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Yu F, Wang Z, Zhang Z, Zhou J, Li J, Chen J, Du G, Zhao X. Biosynthesis, acquisition, regulation, and upcycling of heme: recent advances. Crit Rev Biotechnol 2024; 44:1422-1438. [PMID: 38228501 DOI: 10.1080/07388551.2023.2291339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/10/2023] [Accepted: 11/25/2023] [Indexed: 01/18/2024]
Abstract
Heme, an iron-containing tetrapyrrole in hemoproteins, including: hemoglobin, myoglobin, catalase, cytochrome c, and cytochrome P450, plays critical physiological roles in different organisms. Heme-derived chemicals, such as biliverdin, bilirubin, and phycocyanobilin, are known for their antioxidant and anti-inflammatory properties and have shown great potential in fighting viruses and diseases. Therefore, more and more attention has been paid to the biosynthesis of hemoproteins and heme derivatives, which depends on the adequate heme supply in various microbial cell factories. The enhancement of endogenous biosynthesis and exogenous uptake can improve the intracellular heme supply, but the excess free heme is toxic to the cells. Therefore, based on the heme-responsive regulators, several sensitive biosensors were developed to fine-tune the intracellular levels of heme. In this review, recent advances in the: biosynthesis, acquisition, regulation, and upcycling of heme were summarized to provide a solid foundation for the efficient production and application of high-value-added hemoproteins and heme derivatives.
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Affiliation(s)
- Fei Yu
- Science Center for Future Foods, Jiangnan University, Wuxi, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
| | - Ziwei Wang
- Science Center for Future Foods, Jiangnan University, Wuxi, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
| | - Zihan Zhang
- Science Center for Future Foods, Jiangnan University, Wuxi, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
| | - Jingwen Zhou
- Science Center for Future Foods, Jiangnan University, Wuxi, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
| | - Jianghua Li
- Science Center for Future Foods, Jiangnan University, Wuxi, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
| | - Jian Chen
- Science Center for Future Foods, Jiangnan University, Wuxi, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
| | - Guocheng Du
- Science Center for Future Foods, Jiangnan University, Wuxi, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Xinrui Zhao
- Science Center for Future Foods, Jiangnan University, Wuxi, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
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Zhou X, Su W, Bao Q, Cui Y, Li X, Yang Y, Yang C, Wang C, Jiao L, Chen D, Huang J. Nitric Oxide Ameliorates the Effects of Hypoxia in Mice by Regulating Oxygen Transport by Hemoglobin. High Alt Med Biol 2024; 25:174-185. [PMID: 38743636 DOI: 10.1089/ham.2023.0044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024] Open
Abstract
Xiaoying Zhou, Wenting Su, Quanwei Bao, Yu Cui, Xiaoxu Li, Yidong Yang, Chengzhong Yang, Chengyuan Wang, Li Jiao, Dewei Chen, and Jian Huang. Nitric oxide ameliorates the effects of hypoxia in mice by regulating oxygen transport by hemoglobin. High Alt Med Biol. 25:174-185, 2024.-Hypoxia is a common pathological and physiological phenomenon in ischemia, cancer, and strenuous exercise. Nitric oxide (NO) acts as an endothelium-derived relaxing factor in hypoxic vasodilation and serves as an allosteric regulator of hemoglobin (Hb). However, the ultimate effects of NO on the hematological system in vivo remain unknown, especially in extreme environmental hypoxia. Whether NO regulation of the structure of Hb improves oxygen transport remains unclear. Hence, we examined whether NO altered the oxygen affinity of Hb (Hb-O2 affinity) to protect extremely hypoxic mice. Mice were exposed to severe hypoxia with various concentrations of NO, and the survival time, exercise capacity, and other physical indexes were recorded. The survival time was prolonged in the 5 ppm NO (6.09 ± 1.29 minutes) and 10 ppm NO (6.39 ± 1.58 minutes) groups compared with the 0 ppm group (4.98 ± 1.23 minutes). Hypoxia of the brain was relieved, and the exercise exhaustion time was prolonged when mice inhaled 20 ppm NO (24.70 ± 6.87 minutes vs. 20.23 ± 6.51 minutes). In addition, the differences in arterial oxygen saturation (SO2%) (49.64 ± 7.29% vs. 42.90 ± 4.30%) and arteriovenous SO2% difference (25.14 ± 8.95% vs. 18.10 ± 6.90%) obviously increased. In ex vivo experiments, the oxygen equilibrium curve (OEC) left shifted as P50 decreased from 43.77 ± 2.49 mmHg (0 ppm NO) to 40.97 ± 1.40 mmHg (100 ppm NO) and 38.36 ± 2.78 mmHg (200 ppm NO). Furthermore, the Bohr effect of Hb was enhanced by the introduction of 200 ppm NO (-0.72 ± 0.062 vs.-0.65 ± 0.051), possibly allowing Hb to more easily offload oxygen in tissue at lower pH. The crystal structure reveals a greater distance between Asp94β-His146β in nitrosyl -Hb(NO-Hb), NO-HbβCSO93, and S-NitrosoHb(SNO-Hb) compared to tense Hb(T-Hb, 3.7 Å, 4.3 Å, and 5.8 Å respectively, versus 3.5 Å for T-Hb). Moreover, hydrogen bonds were less likely to form, representing a key limitation of relaxed Hb (R-Hb). Upon NO interaction with Hb, hydrogen bonds and salt bridges were less favored, facilitating relaxation. We speculated that NO ameliorated the effects of hypoxia in mice by promoting erythrocyte oxygen loading in the lung and offloading in tissues.
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Affiliation(s)
- Xiaoying Zhou
- Department of High Altitude Physiology and Pathology, College of High Altitude Military Medicine, Army Medical University, Chongqing, China
- High Altitude Medical Research Center, PLA, Chongqing, China
- Key Laboratory of High Altitude and Frigidzone Medical Surpport, PLA, Chongqing, China
- Key Laboratory of Extreme Environmental Medicine, Ministry of Education, Chongqing, China
| | - Wenting Su
- Department of High Altitude Physiology and Pathology, College of High Altitude Military Medicine, Army Medical University, Chongqing, China
- High Altitude Medical Research Center, PLA, Chongqing, China
- Key Laboratory of High Altitude and Frigidzone Medical Surpport, PLA, Chongqing, China
- Key Laboratory of Extreme Environmental Medicine, Ministry of Education, Chongqing, China
| | - Quanwei Bao
- Department of Emergency Medicine, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Yu Cui
- Department of High Altitude Physiology and Pathology, College of High Altitude Military Medicine, Army Medical University, Chongqing, China
- High Altitude Medical Research Center, PLA, Chongqing, China
- Key Laboratory of High Altitude and Frigidzone Medical Surpport, PLA, Chongqing, China
- Key Laboratory of Extreme Environmental Medicine, Ministry of Education, Chongqing, China
| | - Xiaoxu Li
- Department of High Altitude Physiology and Pathology, College of High Altitude Military Medicine, Army Medical University, Chongqing, China
- High Altitude Medical Research Center, PLA, Chongqing, China
- Key Laboratory of High Altitude and Frigidzone Medical Surpport, PLA, Chongqing, China
- Key Laboratory of Extreme Environmental Medicine, Ministry of Education, Chongqing, China
| | - Yidong Yang
- Department of High Altitude Physiology and Pathology, College of High Altitude Military Medicine, Army Medical University, Chongqing, China
- High Altitude Medical Research Center, PLA, Chongqing, China
- Key Laboratory of High Altitude and Frigidzone Medical Surpport, PLA, Chongqing, China
- Key Laboratory of Extreme Environmental Medicine, Ministry of Education, Chongqing, China
| | - Chengzhong Yang
- Department of High Altitude Physiology and Pathology, College of High Altitude Military Medicine, Army Medical University, Chongqing, China
- High Altitude Medical Research Center, PLA, Chongqing, China
- Key Laboratory of High Altitude and Frigidzone Medical Surpport, PLA, Chongqing, China
- Key Laboratory of Extreme Environmental Medicine, Ministry of Education, Chongqing, China
| | - Chengyuan Wang
- Department of High Altitude Physiology and Pathology, College of High Altitude Military Medicine, Army Medical University, Chongqing, China
- High Altitude Medical Research Center, PLA, Chongqing, China
- Key Laboratory of High Altitude and Frigidzone Medical Surpport, PLA, Chongqing, China
- Key Laboratory of Extreme Environmental Medicine, Ministry of Education, Chongqing, China
| | - Li Jiao
- Department of High Altitude Physiology and Pathology, College of High Altitude Military Medicine, Army Medical University, Chongqing, China
- High Altitude Medical Research Center, PLA, Chongqing, China
- Key Laboratory of High Altitude and Frigidzone Medical Surpport, PLA, Chongqing, China
- Key Laboratory of Extreme Environmental Medicine, Ministry of Education, Chongqing, China
| | - Dewei Chen
- Department of High Altitude Physiology and Pathology, College of High Altitude Military Medicine, Army Medical University, Chongqing, China
- High Altitude Medical Research Center, PLA, Chongqing, China
- Key Laboratory of High Altitude and Frigidzone Medical Surpport, PLA, Chongqing, China
- Key Laboratory of Extreme Environmental Medicine, Ministry of Education, Chongqing, China
| | - Jian Huang
- Department of High Altitude Physiology and Pathology, College of High Altitude Military Medicine, Army Medical University, Chongqing, China
- High Altitude Medical Research Center, PLA, Chongqing, China
- Key Laboratory of High Altitude and Frigidzone Medical Surpport, PLA, Chongqing, China
- Key Laboratory of Extreme Environmental Medicine, Ministry of Education, Chongqing, China
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De Simone G, di Masi A, Sbardella D, Ascenzi P, Coletta M. Nitric Oxide Binding Geometry in Heme-Proteins: Relevance for Signal Transduction. Antioxidants (Basel) 2024; 13:666. [PMID: 38929104 PMCID: PMC11201058 DOI: 10.3390/antiox13060666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024] Open
Abstract
Nitric oxide (NO) synthesis, signaling, and scavenging is associated to relevant physiological and pathological events. In all tissues and organs, NO levels and related functions are regulated at different levels, with heme proteins playing pivotal roles. Here, we focus on the structural changes related to the different binding modes of NO to heme-Fe(II), as well as the modulatory effects of this diatomic messenger on heme-protein functions. Specifically, the ability of heme proteins to bind NO at either the distal or proximal side of the heme and the transient interchanging of the binding site is reported. This sheds light on the regulation of O2 supply to tissues with high metabolic activity, such as the retina, where a precise regulation of blood flow is necessary to meet the demand of nutrients.
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Affiliation(s)
- Giovanna De Simone
- Dipartimento di Scienze, Università degli Studi Roma Tre, 00146 Rome, Italy; (G.D.S.); (A.d.M.)
| | - Alessandra di Masi
- Dipartimento di Scienze, Università degli Studi Roma Tre, 00146 Rome, Italy; (G.D.S.); (A.d.M.)
- Centro Linceo Interdisciplinare “Beniamino Segre”, Accademia dei Lincei, 00165 Rome, Italy
| | | | - Paolo Ascenzi
- Dipartimento di Scienze, Università degli Studi Roma Tre, 00146 Rome, Italy; (G.D.S.); (A.d.M.)
- Accademia Nazionale dei Lincei, 00165 Rome, Italy
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Giraudon--Colas G, Devineau S, Marichal L, Barruet E, Zitolo A, Renault JP, Pin S. How Nanoparticles Modify Adsorbed Proteins: Impact of Silica Nanoparticles on the Hemoglobin Active Site. Int J Mol Sci 2023; 24:3659. [PMID: 36835069 PMCID: PMC9967434 DOI: 10.3390/ijms24043659] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
The adsorption of proteins on surfaces has been studied for a long time, but the relationship between the structural and functional properties of the adsorbed protein and the adsorption mechanism remains unclear. Using hemoglobin adsorbed on silica nanoparticles, we have previously shown that hemoglobin's affinity towards oxygen increases with adsorption. Nevertheless, it was also shown that there were no significant changes in the quaternary and secondary structures. In order to understand the change in activity, we decided in this work to focus on the active sites of hemoglobin, the heme and its iron. After measuring adsorption isotherms of porcine hemoglobin on Ludox silica nanoparticles, we analyzed the structural modifications of adsorbed hemoglobin by X-ray absorption spectroscopy and circular dichroism spectra in the Soret region. It was found that upon adsorption, there were modifications in the heme pocket environment due to changes in the angles of the heme vinyl functions. These alterations can explain the greater affinity observed.
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Affiliation(s)
| | - Stéphanie Devineau
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, 75013 Paris, France
| | - Laurent Marichal
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91191 Gif-sur-Yvette, France
| | - Elodie Barruet
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91191 Gif-sur-Yvette, France
| | - Andrea Zitolo
- Synchrotron SOLEIL, L’Orme des Merisiers, BP 48 Saint Aubin, 91192 Gif-sur-Yvette, France
| | | | - Serge Pin
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91191 Gif-sur-Yvette, France
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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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Kurisaki I, Tanaka S. Elucidating microscopic events driven by GTP hydrolysis reaction in the Ras-GAP system with semi-reactive molecular dynamics simulations: the alternative role of a phosphate binding loop for mechanical energy storage. Phys Chem Chem Phys 2021; 23:26151-26164. [PMID: 34797363 DOI: 10.1039/d1cp04061h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
ATPase and GTPase have been widely found as chemical energy-mechanical work transducers, whereas the physicochemical mechanisms are not satisfactorily understood. We addressed the problem by examining John Ross' conjecture that repulsive Coulomb interaction between ADP/GDP and inorganic phosphate (Pi) does the mechanical work upon the system. We effectively simulated the consequence of a GTP hydrolysis reaction in a complex system of Rat sarcoma (Ras) and GTPase activation protein (GAP) in the framework of classical molecular dynamics by switching force field parameters between the reactant and product systems. We then observed a ca. 5 kcal mol-1 increase of potential energy about the phosphate-binding loop (P-loop) in the Ras protein, indicating that the mechanical work generated via the GTP hydrolysis is converted into the local interaction energy and stored in the P-loop. Interestingly, this local energy storage in the P-loop depends on neither impulsive nor consecutive collisions of GDP and Pi with the P-loop. Instead, GTP-GDP conversion itself does work on the Ras system, elevating the potential energy. These observations encourage us to challenge a conjecture previously given by Ross. We assert that triphosphate nucleotide hydrolyses do mechanical work by producing emergent steric interaction accompanied by relaxation, namely, a shift of the biomolecular system to the non-equilibrium state on the reshaped potential energy landscape. Recalling the universality of the P-loop motif among GTPases and ATPases, the observations that we obtained through this study would progress the physicochemical understanding of the operating principles of GTP/ATP hydrolysis-driven biological nano-machines.
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Affiliation(s)
- Ikuo Kurisaki
- Department of Computational Science, Graduate School of System Informatics, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan.
| | - Shigenori Tanaka
- Department of Computational Science, Graduate School of System Informatics, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan.
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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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8
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Olson JS. Kinetic mechanisms for O 2 binding to myoglobins and hemoglobins. Mol Aspects Med 2021; 84:101024. [PMID: 34544605 DOI: 10.1016/j.mam.2021.101024] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/06/2021] [Accepted: 09/12/2021] [Indexed: 11/29/2022]
Abstract
Antonini and Brunori's 1971 book "Hemoglobin and Myoglobin in Their Reactions with Ligands" was a truly remarkable publication that summarized almost 100 years of research on O2 binding to these globins. Over the ensuing 50 years, ultra-fast laser photolysis techniques, high-resolution and time resolved X-ray crystallography, molecular dynamics simulations, and libraries of recombinant myoglobin (Mb) and hemoglobin (Hb) variants have provided structural interpretations of O2 binding to these proteins. The resultant mechanisms provide quantitative descriptions of the stereochemical factors that govern overall affinity, including proximal and distal steric restrictions that affect iron reactivity and favorable positive electrostatic interactions that preferentially stabilize bound O2. The pathway for O2 uptake and release by Mb and subunits of Hb has been mapped by screening libraries of site-directed mutants in laser photolysis experiments. O2 enters mammalian Mb and the α and β subunits of human HbA through a channel created by upward and outward rotation of the distal His at the E7 helical position, is non-covalently captured in the interior of the distal cavity, and then internally forms a bond with the heme Fe(II) atom. O2 dissociation is governed by disruption of hydrogen bonding interactions with His (E7), breakage of the Fe(II)-O2 bond, and then competition between rebinding and escape through the E7-gate. The structural features that govern the rates of both the individual steps and overall reactions have been determined and provide the framework for: (1) defining the physiological functions of specific globins and their evolution; (2) understanding the clinical features of hemoglobinopathies; and (3) designing safer and more efficient acellular hemoglobin-based oxygen carriers (HBOCs) for transfusion therapy, organ preservation, and other commercially relevant O2 transport and storage processes.
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Affiliation(s)
- John S Olson
- Department of Biosciences, Rice University, Houston, TX, 77005, USA.
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9
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Lepeshkevich SV, Sazanovich IV, Parkhats MV, Gilevich SN, Dzhagarov BM. Towards understanding non-equivalence of α and β subunits within human hemoglobin in conformational relaxation and molecular oxygen rebinding. Chem Sci 2021; 12:7033-7047. [PMID: 34123331 PMCID: PMC8153241 DOI: 10.1039/d1sc00712b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Picosecond to millisecond laser time-resolved transient absorption spectroscopy was used to study molecular oxygen (O2) rebinding and conformational relaxation following O2 photodissociation in the α and β subunits within human hemoglobin in the quaternary R-like structure. Oxy-cyanomet valency hybrids, α2(Fe2+-O2)β2(Fe3+-CN) and α2(Fe3+-CN)β2(Fe2+-O2), were used as models for oxygenated R-state hemoglobin. An extended kinetic model for geminate O2 rebinding in the ferrous hemoglobin subunits, ligand migration between the primary and secondary docking site(s), and nonexponential tertiary relaxation within the R quaternary structure, was introduced and discussed. Significant functional non-equivalence of the α and β subunits in both the geminate O2 rebinding and concomitant structural relaxation was revealed. For the β subunits, the rate constant for the geminate O2 rebinding to the unrelaxed tertiary structure and the tertiary transition rate were found to be greater than the corresponding values for the α subunits. The conformational relaxation following the O2 photodissociation in the α and β subunits was found to decrease the rate constant for the geminate O2 rebinding, this effect being more than one order of magnitude greater for the β subunits than for the α subunits. Evidence was provided for the modulation of the O2 rebinding to the individual α and β subunits within human hemoglobin in the R-state structure by the intrinsic heme reactivity through a change in proximal constraints upon the relaxation of the tertiary structure on a picosecond to microsecond time scale. Our results demonstrate that, for native R-state oxyhemoglobin, O2 rebinding properties and spectral changes following the O2 photodissociation can be adequately described as the sum of those for the α and β subunits within the valency hybrids. The isolated β chains (hemoglobin H) show similar behavior to the β subunits within the valency hybrids and can be used as a model for the β subunits within the R-state oxyhemoglobin. At the same time, the isolated α chains behave differently to the α subunits within the valency hybrids.
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Affiliation(s)
- Sergei V Lepeshkevich
- B. I. Stepanov Institute of Physics, National Academy of Sciences of Belarus 68 Nezavisimosti Ave Minsk 220072 Belarus
| | - Igor V Sazanovich
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory Harwell Campus OX11 0QX UK
| | - Marina V Parkhats
- B. I. Stepanov Institute of Physics, National Academy of Sciences of Belarus 68 Nezavisimosti Ave Minsk 220072 Belarus
| | - Syargey N Gilevich
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus 5 Academician V. F. Kuprevich Street Minsk 220141 Belarus
| | - Boris M Dzhagarov
- B. I. Stepanov Institute of Physics, National Academy of Sciences of Belarus 68 Nezavisimosti Ave Minsk 220072 Belarus
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Morita Y, Saito A, Yamaguchi J, Komatsu T. Haemoglobin(βK120C)-albumin trimer as an artificial O 2 carrier with sufficient haemoglobin allostery. RSC Chem Biol 2020; 1:128-136. [PMID: 34458753 PMCID: PMC8341959 DOI: 10.1039/d0cb00056f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 06/25/2020] [Indexed: 11/21/2022] Open
Abstract
The allosteric O2 release of haemoglobin (Hb) allows for efficient O2 delivery from the lungs to the tissues. However, allostery is weakened in Hb-based O2 carriers because the chemical modifications of the Lys- and Cys-β93 residues prevent the quaternary transition of Hb. In this paper, we describe the synthesis and O2 binding properties of a recombinant Hb [rHb(βK120C)]–albumin heterotrimer that maintains sufficient Hb allostery. The rHb(βK120C) core, with two additional cysteine residues at the symmetrical positions on its protein surface, was expressed using yeast cells. The mutations did not influence either the O2 binding characteristics or the quaternary transition of Hb. Maleimide-activated human serum albumins (HSAs) were coupled with rHb(βK120C) at the two Cys-β120 positions, yielding the rHb(βK120C)–HSA2 trimer, in which the Cys-β93 residues were unreacted. Molecular dynamics simulation demonstrated that the HSA moiety does not interact with the amino acid residues around the haem pockets and the α1β2 surfaces of the rHb(βK120C) core, the alteration of which retards Hb allostery. Circular dichroism spectroscopy demonstrated that the quaternary transition between the relaxed (R) state and the tense (T) state of the Hb core occurred upon both the association and dissociation of O2. In phosphate-buffered saline solution (pH 7.4) at 37 °C, the rHb(βK120C)–HSA2 trimer exhibited a sigmoidal O2 equilibrium curve with the O2 affinity and cooperativity identical to those of native Hb (p50 = 12 Torr, n = 2.4). Moreover, we observed an equal Bohr effect and 2,3-diphosphoglycerate response in the rHb(βK120C)–HSA2 trimer compared with naked Hb. Recombinant haemoglobin [rHb(βK120C)] was coupled with two human serum albumins (HSAs), yielding a rHb(βK120C)–HSA2 heterotrimer, which shows a sigmoidal O2 equilibrium curve and sufficient Hb allostery identical to those of native Hb.![]()
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Affiliation(s)
- Yoshitsugu Morita
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku Tokyo 112-8551 Japan
| | - Asuka Saito
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku Tokyo 112-8551 Japan
| | - Jun Yamaguchi
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku Tokyo 112-8551 Japan
| | - Teruyuki Komatsu
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku Tokyo 112-8551 Japan
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