1
|
Zheng Y, Deng W, Liu D, Li Y, Peng K, Lorimer GH, Wang J. Redox and spectroscopic properties of mammalian nitrite reductase-like hemoproteins. J Inorg Biochem 2022; 237:111982. [PMID: 36116154 DOI: 10.1016/j.jinorgbio.2022.111982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 01/18/2023]
Abstract
Besides the canonical pathway of L-arginine oxidation to produce nitric oxide (NO) in vivo, the nitrate-nitrite-NO pathway has been widely accepted as another source for circulating NO in mammals, especially under hypoxia. To date, there have been at least ten heme-containing nitrite reductase-like proteins discovered in mammals with activities mainly identified in vitro, including four globins (hemoglobin, myoglobin, neuroglobin (Ngb), cytoglobin (Cygb)), three mitochondrial respiratory chain enzymes (cytochrome c oxidase, cytochrome bc1, cytochrome c), and three other heme proteins (endothelial nitric oxide synthase, cytochrome P450 and indoleamine 2,3-dioxygenase 1 (IDO1)). The pathophysiological functions of these proteins are closely related to their redox and spectroscopic properties, as well as their protein structure, although the physiological roles of Ngb, Cygb and IDO1 remain unclear. So far, comprehensive summaries of the redox and spectroscopic properties of these nitrite reductase-like hemoproteins are still lacking. In this review, we have mainly summarized the published data on the application of ultraviolet-visible, electron paramagnetic resonance, circular dichroism and resonance Raman spectroscopies, and X-ray crystallography in studying nitrite reductase-like activity of these 10 proteins, in order to sort out the relationships among enzymatic function, structure and spectroscopic characterization, which might help in understanding their roles in redox biology and medicine.
Collapse
Affiliation(s)
- Yunlong Zheng
- Hubei University of Technology Autism & Depression Diagnosis and Intervention Institute, Hubei University of Technology, Wuhan, Hubei, China; International Joint Research Center for General Health, Precision Medicine & Nutrition, Hubei University of Technology, Wuhan, Hubei, China; Department of Biomedicine and Biopharmacology, Hubei University of Technology, Wuhan, Hubei, China
| | - Wenwen Deng
- Hubei University of Technology Autism & Depression Diagnosis and Intervention Institute, Hubei University of Technology, Wuhan, Hubei, China; International Joint Research Center for General Health, Precision Medicine & Nutrition, Hubei University of Technology, Wuhan, Hubei, China; Department of Biomedicine and Biopharmacology, Hubei University of Technology, Wuhan, Hubei, China
| | - Di Liu
- Hubei University of Technology Autism & Depression Diagnosis and Intervention Institute, Hubei University of Technology, Wuhan, Hubei, China; International Joint Research Center for General Health, Precision Medicine & Nutrition, Hubei University of Technology, Wuhan, Hubei, China; Department of Biomedicine and Biopharmacology, Hubei University of Technology, Wuhan, Hubei, China
| | - Youheng Li
- Hubei University of Technology Autism & Depression Diagnosis and Intervention Institute, Hubei University of Technology, Wuhan, Hubei, China; International Joint Research Center for General Health, Precision Medicine & Nutrition, Hubei University of Technology, Wuhan, Hubei, China; Department of Biomedicine and Biopharmacology, Hubei University of Technology, Wuhan, Hubei, China
| | - Kang Peng
- Hubei University of Technology Autism & Depression Diagnosis and Intervention Institute, Hubei University of Technology, Wuhan, Hubei, China; International Joint Research Center for General Health, Precision Medicine & Nutrition, Hubei University of Technology, Wuhan, Hubei, China; Department of Biomedicine and Biopharmacology, Hubei University of Technology, Wuhan, Hubei, China
| | | | - Jun Wang
- Hubei University of Technology Autism & Depression Diagnosis and Intervention Institute, Hubei University of Technology, Wuhan, Hubei, China; International Joint Research Center for General Health, Precision Medicine & Nutrition, Hubei University of Technology, Wuhan, Hubei, China; Department of Biomedicine and Biopharmacology, Hubei University of Technology, Wuhan, Hubei, China.
| |
Collapse
|
2
|
Freindorf M, Delgado AAA, Kraka E. CO bonding in hexa‐ and pentacoordinate carboxy‐neuroglobin: A quantum mechanics/molecular mechanics and local vibrational mode study. J Comput Chem 2022. [DOI: 10.1002/jcc.26973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Marek Freindorf
- Department of Chemistry Southern Methodist University Dallas Texas USA
| | | | - Elfi Kraka
- Department of Chemistry Southern Methodist University Dallas Texas USA
| |
Collapse
|
3
|
De Simone G, Sbardella D, Oddone F, Pesce A, Coletta M, Ascenzi P. Structural and (Pseudo-)Enzymatic Properties of Neuroglobin: Its Possible Role in Neuroprotection. Cells 2021; 10:cells10123366. [PMID: 34943874 PMCID: PMC8699588 DOI: 10.3390/cells10123366] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/20/2021] [Accepted: 11/23/2021] [Indexed: 12/17/2022] Open
Abstract
Neuroglobin (Ngb), the third member of the globin family, was discovered in human and murine brains in 2000. This monomeric globin is structurally similar to myoglobin (Mb) and hemoglobin (Hb) α and β subunits, but it hosts a bis-histidyl six-coordinated heme-Fe atom. Therefore, the heme-based reactivity of Ngb is modulated by the dissociation of the distal HisE7-heme-Fe bond, which reflects in turn the redox state of the cell. The high Ngb levels (~100–200 μM) present in the retinal ganglion cell layer and in the optic nerve facilitate the O2 buffer and delivery. In contrast, the very low levels of Ngb (~1 μM) in most tissues and organs support (pseudo-)enzymatic properties including NO/O2 metabolism, peroxynitrite and free radical scavenging, nitrite, hydroxylamine, hydrogen sulfide reduction, and the nitration of aromatic compounds. Here, structural and (pseudo-)enzymatic properties of Ngb, which are at the root of tissue and organ protection, are reviewed, envisaging a possible role in the protection from neuronal degeneration of the retina and the optic nerve.
Collapse
Affiliation(s)
- Giovanna De Simone
- Dipartimento di Scienze, Università Roma Tre, Viale Marconi 446, 00146 Roma, Italy;
| | | | | | - Alessandra Pesce
- Dipartimento di Fisica, Università di Genova, Via Dodecaneso 33, 16100 Genova, Italy;
| | - Massimo Coletta
- IRCCS Fondazione Bietti, 00198 Roma, Italy; (D.S.); (F.O.)
- Dipartmento di Scienze Cliniche e Medicina Traslazionale, Università di Roma “Tor Vergata”, Via Montpellier 1, 00133 Roma, Italy
- Correspondence: (M.C.); (P.A.); Tel.: +39-06-72596365 (M.C.); +39-06-57336321 (P.A.)
| | - Paolo Ascenzi
- Dipartimento di Scienze, Università Roma Tre, Viale Marconi 446, 00146 Roma, Italy;
- Accademia Nazionale dei Lincei, Via della Lungara 10, 00165 Roma, Italy
- Unità di Neuroendocrinologia, Metabolismo e Neurofarmacologia, IRCSS Fondazione Santa Lucia, 00179 Roma, Italy
- Correspondence: (M.C.); (P.A.); Tel.: +39-06-72596365 (M.C.); +39-06-57336321 (P.A.)
| |
Collapse
|
4
|
Julió Plana L, Martinez Grundman JE, Estrin DA, Lecomte JTJ, Capece L. Distal lysine (de)coordination in the algal hemoglobin THB1: A combined computer simulation and experimental study. J Inorg Biochem 2021; 220:111455. [PMID: 33882423 DOI: 10.1016/j.jinorgbio.2021.111455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 03/26/2021] [Accepted: 03/27/2021] [Indexed: 11/26/2022]
Abstract
THB1 is a monomeric truncated hemoglobin from the green alga Chlamydomonas reinhardtii. In the absence of exogenous ligands and at neutral pH, the heme group of THB1 is coordinated by two protein residues, Lys53 and His77. THB1 is thought to function as a nitric oxide dioxygenase, and the distal binding of O2 requires the cleavage of the Fe-Lys53 bond accompanied by protonation and expulsion of the lysine from the heme cavity into the solvent. Nuclear magnetic resonance spectroscopy and crystallographic data have provided dynamic and structural insights of the process, but the details of the mechanism have not been fully elucidated. We applied a combination of computer simulations and site-directed mutagenesis experiments to shed light on this issue. Molecular dynamics simulations and hybrid quantum mechanics/molecular mechanics restrained optimizations were performed to explore the nature of the transition between the decoordinated and lysine-bound states of the ferrous heme in THB1. Lys49 and Arg52, which form ionic interactions with the heme propionates in the X-ray structure of lysine-bound THB1, were observed to assist in maintaining Lys53 inside the protein cavity and play a key role in the transition. Lys49Ala, Arg52Ala and Lys49Ala/Arg52Ala THB1 variants were prepared, and the consequences of the replacements on the Lys (de)coordination equilibrium were characterized experimentally for comparison with computational prediction. The results reinforced the dynamic role of protein-propionate interactions and strongly suggested that cleavage of the Fe-Lys53 bond and ensuing conformational rearrangement is facilitated by protonation of the amino group inside the distal cavity.
Collapse
Affiliation(s)
- Laia Julió Plana
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Jaime E Martinez Grundman
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Darío A Estrin
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Juliette T J Lecomte
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, United States.
| | - Luciana Capece
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
| |
Collapse
|
5
|
Control of distal lysine coordination in a monomeric hemoglobin: A role for heme peripheral interactions. J Inorg Biochem 2021; 219:111437. [PMID: 33892380 DOI: 10.1016/j.jinorgbio.2021.111437] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 03/20/2021] [Accepted: 03/20/2021] [Indexed: 12/25/2022]
Abstract
THB1 is a monomeric truncated hemoglobin (TrHb) found in the cytoplasm of the green alga Chlamydomonas reinhardtii. The canonical heme coordination scheme in hemoglobins is a proximal histidine ligand and an open distal site. In THB1, the latter site is occupied by Lys53, which is likely to facilitate Fe(II)/Fe(III) redox cycling but hinders dioxygen binding, two features inherent to the NO dioxygenase activity of the protein. TrHb surveys show that a lysine at a position aligning with Lys53 is an insufficient determinant of coordination, and in this study, we sought to identify factors controlling lysine affinity for the heme iron. We solved the "Lys-off" X-ray structure of THB1, represented by the cyanide adduct of the Fe(III) protein, and hypothesized that interactions that differ between the known "Lys-on" structure and the Lys-off structure participate in the control of Lys53 affinity for the heme iron. We applied an experimental approach (site-directed mutagenesis, heme modification, pH titrations in the Fe(III) and Fe(II) states) and a computational approach (MD simulations in the Fe(II) state) to assess the role of heme propionate-protein interactions, distal helix capping, and the composition of the distal pocket. All THB1 modifications resulted in a weakening of lysine affinity and affected the coupling between Lys53 proton binding and heme redox potential. The results supported the importance of specific heme peripheral interactions for the pH stability of iron coordination and the ability of the protein to undergo redox reactions.
Collapse
|
6
|
Astegno A, Conter C, Bertoldi M, Dominici P. Structural Insights into the Heme Pocket and Oligomeric State of Non-Symbiotic Hemoglobins from Arabidopsis thaliana. Biomolecules 2020; 10:E1615. [PMID: 33260415 PMCID: PMC7761212 DOI: 10.3390/biom10121615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/23/2020] [Accepted: 11/25/2020] [Indexed: 11/18/2022] Open
Abstract
Non-symbiotic hemoglobins AHb1 and AHb2 from Arabidopsis thaliana are hexacoordinate heme-proteins that likely have different biological roles, in view of diverse tissue localization, expression pattern, and ligand binding properties. Herein, we expand upon previous biophysical studies on these isoforms, focusing on their oligomeric states and circular dichroism (CD) characteristics. We found that AHb1 exists in solution in a concentration-dependent monomer-dimer equilibrium, while AHb2 is present only as a monomer. The quaternary structure of AHb1 affects its degree of hexacoordination with the formation of the dimer that enhances pentacoordination. Accordingly, the mutant of a conserved residue within the dimeric interface, AHb1-T45A, which is mostly monomeric in solution, has an equilibrium that is shifted toward a hexacoordinate form compared to the wild-type protein. CD studies further support differences in the globin's structure and heme moiety. The Soret CD spectra for AHb2 are opposite in sense to those for AHb1, reflecting different patterns of heme-protein side chain contacts in the two proteins. Moreover, the smaller contribution of the heme to the near-UV CD in AHb2 compared to AHb1 suggests a weaker heme-protein association in AHb2. Our data corroborate the structural diversity of AHb1 and AHb2 and confirm the leghemoglobin-like structural properties of AHb2.
Collapse
Affiliation(s)
- Alessandra Astegno
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy; (A.A.); (C.C.)
| | - Carolina Conter
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy; (A.A.); (C.C.)
| | - Mariarita Bertoldi
- Department of Neuroscience, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Strada Le Grazie, 8, 37134 Verona, Italy;
| | - Paola Dominici
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy; (A.A.); (C.C.)
| |
Collapse
|
7
|
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.
Collapse
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
Collapse
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
| |
Collapse
|
8
|
Zhang P, Yuan H, Xu J, Wang XJ, Gao SQ, Tan X, Lin YW. A Catalytic Binding Site Together with a Distal Tyr in Myoglobin Affords Catalytic Efficiencies Similar to Natural Peroxidases. ACS Catal 2019. [DOI: 10.1021/acscatal.9b05080] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Ping Zhang
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Hong Yuan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai 200433, China
| | - Jiakun Xu
- Key Lab of Sustainable Development of Polar Fisheries, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Xiao-Juan Wang
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Shu-Qin Gao
- Lab of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Xiangshi Tan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai 200433, China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
- Lab of Protein Structure and Function, University of South China, Hengyang 421001, China
| |
Collapse
|
9
|
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.
Collapse
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.
| |
Collapse
|
10
|
Herrera MG, Noguera ME, Sewell KE, Agudelo Suárez WA, Capece L, Klinke S, Santos J. Structure of the Human ACP-ISD11 Heterodimer. Biochemistry 2019; 58:4596-4609. [PMID: 31664822 DOI: 10.1021/acs.biochem.9b00539] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In recent years, the mammalian mitochondrial protein complex for iron-sulfur cluster assembly has been the focus of important studies. This is partly because of its high degree of relevance in cell metabolism and because mutations of the involved proteins are the cause of several human diseases. Cysteine desulfurase NFS1 is the key enzyme of the complex. At present, it is well-known that the active form of NFS1 is stabilized by the small protein ISD11. In this work, the structure of the human mitochondrial ACP-ISD11 heterodimer was determined at 2.0 Å resolution. ACP-ISD11 forms a cooperative unit stabilized by several ionic interactions, hydrogen bonds, and apolar interactions. The 4'-phosphopantetheine-acyl chain, which is covalently bound to ACP, interacts with several residues of ISD11, modulating together with ACP the foldability of ISD11. Recombinant human ACP-ISD11 was able to interact with the NFS1 desulfurase, thus yielding an active enzyme, and the NFS1/ACP-ISD11 core complex was activated by frataxin and ISCU proteins. Internal motions of ACP-ISD11 were studied by molecular dynamics simulations, showing the persistence of the interactions between both protein chains. The conformation of the dimer is similar to that found in the context of the (NFS1/ACP-ISD11)2 supercomplex core, which contains the Escherichia coli ACP instead of the human variant. This fact suggests a sequential mechanism for supercomplex consolidation, in which the ACP-ISD11 complex may fold independently and, after that, the NFS1 dimer would be stabilized.
Collapse
Affiliation(s)
- María Georgina Herrera
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Intendente Güiraldes 2160-Ciudad Universitaria , C1428EGA Buenos Aires , Argentina
| | - Martín Ezequiel Noguera
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Intendente Güiraldes 2160-Ciudad Universitaria , C1428EGA Buenos Aires , Argentina.,Instituto de Química y Fisicoquímica Biológicas , Dr. Alejandro Paladini, Universidad de Buenos Aires, CONICET , Junín 956 , C1113AAD Buenos Aires , Argentina
| | - Karl Ellioth Sewell
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Intendente Güiraldes 2160-Ciudad Universitaria , C1428EGA Buenos Aires , Argentina
| | - William Armando Agudelo Suárez
- Fundación Instituto de Inmunología de Colombia (FIDIC) , Av. 50 No. 26-20 , Bogotá D.C. , Colombia.,Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE CONICET) , C1428EGA Buenos Aires , Argentina
| | - Luciana Capece
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE CONICET) , C1428EGA Buenos Aires , Argentina
| | - Sebastián Klinke
- Fundación Instituto Leloir , IIBBA-CONICET, and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM , Av. Patricias Argentinas 435 , C1405BWE Buenos Aires , Argentina
| | - Javier Santos
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Intendente Güiraldes 2160-Ciudad Universitaria , C1428EGA Buenos Aires , Argentina
| |
Collapse
|
11
|
Julió Plana L, Nadra AD, Estrin DA, Luque FJ, Capece L. Thermal Stability of Globins: Implications of Flexibility and Heme Coordination Studied by Molecular Dynamics Simulations. J Chem Inf Model 2018; 59:441-452. [PMID: 30516994 DOI: 10.1021/acs.jcim.8b00840] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Proteins are sensitive to temperature, and abrupt changes in the normal temperature conditions can have a profound impact on both structure and function, leading to protein unfolding. However, the adaptation of certain organisms to extreme conditions raises questions about the structural features that permit the structure and function of proteins to be preserved under these adverse conditions. To gain insight into the molecular basis of protein thermostability in the globin family, we have examined three representative examples: human neuroglobin, horse heart myoglobin, and Drosophila hemoglobin, which differ in their melting temperatures and coordination states of the heme iron in the absence of external ligands. In order to elucidate the possible mechanisms that govern the thermostability of these proteins, microsecond-scale classical molecular dynamics simulations were performed at different temperatures. Structural fluctuations and essential dynamics were analyzed, indicating that the flexibility of the CD region, which includes the two short C and D helixes and the connecting CD loop, is directly related to the thermostability. We observed that a larger inherent flexibility of the protein produces higher thermostability, probably concentrating the thermal fluctuations observed at high temperature in flexible regions, preventing unfolding. Globally, the results of this work improve our understanding of thermostability in the globin family.
Collapse
Affiliation(s)
- Laia Julió Plana
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires/Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE-CONICET) , C1428EGA Buenos Aires , Argentina
| | - Alejandro D Nadra
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires/IQUIBICEN-CONICET , C1428EGA Buenos Aires , Argentina
| | - Dario A Estrin
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires/Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE-CONICET) , C1428EGA Buenos Aires , Argentina
| | - F Javier Luque
- Department of Nutrition, Food Sciences and Gastronomy, Faculty of Pharmacy and Food Sciences , University of Barcelona , Campus Torribera , 08921 Santa Coloma de Gramenet , Spain.,Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (IQTCUB) , University of Barcelona , 08028 Barcelona , Spain
| | - Luciana Capece
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires/Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE-CONICET) , C1428EGA Buenos Aires , Argentina
| |
Collapse
|
12
|
Sweeny EA, Singh AB, Chakravarti R, Martinez-Guzman O, Saini A, Haque MM, Garee G, Dans PD, Hannibal L, Reddi AR, Stuehr DJ. Glyceraldehyde-3-phosphate dehydrogenase is a chaperone that allocates labile heme in cells. J Biol Chem 2018; 293:14557-14568. [PMID: 30012884 DOI: 10.1074/jbc.ra118.004169] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 07/05/2018] [Indexed: 11/06/2022] Open
Abstract
Cellular heme is thought to be distributed between a pool of sequestered heme that is tightly bound within hemeproteins and a labile heme pool required for signaling and transfer into proteins. A heme chaperone that can hold and allocate labile heme within cells has long been proposed but never been identified. Here, we show that the glycolytic protein glyceraldehyde-3-phosphate dehydrogenase (GAPDH) fulfills this role by acting as an essential repository and allocator of bioavailable heme to downstream protein targets. We identified a conserved histidine in GAPDH that is needed for its robust heme binding both in vitro and in mammalian cells. Substitution of this histidine, and the consequent decreases in GAPDH heme binding, antagonized heme delivery to both cytosolic and nuclear hemeprotein targets, including inducible nitric-oxide synthase (iNOS) in murine macrophages and the nuclear transcription factor Hap1 in yeast, even though this GAPDH variant caused cellular levels of labile heme to rise dramatically. We conclude that by virtue of its heme-binding property, GAPDH binds and chaperones labile heme to create a heme pool that is bioavailable to downstream proteins. Our finding solves a fundamental question in cell biology and provides a new foundation for exploring heme homeostasis in health and disease.
Collapse
Affiliation(s)
- Elizabeth A Sweeny
- From the Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio 44195
| | - Anuradha Bharara Singh
- From the Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio 44195
| | - Ritu Chakravarti
- From the Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio 44195
| | - Osiris Martinez-Guzman
- the School of Chemistry and Biochemistry and Parker Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Arushi Saini
- the School of Chemistry and Biochemistry and Parker Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Mohammad Mahfuzul Haque
- From the Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio 44195
| | - Greer Garee
- From the Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio 44195
| | - Pablo D Dans
- the Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Balidiri Reixac 10-12, Barcelona 08028, Spain, and
| | - Luciana Hannibal
- the Laboratory of Clinical Biochemistry and Metabolism, Center of Pediatrics, Medical Center, University of Freiburg, D-79106 Freiburg, Germany
| | - Amit R Reddi
- the School of Chemistry and Biochemistry and Parker Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Dennis J Stuehr
- From the Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio 44195,
| |
Collapse
|
13
|
Lin YW. Structure and function of heme proteins regulated by diverse post-translational modifications. Arch Biochem Biophys 2018; 641:1-30. [DOI: 10.1016/j.abb.2018.01.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/10/2018] [Accepted: 01/13/2018] [Indexed: 01/08/2023]
|
14
|
Gell DA. Structure and function of haemoglobins. Blood Cells Mol Dis 2017; 70:13-42. [PMID: 29126700 DOI: 10.1016/j.bcmd.2017.10.006] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 10/29/2017] [Accepted: 10/30/2017] [Indexed: 12/18/2022]
Abstract
Haemoglobin (Hb) is widely known as the iron-containing protein in blood that is essential for O2 transport in mammals. Less widely recognised is that erythrocyte Hb belongs to a large family of Hb proteins with members distributed across all three domains of life-bacteria, archaea and eukaryotes. This review, aimed chiefly at researchers new to the field, attempts a broad overview of the diversity, and common features, in Hb structure and function. Topics include structural and functional classification of Hbs; principles of O2 binding affinity and selectivity between O2/NO/CO and other small ligands; hexacoordinate (containing bis-imidazole coordinated haem) Hbs; bacterial truncated Hbs; flavohaemoglobins; enzymatic reactions of Hbs with bioactive gases, particularly NO, and protection from nitrosative stress; and, sensor Hbs. A final section sketches the evolution of work on the structural basis for allosteric O2 binding by mammalian RBC Hb, including the development of newer kinetic models. Where possible, reference to historical works is included, in order to provide context for current advances in Hb research.
Collapse
Affiliation(s)
- David A Gell
- School of Medicine, University of Tasmania, TAS 7000, Australia.
| |
Collapse
|
15
|
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]
|
16
|
Structural Plasticity in Globins: Role of Protein Dynamics in Defining Ligand Migration Pathways. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2016; 105:59-80. [PMID: 27567484 DOI: 10.1016/bs.apcsb.2016.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Globins are a family of proteins characterized by the presence of the heme prosthetic group and involved in variety of biological functions in the cell. Due to their biological relevance and widespread distribution in all kingdoms of life, intense research efforts have been devoted to disclosing the relationships between structural features, protein dynamics, and function. Particular attention has been paid to the impact of differences in amino acid sequence on the topological features of docking sites and cavities and to the influence of conformational flexibility in facilitating the migration of small ligands through these cavities. Often, tunnels are carved in the interior of globins, and ligand exchange is regulated by gating residues. Understanding the subtle intricacies that relate the differences in sequence with the structural and dynamical features of globins with the ultimate aim of rationalizing the thermodynamics and kinetics of ligand binding continues to be a major challenge in the field. Due to the evolution of computational techniques, significant advances into our understanding of these questions have been made. In this review we focus our attention on the analysis of the ligand migration pathways as well as the function of the structural cavities and tunnels in a series of representative globins, emphasizing the synergy between experimental and theoretical approaches to gain a comprehensive knowledge into the molecular mechanisms of this diverse family of proteins.
Collapse
|
17
|
Ramírez CL, Petruk A, Bringas M, Estrin DA, Roitberg AE, Marti MA, Capece L. Coarse-Grained Simulations of Heme Proteins: Validation and Study of Large Conformational Transitions. J Chem Theory Comput 2016; 12:3390-7. [DOI: 10.1021/acs.jctc.6b00278] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Claudia L. Ramírez
- Dto.
de Química Inorgánica, Analítica y Química
Física, Fac. de Ciencias Exactas y Naturales, Univ. de Buenos Aires/INQUIMAE-CONICET, Buenos Aires, C1428EGA, Argentina
- Dto.
de Química Biologica Fac. de Ciencias Exactas y Naturales, Univ. de Buenos Aires/IQUIBICEN-CONICET, Buenos Aires, C1428EGA, Argentina
| | - Ariel Petruk
- Dto.
de Química Inorgánica, Analítica y Química
Física, Fac. de Ciencias Exactas y Naturales, Univ. de Buenos Aires/INQUIMAE-CONICET, Buenos Aires, C1428EGA, Argentina
| | - Mauro Bringas
- Dto.
de Química Inorgánica, Analítica y Química
Física, Fac. de Ciencias Exactas y Naturales, Univ. de Buenos Aires/INQUIMAE-CONICET, Buenos Aires, C1428EGA, Argentina
| | - Dario A. Estrin
- Dto.
de Química Inorgánica, Analítica y Química
Física, Fac. de Ciencias Exactas y Naturales, Univ. de Buenos Aires/INQUIMAE-CONICET, Buenos Aires, C1428EGA, Argentina
| | - Adrian E. Roitberg
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Marcelo A. Marti
- Dto.
de Química Biologica Fac. de Ciencias Exactas y Naturales, Univ. de Buenos Aires/IQUIBICEN-CONICET, Buenos Aires, C1428EGA, Argentina
| | - Luciana Capece
- Dto.
de Química Inorgánica, Analítica y Química
Física, Fac. de Ciencias Exactas y Naturales, Univ. de Buenos Aires/INQUIMAE-CONICET, Buenos Aires, C1428EGA, Argentina
| |
Collapse
|
18
|
Wu LB, Yuan H, Zhou H, Gao SQ, Nie CM, Tan X, Wen GB, Lin YW. An intramolecular disulfide bond designed in myoglobin fine-tunes both protein structure and peroxidase activity. Arch Biochem Biophys 2016; 600:47-55. [DOI: 10.1016/j.abb.2016.04.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/12/2016] [Accepted: 04/23/2016] [Indexed: 01/08/2023]
|
19
|
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]
|
20
|
Medvedev KE, Alemasov NA, Vorobjev YN, Boldyreva EV, Kolchanov NA, Afonnikov DA. Molecular dynamics simulations of the Nip7 proteins from the marine deep- and shallow-water Pyrococcus species. BMC STRUCTURAL BIOLOGY 2014; 14:23. [PMID: 25315147 PMCID: PMC4209456 DOI: 10.1186/s12900-014-0023-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Accepted: 10/03/2014] [Indexed: 11/13/2022]
Abstract
Background The identification of the mechanisms of adaptation of protein structures to extreme environmental conditions is a challenging task of structural biology. We performed molecular dynamics (MD) simulations of the Nip7 protein involved in RNA processing from the shallow-water (P. furiosus) and the deep-water (P. abyssi) marine hyperthermophylic archaea at different temperatures (300 and 373 K) and pressures (0.1, 50 and 100 MPa). The aim was to disclose similarities and differences between the deep- and shallow-sea protein models at different temperatures and pressures. Results The current results demonstrate that the 3D models of the two proteins at all the examined values of pressures and temperatures are compact, stable and similar to the known crystal structure of the P. abyssi Nip7. The structural deviations and fluctuations in the polypeptide chain during the MD simulations were the most pronounced in the loop regions, their magnitude being larger for the C-terminal domain in both proteins. A number of highly mobile segments the protein globule presumably involved in protein-protein interactions were identified. Regions of the polypeptide chain with significant difference in conformational dynamics between the deep- and shallow-water proteins were identified. Conclusions The results of our analysis demonstrated that in the examined ranges of temperatures and pressures, increase in temperature has a stronger effect on change in the dynamic properties of the protein globule than the increase in pressure. The conformational changes of both the deep- and shallow-sea protein models under increasing temperature and pressure are non-uniform. Our current results indicate that amino acid substitutions between shallow- and deep-water proteins only slightly affect overall stability of two proteins. Rather, they may affect the interactions of the Nip7 protein with its protein or RNA partners.
Collapse
Affiliation(s)
- Kirill E Medvedev
- Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia.
| | - Nikolay A Alemasov
- Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia.
| | - Yuri N Vorobjev
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Prospekt Lavrentyeva 8, Novosibirsk, 630090, Russia.
| | - Elena V Boldyreva
- Novosibirsk State University, Pirogova str. 2, Novosibirsk, 630090, Russia. .,Institute of Solid Chemistry and Mechanochemistry, SB RAS, Novosibirsk, 630090, Russia.
| | - Nikolay A Kolchanov
- Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Pirogova str. 2, Novosibirsk, 630090, Russia. .,NRC Kurchatov Institute, 1, Akademika Kurchatova pl., Moscow, 123182, Russia.
| | - Dmitry A Afonnikov
- Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Pirogova str. 2, Novosibirsk, 630090, Russia.
| |
Collapse
|
21
|
Molecular basis of thermal stability in truncated (2/2) hemoglobins. Biochim Biophys Acta Gen Subj 2014; 1840:2281-8. [PMID: 24704259 DOI: 10.1016/j.bbagen.2014.03.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 03/14/2014] [Accepted: 03/25/2014] [Indexed: 11/23/2022]
Abstract
BACKGROUND Understanding the molecular mechanism through which proteins are functional at extreme high and low temperatures is one of the key issues in structural biology. To investigate this phenomenon, we have focused on two instructive truncated hemoglobins from Thermobifida fusca (Tf-trHbO) and Mycobacterium tuberculosis (Mt-trHbO); although the two proteins are structurally nearly identical, only the former is stable at high temperatures. METHODS We used molecular dynamics simulations at different temperatures as well as thermal melting profile measurements of both wild type proteins and two mutants designed to interchange the amino acid residue, either Pro or Gly, at E3 position. RESULTS The results show that the presence of a Pro at the E3 position is able to increase (by 8°) or decrease (by 4°) the melting temperature of Mt-trHbO and Tf-trHbO, respectively. We observed that the ProE3 alters the structure of the CD loop, making it more flexible. CONCLUSIONS This gain in flexibility allows the protein to concentrate its fluctuations in this single loop and avoid unfolding. The alternate conformations of the CD loop also favor the formation of more salt-bridge interactions, together augmenting the protein's thermostability. GENERAL SIGNIFICANCE These results indicate a clear structural and dynamical role of a key residue for thermal stability in truncated hemoglobins.
Collapse
|
22
|
Dumas VG, Defelipe LA, Petruk AA, Turjanski AG, Marti MA. QM/MM study of the C-C coupling reaction mechanism of CYP121, an essential cytochrome p450 of Mycobacterium tuberculosis. Proteins 2013; 82:1004-21. [PMID: 24356896 DOI: 10.1002/prot.24474] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 10/15/2013] [Accepted: 11/04/2013] [Indexed: 11/06/2022]
Abstract
Among 20 p450s of Mycobacterium tuberculosis (Mt), CYP121 has received an outstanding interest, not only due to its essentiality for bacterial viability but also because it catalyzes an unusual carbon-carbon coupling reaction. Based on the structure of the substrate bound enzyme, several reaction mechanisms were proposed involving first Tyr radical formation, second Tyr radical formation, and C-C coupling. Key and unknown features, being the nature of the species that generate the first and second radicals, and the role played by the protein scaffold each step. In the present work we have used classical and quantum based computer simulation methods to study in detail its reaction mechanism. Our results show that substrate binding promotes formation of the initial oxy complex, Compound I is the responsible for first Tyr radical formation, and that the second Tyr radical is formed subsequently, through a PCET reaction, promoted by the presence of key residue Arg386. The final C-C coupling reaction possibly occurs in bulk solution, thus yielding the product in one oxygen reduction cycle. Our results thus contribute to a better comprehension of MtCYP121 reaction mechanism, with direct implications for inhibitor design, and also contribute to our general understanding of these type of enzymes.
Collapse
Affiliation(s)
- Victoria G Dumas
- Departamento de Quimica Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes, 2160, C1428EGA, Ciudad Autónoma de Buenos Aires, Argentina; Instituto de Química Física de los Materiales Medio Ambiente y Energia (INQUIMAE), UBA-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Intendente Güiraldes, 2160, C1428EGA, Ciudad Autónoma de Buenos Aires, Argentina
| | | | | | | | | |
Collapse
|
23
|
Li WD, Sun Q, Zhang XS, Wang CX, Li S, Li W, Hang CH. Expression and cell distribution of neuroglobin in the brain tissue after experimental subarachnoid hemorrhage in rats: a pilot study. Cell Mol Neurobiol 2013; 34:247-55. [PMID: 24281943 DOI: 10.1007/s10571-013-0008-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 11/17/2013] [Indexed: 12/30/2022]
Abstract
Neuroglobin (Ngb) is a member of the globin superfamily expressed mainly in the nervous system and retina of vertebrates. Accumulated evidence has clearly demonstrated that Ngb has a neuro-protective role enhancing cell viability under hypoxia and other types of oxidative stress. It was suggested that oxidant stress could play an important role in neuronal injury after subarachnoid hemorrhage (SAH). The present study aims to examine the expression of Ngb in the temporal cortex and its cellular localization after SAH. We used a prechiasmatic cistern model of SAH. Ngb expression was examined at 3, 6, 12, 24, 48, and 72 h after SAH by western blot analysis and real-time polymerase chain reaction (PCR). Immunohistochemistry and immunofluorescence were performed to detect the localization of Ngb. Real-time PCR demonstrated that Ngb mRNA levels increased from 3 h after SAH, peaked at 6 h. Western blot showed Ngb protein levels were significantly increased in SAH groups in the temporal cortex and reached the peak at 24 h after SAH. The immunohistochemical staining demonstrated that Ngb was weakly expressed in the cortex in the control group while the enhanced expression of Ngb could be detected in the SAH groups. In addition, immunofluorescence results revealed that the over-expressed Ngb was located in the neuronal and microglia cell cytoplasm. These findings indicated that Ngb might play an important neuro-protective effect after SAH.
Collapse
Affiliation(s)
- Wei-De Li
- Department of Neurosurgery, School of Medicine, Southern Medical University (Guangzhou), Jinling Hospital, 305 East Zhongshan Road, Nanjing, 210002, Jiangsu Province, People's Republic of China
| | | | | | | | | | | | | |
Collapse
|
24
|
Dellarole M, Roumestand C, Royer C, Lecomte JTJ. Volumetric properties underlying ligand binding in a monomeric hemoglobin: a high-pressure NMR study. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1910-22. [PMID: 23619242 DOI: 10.1016/j.bbapap.2013.04.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 04/09/2013] [Accepted: 04/15/2013] [Indexed: 11/16/2022]
Abstract
The 2/2 hemoglobin of the cyanobacterium Synechococcus sp. PCC 7002, GlbN, coordinates the heme iron with two histidines and exists either with a b heme or with a covalently attached heme. The binding of exogenous ligands displaces the distal histidine and induces a conformational rearrangement involving the reorganization of internal void volumes. The formation of passageways within the resulting conformation is thought to facilitate ligand exchange and play a functional role. Here we monitored the perturbation induced by pressure on the ferric bis-histidine and cyanide-bound states of GlbN using (1)H-(15)N HSQC NMR spectroscopy. We inspected the outcome with a statistical analysis of 170 homologous 2/2 hemoglobin sequences. We found that the compression landscape of GlbN, as represented by the variation of an average chemical shift parameter, was highly sensitive to ligand swapping and heme covalent attachment. Stabilization of rare conformers was observed at high pressures and consistent with cavity redistribution upon ligand binding. In all states, the EF loop was found to be exceptionally labile to pressure, suggesting a functional role as a semi-flexible hinge between the adjacent helices. Finally, coevolved clusters presented a common pattern of compensating pressure responses. The high-pressure dissection combined with protein sequence analysis established locations with volumetric signatures relevant to residual communication of 2/2 hemoglobins. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.
Collapse
Affiliation(s)
- Mariano Dellarole
- Centre de Biochimie Structurale, CNRS, UMR 5048, Montpellier, France
| | | | | | | |
Collapse
|
25
|
Spyrakis F, Lucas F, Bidon-Chanal A, Viappiani C, Guallar V, Luque FJ. Comparative analysis of inner cavities and ligand migration in non-symbiotic AHb1 and AHb2. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1957-67. [PMID: 23583621 DOI: 10.1016/j.bbapap.2013.04.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 03/30/2013] [Accepted: 04/03/2013] [Indexed: 10/27/2022]
Abstract
This study reports a comparative analysis of the topological properties of inner cavities and the intrinsic dynamics of non-symbiotic hemoglobins AHb1 and AHb2 from Arabidopsis thaliana. The two proteins belong to the 3/3 globin fold and have a sequence identity of about 60%. However, it is widely assumed that they have distinct physiological roles. In order to investigate the structure-function relationships in these proteins, we have examined the bis-histidyl and ligand-bound hexacoordinated states by atomistic simulations using in silico structural models. The results allow us to identify two main pathways to the distal cavity in the bis-histidyl hexacoordinated proteins. Nevertheless, a larger accessibility to small gaseous molecules is found in AHb2. This effect can be attributed to three factors: the mutation Leu35(AHb1)→Phe32(AHb2), the enhanced flexibility of helix B, and the more favorable energetic profile for ligand migration to the distal cavity. The net effect of these factors would be to facilitate the access of ligands, thus compensating the preference for the fully hexacoordination of AHb2, in contrast to the equilibrium between hexa- and pentacoordinated species in AHb1. On the other hand, binding of the exogenous ligand introduces distinct structural changes in the two proteins. A well-defined tunnel is formed in AHb1, which might be relevant to accomplish the proposed NO detoxification reaction. In contrast, no similar tunnel is found in AHb2, which can be ascribed to the reduced flexibility of helix E imposed by the larger number of salt bridges compared to AHb1. This feature would thus support the storage and transport functions proposed for AHb2. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.
Collapse
Affiliation(s)
- Francesca Spyrakis
- Dipartimento di Scienze degli Alimenti, Università degli Studi di Parma, Parma, Italy.
| | | | | | | | | | | |
Collapse
|
26
|
Morzan UN, Capece L, Marti MA, Estrin DA. Quaternary structure effects on the hexacoordination equilibrium in rice hemoglobin rHb1: Insights from molecular dynamics simulations. Proteins 2013; 81:863-73. [DOI: 10.1002/prot.24245] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 12/11/2012] [Accepted: 12/14/2012] [Indexed: 11/09/2022]
|
27
|
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.
Collapse
Affiliation(s)
- Luca Ronda
- Department of Pharmacy, University of Parma, Parma, Italy
| | | | | | | | | | | | | | | |
Collapse
|
28
|
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.
Collapse
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
| | | | | | | | | | | |
Collapse
|
29
|
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.
Collapse
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
| |
Collapse
|
30
|
Hota KB, Hota SK, Srivastava RB, Singh SB. Neuroglobin regulates hypoxic response of neuronal cells through Hif-1α- and Nrf2-mediated mechanism. J Cereb Blood Flow Metab 2012; 32:1046-60. [PMID: 22472608 PMCID: PMC3367222 DOI: 10.1038/jcbfm.2012.21] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Oxygen sensing in hypoxic neurons has been classically attributed to cytochrome c oxidase and prolyl-4-hydroxylases and involves stabilization of transcription factors, hypoxia-inducible factor-1α (Hif-1α) and nuclear factor erythroid 2-related factor 2 (Nrf2) that mediate survival responses. On the contrary, release of cytochrome c into the cytosol during hypoxic stress triggers apoptosis in neuronal cells. We, here advocate that the redox state of neuroglobin (Ngb) could regulate both Hif-1α and Nrf2 stabilization and cytochrome c release during hypoxia. The hippocampal regions showing higher expression of Ngb were less susceptible to global hypoxia-mediated neurodegeneration. During normoxia, Ngb maintained cytochrome c in the reduced state and prevented its release from mitochondria by using cellular antioxidants. Greater turnover of oxidized cytochrome c and increased utilization of cellular antioxidants during acute hypoxia altered cellular redox status and stabilized Hif-1α and Nrf2 through Ngb-mediated mechanism. Chronic hypoxia, however, resulted in oxidation and degradation of Ngb, accumulation of ferric ions and release of cytochrome c that triggered apoptosis. Administration of N-acetyl-cysteine during hypoxic conditions improved neuronal survival by preventing Ngb oxidation and degradation. Taken together, these results establish a role for Ngb in regulating both the survival and apoptotic mechanisms associated with hypoxia.
Collapse
Affiliation(s)
- Kalpana B Hota
- High Altitude Physiology Laboratory, Defence Institute of High Altitude Research, Jammu and Kashmir, India
| | | | | | | |
Collapse
|
31
|
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]
|
32
|
Boron I, Russo R, Boechi L, Cheng CHC, di Prisco G, Estrin DA, Verde C, Nadra AD. Structure and dynamics of Antarctic fish neuroglobin assessed by computer simulations. IUBMB Life 2011; 63:206-13. [PMID: 21445852 DOI: 10.1002/iub.444] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Neuroglobin (Ngb) is a heme protein, highly conserved along evolution, predominantly found in the nervous system. It is upregulated by hypoxia and ischemia and may have a neuroprotective role under hypoxic stress. Although many other roles have been proposed, the physiological function is still unclear. Antarctic icefishes lack hemoglobin and some species also lack myoglobin, but all have Ngb and thus may help the elucidation of Ngb function. We present the first theoretically derived structure of fish Ngb and describe its behavior using molecular dynamics simulations. Specifically, we sequenced and analyzed Ngbs from a colorless-blooded Antarctic icefish species Chaenocephalus aceratus and a related red-blooded species (Dissostichus mawsoni). Both fish Ngbs are 6-coordinated but have some peculiarities that differentiate them from mammalian counterparts: they have extensions in the N and C termini that can interact with the EF loop, and a gap in the alignment that changes the CD-region structure/dynamics that has been found to play a key role in human neuroglobin. Our results suggest that a single mutation between both fish Ngbs is responsible for significant difference in the behavior of the proteins. The functional role of these characteristics is discussed.
Collapse
Affiliation(s)
- Ignacio Boron
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
| | | | | | | | | | | | | | | |
Collapse
|
33
|
Guardia CMA, Gauto DF, Di Lella S, Rabinovich GA, Martí MA, Estrin DA. An integrated computational analysis of the structure, dynamics, and ligand binding interactions of the human galectin network. J Chem Inf Model 2011; 51:1918-30. [PMID: 21702482 DOI: 10.1021/ci200180h] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Galectins, a family of evolutionarily conserved animal lectins, have been shown to modulate signaling processes leading to inflammation, apoptosis, immunoregulation, and angiogenesis through their ability to interact with poly-N-acetyllactosamine-enriched glycoconjugates. To date 16 human galectin carbohydrate recognition domains have been established by sequence analysis and found to be expressed in several tissues. Given the divergent functions of these lectins, it is of vital importance to understand common and differential features in order to search for specific inhibitors of individual members of the human galectin family. In this work we performed an integrated computational analysis of all individual members of the human galectin family. In the first place, we have built homology-based models for galectin-4 and -12 N-terminus, placental protein 13 (PP13) and PP13-like protein for which no experimental structural information is available. We have then performed classical molecular dynamics simulations of the whole 15 members family in free and ligand-bound states to analyze protein and protein-ligand interaction dynamics. Our results show that all galectins adopt the same fold, and the carbohydrate recognition domains are very similar with structural differences located in specific loops. These differences are reflected in the dynamics characteristics, where mobility differences translate into entropy values which significantly influence their ligand affinity. Thus, ligand selectivity appears to be modulated by subtle differences in the monosaccharide binding sites. Taken together, our results may contribute to the understanding, at a molecular level, of the structural and dynamical determinants that distinguish individual human galectins.
Collapse
Affiliation(s)
- Carlos M A Guardia
- Departamento de Química Inorgánica, Analítica y Química Física, INQUIMAE-CONICET, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, C1428EHA Ciudad de Buenos Aires, Argentina
| | | | | | | | | | | |
Collapse
|
34
|
Mañez PA, Lu C, Boechi L, Martí MA, Shepherd M, Wilson JL, Poole RK, Luque FJ, Yeh SR, Estrin DA. Role of the distal hydrogen-bonding network in regulating oxygen affinity in the truncated hemoglobin III from Campylobacter jejuni. Biochemistry 2011; 50:3946-56. [PMID: 21476539 PMCID: PMC4535342 DOI: 10.1021/bi101137n] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Oxygen affinity in heme-containing proteins is determined by a number of factors, such as the nature and conformation of the distal residues that stabilize the heme bound-oxygen via hydrogen-bonding interactions. The truncated hemoglobin III from Campylobacter jejuni (Ctb) contains three potential hydrogen-bond donors in the distal site: TyrB10, TrpG8, and HisE7. Previous studies suggested that Ctb exhibits an extremely slow oxygen dissociation rate due to an interlaced hydrogen-bonding network involving the three distal residues. Here we have studied the structural and kinetic properties of the G8(WF) mutant of Ctb and employed state-of-the-art computer simulation methods to investigate the properties of the O(2) adduct of the G8(WF) mutant, with respect to those of the wild-type protein and the previously studied E7(HL) and/or B10(YF) mutants. Our data indicate that the unique oxygen binding properties of Ctb are determined by the interplay of hydrogen-bonding interactions between the heme-bound ligand and the surrounding TyrB10, TrpG8, and HisE7 residues.
Collapse
Affiliation(s)
- Pau Arroyo Mañez
- Departamento de Química Inorgánica, Analítica, y Química Fisica, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Ciudad Universitaria, Buenos Aires, Argentina
| | - Changyuan Lu
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Leonardo Boechi
- Departamento de Química Inorgánica, Analítica, y Química Fisica, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Ciudad Universitaria, Buenos Aires, Argentina
| | - Marcelo A. Martí
- Departamento de Química Inorgánica, Analítica, y Química Fisica, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Ciudad Universitaria, Buenos Aires, Argentina
| | - Mark Shepherd
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, United Kingdom
| | - Jayne Louise Wilson
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, United Kingdom
| | - Robert K. Poole
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, United Kingdom
| | - F. Javier Luque
- Department de Fisicoquimica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Spain
| | - Syun-Ru Yeh
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Darío A. Estrin
- Departamento de Química Inorgánica, Analítica, y Química Fisica, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Ciudad Universitaria, Buenos Aires, Argentina
| |
Collapse
|
35
|
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]
|
36
|
Tiso M, Tejero J, Basu S, Azarov I, Wang X, Simplaceanu V, Frizzell S, Jayaraman T, Geary L, Shapiro C, Ho C, Shiva S, Kim-Shapiro DB, Gladwin MT. Human neuroglobin functions as a redox-regulated nitrite reductase. J Biol Chem 2011; 286:18277-89. [PMID: 21296891 DOI: 10.1074/jbc.m110.159541] [Citation(s) in RCA: 216] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Neuroglobin is a highly conserved hemoprotein of uncertain physiological function that evolved from a common ancestor to hemoglobin and myoglobin. It possesses a six-coordinate heme geometry with proximal and distal histidines directly bound to the heme iron, although coordination of the sixth ligand is reversible. We show that deoxygenated human neuroglobin reacts with nitrite to form nitric oxide (NO). This reaction is regulated by redox-sensitive surface thiols, cysteine 55 and 46, which regulate the fraction of the five-coordinated heme, nitrite binding, and NO formation. Replacement of the distal histidine by leucine or glutamine leads to a stable five-coordinated geometry; these neuroglobin mutants reduce nitrite to NO ∼2000 times faster than the wild type, whereas mutation of either Cys-55 or Cys-46 to alanine stabilizes the six-coordinate structure and slows the reaction. Using lentivirus expression systems, we show that the nitrite reductase activity of neuroglobin inhibits cellular respiration via NO binding to cytochrome c oxidase and confirm that the six-to-five-coordinate status of neuroglobin regulates intracellular hypoxic NO-signaling pathways. These studies suggest that neuroglobin may function as a physiological oxidative stress sensor and a post-translationally redox-regulated nitrite reductase that generates NO under six-to-five-coordinate heme pocket control. We hypothesize that the six-coordinate heme globin superfamily may subserve a function as primordial hypoxic and redox-regulated NO-signaling proteins.
Collapse
Affiliation(s)
- Mauro Tiso
- Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Structural insights into a low-spin myoglobin variant with bis-histidine coordination from molecular modeling. Proteins 2010; 79:679-84. [DOI: 10.1002/prot.22928] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Revised: 10/20/2010] [Accepted: 10/25/2010] [Indexed: 11/07/2022]
|
38
|
Arroyo-Mañez P, Bikiel DE, Boechi L, Capece L, Di Lella S, Estrin DA, Martí MA, Moreno DM, Nadra AD, Petruk AA. Protein dynamics and ligand migration interplay as studied by computer simulation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:1054-64. [PMID: 20797453 DOI: 10.1016/j.bbapap.2010.08.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Revised: 08/12/2010] [Accepted: 08/13/2010] [Indexed: 10/19/2022]
Abstract
Since proteins are dynamic systems in living organisms, the employment of methodologies contemplating this crucial characteristic results fundamental to allow revealing several aspects of their function. In this work, we present results obtained using classical mechanical atomistic simulation tools applied to understand the connection between protein dynamics and ligand migration. Firstly, we will present a review of the different sampling schemes used in the last years to obtain both ligand migration pathways and the thermodynamic information associated with the process. Secondly, we will focus on representative examples in which the schemes previously presented are employed, concerning the following: i) ligand migration, tunnels, and cavities in myoglobin and neuroglobin; ii) ligand migration in truncated hemoglobin members; iii) NO escape and conformational changes in nitrophorins; iv) ligand selectivity in catalase and hydrogenase; and v) larger ligand migration: the P450 and haloalkane dehalogenase cases. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
Collapse
Affiliation(s)
- Pau Arroyo-Mañez
- Departamento de Química Inorgánica, Analítica y Química-Física (INQUIMAE-CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
| | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Capece L, Lewis-Ballester A, Batabyal D, Di Russo N, Yeh SR, Estrin DA, Marti MA. The first step of the dioxygenation reaction carried out by tryptophan dioxygenase and indoleamine 2,3-dioxygenase as revealed by quantum mechanical/molecular mechanical studies. J Biol Inorg Chem 2010; 15:811-23. [PMID: 20361220 DOI: 10.1007/s00775-010-0646-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2009] [Accepted: 03/10/2010] [Indexed: 10/19/2022]
Abstract
Tryptophan dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO) are two heme-containing enzymes which catalyze the conversion of L: -tryptophan to N-formylkynurenine (NFK). In mammals, TDO is mostly expressed in liver and is involved in controlling homeostatic serum tryptophan concentrations, whereas IDO is ubiquitous and is involved in modulating immune responses. Previous studies suggested that the first step of the dioxygenase reaction involves the deprotonation of the indoleamine group of the substrate by an evolutionarily conserved distal histidine residue in TDO and the heme-bound dioxygen in IDO. Here, we used classical molecular dynamics and hybrid quantum mechanical/molecular mechanical methods to evaluate the base-catalyzed mechanism. Our data suggest that the deprotonation of the indoleamine group of the substrate by either histidine in TDO or heme-bound dioxygen in IDO is not energetically favorable. Instead, the dioxygenase reaction can be initiated by a direct attack of heme-bound dioxygen on the C(2)=C(3) bond of the indole ring, leading to a protein-stabilized 2,3-alkylperoxide transition state and a ferryl epoxide intermediate, which subsequently recombine to generate NFK. The novel sequential two-step oxygen addition mechanism is fully supported by our recent resonance Raman data that allowed identification of the ferryl intermediate (Lewis-Ballester et al. in Proc Natl Acad Sci USA 106:17371-17376, 2009). The results reveal the subtle differences between the TDO and IDO reactions and highlight the importance of protein matrix in modulating stereoelectronic factors for oxygen activation and the stabilization of both transition and intermediate states.
Collapse
Affiliation(s)
- Luciana Capece
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA, Buenos Aires, Argentina
| | | | | | | | | | | | | |
Collapse
|
40
|
Bocahut A, Bernad S, Sebban P, Sacquin-Mora S. Relating the Diffusion of Small Ligands in Human Neuroglobin to Its Structural and Mechanical Properties. J Phys Chem B 2009; 113:16257-67. [DOI: 10.1021/jp906854x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anthony Bocahut
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France, Laboratoire de Chimie Physique, Université Paris-sud 11, CNRS UMR8000 Bât. 350, 91405 Orsay, France
| | - Sophie Bernad
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France, Laboratoire de Chimie Physique, Université Paris-sud 11, CNRS UMR8000 Bât. 350, 91405 Orsay, France
| | - Pierre Sebban
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France, Laboratoire de Chimie Physique, Université Paris-sud 11, CNRS UMR8000 Bât. 350, 91405 Orsay, France
| | - Sophie Sacquin-Mora
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France, Laboratoire de Chimie Physique, Université Paris-sud 11, CNRS UMR8000 Bât. 350, 91405 Orsay, France
| |
Collapse
|
41
|
Ochiai Y, Ueki N, Watabe S. Effects of point mutations on the structural stability of tuna myoglobins. Comp Biochem Physiol B Biochem Mol Biol 2009; 153:223-8. [PMID: 19285151 DOI: 10.1016/j.cbpb.2009.03.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2009] [Revised: 03/04/2009] [Accepted: 03/04/2009] [Indexed: 11/27/2022]
Abstract
Structural stabilities of myoglobin (Mb) from several tuna fish species significantly differ from each other, although the amino acid sequence identities are very high (>95%), suggesting that limited number of substitutions greatly affect the stability of Mb. To address this hypothesis, attempts were made to elaborate recombinant tuna Mbs with point mutations on the different residues among fish Mbs. The expression plasmid constructs were based on bigeye tuna Mb cDNA sequence, and the recombinant proteins were expressed as GST-fusion proteins in Escherichia coli. After removal of the GST segment and affinity purification, the stability of five Mb mutants, namely, A49G, T91K, K92Q, V108A, and H112Q, together with the wild type (WT) were measured, taking temperature dependency of alpha-helical content and denaturant (urea and guanidine-HCl) concentration dependency of Soret band absorbance as parameters. As a result, the mutant H112Q showed much higher stability than WT, while the structures of K92Q, T91K and A49G mutants were destabilized. No essential change in helical content was observed for V108A, but the mutant was found to be destabilized easier by the denaturants. These findings suggested that the highly conserved residues among tuna species are responsible for their stability of Mbs, but a few non-conserved residues dramatically give rise to the differences in stability of Mbs among species.
Collapse
Affiliation(s)
- Yoshihiro Ochiai
- Laboratory of Aquatic Molecular Biology and Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan.
| | | | | |
Collapse
|