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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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Scheps KG, Hasenahuer MA, Parisi G, Targovnik HM, Fornasari MS. Curating the gnomAD database: Report of novel variants in the globin-coding genes and bioinformatics analysis. Hum Mutat 2019; 41:81-102. [PMID: 31553106 DOI: 10.1002/humu.23925] [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: 05/18/2019] [Revised: 09/14/2019] [Accepted: 09/23/2019] [Indexed: 02/02/2023]
Abstract
Massive parallel sequencing technologies are facilitating the faster identification of sequence variants with the consequent capability of untangling the molecular bases of many human genetic syndromes. However, it is not always easy to understand the impact of novel variants, especially for missense changes, which can lead to a spectrum of phenotypes. This study presents a custom-designed multistep methodology to evaluate the impact of novel variants aggregated in the genome aggregation database for the HBB, HBA2, and HBA1 genes, by testing and improving its performance with a dataset of previously described alterations affecting those same genes. This approach scored high sensitivity and specificity values and showed an overall better performance than sequence-derived predictors, highlighting the importance of protein conformation and interaction specific analyses in curating variant databases. This study also describes the strengths and limitations of these structural studies and allows identifying residues in the globin chains more prone to tolerate substitutions.
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Affiliation(s)
- Karen G Scheps
- Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra de Genética, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Inmunología, Genética y Metabolismo (INIGEM), Universidad de Buenos Aires - CONICET, Buenos Aires, Argentina
| | - Marcia A Hasenahuer
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Argentina.,European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, United Kingdom.,Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Gustavo Parisi
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Héctor M Targovnik
- Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra de Genética, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Inmunología, Genética y Metabolismo (INIGEM), Universidad de Buenos Aires - CONICET, Buenos Aires, Argentina
| | - María S Fornasari
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Argentina
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Mania M, Bruschetta G, Avenoso A, D'Ascola A, Scuruchi M, Campo A, Acri G, Campo S. Evidence for embryonic haemoglobins from Sparus aurata under normal and hypoxic conditions. FISH PHYSIOLOGY AND BIOCHEMISTRY 2019; 45:943-954. [PMID: 30627834 DOI: 10.1007/s10695-018-0605-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 12/26/2018] [Indexed: 06/09/2023]
Abstract
Teleost haemoglobins vary in polymorphisms and primary structure, although display similar functional properties. Key amino acids for Root effect (a reduction in oxygen-carrying capacity and loss of cooperativity with declining pH) are conserved throughout fish evolution. For the first time, we cloned and characterised Sparus aurata L. embryonic globin chains (eα1, eα2, eβ). We also studied haemoglobins (eHbI, eHbII) behaviour in normal and low-oxygen conditions. Several amino acids in fry globins are different in chemical type (e.g. polar → non-polar and vice versa), compared to adult globins. His55α1, crucial for Root effect, is substituted by Ala in fry, presumably enhancing oxygen capture, transport and reducing the dependence of Root effect from pH. Phylogenetic trees demonstrate that eα1 globin diversified more recently than eα2; moreover, eα1, eα2 and eβ globins evolved earlier than adult α and β globins. In low-oxygen conditions, fry haemoglobins display the same behaviour of the adult haemoglobins (probably, embryonic and adult-type I Hbs display a higher oxygen affinity than type II Hbs, operating through a rapid cycle of heme-Fe auto-oxidation/reduction). Therefore, based on our results and on the comparison with adult haemoglobins, we hypothesise that embryonic haemoglobins have evolved to better adapt fry to variable habitats. We studied Sparus aurata for its economical relevance in Mediterranean aquaculture. The information we provide can help understand Sparus aurata behaviour in the wild and in rearing conditions. Further studies with functional assays will deepen the knowledge on the molecular mechanisms of fry haemoglobin physiology.
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Affiliation(s)
- Manuela Mania
- Department of Biochemical and Dental Sciences and Morphofunctional Images, University of Messina, Messina, Italy
| | | | - Angela Avenoso
- Department of Biochemical and Dental Sciences and Morphofunctional Images, University of Messina, Messina, Italy
| | - Angela D'Ascola
- Department of Biochemical and Dental Sciences and Morphofunctional Images, University of Messina, Messina, Italy
| | - Michele Scuruchi
- Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - Adele Campo
- Department of Biochemical and Dental Sciences and Morphofunctional Images, University of Messina, Messina, Italy
| | - Giuseppe Acri
- Department of Biochemical and Dental Sciences and Morphofunctional Images, University of Messina, Messina, Italy
| | - Salvatore Campo
- Department of Biochemical and Dental Sciences and Morphofunctional Images, University of Messina, Messina, Italy.
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Nategholeslam M, Gray CG, Tomberli B. Stiff Spring Approximation Revisited: Inertial Effects in Nonequilibrium Trajectories. J Phys Chem B 2017; 121:391-403. [DOI: 10.1021/acs.jpcb.6b08701] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - C. G. Gray
- Guelph-Waterloo
Physics Institute and Department of Physics, University of Guelph, Guelph, Ontario N1G 2W1, Canada
- Department
of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Bruno Tomberli
- Department
of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario N1G 2W1, Canada
- Department
of Physics, Capilano University, North Vancouver, British
Columbia V7J 3H5, Canada
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5
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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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Nategholeslam M, Gray CG, Tomberli B. Implementation of the Forward–Reverse Method for Calculating the Potential of Mean Force Using a Dynamic Restraining Protocol. J Phys Chem B 2014; 118:14203-14. [DOI: 10.1021/jp504942t] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Mostafa Nategholeslam
- Department
of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada
| | - C. G. Gray
- Guelph-Waterloo
Physics Institute and Department of Physics, University of Guelph, Guelph, Ontario, Canada
| | - Bruno Tomberli
- Department
of Physics, Capilano University, North Vancouver, British
Columbia, Canada
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Petruk AA, Vergara A, Marasco D, Bikiel D, Doctorovich F, Estrin DA, Merlino A. Interaction between Proteins and Ir Based CO Releasing Molecules: Mechanism of Adduct Formation and CO Release. Inorg Chem 2014; 53:10456-62. [DOI: 10.1021/ic501498g] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Ariel A. Petruk
- Departamento de
Química Inorgánica, Analítica y Química
Física/INQUIMAE-CONICET, University of Buenos Aires, Ciudad
Universitaria, Pab. 2, C1428EHA Buenos Aires, Argentina
| | - Alessandro Vergara
- Department
of Chemical Sciences, University of Naples Federico II, via Cintia I-80126, Napoli, Italy
- CNR Institute of Biostructures and Bioimages, Via Mezzocannone 16 I-80100, Napoli, Italy
| | - Daniela Marasco
- CNR Institute of Biostructures and Bioimages, Via Mezzocannone 16 I-80100, Napoli, Italy
- Department of Pharmacy, CIRPEB: Centro Interuniversitario
di Ricerca sui Peptidi Bioattivi- University of Naples Federico II, DFM-Scarl, Via Mezzocannone, 16 80134, Napoli, Italy
| | - Damian Bikiel
- Departamento de
Química Inorgánica, Analítica y Química
Física/INQUIMAE-CONICET, University of Buenos Aires, Ciudad
Universitaria, Pab. 2, C1428EHA Buenos Aires, Argentina
| | - Fabio Doctorovich
- Departamento de
Química Inorgánica, Analítica y Química
Física/INQUIMAE-CONICET, University of Buenos Aires, Ciudad
Universitaria, Pab. 2, C1428EHA Buenos Aires, Argentina
| | - Dario A. Estrin
- Departamento de
Química Inorgánica, Analítica y Química
Física/INQUIMAE-CONICET, University of Buenos Aires, Ciudad
Universitaria, Pab. 2, C1428EHA Buenos Aires, Argentina
| | - Antonello Merlino
- Department
of Chemical Sciences, University of Naples Federico II, via Cintia I-80126, Napoli, Italy
- CNR Institute of Biostructures and Bioimages, Via Mezzocannone 16 I-80100, Napoli, Italy
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Petruk AA, Vergara A, Estrin D, Merlino A. Molecular basis of the NO trans influence in quaternary T-state human hemoglobin: A computational study. FEBS Lett 2013; 587:2393-8. [DOI: 10.1016/j.febslet.2013.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 05/31/2013] [Accepted: 06/03/2013] [Indexed: 11/29/2022]
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Small ligand-globin interactions: reviewing lessons derived from computer simulation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1722-38. [PMID: 23470499 DOI: 10.1016/j.bbapap.2013.02.038] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 02/22/2013] [Accepted: 02/26/2013] [Indexed: 11/24/2022]
Abstract
In this work we review the application of classical and quantum-mechanical atomistic computer simulation tools to the investigation of small ligand interaction with globins. In the first part, studies of ligand migration, with its connection to kinetic association rate constants (kon), are presented. In the second part, we review studies for a variety of ligands such as O2, NO, CO, HS(-), F(-), and NO2(-) showing how the heme structure, proximal effects, and the interactions with the distal amino acids can modulate protein ligand binding. The review presents mainly results derived from our previous works on the subject, in the context of other theoretical and experimental studies performed by others. The variety and extent of the presented data yield a clear example of how computer simulation tools have, in the last decade, contributed to our deeper understanding of small ligand interactions with globins. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.
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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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Boechi L, Arrar M, Martí MA, Olson JS, Roitberg AE, Estrin DA. Hydrophobic effect drives oxygen uptake in myoglobin via histidine E7. J Biol Chem 2013; 288:6754-62. [PMID: 23297402 DOI: 10.1074/jbc.m112.426056] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Since the elucidation of the myoglobin (Mb) structure, a histidine residue on the E helix (His-E7) has been proposed to act as a gate with an open or closed conformation controlling access to the active site. Although it is believed that at low pH, the His-E7 gate is in its open conformation, the full relationship between the His-E7 protonation state, its conformation, and ligand migration in Mb is hotly debated. We used molecular dynamics simulations to first address the effect of His-E7 protonation on its conformation. We observed the expected shift from the closed to the open conformation upon protonation, but more importantly, noted a significant difference between the conformations of the two neutral histidine tautomers. We further computed free energy profiles for oxygen migration in each of the possible His-E7 states as well as in two instructive Mb mutants: Ala-E7 and Trp-E7. Our results show that even in the closed conformation, the His-E7 gate does not create a large barrier to oxygen migration and permits oxygen entry with only a small rotation of the imidazole side chain and movement of the E helix. We identify, instead, a hydrophobic site in the E7 channel that can accommodate an apolar diatomic ligand and enhances ligand uptake particularly in the open His-E7 conformation. This rate enhancement is diminished in the closed conformation. Taken together, our results provide a new conceptual framework for the histidine gate hypothesis.
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Affiliation(s)
- Leonardo Boechi
- Departamento de Química Inorgánica, Analítica, y Química Física/Inquimae-Conicet, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Ciudad Universitaria, Pabellon 2, C1428EHA Buenos Aires, Argentina
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12
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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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