1
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Pantaleone S, Sodupe M, Ugliengo P, Rimola A. On the stability of peptide secondary structures on the TiO 2 (101) anatase surface: a computational insight. Phys Chem Chem Phys 2022; 25:392-401. [PMID: 36477070 DOI: 10.1039/d2cp04395e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The biological activity of proteins is partly due to their secondary structures and conformational states. Peptide chains are rather flexible so that finding ways inducing protein folding in a well-defined state is of great importance. Among the different constraint techniques, the interaction of proteins with inorganic surfaces is a fruitful strategy to stabilize selected folded states. Surface-induced peptide folding can have potential applications in different biomedicine areas, but it can also be of fundamental interest in prebiotic chemistry since the biological activity of a peptide can turn-on when folded in a given state. In this work, periodic quantum mechanical simulations (including implicit solvation effects) at the PBE-D2* level have been carried out to study the adsorption and the stability of the secondary structures (α-helix and β-sheet) of polypeptides with different chemical composition (i.e., polyglycine, polyalanine, polyglutamic acid, polylysine, and polyarginine) on the TiO2 (101) anatase surface. The computational cost is reduced by applying periodic boundary conditions to both the surface and the peptides, thus obtaining full periodic polypeptide/TiO2 surface systems. At variance with polyglycine, the interaction of the other polypeptides with the surface takes place with the lateral chain functionalities, leaving the secondary structures almost undistorted. Results indicate that the preferred conformation upon adsorption is the α-helix over the β-sheet, with the exception of the polyglutamic acid. According to the calculated adsorption energies, the affinity trend of the polypeptides with the (101) anatase surface is: polyarginine ≈ polylysine > polyglutamic acid > polyglycine ≈ polyalanine, both when adsorbed in gas phase and in presence of the implicit water solvent, which is very similar to the trend for the single amino acids. A set of implications related to the areas of surface-induced peptide folding, biomedicine and prebiotic chemistry are finally discussed.
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Affiliation(s)
- Stefano Pantaleone
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain. .,Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS) Inter-Departmental Centre, Università degli Studi di Torino, Via P. Giuria 7, 10125, Torino, Italy
| | - Mariona Sodupe
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain.
| | - Piero Ugliengo
- Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS) Inter-Departmental Centre, Università degli Studi di Torino, Via P. Giuria 7, 10125, Torino, Italy
| | - Albert Rimola
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain.
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2
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Balasco N, Paladino A, Graziano G, D'Abramo M, Vitagliano L. Atomic-Level View of the Functional Transition in Vertebrate Hemoglobins: The Case of Antarctic Fish Hbs. J Chem Inf Model 2022; 62:3874-3884. [PMID: 35930673 PMCID: PMC9400108 DOI: 10.1021/acs.jcim.2c00727] [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
Tetrameric hemoglobins (Hbs) are prototypal systems for studies aimed at unveiling basic structure-function relationships as well as investigating the molecular/structural basis of adaptation of living organisms to extreme conditions. However, a chronological analysis of decade-long studies conducted on Hbs is illuminating on the difficulties associated with the attempts of gaining functional insights from static structures. Here, we applied molecular dynamics (MD) simulations to explore the functional transition from the T to the R state of the hemoglobin of the Antarctic fish Trematomus bernacchii (HbTb). Our study clearly demonstrates the ability of the MD technique to accurately describe the transition of HbTb from the T to R-like states, as shown by a number of global and local structural indicators. A comparative analysis of the structural states that HbTb assumes in the simulations with those detected in previous MD analyses conducted on HbA (human Hb) highlights interesting analogies (similarity of the transition pathway) and differences (distinct population of intermediate states). In particular, the ability of HbTb to significantly populate intermediate states along the functional pathway explains the observed propensity of this protein to assume these structures in the crystalline state. It also explains some functional data reported on the protein that indicate the occurrence of other functional states in addition to the canonical R and T ones. These findings are in line with the emerging idea that the classical two-state view underlying tetrameric Hb functionality is probably an oversimplification and that other structural states play important roles in these proteins. The ability of MD simulations to accurately describe the functional pathway in tetrameric Hbs suggests that this approach may be effectively applied to unravel the molecular and structural basis of Hbs exhibiting peculiar functional properties as a consequence of the environmental adaptation of the host organism.
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Affiliation(s)
- Nicole Balasco
- Institute of Molecular Biology and Pathology, CNR c/o Dep. Chemistry, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
| | - Antonella Paladino
- Institute of Biostructures and Bioimaging, CNR, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Giuseppe Graziano
- Department of Science and Technology, University of Sannio, via Francesco de Sanctis snc, Benevento 82100, Italy
| | - Marco D'Abramo
- Department of Chemistry, University of Rome Sapienza, P.le A.Moro 5, 00185 Rome, Italy
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, CNR, Via Pietro Castellino 111, 80131 Naples, Italy
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3
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Giordano D, Verde C, Corti P. Nitric Oxide Production and Regulation in the Teleost Cardiovascular System. Antioxidants (Basel) 2022; 11:957. [PMID: 35624821 PMCID: PMC9137985 DOI: 10.3390/antiox11050957] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [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
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4
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Balasco N, Alba J, D'Abramo M, Vitagliano L. Quaternary Structure Transitions of Human Hemoglobin: An Atomic-Level View of the Functional Intermediate States. J Chem Inf Model 2021; 61:3988-3999. [PMID: 34375114 PMCID: PMC9473481 DOI: 10.1021/acs.jcim.1c00315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Human hemoglobin (HbA) is one of the prototypal systems used to investigate structure-function relationships in proteins. Indeed, HbA has been used to develop the basic concepts of protein allostery, although the atomic-level mechanism underlying the HbA functionality is still highly debated. This is due to the fact that most of the three-dimensional structural information collected over the decades refers to the endpoints of HbA functional transition with little data available for the intermediate states. Here, we report molecular dynamics (MD) simulations by focusing on the relevance of the intermediate states of the protein functional transition unraveled by the crystallographic studies carried out on vertebrate Hbs. Fully atomistic simulations of the HbA T-state indicate that the protein undergoes a spontaneous transition toward the R-state. The inspection of the trajectory structures indicates that the protein significantly populates the intermediate HL-(C) state previously unraveled by crystallography. In the structural transition, it also assumes the intermediate states crystallographically detected in Antarctic fish Hbs. This finding suggests that HbA and Antarctic fish Hbs, in addition to the endpoints of the transitions, also share a similar deoxygenation pathway despite a distace of hundreds of millions of years in the evolution scale. Finally, using the essential dynamic sampling methodology, we gained some insights into the reverse R to T transition that is not spontaneously observed in classic MD simulations.
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Affiliation(s)
- Nicole Balasco
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Josephine Alba
- Department of Chemistry, University of Rome Sapienza, P.le A.Moro 5, 00185 Rome, Italy
| | - Marco D'Abramo
- Department of Chemistry, University of Rome Sapienza, P.le A.Moro 5, 00185 Rome, Italy
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, 80134 Naples, Italy
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5
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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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6
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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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7
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Balasco N, Vitagliano L, Merlino A, Verde C, Mazzarella L, Vergara A. The unique structural features of carbonmonoxy hemoglobin from the sub-Antarctic fish Eleginops maclovinus. Sci Rep 2019; 9:18987. [PMID: 31831781 PMCID: PMC6908587 DOI: 10.1038/s41598-019-55331-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/11/2019] [Indexed: 01/14/2023] Open
Abstract
Tetrameric hemoglobins (Hbs) are prototypical systems for the investigations of fundamental properties of proteins. Although the structure of these proteins has been known for nearly sixty years, there are many aspects related to their function/structure that are still obscure. Here, we report the crystal structure of a carbonmonoxy form of the Hb isolated from the sub-Antarctic notothenioid fish Eleginops maclovinus characterised by either rare or unique features. In particular, the distal site of the α chain results to be very unusual since the distal His is displaced from its canonical position. This displacement is coupled with a shortening of the highly conserved E helix and the formation of novel interactions at tertiary structure level. Interestingly, the quaternary structure is closer to the T-deoxy state of Hbs than to the R-state despite the full coordination of all chains. Notably, these peculiar structural features provide a rationale for some spectroscopic properties exhibited by the protein in solution. Finally, this unexpected structural plasticity of the heme distal side has been associated with specific sequence signatures of various Hbs.
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Affiliation(s)
- Nicole Balasco
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, Naples, Italy
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, Naples, Italy.
| | - Antonello Merlino
- Dept. Chemical Sciences, University of Napoli "Federico II", Via Cinthia, 80126, Naples, Italy
| | - Cinzia Verde
- Institute of Biosciences and BioResources, CNR, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Lelio Mazzarella
- Dept. Chemical Sciences, University of Napoli "Federico II", Via Cinthia, 80126, Naples, Italy
| | - Alessandro Vergara
- Dept. Chemical Sciences, University of Napoli "Federico II", Via Cinthia, 80126, Naples, Italy.
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8
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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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9
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Helland R, Bjørkeng EK, Rothweiler U, Sydnes MO, Pampanin DM. The crystal structure of haemoglobin from Atlantic cod. Acta Crystallogr F Struct Biol Commun 2019; 75:537-542. [PMID: 31397324 PMCID: PMC6688665 DOI: 10.1107/s2053230x1900904x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 06/24/2019] [Indexed: 11/15/2022] Open
Abstract
The crystal structure of haemoglobin from Atlantic cod has been solved to 2.54 Å resolution. The structure consists of two tetramers in the crystallographic asymmetric unit. The structure of haemoglobin obtained from one individual cod suggests polymorphism in the tetrameric assembly.
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Affiliation(s)
- Ronny Helland
- NorStruct, Department of Chemistry, Faculty of Science and Technology, UiT – The Arctic University of Norway, NO-9037 Tromsø, Norway
| | - Eva Katrin Bjørkeng
- NorStruct, Department of Chemistry, Faculty of Science and Technology, UiT – The Arctic University of Norway, NO-9037 Tromsø, Norway
| | - Ulli Rothweiler
- NorStruct, Department of Chemistry, Faculty of Science and Technology, UiT – The Arctic University of Norway, NO-9037 Tromsø, Norway
| | - Magne Olav Sydnes
- Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, Faculty of Science and Technology, NO-4036 Stavanger, Norway
| | - Daniela Maria Pampanin
- Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, Faculty of Science and Technology, NO-4036 Stavanger, Norway
- NORCE AS, Prof. Olav Hanssensvei 15, NO-4021 Stavanger, Norway
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10
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Crystal structure of the ferric homotetrameric β 4 human hemoglobin. Biophys Chem 2018; 240:9-14. [DOI: 10.1016/j.bpc.2018.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 05/18/2018] [Accepted: 05/18/2018] [Indexed: 11/21/2022]
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11
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Vergara A, Caterino M, Merlino A. Raman-markers of X-ray radiation damage of proteins. Int J Biol Macromol 2018; 111:1194-1205. [PMID: 29374529 DOI: 10.1016/j.ijbiomac.2018.01.135] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 01/10/2018] [Accepted: 01/19/2018] [Indexed: 12/25/2022]
Abstract
Despite their high relevance, the mechanisms of X-ray radiation damage on protein structure yet have to be completely established. Here, we used Raman microspectrophotometry to follow X-ray-induced chemical modifications on the structure of the model protein bovine pancreatic ribonuclease (RNase A). The combination of dose-dependent Raman spectra and ultrahigh resolution (eight structures solved using data collected between 0.85 and 1.17 Å resolution on the same single crystal) allowed direct observation of several radiation damage events, including covalent bond breakages and formation of radicals. Our results are relevant for analytical photodamage detection and provide implications for a detailed understanding of the mechanisms of photoproduct formation.
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Affiliation(s)
- Alessandro Vergara
- Department of Chemical Sciences, University of Naples "Federico II", Via Cinthia, Naples I-80126, Italy; CEINGE Biotecnologie Avanzate Scarl, Via G. Salvatore, Napoli, Italy
| | - Marco Caterino
- Department of Chemical Sciences, University of Naples "Federico II", Via Cinthia, Naples I-80126, Italy
| | - Antonello Merlino
- Department of Chemical Sciences, University of Naples "Federico II", Via Cinthia, Naples I-80126, Italy.
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12
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Vitagliano L, Mazzarella L, Merlino A, Vergara A. Fine Sampling of the R→T Quaternary-Structure Transition of a Tetrameric Hemoglobin. Chemistry 2016; 23:605-613. [DOI: 10.1002/chem.201603421] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Luigi Vitagliano
- Institute of Biostructures and Biomaging; CNR; Via Mezzocannone 16 80134 Napoli Italy
| | - Lelio Mazzarella
- Dept. Chemical Sciences; University of Napoli “Federico II”; Via Cinthia 80126 Napoli Italy
| | - Antonello Merlino
- Institute of Biostructures and Biomaging; CNR; Via Mezzocannone 16 80134 Napoli Italy
- Dept. Chemical Sciences; University of Napoli “Federico II”; Via Cinthia 80126 Napoli Italy
| | - Alessandro Vergara
- Institute of Biostructures and Biomaging; CNR; Via Mezzocannone 16 80134 Napoli Italy
- Dept. Chemical Sciences; University of Napoli “Federico II”; Via Cinthia 80126 Napoli Italy
- CEINGE Biotecnologie Avanzate scarlm; Via G. Salvatore Napoli Italy
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Ramesh P, Sundaresan SS, Sathya Moorthy P, Balasubramanian M, Ponnuswamy MN. Response to comments on structural studies of haemoglobin from pisces species shortfin mako shark (Isurus oxyrinchus) at 1.9 Å resolution by P. Ramesh et al. (2013). J. Synchrotron Rad. 20, 843-847. JOURNAL OF SYNCHROTRON RADIATION 2014; 21:834. [PMID: 24971984 DOI: 10.1107/s1600577514010285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 05/05/2014] [Indexed: 06/03/2023]
Affiliation(s)
- Pandian Ramesh
- Laboratory of Structural Biology, Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, South Korea
| | - S S Sundaresan
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Maraimalai Campus (Guindy), Chennai 600 025, India
| | - Pon Sathya Moorthy
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Maraimalai Campus (Guindy), Chennai 600 025, India
| | - M Balasubramanian
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Maraimalai Campus (Guindy), Chennai 600 025, India
| | - M N Ponnuswamy
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Maraimalai Campus (Guindy), Chennai 600 025, India
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Merlino A, Vergara A, Vitagliano L. Comments on structural studies of haemoglobin from pisces species shortfin mako shark (Isurus oxyrinchus) at 1.9 Å resolution by P. Ramesh et al. (2013). J. Synchrotron Rad.20, 843-847. JOURNAL OF SYNCHROTRON RADIATION 2014; 21:832-833. [PMID: 24971983 DOI: 10.1107/s1600577514010170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 05/05/2014] [Indexed: 06/03/2023]
Affiliation(s)
- Antonello Merlino
- Department of Chemical Sciences, University of Naples `Federico II', Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy
| | - Alessandro Vergara
- Department of Chemical Sciences, University of Naples `Federico II', Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, I-80134 Naples, Italy
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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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Mazzarella L, Merlino A, Vitagliano L, Verde C, di Prisco G, Peisach J, Vergara A. Structural modifications induced by the switch from an endogenous bis-histidyl to an exogenous cyanomet hexa-coordination in a tetrameric haemoglobin. RSC Adv 2014. [DOI: 10.1039/c4ra03317e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Two EPR- and structurally-distinct bis-histidyl conformers of the ferric haemoglobin from Trematomus bernacchii react differently with CN−
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Affiliation(s)
- Lelio Mazzarella
- Dept of Chemical Sciences
- University of Naples “Federico II”
- Naples, Italy
| | - Antonello Merlino
- Dept of Chemical Sciences
- University of Naples “Federico II”
- Naples, Italy
- Institute of Biostructures and Bioimaging
- CNR
| | | | - Cinzia Verde
- Institute of Biosciences and BioResources
- CNR
- Naples, Italy
- Roma 3 University
- Dept of Biology
| | | | - Jack Peisach
- Dept of Biophysics and Physiology
- Albert Einstein College of Medicine
- New York, USA
| | - Alessandro Vergara
- Dept of Chemical Sciences
- University of Naples “Federico II”
- Naples, Italy
- Institute of Biostructures and Bioimaging
- CNR
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17
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Reaction of Hg2+ Insertion into Cysteine Pairs Within Bovine Insulin Crystals Followed via Raman Spectroscopy. J SOLUTION CHEM 2013. [DOI: 10.1007/s10953-013-0066-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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18
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Coppola D, Abbruzzetti S, Nicoletti F, Merlino A, Gambacurta A, Giordano D, Howes BD, De Sanctis G, Vitagliano L, Bruno S, di Prisco G, Mazzarella L, Smulevich G, Coletta M, Viappiani C, Vergara A, Verde C. ATP regulation of the ligand-binding properties in temperate and cold-adapted haemoglobins. X-ray structure and ligand-binding kinetics in the sub-Antarctic fish Eleginops maclovinus. MOLECULAR BIOSYSTEMS 2013; 8:3295-304. [PMID: 23086282 DOI: 10.1039/c2mb25210d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The major haemoglobin of the sub-Antarctic fish Eleginops maclovinus was structurally and functionally characterised with the aim to compare molecular environmental adaptations in the O(2)-transport system of sub-Antarctic fishes of the suborder Notothenioidei with those of their high-latitude relatives. Ligand-binding kinetics of the major haemoglobin of E. maclovinus indicated strong stabilisation of the liganded quaternary T state, enhanced in the presence of the physiological allosteric effector ATP, compared to that of high-Antarctic Trematomus bernacchii. The activation enthalpy for O(2) dissociation was dramatically lower than that in T. bernacchii haemoglobin, suggesting remarkable differences in temperature sensitivity and structural changes associated with O(2) release and exit from the protein. The haemoglobin functional properties, together with the X-ray structure of the CO form at 1.49 Å resolution, the first of a temperate notothenioid, strongly support the hypothesis that in E. maclovinus, whose life-style varies according to changes in habitat, the mechanisms that regulate O(2) affinity and the ATP-induced Root effect differ from those of high-Antarctic Notothenioids.
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Affiliation(s)
- Daniela Coppola
- Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, I-80131 Naples, 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. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 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] [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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20
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Merlino A, Fuchs MR, Pica A, Balsamo A, Dworkowski FSN, Pompidor G, Mazzarella L, Vergara A. Selective X-ray-induced NO photodissociation in haemoglobin crystals: evidence from a Raman-assisted crystallographic study. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 69:137-40. [DOI: 10.1107/s0907444912042229] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 10/09/2012] [Indexed: 11/10/2022]
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21
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Giordano D, Boron I, Abbruzzetti S, Van Leuven W, Nicoletti FP, Forti F, Bruno S, Cheng CHC, Moens L, di Prisco G, Nadra AD, Estrin D, Smulevich G, Dewilde S, Viappiani C, Verde C. Biophysical characterisation of neuroglobin of the icefish, a natural knockout for hemoglobin and myoglobin. Comparison with human neuroglobin. PLoS One 2012; 7:e44508. [PMID: 23226490 PMCID: PMC3513292 DOI: 10.1371/journal.pone.0044508] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Accepted: 08/03/2012] [Indexed: 11/19/2022] Open
Abstract
The Antarctic icefish Chaenocephalus aceratus lacks the globins common to most vertebrates, hemoglobin and myoglobin, but has retained neuroglobin in the brain. This conserved globin has been cloned, over-expressed and purified. To highlight similarities and differences, the structural features of the neuroglobin of this colourless-blooded fish were compared with those of the well characterised human neuroglobin as well as with the neuroglobin from the retina of the red blooded, hemoglobin and myoglobin-containing, closely related Antarctic notothenioid Dissostichus mawsoni. A detailed structural and functional analysis of the two Antarctic fish neuroglobins was carried out by UV-visible and Resonance Raman spectroscopies, molecular dynamics simulations and laser-flash photolysis. Similar to the human protein, Antarctic fish neuroglobins can reversibly bind oxygen and CO in the Fe(2+) form, and show six-coordination by distal His in the absence of exogenous ligands. A very large and structured internal cavity, with discrete docking sites, was identified in the modelled three-dimensional structures of the Antarctic neuroglobins. Estimate of the free-energy barriers from laser-flash photolysis and Implicit Ligand Sampling showed that the cavities are accessible from the solvent in both proteins.Comparison of structural and functional properties suggests that the two Antarctic fish neuroglobins most likely preserved and possibly improved the function recently proposed for human neuroglobin in ligand multichemistry. Despite subtle differences, the adaptation of Antarctic fish neuroglobins does not seem to parallel the dramatic adaptation of the oxygen carrying globins, hemoglobin and myoglobin, in the same organisms.
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Affiliation(s)
| | - Ignacio Boron
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires, Argentina
| | - Stefania Abbruzzetti
- Department of Physics, University of Parma, NEST Istituto Nanoscienze-CNR, Parma, Italy
| | - Wendy Van Leuven
- Department of Biomedical Sciences, PPES, University of Antwerp, Universiteitsplein 1, Wilrijk, Belgium
| | - Francesco P. Nicoletti
- Dipartimento di Chimica “Ugo Schiff”, Università di Firenze, Sesto Fiorentino (FI), Italy
| | - Flavio Forti
- Facultat de Farmacia, Departament de Fisicoquímica and Institut de Biomedicina, Universitat de Barcelona, Barcelona, Spain
| | - Stefano Bruno
- Department of Biochemistry and Molecular Biology, University of Parma, Parma, Italy
| | - C-H. Christina Cheng
- Department of Animal Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Luc Moens
- Department of Biomedical Sciences, PPES, University of Antwerp, Universiteitsplein 1, Wilrijk, Belgium
| | | | - Alejandro D. Nadra
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
| | - Darío Estrin
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
| | - Giulietta Smulevich
- Dipartimento di Chimica “Ugo Schiff”, Università di Firenze, Sesto Fiorentino (FI), Italy
- Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici, Bari, Italy
| | - Sylvia Dewilde
- Department of Biomedical Sciences, PPES, University of Antwerp, Universiteitsplein 1, Wilrijk, Belgium
| | - Cristiano Viappiani
- Department of Physics, University of Parma, NEST Istituto Nanoscienze-CNR, Parma, Italy
| | - Cinzia Verde
- Institute of Protein Biochemistry, CNR, Naples, Italy
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Balsamo A, Sannino F, Merlino A, Parrilli E, Tutino ML, Mazzarella L, Vergara A. Role of the tertiary and quaternary structure in the formation of bis-histidyl adducts in cold-adapted hemoglobins. Biochimie 2012; 94:953-60. [DOI: 10.1016/j.biochi.2011.12.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 12/14/2011] [Indexed: 10/14/2022]
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New Roles Assigned to the α1–β1 (and α2–β2) Interface of the Human Hemoglobin Molecule from Physiological to Cellular. APPLIED SCIENCES-BASEL 2011. [DOI: 10.3390/app1010013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Merlino A, Howes BD, Prisco GD, Verde C, Smulevich G, Mazzarella L, Vergara A. Occurrence and formation of endogenous histidine hexa-coordination in cold-adapted hemoglobins. IUBMB Life 2011; 63:295-303. [PMID: 21491555 DOI: 10.1002/iub.446] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 02/11/2011] [Indexed: 11/06/2022]
Abstract
Spectroscopic and crystallographic evidence of endogenous (His) ligation at the sixth coordination site of the heme iron has been reported for monomeric, dimeric, and tetrameric hemoglobins (Hbs) in both ferrous (hemochrome) and ferric (hemichrome) oxidation states. In particular, the ferric bis- histidyl adduct represents a common accessible ordered state for the β chains of all tetrameric Hbs isolated from Antarctic and sub-Antarctic fish. Indeed, the crystal structures of known tetrameric Hbs in the bis-His state are characterized by a different binding state of the α and β chains. An overall analysis of the bis-histidyl adduct of globin structures deposited in the Protein Data Bank reveals a marked difference between hemichromes in tetrameric Hbs compared to monomeric/dimeric Hbs. Herein, we review the structural, spectroscopic and stability features of hemichromes in tetrameric Antarctic fish Hbs. The role of bis-histidyl adducts is also addressed in a more evolutionary context alongside the concept of its potential physiological role.
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Affiliation(s)
- Antonello Merlino
- Department of Chemistry "Paolo Corradini," University of Naples "Federico II," Complesso Universitario Monte S. Angelo, Italy
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Boechi L, Martì MA, Vergara A, Sica F, Mazzarella L, Estrin DA, Merlino A. Protonation of histidine 55 affects the oxygen access to heme in the alpha chain of the hemoglobin from the Antarctic fish Trematomus bernacchii. IUBMB Life 2011; 63:175-82. [DOI: 10.1002/iub.436] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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26
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Vergara A, Vitagliano L, Merlino A, Sica F, Marino K, Verde C, di Prisco G, Mazzarella L. An order-disorder transition plays a role in switching off the root effect in fish hemoglobins. J Biol Chem 2010; 285:32568-75. [PMID: 20610398 PMCID: PMC2952259 DOI: 10.1074/jbc.m110.143537] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Revised: 06/17/2010] [Indexed: 11/06/2022] Open
Abstract
The Root effect is a widespread property among fish hemoglobins whose structural basis remains largely obscure. Here we report a crystallographic and spectroscopic characterization of the non-Root-effect hemoglobin isolated from the Antarctic fish Trematomus newnesi in the deoxygenated form. The crystal structure unveils that the T state of this hemoglobin is stabilized by a strong H-bond between the side chains of Asp95α and Asp101β at the α(1)β(2) and α(2)β(1) interfaces. This unexpected finding undermines the accepted paradigm that correlates the presence of this unusual H-bond with the occurrence of the Root effect. Surprisingly, the T state is characterized by an atypical flexibility of two α chains within the tetramer. Indeed, regions such as the CDα corner and the EFα pocket, which are normally well ordered in the T state of tetrameric hemoglobins, display high B-factors and non-continuous electron densities. This flexibility also leads to unusual distances between the heme iron and the proximal and distal His residues. These observations are in line with Raman micro-spectroscopy studies carried out both in solution and in the crystal state. The findings here presented suggest that in fish hemoglobins the Root effect may be switched off through a significant destabilization of the T state regardless of the presence of the inter-aspartic H-bond. Similar mechanisms may also operate for other non-Root effect hemoglobins. The implications of the flexibility of the CDα corner for the mechanism of the T-R transition in tetrameric hemoglobins are also discussed.
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Affiliation(s)
- Alessandro Vergara
- From the Department of Chemistry, University of Naples “Federico II,” Naples I-80126, Italy
- the Istituto di Biostrutture e Bioimmagini, CNR, Naples I-80134, Italy, and
| | - Luigi Vitagliano
- the Istituto di Biostrutture e Bioimmagini, CNR, Naples I-80134, Italy, and
| | - Antonello Merlino
- From the Department of Chemistry, University of Naples “Federico II,” Naples I-80126, Italy
- the Istituto di Biostrutture e Bioimmagini, CNR, Naples I-80134, Italy, and
| | - Filomena Sica
- From the Department of Chemistry, University of Naples “Federico II,” Naples I-80126, Italy
- the Istituto di Biostrutture e Bioimmagini, CNR, Naples I-80134, Italy, and
| | - Katia Marino
- From the Department of Chemistry, University of Naples “Federico II,” Naples I-80126, Italy
- the Institute of Protein Biochemistry, CNR, Naples I-80131, Italy
| | - Cinzia Verde
- the Institute of Protein Biochemistry, CNR, Naples I-80131, Italy
| | - Guido di Prisco
- the Institute of Protein Biochemistry, CNR, Naples I-80131, Italy
| | - Lelio Mazzarella
- From the Department of Chemistry, University of Naples “Federico II,” Naples I-80126, Italy
- the Istituto di Biostrutture e Bioimmagini, CNR, Naples I-80134, Italy, and
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Russo R, Giordano D, Riccio A, di Prisco G, Verde C. Cold-adapted bacteria and the globin case study in the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125. Mar Genomics 2010; 3:125-31. [PMID: 21798206 DOI: 10.1016/j.margen.2010.09.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Revised: 08/31/2010] [Accepted: 09/01/2010] [Indexed: 11/15/2022]
Abstract
Environmental oxygen availability may play an important role in the evolution of polar marine organisms, as suggested by the physiological and biochemical strategies adopted by these organisms to acquire, deliver and scavenge oxygen. Stress conditions such as extreme temperatures increase the production of reactive oxygen species (ROS) in cells. Thus, in order to prevent cellular damage, adjustments in antioxidant defences are needed to maintain the steady-state concentration of ROS. Cold-adapted bacteria are generally acknowledged to achieve their physiological and ecological success in cold environments through structural and functional properties developed in their genomes. A short overview on the molecular adaptations of polar bacteria and in particular on the biological function of oxygen-binding proteins in Pseudoalteromonas haloplanktis TAC125, selected as a model, will be provided together with the role of oxygen and oxidative/nitrosative stress in regulating adaptive responses at cellular and molecular levels.
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Merlino A, Vergara A, Sica F, Aschi M, Amadei A, Di Nola A, Mazzarella L. Free-Energy Profile for CO Binding to Separated Chains of Human and Trematomus newnesi Hemoglobin: Insights from Molecular Dynamics Simulations and Perturbed Matrix Method. J Phys Chem B 2010; 114:7002-8. [DOI: 10.1021/jp908525s] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Antonello Merlino
- Dipartimento di Chimica, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy, Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Naples, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali, University of L’Aquila, Via Vetoio, I-67010, L’Aquila, Italy, Dipartimento di Scienze e Tecnologie Chimiche, University of Rome “Tor Vergata”, Via della Ricerca scientifica 1, I-00133 Roma, Italy, and Dipartimento di Chimica,
| | - Alessandro Vergara
- Dipartimento di Chimica, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy, Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Naples, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali, University of L’Aquila, Via Vetoio, I-67010, L’Aquila, Italy, Dipartimento di Scienze e Tecnologie Chimiche, University of Rome “Tor Vergata”, Via della Ricerca scientifica 1, I-00133 Roma, Italy, and Dipartimento di Chimica,
| | - Filomena Sica
- Dipartimento di Chimica, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy, Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Naples, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali, University of L’Aquila, Via Vetoio, I-67010, L’Aquila, Italy, Dipartimento di Scienze e Tecnologie Chimiche, University of Rome “Tor Vergata”, Via della Ricerca scientifica 1, I-00133 Roma, Italy, and Dipartimento di Chimica,
| | - Massimiliano Aschi
- Dipartimento di Chimica, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy, Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Naples, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali, University of L’Aquila, Via Vetoio, I-67010, L’Aquila, Italy, Dipartimento di Scienze e Tecnologie Chimiche, University of Rome “Tor Vergata”, Via della Ricerca scientifica 1, I-00133 Roma, Italy, and Dipartimento di Chimica,
| | - Andrea Amadei
- Dipartimento di Chimica, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy, Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Naples, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali, University of L’Aquila, Via Vetoio, I-67010, L’Aquila, Italy, Dipartimento di Scienze e Tecnologie Chimiche, University of Rome “Tor Vergata”, Via della Ricerca scientifica 1, I-00133 Roma, Italy, and Dipartimento di Chimica,
| | - Alfredo Di Nola
- Dipartimento di Chimica, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy, Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Naples, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali, University of L’Aquila, Via Vetoio, I-67010, L’Aquila, Italy, Dipartimento di Scienze e Tecnologie Chimiche, University of Rome “Tor Vergata”, Via della Ricerca scientifica 1, I-00133 Roma, Italy, and Dipartimento di Chimica,
| | - Lelio Mazzarella
- Dipartimento di Chimica, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy, Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Naples, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali, University of L’Aquila, Via Vetoio, I-67010, L’Aquila, Italy, Dipartimento di Scienze e Tecnologie Chimiche, University of Rome “Tor Vergata”, Via della Ricerca scientifica 1, I-00133 Roma, Italy, and Dipartimento di Chimica,
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Giordano D, Russo R, Coppola D, di Prisco G, Verde C. Molecular adaptations in haemoglobins of notothenioid fishes. JOURNAL OF FISH BIOLOGY 2010; 76:301-318. [PMID: 20738709 DOI: 10.1111/j.1095-8649.2009.02528.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Since haemoglobins of all animal species have the same haem group, differences in their properties, including oxygen affinity, electrophoretic mobility and pH sensitivity, must result from the interaction of the prosthetic group with specific amino-acid residues in the primary structure. For this reason, fish globins have been the subject of extensive studies in recent years, not only for their structural characteristics, but also because they offer the possibility to investigate the evolutionary history of these ancient molecules in marine and freshwater species living in a great variety of environmental conditions. This review summarizes the current knowledge on the structure, function and phylogeny of haemoglobins of notothenioid fishes. On the basis of crystallographic analysis, the evolution of the Root effect is analysed. Adaptation of the oxygen transport system in notothenioids seems to be based on evolutionary changes, involving levels of biological organization higher than the structure of haemoglobin. These include changes in the rate of haemoglobin synthesis or in regulation by allosteric effectors, which affect the amount of oxygen transported in blood. These factors are thought to be more important for short-term response to environmental challenges than previously believed.
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Affiliation(s)
- D Giordano
- Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, I-80131 Naples, Italy
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30
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Pan W, Uzunova VV, Vekilov PG. Free heme in micromolar amounts enhances the attraction between sickle cell hemoglobin molecules. Biopolymers 2010; 91:1108-16. [PMID: 19322821 DOI: 10.1002/bip.21191] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We probe the role of free heme in the interactions between sickle cell hemoglobin (HbS) molecules in simulated physiological solutions: polymerization of deoxy-HbS is the primary pathogenic event of sickle cell anemia, and HbS releases heme after autoxidation more readily than normal adult hemoglobin. We characterize these interactions in terms of osmotic virial coefficients, which we determine by static light scattering. We analyze the results in the heme-hemoglobin system using the Kirkwood-Goldberg model. We show that in the absence of heme, the HbS molecules weakly attract and the attraction is not due to the lowered-as a result of the sickle cell mutation-molecular charge. We show that the part of the interface between the two alphabeta dimers, exposed in the deoxy-state, plays a crucial role in this attraction. We show that heme at micromolar concentrations induces strong attraction between the hemoglobin molecules. We show that the high efficacy of the heme results from the statistics of electrostatic and hydrophobic interactions between the heme and hemoglobin molecules.
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Affiliation(s)
- Weichun Pan
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204-4004, USA
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31
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Combined crystallographic and spectroscopic analysis ofTrematomus bernacchiihemoglobin highlights analogies and differences in the peculiar oxidation pathway of Antarctic fish hemoglobins. Biopolymers 2009; 91:1117-25. [DOI: 10.1002/bip.21206] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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32
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Vergara A, Franzese M, Merlino A, Bonomi G, Verde C, Giordano D, di Prisco G, Lee HC, Peisach J, Mazzarella L. Correlation between hemichrome stability and the root effect in tetrameric hemoglobins. Biophys J 2009; 97:866-74. [PMID: 19651045 DOI: 10.1016/j.bpj.2009.04.056] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Revised: 04/23/2009] [Accepted: 04/28/2009] [Indexed: 10/20/2022] Open
Abstract
Oxidation of Hbs leads to the formation of different forms of Fe(III) that are relevant to a range of biochemical and physiological functions. Here we report a combined EPR/x-ray crystallography study performed at acidic pH on six ferric tetrameric Hbs. Five of the Hbs were isolated from the high-Antarctic notothenioid fishes Trematomus bernacchii, Trematomus newnesi, and Gymnodraco acuticeps, and one was isolated from the sub-Antarctic notothenioid Cottoperca gobio. Our EPR analysis reveals that 1), in all of these Hbs, at acidic pH the aquomet form and two hemichromes coexist; and 2), only in the three Hbs that exhibit the Root effect is a significant amount of the pentacoordinate (5C) high-spin Fe(III) form found. The crystal structure at acidic pH of the ferric form of the Root-effect Hb from T. bernacchii is also reported at 1.7 A resolution. This structure reveals a 5C state of the heme iron for both the alpha- and beta-chains within a T quaternary structure. Altogether, the spectroscopic and crystallographic results indicate that the Root effect and hemichrome stability at acidic pH are correlated in tetrameric Hbs. Furthermore, Antarctic fish Hbs exhibit higher peroxidase activity than mammalian and temperate fish Hbs, suggesting that a partial hemichrome state in tetrameric Hbs, unlike in monomeric Hbs, does not remove the need for protection from peroxide attack, in contrast to previous results from monomeric Hbs.
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Affiliation(s)
- Alessandro Vergara
- Department of Chemistry, University of Naples Federico II, Complesso Universitario Monte S. Angelo, Naples, Italy
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Balakrishnan G, Ibrahim M, Mak PJ, Hata J, Kincaid JR, Spiro TG. Linking conformation change to hemoglobin activation via chain-selective time-resolved resonance Raman spectroscopy of protoheme/mesoheme hybrids. J Biol Inorg Chem 2009; 14:741-50. [PMID: 19288145 PMCID: PMC2880192 DOI: 10.1007/s00775-009-0487-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2008] [Accepted: 02/19/2009] [Indexed: 11/28/2022]
Abstract
Time-resolved resonance Raman (RR) spectra are reported for hemoglobin (Hb) tetramers, in which the alpha and beta chains are selectively substituted with mesoheme. The Soret absorption band shift in mesoheme relative to protoheme permits chain-selective recording of heme RR spectra. The evolution of these spectra following HbCO photolysis shows that the geminate recombination rates and the yields are the same for the two chains, consistent with recent results on (15)N-heme isotopomer hybrids. The spectra also reveal systematic shifts in the deoxyheme nu (4) and nu (Fe-His) RR bands, which are anticorrelated. These shifts are resolved for the successive intermediates in the protein structure, which have previously been determined from time-resolved UV RR spectra. Both chains show Fe-His bond compression in the immediate photoproduct, which relaxes during the formation of the first intermediate, R(deoxy) (0.07 micros), in which the proximal F-helix is proposed to move away from the heme. Subsequently, the Fe-His bond weakens, more so for the alpha chains than for the beta chains. The weakening is gradual for the beta chains, but is abrupt for the alpha chains, coinciding with completion of the R-T quaternary transition, at 20 micros. Since the transition from fast- to slow-rebinding Hb also occurs at 20 micros, the drop in the alpha chain nu (Fe-His) supports the localization of ligation restraint to tension in the Fe-His bond, at least in the alpha chains. The mechanism is more complex in the beta chains.
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Merlino A, Vergara A, Sica F, Mazzarella L. The bis-histidyl complex in hemoproteins: A detailed conformational analysis of database protein structures and the case of Antarctic fish hemoglobins. Mar Genomics 2009; 2:51-6. [DOI: 10.1016/j.margen.2009.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2008] [Revised: 04/09/2009] [Accepted: 04/16/2009] [Indexed: 10/20/2022]
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35
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Verde C, Giordano D, Russo R, Riccio A, Vergara A, Mazzarella L, di Prisco G. Hemoproteins in the cold. Mar Genomics 2009; 2:67-73. [DOI: 10.1016/j.margen.2009.03.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2008] [Revised: 01/16/2009] [Accepted: 03/02/2009] [Indexed: 11/25/2022]
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