, Napoli, Italy
| | - Dario A Estrin
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | | | - Cristiano Viappiani
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parma, Italy
| | - Cinzia Verde
- Institute of Biosciences and BioResources (IBBR), CNR, Napoli, Italy.,Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
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12
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Daane JM, Giordano D, Coppola D, di Prisco G, Detrich HW, Verde C. Adaptations to environmental change: Globin superfamily evolution in Antarctic fishes. Mar Genomics 2019; 49:100724. [PMID: 31735579 DOI: 10.1016/j.margen.2019.100724] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 10/27/2019] [Accepted: 11/01/2019] [Indexed: 02/08/2023]
Abstract
The ancient origins and functional versatility of globins make them ideal subjects for studying physiological adaptation to environmental change. Our goals in this review are to describe the evolution of the vertebrate globin gene superfamily and to explore the structure/function relationships of hemoglobin, myoglobin, neuroglobin and cytoglobin in teleost fishes. We focus on the globins of Antarctic notothenioids, emphasizing their adaptive features as inferred from comparisons with human proteins. We dedicate this review to Guido di Prisco, our co-author, colleague, friend, and husband of C.V. Ever thoughtful, creative, and enthusiastic, Guido spearheaded study of the structure, function, and evolution of the hemoglobins of polar fishes - this review is testimony to his wide-ranging contributions. Throughout his career, Guido inspired younger scientists to embrace polar biological research, and he challenged researchers of all ages to explore evolutionary adaptation in the context of global climate change. Beyond his scientific contributions, we will miss his warmth, his culture, and his great intellect. Guido has left an outstanding legacy, one that will continue to inspire us and our research.
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Affiliation(s)
- Jacob M Daane
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, MA 01908, USA
| | - Daniela Giordano
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111, 80131 Napoli, Italy; Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Daniela Coppola
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111, 80131 Napoli, Italy; Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Guido di Prisco
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - H William Detrich
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, MA 01908, USA
| | - Cinzia Verde
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111, 80131 Napoli, Italy; Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy.
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13
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Proximal and distal control for ligand binding in neuroglobin: role of the CD loop and evidence for His64 gating. Sci Rep 2019; 9:5326. [PMID: 30926858 PMCID: PMC6441039 DOI: 10.1038/s41598-019-41780-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 03/13/2019] [Indexed: 11/24/2022] Open
Abstract
Neuroglobin (Ngb) is predominantly expressed in neurons of the central and peripheral nervous systems and it clearly seems to be involved in neuroprotection. Engineering Ngb to observe structural and dynamic alterations associated with perturbation in ligand binding might reveal important structural determinants, and could shed light on key features related to its mechanism of action. Our results highlight the relevance of the CD loop and of Phe106 as distal and proximal controls involved in ligand binding in murine neuroglobin. We observed the effects of individual and combined mutations of the CD loop and Phe106 that conferred to Ngb higher CO binding velocities, which we correlate with the following structural observations: the mutant F106A shows, upon CO binding, a reduced heme sliding hindrance, with the heme present in a peculiar double conformation, whereas in the CD loop mutant “Gly-loop”, the original network of interactions between the loop and the heme was abolished, enhancing binding via facilitated gating out of the distal His64. Finally, the double mutant, combining both mutations, showed a synergistic effect on CO binding rates. Resonance Raman spectroscopy and MD simulations support our findings on structural dynamics and heme interactions in wild type and mutated Ngbs.
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14
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Fiocchetti M, Cipolletti M, Brandi V, Polticelli F, Ascenzi P. Neuroglobin and friends. J Mol Recognit 2017; 30. [DOI: 10.1002/jmr.2654] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 06/05/2017] [Accepted: 06/14/2017] [Indexed: 01/02/2023]
Affiliation(s)
| | | | | | - Fabio Polticelli
- Dipartimento di Scienze; Università Roma Tre; Rome Italy
- Istituto Nazionale di Fisica Nucleare; Sezione dell'Università Roma Tre; Rome Italy
| | - Paolo Ascenzi
- Laboratorio Interdipartimentale di Microscopia Elettronica; Università Roma Tre; Rome Italy
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15
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Solomon LA, Kronenberg JB, Fry HC. Control of Heme Coordination and Catalytic Activity by Conformational Changes in Peptide-Amphiphile Assemblies. J Am Chem Soc 2017; 139:8497-8507. [PMID: 28505436 DOI: 10.1021/jacs.7b01588] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Self-assembling peptide materials have gained significant attention, due to well-demonstrated applications, but they are functionally underutilized. To advance their utility, we use noncovalent interactions to incorporate the biological cofactor heme-B for catalysis. Heme-proteins achieve differing functions through structural and coordinative variations. Here, we replicate this phenomenon by highlighting changes in heme reactivity as a function of coordination, sequence, and morphology (micelles versus fibers) in a series of simple peptide amphiphiles with the sequence c16-xyL3K3-CO2H where c16 is a palmitoyl moiety and xy represents the heme binding region: AA, AH, HH, and MH. The morphology of this peptide series is characterized using transmission electron and atomic force microscopies as well as dynamic light scattering. Within this small library of peptide constructs, we show that three spectroscopically (UV/visible and electron paramagnetic resonance) distinct heme environments were generated: noncoordinated/embedded high-spin, five-coordinate high-spin, and six-coordinate low-spin. The resulting material's functional dependence on sequence and supramolecular morphology is highlighted 2-fold. First, the heme active site binds carbon monoxide in both micelles and fibers, demonstrating that the heme active site in both morphologies is accessible to small molecules for catalysis. Second, peroxidase activity was observed in heme-containing micelles yet was significantly reduced in heme-containing fibers. We briefly discuss the implications these findings have in the production of functional, self-assembling peptide materials.
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Affiliation(s)
- Lee A Solomon
- Argonne National Laboratory , 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - Jacob B Kronenberg
- Illinois Math and Science Academy , 1500 West Sullivan Road, Aurora, Illinois 60506, United States
| | - H Christopher Fry
- Argonne National Laboratory , 9700 South Cass Avenue, Argonne, Illinois 60439, United States
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16
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Cuypers B, Vermeylen S, Hammerschmid D, Trashin S, Rahemi V, Konijnenberg A, De Schutter A, Cheng CHC, Giordano D, Verde C, De Wael K, Sobott F, Dewilde S, Van Doorslaer S. Antarctic fish versus human cytoglobins - The same but yet so different. J Inorg Biochem 2017; 173:66-78. [PMID: 28501743 DOI: 10.1016/j.jinorgbio.2017.04.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 03/23/2017] [Accepted: 04/26/2017] [Indexed: 10/19/2022]
Abstract
The cytoglobins of the Antarctic fish Chaenocephalus aceratus and Dissostichus mawsoni have many features in common with human cytoglobin. These cytoglobins are heme proteins in which the ferric and ferrous forms have a characteristic hexacoordination of the heme iron, i.e. axial ligation of two endogenous histidine residues, as confirmed by electron paramagnetic resonance, resonance Raman and optical absorption spectroscopy. The combined spectroscopic analysis revealed only small variations in the heme-pocket structure, in line with the small variations observed for the redox potential. Nevertheless, some striking differences were also discovered. Resonance Raman spectroscopy showed that the stabilization of an exogenous heme ligand, such as CO, occurs differently in human cytoglobin in comparison with Antarctic fish cytoglobins. Furthermore, while it has been extensively reported that human cytoglobin is essentially monomeric and can form an intramolecular disulfide bridge that can influence the ligand binding kinetics, 3D modeling of the Antarctic fish cytoglobins indicates that the cysteine residues are too far apart to form such an intramolecular bridge. Moreover, gel filtration and mass spectrometry reveal the occurrence of non-covalent multimers (up to pentamers) in the Antarctic fish cytoglobins that are formed at low concentrations. Stabilization of these oligomers by disulfide-bridge formation is possible, but not essential. If intermolecular disulfide bridges are formed, they influence the heme-pocket structure, as is shown by EPR measurements.
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Affiliation(s)
- Bert Cuypers
- BIMEF Laboratory, Department of Physics, University of Antwerp, Belgium
| | - Stijn Vermeylen
- PPES Laboratory, Department of Biomedical Sciences, University of Antwerp, Belgium
| | - Dietmar Hammerschmid
- PPES Laboratory, Department of Biomedical Sciences, University of Antwerp, Belgium; BAMS Laboratory, Department of Chemistry, University of Antwerp, Belgium
| | - Stanislav Trashin
- AXES Laboratory, Department of Chemistry, University of Antwerp, Belgium
| | - Vanoushe Rahemi
- AXES Laboratory, Department of Chemistry, University of Antwerp, Belgium
| | | | - Amy De Schutter
- BIMEF Laboratory, Department of Physics, University of Antwerp, Belgium
| | | | - Daniela Giordano
- Institute of Biosciences and BioResources, CNR, Naples, Italy; Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Cinzia Verde
- Institute of Biosciences and BioResources, CNR, Naples, Italy; Department of Biology, University Roma 3, Rome, Italy; Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Karolien De Wael
- AXES Laboratory, Department of Chemistry, University of Antwerp, Belgium
| | - Frank Sobott
- BAMS Laboratory, Department of Chemistry, University of Antwerp, Belgium
| | - Sylvia Dewilde
- PPES Laboratory, Department of Biomedical Sciences, University of Antwerp, Belgium
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17
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Ruetz M, Kumutima J, Lewis BE, Filipovic MR, Lehnert N, Stemmler TL, Banerjee R. A distal ligand mutes the interaction of hydrogen sulfide with human neuroglobin. J Biol Chem 2017; 292:6512-6528. [PMID: 28246171 DOI: 10.1074/jbc.m116.770370] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 02/16/2017] [Indexed: 11/06/2022] Open
Abstract
Hydrogen sulfide is a critical signaling molecule, but high concentrations cause cellular toxicity. A four-enzyme pathway in the mitochondrion detoxifies H2S by converting it to thiosulfate and sulfate. Recent studies have shown that globins like hemoglobin and myoglobin can also oxidize H2S to thiosulfate and hydropolysulfides. Neuroglobin, a globin enriched in the brain, was reported to bind H2S tightly and was postulated to play a role in modulating neuronal sensitivity to H2S in conditions such as stroke. However, the H2S reactivity of the coordinately saturated heme in neuroglobin is expected a priori to be substantially lower than that of the 5-coordinate hemes present in myoglobin and hemoglobin. To resolve this discrepancy, we explored the role of the distal histidine residue in muting the reactivity of human neuroglobin toward H2S. Ferric neuroglobin is slowly reduced by H2S and catalyzes its inefficient oxidative conversion to thiosulfate. Mutation of the distal His64 residue to alanine promotes rapid binding of H2S and its efficient conversion to oxidized products. X-ray absorption, EPR, and resonance Raman spectroscopy highlight the chemically different reaction options influenced by the distal histidine ligand. This study provides mechanistic insights into how the distal heme ligand in neuroglobin caps its reactivity toward H2S and identifies by cryo-mass spectrometry a range of sulfide oxidation products with 2-6 catenated sulfur atoms with or without oxygen insertion, which accumulate in the absence of the His64 ligand.
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Affiliation(s)
| | - Jacques Kumutima
- the Departments of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109
| | - Brianne E Lewis
- the Department of Pharmaceutical Science, Wayne State University, Detroit, Michigan 48201-2417
| | - Milos R Filipovic
- the University of Bordeaux, IBGC, UMR 5090, F33077 Bordeaux, France, and.,CNRS, Institute of Biochemistry and Cellular Genetics, UMR 5095, F33077 Bordeaux, France
| | - Nicolai Lehnert
- the Departments of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109
| | - Timothy L Stemmler
- the Department of Pharmaceutical Science, Wayne State University, Detroit, Michigan 48201-2417
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18
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Christopher Fry H, Wood AR, Solomon LA. Supramolecular control of heme binding and electronic states in multi-heme peptide assemblies. Org Biomol Chem 2017; 15:6725-6730. [DOI: 10.1039/c7ob01081h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Three peptides that are compositionally identical but sequentially distinct have been designed to study the impact of morphology and hydrophobicity on heme coordination and function.
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Affiliation(s)
| | - Anna R. Wood
- Argonne National Laboratory
- Center for Nanoscale Materials
- Lemont
- USA
| | - Lee A. Solomon
- Argonne National Laboratory
- Center for Nanoscale Materials
- Lemont
- USA
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19
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Ascenzi P, di Masi A, Leboffe L, Fiocchetti M, Nuzzo MT, Brunori M, Marino M. Neuroglobin: From structure to function in health and disease. Mol Aspects Med 2016; 52:1-48. [DOI: 10.1016/j.mam.2016.10.004] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 10/27/2016] [Accepted: 10/27/2016] [Indexed: 01/01/2023]
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20
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Zare H, Moosavi-Movahedi AA, Salami M, Sheibani N, Khajeh K, Habibi-Rezaei M. Autolysis control and structural changes of purified ficin from Iranian fig latex with synthetic inhibitors. Int J Biol Macromol 2016; 84:464-71. [PMID: 26718871 PMCID: PMC5223272 DOI: 10.1016/j.ijbiomac.2015.12.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 12/06/2015] [Accepted: 12/09/2015] [Indexed: 12/13/2022]
Abstract
The fig's ficin is a cysteine endoproteolytic enzyme, which plays fundamental roles in many plant physiological processes, and has many applications in different industries such as pharmaceutical and food. In this work, we report the inhibition and activation of autolysis and structural changes associated with reaction of ficin with iodoacetamide and tetrathionate using high-performance liquid chromatography (HPLC), ultra filtration membrane, and dynamic light scattering (DLS) methods. The ficin structural changes were also determined using UV-absorption, circular dichroism (CD), fluorescence spectroscopy, and differential scanning calorimetry (DSC) techniques. These techniques demonstrated that iodoacetamide completely inhibited ficin autolysis, which was irreversible. However, tetrathionate partially and reversibility inhibited its autolysis. The ficin structural changes with two synthetic inhibitors were associated with secondary structural changes related to decreased alpha-helix and increased beta sheet and random coil conformations, contributing to its aggregation.
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Affiliation(s)
- H Zare
- Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran; Estahban Fig Research Station, Fars Agricultural and Natural Resources Research and Training Center, AREEO, Shiraz, Iran
| | - A A Moosavi-Movahedi
- Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran; Center of Excellence in Biothermodynamics (CEBiotherm), University of Tehran, Tehran, Iran.
| | - M Salami
- Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran; Department of Food Science and Engineering, University College of Agriculture & Natural Resources, University of Tehran, Karaj, Iran
| | - N Sheibani
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA; Department of Pharmacology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - K Khajeh
- Faculty of Biological Sciences, Department of Biochemistry, Tarbiat Modares University, Tehran, Iran
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21
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Interaction of apoNeuroglobin with heme–Aβ complexes relevant to Alzheimer’s disease. J Biol Inorg Chem 2015; 20:563-74. [DOI: 10.1007/s00775-015-1241-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 01/13/2015] [Indexed: 01/09/2023]
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22
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Engineered chimeras reveal the structural basis of hexacoordination in globins: A case study of neuroglobin and myoglobin. Biochim Biophys Acta Gen Subj 2015; 1850:169-77. [DOI: 10.1016/j.bbagen.2014.10.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 09/12/2014] [Accepted: 10/06/2014] [Indexed: 11/18/2022]
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23
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Giordano D, Coppola D, Russo R, Tinajero-Trejo M, di Prisco G, Lauro F, Ascenzi P, Verde C. The globins of cold-adapted Pseudoalteromonas haloplanktis TAC125: from the structure to the physiological functions. Adv Microb Physiol 2014; 63:329-89. [PMID: 24054800 DOI: 10.1016/b978-0-12-407693-8.00008-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Evolution allowed Antarctic microorganisms to grow successfully under extreme conditions (low temperature and high O2 content), through a variety of structural and physiological adjustments in their genomes and development of programmed responses to strong oxidative and nitrosative stress. The availability of genomic sequences from an increasing number of cold-adapted species is providing insights to understand the molecular mechanisms underlying crucial physiological processes in polar organisms. The genome of Pseudoalteromonas haloplanktis TAC125 contains multiple genes encoding three distinct truncated globins exhibiting the 2/2 α-helical fold. One of these globins has been extensively characterised by spectroscopic analysis, kinetic measurements and computer simulation. The results indicate unique adaptive structural properties that enhance the overall flexibility of the protein, so that the structure appears to be resistant to pressure-induced stress. Recent results on a genomic mutant strain highlight the involvement of the cold-adapted globin in the protection against the stress induced by high O2 concentration. Moreover, the protein was shown to catalyse peroxynitrite isomerisation in vitro. In this review, we first summarise how cold temperatures affect the physiology of microorganisms and focus on the molecular mechanisms of cold adaptation revealed by recent biochemical and genetic studies. Next, since only in a very few cases the physiological role of truncated globins has been demonstrated, we also discuss the structural and functional features of the cold-adapted globin in an attempt to put into perspective what has been learnt about these proteins and their potential role in the biology of cold-adapted microorganisms.
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24
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Abbruzzetti S, Spyrakis F, Bidon-Chanal A, Luque FJ, Viappiani C. Ligand migration through hemeprotein cavities: insights from laser flash photolysis and molecular dynamics simulations. Phys Chem Chem Phys 2013; 15:10686-701. [PMID: 23733145 DOI: 10.1039/c3cp51149a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The presence of cavities and tunnels in the interior of proteins, in conjunction with the structural plasticity arising from the coupling to the thermal fluctuations of the protein scaffold, has profound consequences on the pathways followed by ligands moving through the protein matrix. In this perspective we discuss how quantitative analysis of experimental rebinding kinetics from laser flash photolysis, trapping of unstable conformational states by embedding proteins within the nanopores of silica gels, and molecular simulations can synergistically converge to gain insight into the migration mechanism of ligands. We show how the evaluation of the free energy landscape for ligand diffusion based on the outcome of computational techniques can assist the definition of sound reaction schemes, leading to a comprehensive understanding of the broad range of chemical events and time scales that encompass the transport of small ligands in hemeproteins.
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Affiliation(s)
- Stefania Abbruzzetti
- Dipartimento di Fisica e Scienze della Terra, Università degli Studi di Parma, viale delle Scienze 7A, 43124, Parma, Italy
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25
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Van Leuven W, Cuypers B, Desmet F, Giordano D, Verde C, Moens L, Van Doorslaer S, Dewilde S. Is the heme pocket region modulated by disulfide-bridge formation in fish and amphibian neuroglobins as in humans? BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1757-63. [PMID: 23403147 DOI: 10.1016/j.bbapap.2013.01.042] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 01/25/2013] [Accepted: 01/29/2013] [Indexed: 12/17/2022]
Abstract
Neuroglobin, a globin characterized by a bis-histidine ligation of the heme iron, has been identified in mammalian and non-mammalian vertebrates, including fish, amphibians and reptiles. In human neuroglobin, the presence of an internal disulfide bond in the CD loop (CD7-D5) is found to modulate the ligand binding through a change in the heme pocket structure. Although the neuroglobin sequences mostly display conserved Cys at positions CD7, D5 and G18/19, a number of exceptions are known. In this study, neuroglobins from amphibian (Xenopus tropicalis) and fish (Chaenocephalus aceratus, Dissostichus mawsoni and Danio rerio) are investigated using electron paramagnetic resonance and optical absorption spectroscopy. All these neuroglobins differ from human neuroglobin in their Cys-positions. It is demonstrated that if disulfide bonds are formed in fish and amphibian neuroglobins, the reduction of these bonds does not result in alteration of the heme pocket in these globins. Furthermore, it is shown that mutagenesis of the Cys residues of X. tropicalis neuroglobin influences the protein structure. The amphibian neuroglobin is also found to be more resistant to H2O2-induced denaturation than the other neuroglobins under study, although all show an overall large stability in high concentrations of this oxidant. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.
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Affiliation(s)
- Wendy Van Leuven
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
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