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Numoto N, Onoda S, Kawano Y, Okumura H, Baba S, Fukumori Y, Miki K, Ito N. Structures of oxygen dissociation intermediates of 400 kDa V2 hemoglobin provide coarse snapshots of the protein allostery. Biophys Physicobiol 2022; 19:1-10. [PMID: 35797404 PMCID: PMC9173864 DOI: 10.2142/biophysico.bppb-v19.0019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/09/2022] [Indexed: 12/01/2022] Open
Abstract
Ever since the historic discovery of the cooperative oxygenation of its multiple subunits, hemoglobin (Hb) has been among the most exhaustively studied allosteric proteins. However, the lack of structural information on the intermediates between oxygenated and deoxygenated forms prevents our detailed understanding of the molecular mechanism of its allostery. It has been difficult to prepare crystals of intact oxy-deoxy intermediates and to individually identify the oxygen saturation for each subunit. However, our recent crystallographic studies have demonstrated that giant Hbs from annelids are suitable for overcoming these problems and can provide abundant information on oxy-deoxy intermediate structures. Here, we report the crystal structures of oxy-deoxy intermediates of a 400 kDa Hb (V2Hb) from the annelid Lamellibrachia satsuma, following up on a series of previous studies of similar giant Hbs. Four intermediate structures had average oxygen saturations of 78%, 69%, 55%, and 26%, as determined by the occupancy refinement of the bound oxygen based on ambient temperature factors. The structures demonstrate that the cooperative oxygen dissociation is weaker, large ternary and quaternary changes are induced at a later stage of the oxygen dissociation process, and the ternary and quaternary changes are smaller with local perturbations. Nonetheless, the overall structural transition seemed to proceed in the manner of the MWC two-state model. Our crystallographic snapshots of the allosteric transition of V2Hb provide important experimental evidence for a more detailed understanding of the allostery of Hbs by extension of the Monod–Wyman–Changeux (MWC) model.
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Affiliation(s)
- Nobutaka Numoto
- Medical Research Institute, Tokyo Medical and Dental University (TMDU)
| | - Seiko Onoda
- Graduate School of Natural Science and Technology, Kanazawa University
| | | | - Hideo Okumura
- Structural Biology Division, Japan Synchrotron Radiation Research Institute
| | - Seiki Baba
- Structural Biology Division, Japan Synchrotron Radiation Research Institute
| | | | - Kunio Miki
- Graduate School of Science, Kyoto University
| | - Nobutoshi Ito
- Medical Research Institute, Tokyo Medical and Dental University (TMDU)
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Numoto N, Kawano Y, Okumura H, Baba S, Fukumori Y, Miki K, Ito N. Coarse snapshots of oxygen-dissociation intermediates of a giant hemoglobin elucidated by determining the oxygen saturation in individual subunits in the crystalline state. IUCRJ 2021; 8:954-962. [PMID: 34804547 PMCID: PMC8562662 DOI: 10.1107/s2052252521009386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 09/08/2021] [Indexed: 06/13/2023]
Abstract
Cooperative oxygen binding of hemoglobin (Hb) has been studied for over half a century as a representative example of the allostericity of proteins. The most important problem remaining to be solved is the lack of structural information on the intermediates between the oxygenated and deoxygenated forms. In order to characterize the intermediate structures, it is necessary to obtain intermediate-state crystals, determine their oxygen saturations and then determine the oxygen saturations of each of their constituent subunits, all of which are challenging issues even now. Here, intermediate forms of the 400 kDa giant Hb from the tubeworm Oligobrachia mashikoi are reported. To overcome the above problems without any artificial modifications to the protein or prosthetic groups, intermediate crystals of the giant Hb were prepared from fully oxygenated crystals by a soaking method. The oxygen saturation of the crystals was measured by in situ observation with a microspectrophotometer using thin plate crystals processed by an ultraviolet laser to avoid saturation of absorption. The oxygen saturation of each subunit was determined by occupancy refinement of the bound oxygen based on ambient temperature factors. The obtained structures reveal the detailed relationship between the structural transition and oxygen dissociation. The dimer subassembly of the giant Hb shows strong correlation with the local structural changes at the heme pockets. Although some local ternary-structural changes occur in the early stages of the structural transition, the associated global ternary-structural and quaternary-structural changes might arise at about 50% oxygen saturation. The models based on coarse snapshots of the allosteric transition support the conventional two-state model of Hbs and provide the missing pieces of the intermediate structures that are required for full understanding of the allosteric nature of Hbs in detail.
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Affiliation(s)
- Nobutaka Numoto
- Medical Research Institute, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Yoshiaki Kawano
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Hideo Okumura
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Seiki Baba
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Yoshihiro Fukumori
- Nano Life Science Institute, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Kunio Miki
- Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Nobutoshi Ito
- Medical Research Institute, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
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Carvalho FAO, Alves FR, Tabak M. Ionic surfactants-Glossoscolex paulistus hemoglobin interactions: Characterization of species in the solution. Int J Biol Macromol 2016; 92:670-681. [PMID: 27456123 DOI: 10.1016/j.ijbiomac.2016.07.072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 07/18/2016] [Accepted: 07/21/2016] [Indexed: 12/18/2022]
Abstract
Glossoscolex paulistus hemoglobin (HbGp) is an oligomeric multisubunit protein with molecular mass of 3600kDa. In the current study, the interaction of sodium dodecyl sulfate (SDS) and cetyl trimethylammonium chloride (CTAC) surfactants with the monomer d and the whole oxy-HbGp, at pH 7.0, was investigated. For pure monomer d solution, SDS promotes the dimerization of subunit d, and the monomeric and dimeric forms have sedimentation coefficient values, s20,w, around 2.1-2.4 S and 2.9-3.2 S, respectively. Analytical ultracentrifugation (AUC) and isothermal titration calorimetry (ITC) data suggest that up to 26 DS- anions are bound to the monomer. In the presence of CTAC, only the monomeric form is observed in solution for subunit d. For the oxy-HbGp, SDS induces the dissociation into smaller subunits, such as, monomer d, trimer abc, and tetramer abcd, and unfolding without promoting the protein aggregation. On the other hand, lower CTAC concentration promotes protein aggregation, mainly of trimer, while higher concentration induces the unfolding of dissociated species. Our study provides strong evidence that surfactant effects upon the HbGp-subunits are different, and depend on the surfactant: protein concentration ratio and the charges of surfactant headgroups.
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Affiliation(s)
- Francisco A O Carvalho
- Instituto de Química de São Carlos, Universidade de São Paulo, Brazil; Faculdade de Química, Universidade Federal do Sul e Sudeste do Pará, Brazil.
| | - Fernanda R Alves
- Instituto de Química de São Carlos, Universidade de São Paulo, Brazil
| | - Marcel Tabak
- Instituto de Química de São Carlos, Universidade de São Paulo, Brazil
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Purification, characterization, and crystallization of Crocodylus siamensis hemoglobin. Protein J 2015; 33:377-85. [PMID: 24928538 DOI: 10.1007/s10930-014-9569-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Crocodylus siamensis hemoglobin was purified by a size exclusion chromatography, Sephacryl S-100 with buffer containing dithiothreitol. The purified Hb was dissociated to be two forms (α chain and β chain) which observed by SDS-PAGE, indicated that the C. siamensis Hb was an unpolymerized form. The unpolymerized Hb (composed of two α chains and two β chains) showed high oxygen affinity at 3.13 mmHg (P(50)) and 1.96 (n value), and a small Bohr effect (δH(+) = -0.29) at a pH of 6.9-8.4. Adenosine triphosphate did not affect the oxygenation properties, whereas bicarbonate ions strongly depressed oxygen affinity. Crude C. siamensis Hb solutions were showed high O(2) affinity at P(50) of 2.5 mmHg which may assure efficient utilization of the lung O(2) reserve during breath holding and diving. The purified Hbs were changed to cyanmethemoglobin forms prior crystallization. Rod- and plate-shaped crystals were obtained by the sitting-drop vapor-diffusion method at 5 °C using equal volumes of protein solution (37 mg/ml) and reservoir [10-13 % (w/v) PEG 4000, with 0.1 M Tris buffer in present of 0.2 M MgCl(2)·6H(2)O] solution at a pH of 7.0-8.5.
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Carvalho FAO, Alves FR, Carvalho JWP, Tabak M. Guanidine hydrochloride and urea effects upon thermal stability of Glossoscolex paulistus hemoglobin (HbGp). Int J Biol Macromol 2014; 74:18-28. [PMID: 25433131 DOI: 10.1016/j.ijbiomac.2014.11.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 11/17/2014] [Accepted: 11/19/2014] [Indexed: 11/16/2022]
Abstract
Glossoscolex paulistus hemoglobin (HbGp) has a molecular mass of 3600kDa. It belongs to the hexagonal bilayer hemoglobin class, which consists of highly cooperative respiratory macromolecules found in mollusks and annelids. The present work focusses on oxy-HbGp thermal stability, in the presence of urea and guanidine hydrochloride (GuHCl), monitored by several techniques. Initially, dynamic light scattering data show that the presence of GuHCl induces the protein oligomeric dissociation, followed by a significant 11-fold increase in the hydrodynamic diameter (DH) values, due to the formation of protein aggregates in solution. In contrast, urea promotes the HbGp oligomeric dissociation, followed by unfolding process at high temperatures, without aggregation. Circular dichroism data show that unfolding critical temperature (Tc) of oxy-HbGp decreases from 57°C, at 0.0 mol/L of the denaturant, to 45°C, in the presence of 3.5 mol/L of urea, suggesting the reduction of HbGp oligomeric stability. Moreover, differential scanning calorimetry results show that at lower GuHCl concentrations, some thermal stabilization of the hemoglobin is observed, whereas at higher concentrations, the reduction of stability takes place. Besides, HbGp is more stable in the presence of urea when compared with the guanidine effect, as deduced from the differences in the concentration range of denaturants.
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Affiliation(s)
| | - Fernanda R Alves
- Instituto de Química de São Carlos-Universidade de São Paulo, Brazil
| | - José W P Carvalho
- Instituto de Química de São Carlos-Universidade de São Paulo, Brazil; Universidade do Estado de Mato Grosso, MT, Brazil
| | - Marcel Tabak
- Instituto de Química de São Carlos-Universidade de São Paulo, Brazil
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Numoto N, Nakagawa T, Ohara R, Hasegawa T, Kita A, Yoshida T, Maruyama T, Imai K, Fukumori Y, Miki K. The structure of a deoxygenated 400 kDa haemoglobin reveals ternary- and quaternary-structural changes of giant haemoglobins. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:1823-31. [PMID: 25004960 DOI: 10.1107/s1399004714008475] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Accepted: 04/14/2014] [Indexed: 11/10/2022]
Abstract
The quaternary structures of invertebrate haemoglobins (Hbs) are quite different from those of vertebrate Hbs. The extracellular giant Hbs of molecular masses of about 400 and 3600 kDa are composed of a dome-shaped dodecameric subassembly which consists of four individual globin subunits. Several crystal structures of 400 kDa Hbs from annelids have been reported, including structures in oxygenated and partially unliganded states, but the structure of the fully deoxygenated state has not been reported. In the present study, crystal structures of V2Hb from the tube worm Lamellibrachia satsuma have been determined in both the fully oxygenated and deoxygenated states. A glycosylation site and novel metal-binding sites for divalent cations were clearly observed with no intersubunit interactions in V2Hb. A comparison of the oxygenated and the deoxygenated forms of V2Hb reveals that the ternary- and quaternary-structural changes occur in a manner that maintains the molecular D3 symmetry. These structures suggest that the mechanisms of quaternary-structural changes between the oxy and deoxy states for the giant Hbs are identical across species.
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Affiliation(s)
- Nobutaka Numoto
- Department of Life Science, Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Taro Nakagawa
- Department of Life Science, Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Ryota Ohara
- Department of Life Science, Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Tomoyo Hasegawa
- Department of Life Science, Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Akiko Kita
- Research Reactor Institute, Kyoto University, Kumatori, Osaka 590-0494, Japan
| | - Takao Yoshida
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Tadashi Maruyama
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Kiyohiro Imai
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo 184-0003, Japan
| | - Yoshihiro Fukumori
- Department of Life Science, Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Kunio Miki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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Tertiary and quaternary effects in the allosteric regulation of animal hemoglobins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1860-72. [PMID: 23523886 DOI: 10.1016/j.bbapap.2013.03.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 03/07/2013] [Accepted: 03/08/2013] [Indexed: 12/16/2022]
Abstract
In the last decade, protein allostery has experienced a major resurgence, boosted by the extension of the concept to systems of increasing complexity and by its exploitation for the development of drugs. Expansion of the field into new directions has not diminished the key role of hemoglobin as a test molecule for theory and experimental validation of allosteric models. Indeed, the diffusion of hemoglobins in all kingdoms of life and the variety of functions and of quaternary assemblies based on a common tertiary fold indicate that this superfamily of proteins is ideally suited for investigating the physical and molecular basis of allostery and firmly maintains its role as a main player in the field. This review is an attempt to briefly recollect common and different strategies adopted by metazoan hemoglobins, from monomeric molecules to giant complexes, exploiting homotropic and heterotropic allostery to increase their functional dynamic range. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.
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Moreira LM, Poli AL, Lyon JP, Aimbire F, Toledo JC, Costa-Filho AJ, Imasato H. Ligand changes in ferric species of the giant extracellular hemoglobin of Glossoscolex paulistusas function of pH: correlations between redox, spectroscopic and oligomeric properties and general implications with different hemoproteins. J PORPHYR PHTHALOCYA 2012. [DOI: 10.1142/s108842461000201x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The present review is focused on the relationship between oligomeric and heme properties of HbGp, emphasizing the characteristics that can be generalized to other hemoproteins. This study represents the state-of-the-art with respect to the approaches for investigating giant extracellular hemoglobins as well as the correlation between oligomeric assembly alterations and their consequent changes in the first coordination sphere. A wide introduction focused on the properties of this hemoglobin is developed. Indeed, this hemoprotein is considered an interesting prototype of blood substitute and biosensor due to its peculiar properties, such as resistance to autoxidation and oligomeric stability. Previous studies by our group employing UV-vis, EPR and CD spectroscopies have been revised in a complete approach, in agreement with recent and relevant data from the literature. In fact, a consistent and inter-related spectroscopic study is described propitiating a wide assignment of "fingerprint" peaks found in the techniques evaluated in this paper. This review furnishes physicochemical information regarding the identification of ferric heme species of hemoproteins and metallic complexes through their spectroscopic bands. This effort at the attribution of UV-vis, EPR and CD peaks is not restricted to HbGp, and includes a comparative analysis of several hemoproteins involving relevant implications regarding several types of iron-porphyrin systems.
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Affiliation(s)
- Leonardo Marmo Moreira
- Instituto de Pesquisa e Desenvolvimento, Universidade do Vale do Paraíba, 12244-000 São José dos Campos SP, Brazil
- Instituto de Química de São Carlos, Universidade de São Paulo, 13560-970 São Carlos SP, Brazil
- Instituto de Pesquisa e Qualidade Acadêmica (IPQA), Universidade Camilo Castelo Branco, São José dos Campos SP, Brazil
| | - Alessandra Lima Poli
- Instituto de Química de São Carlos, Universidade de São Paulo, 13560-970 São Carlos SP, Brazil
| | - Juliana Pereira Lyon
- Instituto de Pesquisa e Desenvolvimento, Universidade do Vale do Paraíba, 12244-000 São José dos Campos SP, Brazil
| | - Flávio Aimbire
- Instituto de Pesquisa e Desenvolvimento, Universidade do Vale do Paraíba, 12244-000 São José dos Campos SP, Brazil
- Instituto de Pesquisa e Qualidade Acadêmica (IPQA), Universidade Camilo Castelo Branco, São José dos Campos SP, Brazil
| | | | | | - Hidetake Imasato
- Instituto de Química de São Carlos, Universidade de São Paulo, 13560-970 São Carlos SP, Brazil
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Nakahama S, Nakagawa T, Kanemori M, Fukumori Y, Sasayama Y. Direct evidence that extracellular giant hemoglobin is produced in chloragogen tissues in a beard worm, Oligobrachia mashikoi (Frenulata, Siboglinidae, Annelida). Zoolog Sci 2009; 25:1247-52. [PMID: 19267652 DOI: 10.2108/zsj.25.1247] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In Oligobrachia mashikoi, a mouthless and gutless polychaete known as a beard worm, sites of production of extra-cellular giant hemoglobin were examined with whole-mount in-situ hybridization and semi-quantitative RT-PCR. An RNA probe was prepared from mRNA of the A2-globin subunit. Clear signals were obtained from a peritoneal membrane covering the trophosome in the posterior body in all seven individuals examined in this study. In addition, weak signals were observed in the peritoneal membrane covering tissues in the middle part of the body in some individuals. Furthermore, in one individual, signals were obtained in complicated bodies invaginated into the dorsal vessel from a peritoneal membrane that also released signals. The results of RT-PCR regarding the expression levels of four kinds of globin-subunit genes suggest that the main site of hemoglobin production is the peritoneal membrane in the posterior body.
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Affiliation(s)
- Shigeyuki Nakahama
- Department of Life Science, Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa 920-1192, Japan
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Numoto N, Nakagawa T, Kita A, Sasayama Y, Fukumori Y, Miki K. Structural basis for the heterotropic and homotropic interactions of invertebrate giant hemoglobin. Biochemistry 2008; 47:11231-8. [PMID: 18834142 DOI: 10.1021/bi8012609] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The oxygen binding properties of extracellular giant hemoglobins (Hbs) in some annelids exhibit features significantly different from those of vertebrate tetrameric Hbs. Annelid giant Hbs show cooperative oxygen binding properties in the presence of inorganic cations, while the cooperativities of vertebrate Hbs are enhanced by small organic anions or chloride ions. To elucidate the structural basis for the cation-mediated cooperative mechanisms of these giant Hbs, we determined the crystal structures of Ca2+- and Mg2+-bound Hbs from Oligobrachia mashikoi at 1.6 and 1.7 A resolution, respectively. Both of the metal-bound structures were determined in the oxygenated state. Four Ca2+-binding sites and one Mg2+-binding site were identified in each tetramer subassembly. These cations are considered to stabilize the oxygenated form and increase affinity and cooperativity for oxygen binding, as almost all of the Ca2+ and Mg2+ cations were bound at the interface regions, forming either direct or hydrogen bond-mediated interactions with the neighboring subunits. A comparison of the structures of the oxygenated form and the partially unliganded form provides structural insight into proton-coupled cooperativity (Bohr effect) and ligand-induced transitions. Two histidine residues are assumed to be primarily associated with the Bohr effect. With regard to the ligand-induced cooperativity, a novel quaternary rotation mechanism is proposed to exist at the interface region of the dimer subassembly. Interactions among conserved residues Arg E10, His F3, Gln F7, and Val E11, together with the bending motion of the heme molecules, appear to be essential for quaternary rearrangement.
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Affiliation(s)
- Nobutaka Numoto
- Department of Chemistry, Graduate School of Science, Kyoto UniVersity, Sakyo-ku, Kyoto 606-8502, Japan
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Moreira LM, Poli AL, Lyon JP, Saade J, Costa-Filho AJ, Imasato H. Ferric species of the giant extracellular hemoglobin of Glossoscolex paulistus as function of pH: An EPR study on the irreversibility of the heme transitions. Comp Biochem Physiol B Biochem Mol Biol 2008; 150:292-300. [DOI: 10.1016/j.cbpb.2008.03.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2008] [Revised: 03/19/2008] [Accepted: 03/21/2008] [Indexed: 10/22/2022]
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