1
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Kondo HX, Fujii M, Tanioka T, Kanematsu Y, Yoshida T, Takano Y. Global Analysis of Heme Proteins Elucidates the Correlation between Heme Distortion and the Heme-Binding Pocket. J Chem Inf Model 2022; 62:775-784. [PMID: 35157473 DOI: 10.1021/acs.jcim.1c01315] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Heme proteins play diverse and important biological roles, from electron transfer and chemical catalysis to oxygen transport and/or storage. Although the distortion of heme porphyrin correlates with the physical properties of heme, such as the redox potential and oxygen affinity, the relationship between heme distortion and the heme protein environment is unclear. Here, we tested the hypothesis that the protein environment of the heme-binding pocket determines heme distortion (conformation). We analyzed the correlations between the amino acid composition of the heme-binding pocket and the magnitude of heme distortion along 12 vibrational modes using machine learning. A correlation was detected in the three lowest vibrational modes. Analysis of heme distortions in nearly the same environments of the heme-binding pocket supported this notion. Our analyses indicate that the heme-binding pocket environment is a major factor impacting the distortion of heme porphyrin along the three lowest vibrational modes. In addition, statistical analysis of the distortion of heme porphyrin revealed that the peaks of distributions of the ruffling and breathing distortions are shifted from 0 (the equilibrium structure). Both the ruffling and breathing distortions are correlated with the redox potential of heme, so that heme molecules with these distortions have a lower redox potential than planar molecules. These findings explain the structure-function relationship of heme.
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Affiliation(s)
- Hiroko X Kondo
- School of Regional Innovation and Social Design Engineering, Faculty of Engineering, Kitami Institute of Technology, 165 Koen-cho, Kitami, Hokkaido 090-8507, Japan.,Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima, Hiroshima 731-3194, Japan.,Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research, 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan
| | - Masanori Fujii
- School of Regional Innovation and Social Design Engineering, Faculty of Engineering, Kitami Institute of Technology, 165 Koen-cho, Kitami, Hokkaido 090-8507, Japan
| | - Takuma Tanioka
- School of Regional Innovation and Social Design Engineering, Faculty of Engineering, Kitami Institute of Technology, 165 Koen-cho, Kitami, Hokkaido 090-8507, Japan
| | - Yusuke Kanematsu
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima, Hiroshima 731-3194, Japan.,Department of Applied Chemistry, Graduate School of Advanced Science and Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8527, Japan
| | - Takashi Yoshida
- School of Regional Innovation and Social Design Engineering, Faculty of Engineering, Kitami Institute of Technology, 165 Koen-cho, Kitami, Hokkaido 090-8507, Japan
| | - Yu Takano
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima, Hiroshima 731-3194, Japan
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2
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Galinato MGI, Trail AM, Steinbeck OR, Si Z, Rodland AM, Gowen J. Influence of heme propionates on the nitrite reductase activity of myoglobin. J Inorg Biochem 2021; 226:111630. [PMID: 34688205 DOI: 10.1016/j.jinorgbio.2021.111630] [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: 07/12/2021] [Revised: 10/06/2021] [Accepted: 10/12/2021] [Indexed: 11/20/2022]
Abstract
The heme propionates in myoglobin (Mb) form a H-bonding network among several residues within its second-sphere coordination, providing a key structural role towards Mb's functional properties. Our work aims to understand the role of the heme propionates on the nitrite reductase (NiR) activity (e.g. reduction of NO2- to NO) of this globin by studying an artificial dimethylester heme-substituted horse heart Mb (DME-Mb). The minor structural change brought about by esterification of the heme propionates causes the NiR rate to increase by more than over two-fold (5.6 ± 0.1 M-1 s-1) relative to wildtype (wt) Mb (2.3 ± 0.1 M-1 s-1). The lower pKa observed in DME-Mb may enhance the tendency of His64 towards protonation, therefore increasing the NiR rate. In addition, the nitrite binding constant (Knitrite) for DME-MbIII is greater than wt MbIII (350 M-1 versus 120 M-1). The disparity in the NiR activity correlates with the differences in electrostatic behavior, which influences the system's reactivity towards the approaching NO2- ion, and thus the formation of the FeII-NO2- intermediate.
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Affiliation(s)
- Mary Grace I Galinato
- School of Science-Chemistry, Penn State Behrend, Erie, PA 16563, United States of America.
| | - Aaron M Trail
- School of Science-Chemistry, Penn State Behrend, Erie, PA 16563, United States of America
| | - Olivia R Steinbeck
- School of Science-Chemistry, Penn State Behrend, Erie, PA 16563, United States of America
| | - Zhuoyan Si
- School of Science-Chemistry, Penn State Behrend, Erie, PA 16563, United States of America
| | - Anthony M Rodland
- School of Science-Chemistry, Penn State Behrend, Erie, PA 16563, United States of America
| | - Jaclyn Gowen
- School of Science-Chemistry, Penn State Behrend, Erie, PA 16563, United States of America
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3
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Kondo HX, Kanematsu Y, Masumoto G, Takano Y. PyDISH: database and analysis tools for heme porphyrin distortion in heme proteins. Database (Oxford) 2020; 2023:baaa066. [PMID: 33002111 PMCID: PMC10755257 DOI: 10.1093/database/baaa066] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 07/09/2020] [Accepted: 07/24/2020] [Indexed: 11/14/2022]
Abstract
Heme participates in a wide range of biological functions such as oxygen transport, electron transport, oxygen reduction, transcriptional regulation and so on. While the mechanism of each function has been investigated for many heme proteins, the origin of the diversity of the heme functions is still unclear and a crucial scientific issue. We have constructed a database of heme proteins, named Python-based database and analyzer for DIStortion of Heme porphyrin (PyDISH), which also contains some analysis tools. The aim of PyDISH is to integrate the information on the structures of hemes and heme proteins and the functions of heme proteins. This database will provide the structure-function relationships focusing on heme porphyrin distortion and lead to the elucidation of the origin of the functional diversity of heme proteins. In addition, the insights obtained from the database can be used for the design of protein function. PyDISH contains the structural data of more than 13 000 hemes extracted from the Protein Data Bank, including heme porphyrin distortion, axial ligands coordinating to the heme and the orientation of the propionate sidechains of heme. PyDISH also has information about the protein domains, including Uniprot ID, protein fold by CATH ID, organism, coordination distance and so on. The analytical tools implemented in PyDISH allow users to not only browse and download the data but also analyze the structures of heme porphyrin by using the analytical tools implemented in PyDISH. PyDISH users will be able to utilize the obtained results for the design of protein function. Database URL: http://pydish.bio.info.hiroshima-cu.ac.jp/.
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Affiliation(s)
- Hiroko X Kondo
- School of Regional Innovation and Social Design Engineering, Faculty of Engineering, Kitami Institute of Technology, 165 Koen-cho, Kitami, Hokkaido 090-8507, Japan
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima 731-3194, Japan
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research, 6-2-3, Furuedai, Suita 565-0874, Japan and
| | - Yusuke Kanematsu
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima 731-3194, Japan
| | - Gen Masumoto
- Information Systems Division, RIKEN Head Office for Information Systems and Cybersecurity, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yu Takano
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima 731-3194, Japan
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4
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Carminati DM, Moore EJ, Fasan R. Strategies for the expression and characterization of artificial myoglobin-based carbene transferases. Methods Enzymol 2020; 644:35-61. [PMID: 32943150 DOI: 10.1016/bs.mie.2020.07.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Myoglobin has recently emerged as a versatile metalloprotein scaffold for the design of efficient and selective biocatalysts for abiological carbene transfer reactions, including asymmetric cyclopropanation reactions. Over the past few years, our group has explored several strategies to modulate the carbene transfer reactivity of myoglobin-based catalysts, including the substitution of the native heme cofactor and conserved histidine axial ligand with non-native porphynoid ligands and alternative natural and unnatural amino acids as the metal-coordinating ligands, respectively. Herein, we report protocols for the generation and reconstitution in vitro and in vivo of myoglobin-based artificial carbene transferases incorporating non-native iron-porphynoid cofactors, also in combination with unnatural amino acids as the proximal ligand. These strategies are effective for imparting these myoglobin-based cyclopropanation biocatalysts with altered and improved function, including tolerance to aerobic conditions and improved reactivity toward electrondeficient olefins.
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Affiliation(s)
- Daniela M Carminati
- Department of Chemistry, University of Rochester, Rochester, NY, United States
| | - Eric J Moore
- Department of Chemistry, University of Rochester, Rochester, NY, United States
| | - Rudi Fasan
- Department of Chemistry, University of Rochester, Rochester, NY, United States.
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5
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Nagai M, Mizusawa N, Kitagawa T, Nagatomo S. A role of heme side-chains of human hemoglobin in its function revealed by circular dichroism and resonance Raman spectroscopy. Biophys Rev 2017; 10:271-284. [PMID: 29260461 DOI: 10.1007/s12551-017-0364-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 11/19/2017] [Indexed: 11/26/2022] Open
Abstract
Structural changes of heme side-chains of human adult hemoglobin (Hb A) upon ligand (O2 or CO) dissociation have been studied by circular dichroism (CD) and resonance Raman (RR) spectroscopies. We point out the occurrence of appreciable deformation of heme side-chains like vinyl and propionate groups prior to the out-of-plane displacement of heme iron. Referring to the recent fine resolved crystal structure of Hb A, the deformations of heme side-chains take place only in the β subunits. However, these changes are not observed in the isolated β chain (β4 homotetramer) and, therefore, are associated with the α-β inter-subunit interactions. For the communications between α and β subunits in Hb A regarding signals of ligand dissociation, possible routes are proposed on the basis of the time-resolved absorption, CD, MCD (magnetic CD), and RR spectroscopies. Our finding of the movements of heme side-chains would serve as one of the clues to solve the cooperative O2 binding mechanism of Hb A.
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Affiliation(s)
- Masako Nagai
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, 184-0003, Japan.
- School of Health Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, 920-0942, Japan.
| | - Naoki Mizusawa
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, 184-0003, Japan
| | - Teizo Kitagawa
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Ako-gun, Hyogo, 678-1297, Japan
| | - Shigenori Nagatomo
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8571, Japan
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6
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Ramos-Santana BJ, López-Garriga J. Tyrosine B10 triggers a heme propionate hydrogen bonding network loop with glutamine E7 moiety. Biochem Biophys Res Commun 2012; 424:771-6. [PMID: 22809503 PMCID: PMC3422640 DOI: 10.1016/j.bbrc.2012.07.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 07/08/2012] [Indexed: 11/27/2022]
Abstract
Propionates, as peripheral groups of the heme active center in hemeproteins have been described to contribute in the modulation of heme reactivity and ligand selection. These electronic characteristics prompted the question of whether the presence of hydrogen bonding networks between propionates and distal amino acids present in the heme ligand moiety can modulate physiological relevant events, like ligand binding association and dissociation activities. Here, the role of these networks was evaluated by NMR spectroscopy using the hemoglobin I PheB10Tyr mutant from Lucina pectinata as model for TyrB10 and GlnE7 hemeproteins. (1)H-NMR results for the rHbICN PheB10Tyr derivative showed chemical shifts of TyrB10 OHη at 31.00ppm, GlnE7N(ε1)H/N(ε2)H at 10.66ppm/-3.27ppm, and PheE11 C(δ)H at 11.75ppm, indicating the presence of a crowded, collapsed, and constrained distal pocket. Strong dipolar contacts and inter-residues crosspeaks between GlnE7/6-propionate group, GlnE7/TyrB10 and TyrB10/CN suggest that this hydrogen bonding network loop between GlnE7, TyrB10, 6-propionate group, and the heme ligand contribute significantly to the modulation of the heme iron electron density as well as the ligand stabilization mechanism. Therefore, the network loop presented here support the fact that the electron withdrawing character of the hydrogen bonding is controlled by the interaction of the propionates and the nearby electronic environments contributing to the modulation of the heme electron density state. Thus, we hypothesize that in hemeproteins with similar electrostatic environment the flexibility of the heme-6-propionate promotes a hydrogen bonding network loop between the 6-propionate, the heme ligand and nearby amino acids, tailoring in this way the electron density in the heme-ligand moiety.
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Affiliation(s)
- Brenda J. Ramos-Santana
- Department of Chemistry, University of Puerto Rico, Mayagüez Campus, PO BOX 9019, Mayagüez, Puerto Rico 00681-9019
| | - Juan López-Garriga
- Department of Chemistry, University of Puerto Rico, Mayagüez Campus, PO BOX 9019, Mayagüez, Puerto Rico 00681-9019
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7
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Sun C, Hu B, Zhao D, Liu Z. Covalently immobilized Mn(III)deuteroporphyrin on chitosan: An efficient and recyclable catalyst for aerobic oxidation of cyclohexane. J Appl Polym Sci 2012. [DOI: 10.1002/app.36672] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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8
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Matsuo T, Hayashi T. Electron transfer and oxidase activities in reconstituted hemoproteins with chemically modified cofactors. J PORPHYR PHTHALOCYA 2012. [DOI: 10.1142/s1088424609001340] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Protoheme IX is a typical iron porphyrin cofactor, showing a variety of reactivities in many hemoproteins under the reaction environments provided by protein matrices. Chemical modification of the protoheme cofactor is expected to be a versatile strategy to design hemoproteins possessing unique functions. This review focuses on the conversion of a hemoprotein, mainly myoglobin (an oxygen-storage hemoprotein), into a protein having different functions from the original ones by replacement of the protoheme cofactor with synthetic cofactors. The myoglobin having anionic patches pended to the heme propionates effectively binds electron-accepting proteins or small cationic organic molecules on the protein surface, resulting in enhanced efficiency of the photoinduced electron transfers from the myoglobin to these electron acceptors. Furthermore, the peroxidase and peroxygenase activities are also enhanced due to the facile substrate accesses. The attachment of the chemically active moiety such as flavin at the heme terminal is also important to give P450-like function to the native myoglobin. The employment of a structural isomer of porphyrin as an artificial cofactor gives rise to remarkably high dioxygen affinity and peroxidase activity in myoglobin, and allows us to easily detect high-valent species of the porphyrin isomer in HRP. These examples provide a clear insight into hemoprotein modifications based on synthetic chemistry as well as genetic amino acid mutations.
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Affiliation(s)
- Takashi Matsuo
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Takashi Hayashi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
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9
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Abstract
Photoactivatable myoglobin containing a DNA oligonucleotide as a structural anchor was designed by using the reconstitution of artificial heme moieties containing Ru(3+) ions. This semisynthetic DNA-enzyme conjugate was successfully used for the oxidation of peroxidase substrates by using visible light instead of H(2)O(2) for the activation. The DNA anchor was utilized for the immobilization of the enzyme on the surface of magnetic microbeads. Enzyme activity measurements not only indicated undisturbed biofunctionality of the tethered DNA but also enabled magnetic separation-based enrichment and recycling of the photoactivatable biocatalyst.
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Affiliation(s)
- Chi-Hsien Kuo
- Technische Universität Dortmund, Fakultät Chemie, Biologisch-Chemische Mikrostrukturtechnik, Otto-Hahn Str. 6, 44227 Dortmund, Germany
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10
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Fruk L, Kuo CH, Torres E, Niemeyer CM. Apoenzyme reconstitution as a chemical tool for structural enzymology and biotechnology. Angew Chem Int Ed Engl 2009; 48:1550-74. [PMID: 19165853 DOI: 10.1002/anie.200803098] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Many enzymes contain a nondiffusible organic cofactor, often termed a prosthetic group, which is located in the active site and essential for the catalytic activity of the enzyme. These cofactors can often be extracted from the protein to yield the respective apoenzyme, which can subsequently be reconstituted with an artificial analogue of the native cofactor. Nowadays a large variety of synthetic cofactors can be used for the reconstitution of apoenzymes and, thus, generate novel semisynthetic enzymes. This approach has been refined over the past decades to become a versatile tool of structural enzymology to elucidate structure-function relationships of enzymes. Moreover, the reconstitution of apoenzymes can also be used to generate enzymes possessing enhanced or even entirely new functionality. This Review gives an overview on historical developments and the current state-of-the-art on apoenzyme reconstitution.
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Affiliation(s)
- Ljiljana Fruk
- Universität Dortmund, Fachbereich Chemie, Biologisch-Chemische Mikrostrukturtechnik, Otto-Hahn Strasse 6, 44227 Dortmund, Germany.
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Fruk L, Kuo CH, Torres E, Niemeyer C. Rekonstitution von Apoenzymen als chemisches Werkzeug für die strukturelle Enzymologie und Biotechnologie. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200803098] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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12
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Matsuo T, Ito K, Nakashima Y, Hisaeda Y, Hayashi T. Effect of peripheral trifluoromethyl groups in artificial iron porphycene cofactor on ligand binding properties of myoglobin. J Inorg Biochem 2008; 102:166-73. [PMID: 17845820 DOI: 10.1016/j.jinorgbio.2007.07.032] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2007] [Revised: 06/30/2007] [Accepted: 07/27/2007] [Indexed: 11/18/2022]
Abstract
An iron porphycene, a structural isomer of iron porphyrin, with trifluoromethyl groups at the peripheral position of the framework was incorporated into sperm whale apomyoglobin. The prepared myoglobin shows the higher O(2) affinity than the native protein. However, the oxygen affinity of the reconstituted myoglobin is lower than that of the myoglobin having an iron porphycene without trifluoromethyl groups, which is mainly originated from the enhancement of the O(2) dissociation. The CO affinity of the myoglobin with the trifluoromethylated iron porphycene is similar to that observed for the reference protein having the iron porphycene without trifluoromethyl groups, although their C-O stretching frequencies are significantly different. The relationship between the electronic states of the porphycene ring and the ligand bindings is discussed.
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Affiliation(s)
- Takashi Matsuo
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
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13
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Harada K, Makino M, Sugimoto H, Hirota S, Matsuo T, Shiro Y, Hisaeda Y, Hayashi T. Structure and Ligand Binding Properties of Myoglobins Reconstituted with Monodepropionated Heme: Functional Role of Each Heme Propionate Side Chain,. Biochemistry 2007; 46:9406-16. [PMID: 17636874 DOI: 10.1021/bi7007068] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Two heme propionate side chains, which are attached at the 6 and 7 positions of the heme framework, are linked with Arg45 and Ser92, respectively, in sperm whale myoglobin. To evaluate the role of each propionate, two kinds of one-legged hemins, 6-depropionated and 7-depropionated protohemins, were prepared and inserted into the apomyoglobin to yield two reconstituted proteins. Structural data of the reconstituted myoglobins were obtained via an X-ray crystallographic analysis at a resolution of 1.1-1.4 A and resonance Raman spectroscopy. It was found that the lack of the 6-propionate reduces the number of hydrogen bonds in the distal site and clearly changes the position of the Arg45 residue with the disrupting Arg45-Asp60 interaction. In contrast, the removal of the 7-propionate does not cause a significant structural change in the residues of the distal and proximal sites. However, the resonance Raman studies suggested that the coordination bond strength of the His93-Fe bond for the protein with the 7-depropionated protoheme slightly increases compared to that for the protein with the native heme. The O2 and CO ligand binding studies for the reconstituted proteins with the one-legged hemes provide an important insight into the functional role of each propionate. The lack of the 6-propionate accelerates the O2 dissociation by ca. 3-fold compared to those of the other reconstituted and native proteins. The lack of the 7-propionate enhances the CO affinity by 2-fold compared to that of the protein with the native heme. These results indicate that the 6-propionate clearly contributes to the stabilization of the bound O2, whereas the 7-propionate plays an important role in the regulation of the Fe-His bond.
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Affiliation(s)
- Katsuyoshi Harada
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan
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14
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Belogortseva N, Rubio M, Terrell W, Miksovská J. The contribution of heme propionate groups to the conformational dynamics associated with CO photodissociation from horse heart myoglobin. J Inorg Biochem 2007; 101:977-86. [PMID: 17499362 DOI: 10.1016/j.jinorgbio.2007.03.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2006] [Revised: 03/09/2007] [Accepted: 03/14/2007] [Indexed: 11/26/2022]
Abstract
Photoacoustic calorimetry and transient absorption spectroscopy were used to study conformational dynamics associated with CO photodissociation from horse heart myoglobin (Mb) reconstituted with either Fe protoporphyrin IX dimethylester (FePPDME), Fe octaethylporphyrin (FeOEP), or with native Fe protoporphyrin IX (FePPIX). The volume and enthalpy changes associated with the Fe-CO bond dissociation and formation of a transient deoxyMb intermediate for the reconstituted Mbs were found to be similar to those determined for native Mb (DeltaV1 = -2.5+/-0.6 ml mol(-1) and DeltaH1 = 8.1+/-3.0 kcal mol(-1)). The replacement of FePPIX by FeOEP significantly alters the conformational dynamics associated with CO release from protein. Ligand escape from FeOEP reconstituted Mb was determined to be roughly a factor of two faster (tau=330 ns) relative to native protein (tau=700 ns) and accompanying reaction volume and enthalpy changes were also found to be smaller (DeltaV2 = 5.4+/-2.5 ml mol(-1) and DeltaH2 = 0.7+/-2.2 kcal mol(-1)) than those for native Mb (DeltaV2 = 14.3+/-0.8 ml mol(-1) and DeltaH2 = 7.8+/-3.5 kcal mol(-1)). On the other hand, volume and enthalpy changes for CO release from FePPIX or FePPDME reconstituted Mb were nearly identical to those of the native protein. These results suggest that the hydrogen bonding network between heme propionate groups and nearby amino acid residues likely play an important role in regulating ligand diffusion through protein matrix. Disruption of this network leads to a partially open conformation of protein with less restricted ligand access to the heme binding pocket.
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Affiliation(s)
- Natalia Belogortseva
- Chemistry Department, Marshall University, One John Marshall Drive, Huntington, WV 25755, USA
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15
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Nicolis S, Casella L, Roncone R, Dallacosta C, Monzani E. Heme-peptide complexes as peroxidase models. CR CHIM 2007. [DOI: 10.1016/j.crci.2006.09.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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16
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Garcia-Serres R, Davydov RM, Matsui T, Ikeda-Saito M, Hoffman BM, Huynh BH. Distinct reaction pathways followed upon reduction of oxy-heme oxygenase and oxy-myoglobin as characterized by Mössbauer spectroscopy. J Am Chem Soc 2007; 129:1402-12. [PMID: 17263425 PMCID: PMC2519892 DOI: 10.1021/ja067209i] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Activation of O(2) by heme-containing monooxygenases generally commences with the common initial steps of reduction to the ferrous heme and binding of O(2) followed by a one-electron reduction of the O(2)-bound heme. Subsequent steps that generate reactive oxygen intermediates diverge and reflect the effects of protein control on the reaction pathway. In this study, Mössbauer and EPR spectroscopies were used to characterize the electronic states and reaction pathways of reactive oxygen intermediates generated by 77 K radiolytic cryoreduction and subsequent annealing of oxy-heme oxygenase (HO) and oxy-myoglobin (Mb). The results confirm that one-electron reduction of (Fe(II)-O(2))HO is accompanied by protonation of the bound O(2) to generate a low-spin (Fe(III)-O(2)H(-))HO that undergoes self-hydroxylation to form the alpha-meso-hydroxyhemin-HO product. In contrast, one-electron reduction of (Fe(II)-O(2))Mb yields a low-spin (Fe(III)-O(2)(2-))Mb. Protonation of this intermediate generates (Fe(III)-O(2)H(-))Mb, which then decays to a ferryl complex, (Fe(IV)=O(2-))Mb, that exhibits magnetic properties characteristic of the compound II species generated in the reactions of peroxide with heme peroxidases and with Mb. Generation of reactive high-valent states with ferryl species via hydroperoxo intermediates is believed to be the key oxygen-activation steps involved in the catalytic cycles of P450-type monooxygenases. The Mössbauer data presented here provide direct spectroscopic evidence supporting the idea that ferric-hydroperoxo hemes are indeed the precursors of the reactive ferryl intermediates. The fact that a ferryl intermediate does not accumulate in HO underscores the determining role played by protein structure in controlling the reactivity of reaction intermediates.
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Affiliation(s)
| | | | | | - Masao Ikeda-Saito
- *To whom correspondence should be addressed. B.H.H: telephone, 404-727-4295; fax, 404-727-0873; email, . B.M.H., telephone, 847-491-3104; fax: 847-491-7713; email, . M.I.S.: telephone, +81-22-217-5116; fax, +81-22-217-5118; email,
| | - Brian M. Hoffman
- *To whom correspondence should be addressed. B.H.H: telephone, 404-727-4295; fax, 404-727-0873; email, . B.M.H., telephone, 847-491-3104; fax: 847-491-7713; email, . M.I.S.: telephone, +81-22-217-5116; fax, +81-22-217-5118; email,
| | - Boi Hanh Huynh
- *To whom correspondence should be addressed. B.H.H: telephone, 404-727-4295; fax, 404-727-0873; email, . B.M.H., telephone, 847-491-3104; fax: 847-491-7713; email, . M.I.S.: telephone, +81-22-217-5116; fax, +81-22-217-5118; email,
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17
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Boerakker MJ, Botterhuis NE, Bomans PHH, Frederik PM, Meijer EM, Nolte RJM, Sommerdijk NAJM. Aggregation Behavior of Giant Amphiphiles Prepared by Cofactor Reconstitution. Chemistry 2006; 12:6071-80. [PMID: 16688714 DOI: 10.1002/chem.200600089] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We report on biohybrid surfactants, termed "giant amphiphiles", in which a protein or an enzyme acts as the polar head group and a synthetic polymer as the apolar tail. It is demonstrated that the modification of horseradish peroxidase (HRP) and myoglobin (Mb) with an apolar polymer chain through the cofactor reconstitution method yields giant amphiphiles that form spherical aggregates (vesicles) in aqueous solution. Both HRP and Mb retain their original functionality when modified with a single polystyrene chain, but reconstitution has an effect on their activities. In the case of HRP the enzymatic activity decreases and for Mb the stability of the dioxygen myoglobin (oxy-Mb) complex is reduced, which is probably the result of a disturbed binding of the heme in the apo-protein or a reduced access of the substrate to the active site of the enzyme or protein.
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Affiliation(s)
- Mark J Boerakker
- Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600MB Eindhoven, The Netherlands
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18
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Matsuo T, Ikegami T, Sato H, Hisaeda Y, Hayashi T. Ligand binding properties of two kinds of reconstituted myoglobins with iron porphycene having propionates: Effect of β-pyrrolic position of two propionate side chains in porphycene framework. J Inorg Biochem 2006; 100:1265-71. [PMID: 16624412 DOI: 10.1016/j.jinorgbio.2006.02.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2005] [Revised: 01/31/2006] [Accepted: 02/03/2006] [Indexed: 10/25/2022]
Abstract
An iron porphycene containing two propionate side chains at the 12th and 17th beta-pyrrolic positions of the porphycene ring was synthesized and incorporated into sperm whale apomyoglobin in order to investigate the O(2) and CO binding properties of the reconstituted ferrous myoglobin. The protein showed a slower O(2) dissociation rate by 1/20, compared to the native myoglobin, whereas the CO dissociation rates were found to be almost the same. This tendency is similar to the result of a previous study on the reconstituted myoglobin with a porphycene having the propionates at the 13th and 16th beta-pyrrolic positions. However, the present myoglobin showed a faster O(2) dissociation than the previously studied myoglobin. This finding suggests that the position of the two propionates as well as the symmetry of the porphycene framework is an important factor for obtaining a stable oxygenated iron porphycene myoglobin.
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Affiliation(s)
- Takashi Matsuo
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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19
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Gilles-Gonzalez MA, Caceres AI, Sousa EHS, Tomchick DR, Brautigam C, Gonzalez C, Machius M. A Proximal Arginine R206 Participates in Switching of the Bradyrhizobium japonicum FixL Oxygen Sensor. J Mol Biol 2006; 360:80-9. [PMID: 16813836 DOI: 10.1016/j.jmb.2006.04.054] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2006] [Revised: 04/20/2006] [Accepted: 04/25/2006] [Indexed: 10/24/2022]
Abstract
In oxygen-sensing PAS domains, a conserved polar residue on the proximal side of the heme cofactor, usually arginine or histidine, interacts alternately with the protein in the "on-state" or the heme edge in the "off-state" but does not contact the bound ligand directly. We assessed the contributions of this residue in Bradyrhizobium japonicum FixL by determining the effects of an R206A substitution on the heme-PAS structure, ligand affinity, and regulatory capacity. The crystal structures of the unliganded forms of the R206A and wild-type BjFixL heme-PAS domains were similar, except for a more ruffled porphyrin ring in R206A BjFixL and a relaxation of the H214 residue and heme propionate 7 due to their lost interactions. The oxygen affinity of R206A BjFixL (Kd approximately 350 microM) was 2.5 times lower than that of BjFixL, and this was due to a higher off-rate constant for the R206A variant. The enzymatic activities of the unliganded "on-state" forms, either deoxy or met-R206A BjFixL, were comparable to each other and slightly lower (twofold less) than those of the corresponding BjFixL species. The most striking difference between the two proteins was in the enzymatic activities of the liganded "off-state" forms. In particular, saturation with a regulatory ligand (the Fe(III) form with cyanide) caused a >2000-fold inhibition of the BjFixL phosphorylation of BjFixJ, but a 140-fold inhibition of this catalytic activity in R206A BjFixL. Thus, in oxygen-sensing PAS domains, the interactions of polar residues with the heme edge couple the heme-binding domain to a transmitter during signal transduction.
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Affiliation(s)
- Marie-Alda Gilles-Gonzalez
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9038, USA.
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20
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Guallar V, Olsen B. The role of the heme propionates in heme biochemistry. J Inorg Biochem 2006; 100:755-60. [PMID: 16513175 DOI: 10.1016/j.jinorgbio.2006.01.019] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2005] [Revised: 01/11/2006] [Accepted: 01/12/2006] [Indexed: 11/28/2022]
Abstract
There are numerous studies, relying on both experimental and theoretical observations, illustrating the active role of the heme propionates in regulating electron delivery to the iron center as well as biochemical properties of the heme. Evidences for this come from a wide variety of heme containing systems: cytochromes, heme peroxidases, globins, etc. Here, we shortly summarize these studies and revisit previous theoretical calculations (V. Guallar, M.H. Baik, S.J. Lippard, R.A. Friesner, Proc. Natl. Acad. Sci. USA 100 (2003) 6998-7002) where the propionate groups induced the delocalization of the spin density in the cytochrome P450cam putative active species, Compound I. We introduce novel data, obtained by means of mixed quantum mechanics and molecular mechanics methods, indicating a larger electron delocalization into the protein. We also present novel results based on the recent migration of spin density observed by Barrows et al. (T.P. Barrows, T.L. Poulos, Biochemistry 44 (2005) 14062-68) on an ascorbate peroxidase mutant. All this data strongly supports the importance of the propionate groups in tuning the heme electronic properties.
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Affiliation(s)
- Victor Guallar
- Department of Biochemistry, Washington University School of Medicine, 700 S. Euclid, Room 112, St. Louis, MO 63108, USA.
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21
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Wang N, Zhao X, Lu Y. Role of heme types in heme-copper oxidases: effects of replacing a heme b with a heme o mimic in an engineered heme-copper center in myoglobin. J Am Chem Soc 2006; 127:16541-7. [PMID: 16305243 DOI: 10.1021/ja052659g] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To address the role of the secondary hydroxyl group of heme a/o in heme-copper oxidases, we incorporated Fe(III)-2,4 (4,2) hydroxyethyl vinyl deuterioporphyrin IX, as a heme o mimic, into the engineered heme-copper center in myoglobin (sperm whale myoglobin L29H/F43H, called Cu(B)Mb). The only difference between the heme b of myoglobin and the heme o mimic is the substitution of one of the vinyl side chains of the former with a hydroxyethyl group of the latter. This substitution resulted in an approximately 4 nm blue shift in the Soret band and approximately 20 mV decrease in the heme reduction potential. In a control experiment, the heme b in Cu(B)Mb was also replaced with a mesoheme, which resulted in an approximately 13 nm blue shift and approximately 30 mV decrease in the heme reduction potential. Kinetic studies of the heme o mimic-substituted Cu(B)Mb showed significantly different reactivity toward copper-dependent oxygen reduction from that of the b-type Cu(B)Mb. In reaction with O2, Cu(B)Mb with a native heme b showed heme oxygenase activity by generating verdoheme in the presence of Cu(I). This heme degradation reaction was slowed by approximately 19-fold in the heme o mimic-substituted Cu(B)Mb (from 0.028 s(-1) to 0.0015 s(-1)), while the mesoheme-substituted Cu(B)Mb shared a similar heme degradation rate with that of Cu(B)Mb (0.023 s(-1)). No correlation was found between the heme reduction potential and its O2 reactivity. These results strongly suggest the critical role of the hydroxyl group of heme o in modulating heme-copper oxidase activity through participation in an extra hydrogen-bonding network.
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Affiliation(s)
- Ningyan Wang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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22
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Sakamoto S, Kudo K. Design and Synthesis of Semi-Artificial Myoglobin Possessing DNA-Binding Peptides on Heme Propionates. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2005. [DOI: 10.1246/bcsj.78.1749] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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23
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Podstawka E, Proniewicz LM. Resonance Raman study of deoxy and ligated (O2 and CO) mesoheme IX-reconstituted myoglobin, hemoglobin and its alpha and beta subunits. J Inorg Biochem 2005; 98:1502-12. [PMID: 15337602 DOI: 10.1016/j.jinorgbio.2004.06.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2004] [Revised: 05/31/2004] [Accepted: 06/01/2004] [Indexed: 11/22/2022]
Abstract
In this work, we corrected the resonance Raman (RR) results presented earlier for deoxy mesoheme IX-reconstituted hemoglobin (mesoHb) alpha and beta subunits implied that mesohemes in these subunits undergo substantial structural changes upon formation of a hemoglobin tetramer (Biochemistry 29 (1990) 5087). We show that these data were probably due to the improper handling of the deoxy mesoheme subunit preparation. Additionally, we discuss the RR spectra of deoxy, oxy, and CO species of mesoheme IX-reconstituted myoglobin (mesoMb) and alpha and beta deoxy meso hemoglobin subunits, including their analogues with deuterium-substituted mesoheme IX in all methyl groups (d(12)). Based on the obtained data, we propose a complete RR band assignment for all of the investigated molecules. The most pronounced changes are observed for the gamma(7) mode (out-of-plane movement of methane carbon atoms) associated with the interaction of the ethyl groups with the globin. We also show that in mesoheme IX-reconstituted proteins, the O(2) molecule binds stronger than in the case of native species. This is manifested by the up-shift of nu(Fe-O(2)).
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Affiliation(s)
- Edyta Podstawka
- Laser Raman Laboratory, Regional Laboratory of Physicochemical Analysis and Structural Research, Jagiellonian University, 3 Ingardena Str., 30-060 Krakow, Poland
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Sato H, Watanabe M, Hisaeda Y, Hayashi T. Unusual ligand discrimination by a myoglobin reconstituted with a hydrophobic domain-linked heme. J Am Chem Soc 2005; 127:56-7. [PMID: 15631446 DOI: 10.1021/ja044984u] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
New, reconstituted horse heart myoglobins possessing a hydrophobic domain at the terminal of the two heme propionate side chains were constructed. The O2 and CO bindings for the reconstituted deoxymyoglobins were examined in detail by laser flash photolysis and stopped-flow rapid mixing techniques. The artificially created domain worked as a barrier against exogenous ligand penetration into the heme pocket, whereas the bound O2 was stabilized in the reconstituted myoglobin as well as in the native one. In contrast, the CO dissociation rate for the reconstituted myoglobin increased by 20-fold compared to the native protein, suggesting that the incorporation of the hydrophobic domain onto the heme pocket perturbs the distal-site structure of the reconstituted myoglobin. As a result, the substantial ligand selectivity for the reconstituted myoglobin significantly increases in favor of O2 over CO with the M' value (= KCO/KO2) of 0.88, whereas, to the best of our knowledge, there is no myoglobin mutant in which the O2 affinity exceeds the CO one. The present work concludes that the O2 selectivity of myoglobin over CO is markedly improved by chemically modifying the heme propionates without any mutation of the amino acid residues in the distal site.
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Affiliation(s)
- Hideaki Sato
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka 812-8581, Japan
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25
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Hayashi T, Nakagawa T, Harada K, Matsuo T, Hitomi Y, Hisaeda Y. Chemical Properties of Sperm Whale Myoglobins Reconstituted with Monopropionate Hemins. CHEM LETT 2004. [DOI: 10.1246/cl.2004.1512] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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