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Ngo HT, Minami K, Imamura G, Shiba K, Yoshikawa G. Effects of Center Metals in Porphines on Nanomechanical Gas Sensing. SENSORS (BASEL, SWITZERLAND) 2018; 18:E1640. [PMID: 29883390 PMCID: PMC5982686 DOI: 10.3390/s18051640] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 05/15/2018] [Accepted: 05/16/2018] [Indexed: 12/13/2022]
Abstract
Porphyrin is one of the most promising materials for realizing a practical artificial olfactory sensor system. In this study, we focus on non-substituted porphyrins—porphines—as receptor materials of nanomechanical membrane-type surface stress sensors (MSS) to investigate the effect of center metals on gas sensing. By omitting the substituents on the tetrapyrrole macrocycle of porphyrin, the peripheral interference by substituents can be avoided. Zinc, nickel, and iron were chosen for the center metals as these metalloporphines show different properties compared to free-base porphine. The present study revealed that iron insertion enhanced sensitivity to various gases, while zinc and nickel insertion led to equivalent or less sensitivity than free-base porphine. Based on the experimental results, we discuss the role of center metals for gas uptake from the view point of molecular interaction. We also report the high robustness of the iron porphine to humidity, showing the high feasibility of porphine-based nanomechanical sensor devices for practical applications in ambient conditions.
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Affiliation(s)
- Huynh Thien Ngo
- World Premier International (WPI) Research Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba 305-0044, Japan.
| | - Kosuke Minami
- World Premier International (WPI) Research Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba 305-0044, Japan.
| | - Gaku Imamura
- World Premier International (WPI) Research Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba 305-0044, Japan.
| | - Kota Shiba
- World Premier International (WPI) Research Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba 305-0044, Japan.
| | - Genki Yoshikawa
- World Premier International (WPI) Research Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba 305-0044, Japan.
- Materials Science and Engineering, Graduate School of Pure and Applied Science, University of Tsukuba, Tennodai 1-1-1 Tsukuba, Ibaraki 305-8571, Japan.
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2
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Kanai Y, Harada A, Shibata T, Nishimura R, Namiki K, Watanabe M, Nakamura S, Yumoto F, Senda T, Suzuki A, Neya S, Yamamoto Y. Characterization of Heme Orientational Disorder in a Myoglobin Reconstituted with a Trifluoromethyl-Group-Substituted Heme Cofactor. Biochemistry 2017; 56:4500-4508. [DOI: 10.1021/acs.biochem.7b00457] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yuki Kanai
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Ayaka Harada
- Structural
Biology Research Center, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Tomokazu Shibata
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Ryu Nishimura
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Kosuke Namiki
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Miho Watanabe
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Shunpei Nakamura
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Fumiaki Yumoto
- Structural
Biology Research Center, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Toshiya Senda
- Structural
Biology Research Center, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Akihiro Suzuki
- Department
of Materials Engineering, National Institute of Technology, Nagaoka College, Nagaoka 940-8532, Japan
| | - Saburo Neya
- Department
of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chuoh-Inohana, Chiba 260-8675, Japan
| | - Yasuhiko Yamamoto
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
- Life
Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba 305-8577, Japan
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3
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Neya S, Nagai M, Nagatomo S, Hoshino T, Yoneda T, Kawaguchi AT. Utility of heme analogues to intentionally modify heme-globin interactions in myoglobin. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:582-588. [PMID: 26435388 DOI: 10.1016/j.bbabio.2015.09.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 09/12/2015] [Accepted: 09/25/2015] [Indexed: 01/01/2023]
Abstract
Myoglobin reconstitution with various synthetic heme analogues was reviewed to follow the consequences of modified heme-globin interactions. Utility of dimethyl sulfoxide as the solvent for water-insoluble hemes was emphasized. Proton NMR spectroscopy revealed that loose heme-globin contacts in the heme pocket eventually caused the dynamic heme rotation around the iron-histidine bond. The full rotational rate was estimated to be about 1400 s(-1) at room temperature for 1,4,5,8-tetramethylhemin. The X-ray analysis of the myoglobin containing iron porphine, the smallest heme without any side chains, showed that the original globin fold was well conserved despite the serious disruption of native heme-globin contacts. Comparison between the two myoglobins with static and rotatory prosthetic groups indicated that the oxygen and carbon monoxide binding profiles were almost unaffected by the heme motion. On the other hand, altered tetrapyrrole array of porphyrin dramatically changed the dissociation constant of oxygen from 0.0005 mm Hg of porphycene-myoglobin to ∞ in oxypyriporphyrin-myoglobin. Heme-globin interactions in myoglobin were also monitored with circular dichroism spectroscopy. The observation on several reconstituted protein revealed an unrecognized role of the propionate groups in protoheme. Shortening of heme 6,7-propionates to carboxylates resulted in almost complete disappearance of the positive circular dichroism band in the Soret region. The theoretical analysis suggested that the disappeared circular dichroism band reflected the cancellation effects between different conformers of the carboxyl groups directly attached to heme periphery. The above techniques were proposed to be applicable to other hemoproteins to create new biocatalysts. This article is part of a Special Issue entitled Biodesign for Bioenergetics--the design and engineering of electronic transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.
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Affiliation(s)
- Saburo Neya
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chuoh-Inohana, Chiba City, Chiba 260-8675, Japan.
| | - Masako Nagai
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo 184-0003, Japan
| | - Shigenori Nagatomo
- Department of Chemistry, Graduate School of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Tyuji Hoshino
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chuoh-Inohana, Chiba City, Chiba 260-8675, Japan
| | - Tomoki Yoneda
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chuoh-Inohana, Chiba City, Chiba 260-8675, Japan
| | - Akira T Kawaguchi
- School of Medicine, Tokai University, Isehara, Kanagawa 259-1193, Japan
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4
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Neya S, Suzuki M, Hoshino T, Kawaguchi AT. Relaxation Analysis of Ligand Binding to the Myoglobin Reconstituted with Cobaltic Heme. Inorg Chem 2013; 52:7387-93. [PMID: 23758139 DOI: 10.1021/ic400078w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Saburo Neya
- Department of Physical Chemistry, Graduate School of Pharmaceutical
Sciences, Chiba University, Chuoh-Inohana,
Chiba 260-8675, Japan
| | - Masaaki Suzuki
- Department of Physical Chemistry, Graduate School of Pharmaceutical
Sciences, Chiba University, Chuoh-Inohana,
Chiba 260-8675, Japan
| | - Tyuji Hoshino
- Department of Physical Chemistry, Graduate School of Pharmaceutical
Sciences, Chiba University, Chuoh-Inohana,
Chiba 260-8675, Japan
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5
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Neya S. Dynamic motion and rearranged molecular shape of heme in myoglobin: structural and functional consequences. Molecules 2013; 18:3168-82. [PMID: 23478515 PMCID: PMC6269712 DOI: 10.3390/molecules18033168] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 03/07/2013] [Accepted: 03/07/2013] [Indexed: 11/16/2022] Open
Abstract
Myoglobin, a simple oxygen binding protein, was reconstituted with various types of synthetic hemes to manipulate the heme-globin interactions. From the paramagnetic NMR analysis, small heme was found to rotate rapidly about the iron-histidine bond upon. This is a novel and typical example for the fluctuation of protein. The dynamic NMR analysis indicated that the 360° rotational rate of a small heme was 1,400 s−1 at room temperature. The X-ray analyses revealed that the tertiary structure of globin containing the smallest heme was closely similar to that of native protein despite extensive destruction of the specific heme-globin interactions. The functional analyses of O2 binding showed that the loose heme-globin contacts do not significantly affect the oxygen binding. On the other hand, the rearrangement of tetrapyrrole array and the non-planar deformation in porphyrin ring significantly affect the functional properties of myoglobin. These results, taken together, indicate that the essential factors to regulate the myoglobin function are hidden under the molecular shape of prosthetic group rather than in the nonbonded heme-globin contacts.
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Affiliation(s)
- Saburo Neya
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chuoh-Inohana, Chiba City, Chiba 260-8675, Japan.
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6
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Nishimura R, Shibata T, Tai H, Ishigami I, Ogura T, Nagao S, Matsuo T, Hirota S, Imai K, Neya S, Suzuki A, Yamamoto Y. Relationship between the Electron Density of the Heme Fe Atom and the Vibrational Frequencies of the Fe-Bound Carbon Monoxide in Myoglobin. Inorg Chem 2013; 52:3349-55. [DOI: 10.1021/ic3028447] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ryu Nishimura
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Tomokazu Shibata
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Hulin Tai
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Izumi Ishigami
- Department of Life Science, Graduate School
of Life Science, University of Hyogo, Kamigori-cho,
Ako-gun, Hyogo 678-1297, Japan
| | - Takashi Ogura
- Department of Life Science, Graduate School
of Life Science, University of Hyogo, Kamigori-cho,
Ako-gun, Hyogo 678-1297, Japan
| | - Satoshi Nagao
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Takashi Matsuo
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Shun Hirota
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Kiyohiro Imai
- Department of Frontier Bioscience,
Faculty of Bioscience and Applied Chemistry, Hosei University, Koganei, Tokyo 184-8584, Japan
| | - Saburo Neya
- Department of Physical Chemistry, Graduate School of Pharmaceutical
Sciences, Chiba University, Chuoh-Inohana,
Chiba 260-8675, Japan
| | - Akihiro Suzuki
- Department
of Materials Engineering, Nagaoka National College of Technology, Nagaoka 940-8532, Japan
| | - Yasuhiko Yamamoto
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
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7
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Juillard S, Chevance S, Bondon A, Simonneaux G. Dynamics of heme in hemoproteins: proton NMR study of myoglobin reconstituted with iron 3-ethyl-2-methylporphyrin. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1188-94. [PMID: 21600316 DOI: 10.1016/j.bbapap.2011.04.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Revised: 04/23/2011] [Accepted: 04/27/2011] [Indexed: 11/19/2022]
Abstract
The asymmetric 3-ethyl-2-methylporphyrin iron complex was synthetized and inserted into apomyoglobin. UV-visible spectroscopic studies demonstrated the capacity of iron to coordinate different exogenous axial ligands in ferrous and ferric forms. The position of synthetic heme into the hydrophobic pocket of the reconstituted myoglobin was investigated by ((1))H NMR spectroscopy. In absence of exogenous ligand, signals of the synthetic prosthetic group were not detected, suggesting a rotational disorder of the synthetic porphyrin into the heme pocket. This direct interconversion behavior is favored since site-specific interactions between the poorly substituted heme and protein in the chiral hydrophobic cavity were weak. Complexion of cyanide to the iron allowed to quench partially the heme reorientation and two interconvertible forms, around the meso-Cα-Cγ axis, were detected in solution.
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Affiliation(s)
- Sandrine Juillard
- UMR 6226 Sciences Chimiques de Rennes, Campus de Beaulieu, Université de Rennes 1, Rennes, France
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8
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Takashima H, Kawahara H, Kitano M, Shibata S, Murakami H, Tsukahara K. Metal ion-dependent fluorescent dynamics of photoexcited zinc-porphyrin and zinc-myoglobin modified with ethylenediaminetetraacetic acid. J Phys Chem B 2009; 112:15493-502. [PMID: 18991435 DOI: 10.1021/jp807692w] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The reconstituted zinc-myoglobin (ZnMb) dyads, ZnMb-[M(II)(edta)], have been prepared by incorporating a zinc-porphyrin (ZnP) cofactor modified with ethylenediaminetetraacetic acid (H(4)edta) into apo-Mb. In case of the monomeric ZnP(edta) cofactor coordinated by one pyridine molecule, ZnP(py)(edta), a spontaneous 1:1 complex with a transient metal ion was formed in an aqueous solvent, and the photoexcited singlet state of ZnP, (1)(ZnP)*, was quenched by the [Cu(II)(edta)] moiety through intramolecular photoinduced electron-transfer (ET) reaction. The rate constant for the intramolecular quenching ET (k(q)) at 25 degrees C was successfully obtained as k(q) = 5.1 x 10(9) s(-1). In the case of Co(2+), Ni(2+), and Mn(2+), intersystem crossing by paramagnetic effect was mainly considered between (1)(ZnP)* and the [M(II)(edta)] complex. For the ZnMb-[M(II)(edta)] systems, the intramolecular ET reaction between the excited singlet state of (1)(ZnMb)* and the [Cu(II)(edta)] moieties provided the slower quenching rate constant, k(q) = 2.1 x 10(8) s(-1), compared with that of the ZnP(py)(edta) one. Kinetic studies also presented the efficient fluorescence quenching of the (1)(ZnMb)*-[Co(II)(edta)] dyad. Our study clearly demonstrates that wrapping of the ZnP cofactor by the apoprotein matrix and synthetic manipulation at the Mb surface ensure metal ion-sensitive fluorescent dynamics of ZnMb and provides valuable information to elucidate the complicated mechanism of the biological photoinduced ET reactions of hemoproteins.
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Affiliation(s)
- Hiroshi Takashima
- Department of Chemistry, Faculty of Science, Nara Women's University, Nara, 630-8506 Japan.
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9
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Juillard S, Bondon A, Simonneaux G. Proton NMR Study of Low‐Spin
meso
‐Unsubstituted β‐Substituted Alkyl Iron Porphyrins: Remarkable Influence of Peripheral Substitution on Spin Density. Eur J Inorg Chem 2007. [DOI: 10.1002/ejic.200700503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Sandrine Juillard
- Laboratoire de Chimie Organométallique et Biologique, UMR CNRS 6226 Campus de Beaulieu,Université de Rennes 1, 35042 Rennes, France
| | - Arnaud Bondon
- RMN‐ILP, UMR CNRS 6026, IFR 140 PRISM, Campus de Villejean, Université de Rennes 1, 35043 Rennes, France
| | - Gérard Simonneaux
- Laboratoire de Chimie Organométallique et Biologique, UMR CNRS 6226 Campus de Beaulieu,Université de Rennes 1, 35042 Rennes, France
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10
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Satake Y, Abe S, Okazaki S, Ban N, Hikage T, Ueno T, Nakajima H, Suzuki A, Yamane T, Nishiyama H, Watanabe Y. Incorporation of a Phebox Rhodium Complex into apo-Myoglobin Affords a Stable Organometallic Protein Showing Unprecedented Arrangement of the Complex in the Cavity. Organometallics 2007. [DOI: 10.1021/om700471a] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuh Satake
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan, PRESTO, Japan Science and Technology Agency (JST) Kawaguchi, Saitama, 332-0012, Japan, Department of Biotechnology, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan, Department of Applied Chemistry, Graduate School of Engineering, High Intensity X-ray Diffraction Laboratory, Nagoya University, Nagoya, 464-8603, Japan, and Research Center of Materials Science, Nagoya University,
| | - Satoshi Abe
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan, PRESTO, Japan Science and Technology Agency (JST) Kawaguchi, Saitama, 332-0012, Japan, Department of Biotechnology, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan, Department of Applied Chemistry, Graduate School of Engineering, High Intensity X-ray Diffraction Laboratory, Nagoya University, Nagoya, 464-8603, Japan, and Research Center of Materials Science, Nagoya University,
| | - Seiji Okazaki
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan, PRESTO, Japan Science and Technology Agency (JST) Kawaguchi, Saitama, 332-0012, Japan, Department of Biotechnology, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan, Department of Applied Chemistry, Graduate School of Engineering, High Intensity X-ray Diffraction Laboratory, Nagoya University, Nagoya, 464-8603, Japan, and Research Center of Materials Science, Nagoya University,
| | - Noritaka Ban
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan, PRESTO, Japan Science and Technology Agency (JST) Kawaguchi, Saitama, 332-0012, Japan, Department of Biotechnology, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan, Department of Applied Chemistry, Graduate School of Engineering, High Intensity X-ray Diffraction Laboratory, Nagoya University, Nagoya, 464-8603, Japan, and Research Center of Materials Science, Nagoya University,
| | - Tatsuo Hikage
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan, PRESTO, Japan Science and Technology Agency (JST) Kawaguchi, Saitama, 332-0012, Japan, Department of Biotechnology, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan, Department of Applied Chemistry, Graduate School of Engineering, High Intensity X-ray Diffraction Laboratory, Nagoya University, Nagoya, 464-8603, Japan, and Research Center of Materials Science, Nagoya University,
| | - Takafumi Ueno
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan, PRESTO, Japan Science and Technology Agency (JST) Kawaguchi, Saitama, 332-0012, Japan, Department of Biotechnology, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan, Department of Applied Chemistry, Graduate School of Engineering, High Intensity X-ray Diffraction Laboratory, Nagoya University, Nagoya, 464-8603, Japan, and Research Center of Materials Science, Nagoya University,
| | - Hiroshi Nakajima
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan, PRESTO, Japan Science and Technology Agency (JST) Kawaguchi, Saitama, 332-0012, Japan, Department of Biotechnology, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan, Department of Applied Chemistry, Graduate School of Engineering, High Intensity X-ray Diffraction Laboratory, Nagoya University, Nagoya, 464-8603, Japan, and Research Center of Materials Science, Nagoya University,
| | - Atsuo Suzuki
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan, PRESTO, Japan Science and Technology Agency (JST) Kawaguchi, Saitama, 332-0012, Japan, Department of Biotechnology, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan, Department of Applied Chemistry, Graduate School of Engineering, High Intensity X-ray Diffraction Laboratory, Nagoya University, Nagoya, 464-8603, Japan, and Research Center of Materials Science, Nagoya University,
| | - Takashi Yamane
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan, PRESTO, Japan Science and Technology Agency (JST) Kawaguchi, Saitama, 332-0012, Japan, Department of Biotechnology, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan, Department of Applied Chemistry, Graduate School of Engineering, High Intensity X-ray Diffraction Laboratory, Nagoya University, Nagoya, 464-8603, Japan, and Research Center of Materials Science, Nagoya University,
| | - Hisao Nishiyama
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan, PRESTO, Japan Science and Technology Agency (JST) Kawaguchi, Saitama, 332-0012, Japan, Department of Biotechnology, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan, Department of Applied Chemistry, Graduate School of Engineering, High Intensity X-ray Diffraction Laboratory, Nagoya University, Nagoya, 464-8603, Japan, and Research Center of Materials Science, Nagoya University,
| | - Yoshihito Watanabe
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan, PRESTO, Japan Science and Technology Agency (JST) Kawaguchi, Saitama, 332-0012, Japan, Department of Biotechnology, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan, Department of Applied Chemistry, Graduate School of Engineering, High Intensity X-ray Diffraction Laboratory, Nagoya University, Nagoya, 464-8603, Japan, and Research Center of Materials Science, Nagoya University,
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11
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Ueno T, Yokoi N, Abe S, Watanabe Y. Crystal structure based design of functional metal/protein hybrids. J Inorg Biochem 2007; 101:1667-75. [PMID: 17675160 DOI: 10.1016/j.jinorgbio.2007.06.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2007] [Revised: 06/11/2007] [Accepted: 06/18/2007] [Indexed: 11/23/2022]
Abstract
Preparation of metal/protein hybrids is growing into important topics in the field of bioinorganic chemistry. X-ray crystal structure analyses of them provide direct information on unique interactions of metal cations or metal cofactors to understand and design enzymatic functions. In this mini review, the authors focus on the recent studies on the metal/protein hybrids concerning crystal structure analyses since 2002 and our related works. The precise structural determination promise us to deeply understand coordination chemistry in protein scaffold and shows intriguing suggestions on rational design and application use for biocatalysts, metal drugs and so on.
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Affiliation(s)
- Takafumi Ueno
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
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12
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Abe S, Ueno T, Reddy PAN, Okazaki S, Hikage T, Suzuki A, Yamane T, Nakajima H, Watanabe Y. Design and structure analysis of artificial metalloproteins: selective coordination of His64 to copper complexes with square-planar structure in the apo-myoglobin scaffold. Inorg Chem 2007; 46:5137-9. [PMID: 17523632 DOI: 10.1021/ic070289m] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
apo-Myoglobin (apo-Mb) was reconstituted with three copper complexes: CuII(Sal-Phe) (1; Sal-Phe = N-salicylidene-L-phenylalanato), CuII(Sal-Leu) (2; Sal-Leu = N-salicylidene-L-leucinato), and CuII(Sal-Ala) (3; Sal-Ala = N-salicylidene-L-alanato). The crystal structures of 1.apo-Mb (1.65 Angstrom resolution) and 2.apo-Mb (1.8 Angstrom resolution) show that the coordination geometry around the CuII atom in apo-Mb is distorted square-planar with tridentate Sal-X and a Nepsilon atom of His64 in the apo-Mb cavity and the plane of these copper complexes is perpendicular to that of heme. These results suggest that the apo-Mb cavity can hold metal complexes with various coordination geometries.
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Affiliation(s)
- Satoshi Abe
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
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13
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Danielsson J, Meuwly M. Molecular Dynamics Simulations of CN− Dynamics and Spectroscopy in Myoglobin. Chemphyschem 2007; 8:1077-84. [PMID: 17436348 DOI: 10.1002/cphc.200700042] [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] [Indexed: 11/07/2022]
Abstract
The vibrational dynamics of the cyanide anion and the heme group in MbCN (CN complexed to Myoglobin) are investigated using molecular dynamics simulations. A previously calculated quantum-chemical heme-ligand potential-energy surface together with a three-center charge model for the iron-ligand center that captures both polarization and ligand-to-metal charge transfer allows for a detailed description of the interactions around the active site. It is found that the CN binding orientation (Fe--CN or Fe--NC) to the heme affects the stretching frequency of the ligand, with a 25 cm-1 difference in the fundamental wavenumber between the two orientations as well as a change in bond length. The charge model also captures such crucial interactions as the possible hydrogen bond between the ligand and the His64 residue. This interaction is weakened when the ligand binds in the Fe--NC conformation but is also sensitive to the protonation state of His64. The structural changes around the active site, the observation of water penetration for the Fe--NC conformation, the computed IR spectrum, and the energetics suggest that the Fe--CN conformation with Hisepsilon64 is the most likely one. The water accessibility of the active site is also found to be related to the protonation state of His64. The presence of water in the active site could also affect the IR band of the C--N stretch mode. Thus, IR spectroscopy of the C--N stretch is a potentially useful reporter of ligand isomers and active-site structure.
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Affiliation(s)
- Jonas Danielsson
- University of Basel, Department of Chemistry, Klingelbergstr. 80, 4056 Basel, Switzerland
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Ueno T, Koshiyama T, Abe S, Yokoi N, Ohashi M, Nakajima H, Watanabe Y. Design of artificial metalloenzymes using non-covalent insertion of a metal complex into a protein scaffold. J Organomet Chem 2007. [DOI: 10.1016/j.jorganchem.2006.08.043] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Takashima H, Tara C, Namikawa S, Kato T, Araki Y, Ito O, Tsukahara K. Photoinduced Intramolecular Electron-Transfer Reactions of Reconstituted Met- and Zinc-Myoglobins Appending Acridine and Methylacridinium Ion as DNA-Binders. J Phys Chem B 2006; 110:26413-23. [PMID: 17181301 DOI: 10.1021/jp0655571] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Three types of reconstituted met- and zinc-myoglobin (metMb and ZnMb) dyads, ZnMbAc(4)Me+, ZnMbAc(6)Me+, and metMbAc(6) have been prepared by incorporating chemically modified metalloporphyrin cofactor appending an acridine (Ac) or a methylacridinium ion ([AcMe]+) into apo-Mb. In the bimolecular system between ZnMb and [AcMe]+, the photoexcited triplet state of ZnMb, 3(ZnMb)*, was successfully quenched by [AcMe]+ to form the radical pair of ZnMb cation (ZnMb*+) and reduced methylacridine ([AcMe]*), followed by a thermal back ET reaction. The rate constants for the intermolecular quenching ET (kq) and the back ET reaction (kb) at 25 degrees C were successfully obtained as kq = (8.8 +/- 0.4) x 10(7) M(-1) s(-1) and kb = (1.2 +/- 0.1) x 10(8) M(-1) s(-1), respectively. On the other hand, in case of the intramolecular photoinduced ET reactions of ZnMbAc(4)Me+ and ZnMbAc(6)Me+ dyads, the first-order quenching rate constants (kET) of 3(ZnMb)* by [AcMe]+ moiety were determined to be kET = 2.6 x 10(3) and 2.5 x 10(3) s(-1), respectively. When such ET occurs along the alkyl spacer via through-bond mechanism at the surface of Mb, the obtained kET is reasonable to provide decay constant of beta (1.0-1.3 A(-1)). Upon photoirradiation of [AcMe]+ moiety, kinetic studies also presented the intramolecular quenching reactions from the excited singlet state, 1([AcMe]+)*, whose likely process is the photoinduced energy-transfer reaction. For metMbAc(6) dyad, steady-state fluorescence was almost quenched, while the signal around 440 nm gradually appeared in the presence of various concentrations of DNA. Our study implies that synthetic manipulation at the Mb surface, by using an artificial DNA-binder coupled with photoinduced reaction, may provide valuable information to construct new Mb-DNA complex and sensitive fluorescent for DNA.
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Affiliation(s)
- Hiroshi Takashima
- Department of Chemistry, Faculty of Science, Nara Women's University, Nara, 630-8506 Japan.
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Juillard S, Bondon A, Simonneaux G. Proton NMR study of myoglobin reconstituted with 3,7-diethyl-2,8-dimethyl iron porphyrin: Remarkable influence of peripheral substitution on heme rotation. J Inorg Biochem 2006; 100:1441-8. [PMID: 16766034 DOI: 10.1016/j.jinorgbio.2006.04.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2005] [Revised: 04/03/2006] [Accepted: 04/06/2006] [Indexed: 11/29/2022]
Abstract
The iron complex of 3,7-diethyl-2,8-dimethylporphyrin was incorporated into horse heart apomyoglobin to investigate the influence of peripheral substitution on artificial heme rotation. The hyperfine-shifted 1H NMR spectrum of the reconstituted deoxymyoglobin (rMb) revealed the proximal imidazole N-H resonance at 82.5 ppm to indicate the formation of the Fe--N (His93) bond. The pyrrole-protons of the hemin of myoglobin in the absence of external ligand appeared as four resonances between -10 and -18 ppm, indicating a mainly low-spin ferric hemin, with a ligated distal histidine (His64). This also indicates the lost of the symmetry of the hemin, according to an absence of free rotation of the prosthetic group. The 1H NMR spectrum of reconstituted rMbCO revealed a set of four pyrrole-protons and a set of four meso-protons. Accordingly, the prosthetic group without acid side chains interacts specifically with the surrounding globin showing a unique heme orientation in the 1H NMR time-scale, despite the presence of only four alkyl substituents on the porphine ring. This also suggests that two ethyl groups are large enough to avoid the free rotation movement of the heme.
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Affiliation(s)
- Sandrine Juillard
- Laboratoire de Chimie Organométallique et Biologique, UMR CNRS 6226, Campus de Beaulieu, Université de Rennes 1, 35042 Rennes, France
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Ueno T, Koshiyama T, Ohashi M, Kondo K, Kono M, Suzuki A, Yamane T, Watanabe Y. Coordinated Design of Cofactor and Active Site Structures in Development of New Protein Catalysts. J Am Chem Soc 2005; 127:6556-62. [PMID: 15869276 DOI: 10.1021/ja045995q] [Citation(s) in RCA: 156] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
New methods for the synthesis of artificial metalloenzymes are important for the construction of novel biocatalysts and biomaterials. Recently, we reported new methodology for the synthesis of artificial metalloenzymes by reconstituting apo-myoglobin with metal complexes (Ohashi, M. et al., Angew Chem., Int. Ed. 2003, 42, 1005-1008). However, it has been difficult to improve their reactivity, since their crystal structures were not available. In this article, we report the crystal structures of M(III)(Schiff base).apo-A71GMbs (M = Cr and Mn). The structures suggest that the position of the metal complex in apo-Mb is regulated by (i) noncovalent interaction between the ligand and surrounding peptides and (ii) the ligation of the metal ion to proximal histidine (His93). In addition, it is proposed that specific interactions of Ile107 with 3- and 3'-substituent groups on the salen ligand control the location of the Schiff base ligand in the active site. On the basis of these results, we have successfully controlled the enantioselectivity in the sulfoxidation of thioanisole by changing the size of substituents at the 3 and 3' positions. This is the first example of an enantioselective enzymatic reaction regulated by the design of metal complex in the protein active site.
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Affiliation(s)
- Takafumi Ueno
- Research Center for Materials Science and Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
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Ueno T, Ohashi M, Kono M, Kondo K, Suzuki A, Yamane T, Watanabe Y. Crystal structures of artificial metalloproteins: tight binding of FeIII(Schiff-Base) by mutation of Ala71 to Gly in apo-myoglobin. Inorg Chem 2004; 43:2852-8. [PMID: 15106972 DOI: 10.1021/ic0498539] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Apo-myoglobin (apo-Mb) and apo-A71GMb were successfully reconstituted with FeIII(salophen) (1) (salophen = N,N'-bis(salicylidene)-1,2-phenilenediamine), Fe(III)(3,3'-Me2-salophen) (2), and FeIII(5,5'-t-Bu2-salophen) (3). The crystal structure of 2.apo-A71GMb shows the tight binding of the complex in the Mb cavity, while in wild-type apo-Mb it is highly disordered due to the steric repulsion with Ala71. Furthermore, the structure of 2.apo-A71GMb suggests a possible accommodation of a small substrate in the cavity. In fact, the cyanide association rate constant of 2.apo-A71GMb is 216-fold larger compared to that of 2.apo-Mb. These results provide us principles for the noncovalent fixation of synthetic metal cofactors at the desired positions in protein matrixes.
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Affiliation(s)
- Takafumi Ueno
- Research Center for Materials Science, Nagoya University, Nagoya 464-8602, Japan
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21
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Ye X, Demidov A, Rosca F, Wang W, Kumar A, Ionascu D, Zhu L, Barrick D, Wharton D, Champion PM. Investigations of Heme Protein Absorption Line Shapes, Vibrational Relaxation, and Resonance Raman Scattering on Ultrafast Time Scales. J Phys Chem A 2003. [DOI: 10.1021/jp0276799] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Xiong Ye
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Andrey Demidov
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Florin Rosca
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Wei Wang
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Anand Kumar
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Dan Ionascu
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Leyun Zhu
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Doug Barrick
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - David Wharton
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Paul M. Champion
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
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Neya S, Imai K, Hori H, Ishikawa H, Ishimori K, Okuno D, Nagatomo S, Hoshino T, Hata M, Funasaki N. Iron hemiporphycene as a functional prosthetic group for myoglobin. Inorg Chem 2003; 42:1456-61. [PMID: 12611510 DOI: 10.1021/ic020504t] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The iron complex of hemiporphycene, a molecular hybrid of porphyrin with porphycene, was incorporated into the apomyoglobin pocket to examine ligand binding ability of the iron atom in the novel porphyrinoid. Apomyoglobin was successfully coupled with a stoichiometric amount of ferric hemiporphycene to afford the reconstituted myoglobin equipped with the iron coordination structure of native protein. Cyanide, imidazole, and fluoride coordinated to the ferric protein with affinities comparable with those for native myoglobin. The ferrous myoglobin was functionally active to bind O(2) and CO reversibly at pH 7.4 and 20 degrees C. The O(2) affinity is 12-fold higher than that of native myoglobin while the CO affinity is slightly lower, suggesting decreased discrimination between O(2) and CO in the heme pocket. The functional anomaly was interpreted to reflect increased sigma-bonding character in the Fe(II)-O(2) bond. In contrast with 6-coordinate native NO protein, the NO myoglobin containing ferrous hemiporphycene is in a mixed 5- and 6-coordinate state. This observation suggests that the in-plane configuration of the iron atom in hemiporphycene is destabilized by NO. Influence of the core deformation was also detected with both the infrared absorption for the ferrous CO derivative and electron paramagnetic resonance for ferric imidazole complex. Anomalies in the ferric and ferrous derivatives were ascribed to the modified iron-N(pyrrole) interactions in the asymmetric metallo core of hemiporphycene.
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Affiliation(s)
- Saburo Neya
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Inage-Yayoi, Japan.
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Hayashi T, Hisaeda Y. New functionalization of myoglobin by chemical modification of heme-propionates. Acc Chem Res 2002; 35:35-43. [PMID: 11790087 DOI: 10.1021/ar000087t] [Citation(s) in RCA: 176] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The reconstitution of myoglobin with an artificially created prosthetic group is a unique method for introducing a new chemical function into the protein. Particularly, the modification of two heme-propionates gives us an effective binding domain or binding site on the protein surface. This Account traces the design and construction of the highly ordered binding domain around the entrance of the heme pocket. The discussion includes the protein-small molecule or protein-protein recognition, electron transfer reaction within the complex, and enhancement of the chemical reactivity of the myoglobin with a substrate binding site. The synthetic approach to modifying a protein will be a new trend in engineering a novel function in naturally occurring hemoprotein.
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Affiliation(s)
- Takashi Hayashi
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka 812-8581, Japan.
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Rosca F, Kumar ATN, Ionascu D, Ye X, Demidov AA, Sjodin T, Wharton D, Barrick D, Sligar SG, Yonetani T, Champion PM. Investigations of Anharmonic Low-Frequency Oscillations in Heme Proteins. J Phys Chem A 2001. [DOI: 10.1021/jp0129277] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Florin Rosca
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Anand T. N. Kumar
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Dan Ionascu
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Xiong Ye
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Andrey A. Demidov
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Theodore Sjodin
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - David Wharton
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Douglas Barrick
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Stephen G. Sligar
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Takashi Yonetani
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Paul M. Champion
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
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Neya S, Nakamura M, Imai K, Funasaki N. Functional analysis of the iron(II) etiocorrphycene incorporated in the myoglobin heme pocket. Chem Pharm Bull (Tokyo) 2001; 49:345-6. [PMID: 11253930 DOI: 10.1248/cpb.49.345] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The iron(III) complex of 2,7,12,17-tetraethyl-3,6,11,18-tetra-methylcorrphycene, an isomeric heme, was complexed with apomyoglobin to examine the ligand binding ability of the novel macrocycle under physiological conditions. The reconstituted holoprotein was found to be functionally active at pH 7.4 and 20 degrees C and to bind oxygen and carbon monoxide reversibly with a half-saturation pressure at 6.7 and 3.5mmHg, respectively. Equilibrium affinities for these ligands are one to two orders of magnitude lower than those reported for native myoglobin. The functional anomaly was ascribed to the geometric and electronic strain on the iron(II) atom in the trapezoidal coordination core of corrphycene.
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Affiliation(s)
- S Neya
- Department of Physical Chemistry, Kyoto Pharmaceutical University, Japan.
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27
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Mie Y, Sonoda K, Kishita M, Krestyn E, Neya S, Funasaki N, Taniguchi I. Effect of rapid heme rotation on electrochemistry of myoglobin. Electrochim Acta 2000. [DOI: 10.1016/s0013-4686(00)00366-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Bolognesi M, Rosano C, Losso R, Borassi A, Rizzi M, Wittenberg JB, Boffi A, Ascenzi P. Cyanide binding to Lucina pectinata hemoglobin I and to sperm whale myoglobin: an x-ray crystallographic study. Biophys J 1999; 77:1093-9. [PMID: 10423453 PMCID: PMC1300399 DOI: 10.1016/s0006-3495(99)76959-6] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The x-ray crystal structures of the cyanide derivative of Lucina pectinata monomeric hemoglobin I (L. pectinata HbI) and sperm whale (Physeter catodon) myoglobin (Mb), generally taken as reference models for monomeric hemoproteins carrying hydrogen sulfide and oxygen, respectively, have been determined at 1.9 A (R-factor = 0. 184), and 1.8 A (R-factor = 0.181) resolution, respectively, at room temperature (lambda = 1.542 A). Moreover, the x-ray crystal structure of the L. pectinata HbI:cyanide derivative has been studied at 1.4-A resolution (R-factor = 0.118) and 100 K (on a synchrotron source lambda = 0.998 A). At room temperature, the cyanide ligand is roughly parallel to the heme plane of L. pectinata HbI, being located approximately 2.5 A from the iron atom. On the other hand, the crystal structure of the L. pectinata HbI:cyanide derivative at 100 K shows that the diatomic ligand is coordinated to the iron atom in an orientation almost perpendicular to the heme (the Fe-C distance being 1.95 A), adopting a coordination geometry strictly reminescent of that observed in sperm whale Mb, at room temperature. The unusual cyanide distal site orientation observed in L. pectinata HbI, at room temperature, may reflect reduction of the heme Fe(III) atom induced by free radical species during x-ray data collection using Cu Kalpha radiation.
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Affiliation(s)
- M Bolognesi
- Dipartimento di Fisica-INFM, Università di Genova, and Centro Biotecnologie Avanzate-IST, I-16132 Genova, Italy.
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Singh UP, Obayashi E, Takahashi S, Iizuka T, Shoun H, Shiro Y. The effects of heme modification on reactivity, ligand binding properties and iron-coordination structures of cytochrome P450nor. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1384:103-11. [PMID: 9602081 DOI: 10.1016/s0167-4838(98)00006-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Artificial cytochrome P450nors (nitric oxide reductase) were prepared by replacing the native protoheme with various 2,4-substituted hemes: meso-, deutero-, and diacetyldeutero-hemes. For these samples, the ratio of low spin/high spin states of the ferric resting enzyme were varied, indicating that the coordination of the water molecule at the iron sixth site was affected by the electron withdrawing capacities of the heme 2,4-substituents. The binding of the water molecule reduces the rate of binding of nitric oxide (NO) to the ferric iron. In addition, the reduction reaction of the ferric-NO complex with NADH, which constitutes the second step in the NO reduction, was facilitated by the electron withdrawing capacity of 2,4-substituents. Consequently, proto- (native-) P450nor exhibited the highest overall enzymatic activity (NO reduction activity), while the enzymes containing diacetyl-, deutero-, and meso-hemes had considerably lower activities, since the NO reduction activity is determined by a balance of the reaction rates of the above two steps. The optical absorption spectra of the ferric-NO and the ferrous-CO complexes of the reconstituted enzymes show that the electron density on the heme in both states was modulated by the substituent groups. However, the resonance Raman spectral measurements showed that the Fe-NO and N-O stretching frequencies in the ferric-NO complex were insensitive to the electron density of the heme while the Fe-CO and C-O stretching frequencies in the ferrous-CO complex were sensitively varied by the electron withdrawing capacity of the 2,4-substituent. The differences are discussed in terms of the difference in the iron-ligand bond characters between the ferric-NO and the ferrous-CO complexes.
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Affiliation(s)
- U P Singh
- Institute of Physical and Chemical Research (RIKEN), Saitama, Japan
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Neya S, Funasaki N, Igarashi N, Ikezaki A, Sato T, Imai K, Tanaka N. Structure and function of 6,7-dicarboxyheme-substituted myoglobin. Biochemistry 1998; 37:5487-93. [PMID: 9548931 DOI: 10.1021/bi972632c] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Myoglobin was reconstituted with 6,7-dicarboxy-1,2,3,4,5, 8-hexamethylheme, a compact synthetic heme with the shortest acid side chains, to pursue the structural and functional consequences after intensive disruption of the heme propionate-apoglobin linkages in the native protein. The electron-withdrawing carboxylate groups directly attached to the porphyrin ring lowered the oxygen affinity by 3-fold as compared with native myoglobin. Autoxidation of the oxy derivative to the ferric protein proceeded with 1.6 x 10(-)2 min-1 at pH 7.0 and 30 degrees C. The crystallographic structure of the cyanomet myoglobin with 1.9 A resolution shows that the heme adopts a unique orientation in the protein pocket to extend the two carboxylates toward solvent sphere. The native globin fold is conserved, and the conformations of globin side chains are almost intact except for those located nearby the heme 6,7-carboxylates. The 7-carboxylate only weakly interacts with Ser92 and His97 through two mediating water molecules. The 6-carboxylate, on the other hand, forms a novel salt bridge with Arg45 owing to conformational flexibility of the guanidinium side chain. The proton NMR shows that the small heme does not fluctuate about the iron-histidine bond even at 55 degreesC, suggesting that the salt bridge between Arg45 and heme 6-carboxylate is of critical importance to recognize and fix the heme in myoglobin.
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Affiliation(s)
- S Neya
- Department of Physical Chemistry, Kyoto Pharmaceutical University, Japan.
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Kroeger KS, Kundrot CE. Structures of a hemoglobin-based blood substitute: insights into the function of allosteric proteins. Structure 1997; 5:227-37. [PMID: 9032082 DOI: 10.1016/s0969-2126(97)00181-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
BACKGROUND . Potential blood substitutes can be based on hemoglobin. Two problems must be overcome with acellular hemoglobin-based blood substitutes, however: the oxygen affinity of purified human hemoglobin is too high for it to deliver oxygen to tissues, and hemoglobin tetramers dissociate into alphabeta dimers that can cause kidney damage. A modified form of hemoglobin, rHb 1.1, has reduced oxygen affinity as the result of an Asnbeta 108-->Lys mutation, and dimerization is prevented by the insertion of a glycine residue between the sequences of the normal alpha chains to produce one covalently continuous di-alpha-chain. Determination of the structure of rHb 1.1 would provide structure-based explanations for the altered properties of rHb 1.1. RESULTS . We determined the structures of the deoxy form of rHb 1.1 at 2.0 resolution and of cyanomet-rHb 1.1 at 2.6 resolution. Deoxy-rHb 1.1 adopts the classic 'T state' quaternary structure, but cyanomet-rHb 1.1 adopts a novel quanternary structure, the B state. The most striking feature of the tertiary structures is a charged hydrogen bond involving Lysbeta 108 that is broken in the T-->B state transition. The glycine bridge within the di-alpha-chain is well defined in both structures and appears to cause adoption of the B state instead of the previously observed ligand-bound quaternary structures R or Y/R2. CONCLUSIONS . A charged hydrogen bond between Lysbeta 108 and Tyrbeta35 is broken in the transition between the deoxy and ligand-bound forms of rHb 1.1. This structural change reduces the oxygen affinity of rHb 1.1 by changing the relative stability of deoxy and ligand-bound states. Furthermore, our observations highlight the importance of small conformational changes in allosteric proteins, even in their most rigid domains. Three ligand-bound quaternary structures of hemoglobin (R, Y/R2 and B) have now been described. In contrast, only one quaternary structure has been observed for deoxyhemoglobin (T). The structural degeneracy of the high oxygen affinity form of hemoglobin is an important reminder that allosteric proteins may have multiple quaternary structures that are functionally very similar. This degeneracy of quaternary structures has important implications for the regulation of allosteric proteins, because different quaternary structures may be stabilized by different allosteric effectors.
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Affiliation(s)
- K S Kroeger
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309-0215, USA
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Fukuyama K, Kunishima N, Amada F, Kubota T, Matsubara H. Crystal structures of cyanide- and triiodide-bound forms of Arthromyces ramosus peroxidase at different pH values. Perturbations of active site residues and their implication in enzyme catalysis. J Biol Chem 1995; 270:21884-92. [PMID: 7665612 DOI: 10.1074/jbc.270.37.21884] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The structures of the cyanide and triiodide complexes of Arthromyces ramosus peroxidase (ARP) at different pH values were investigated by x-ray crystallography in order to examine the behavior of the invariant residues of arginine (Arg-52) and distal histidine (His-56) during the enzyme reaction as well as to provide the structural basis of the active site of peroxidase. The models of the cyanide complexes at pH 7.5, 5.0, and 4.0, respectively, were refined to the R-factors of 17.8, 17.8, and 18.5% using 7.0-1.6-A resolution data, and those of the triiodide complexes at pH 6.5 and 5.0 refined to 16.9 and 16.8% using 7.0-1.9-A resolution data. The structures of the cyanide complexes at pH 7.5, 5.0, and 4.0 are identical within experimental error. Cyanide ion bound to the heme in the bent conformation rather than in the tilt conformation. Upon cyanide ion binding, the N epsilon atom of His-56 moved toward the ion by rotation of the imidazole ring around the C beta-C gamma bond, but there was little conformational change in the remaining residues. The distance between the N epsilon atom of His-56 and the nitrogen atom of the cyanide suggests the presence of a hydrogen bond between them in the pH range investigated. In the triiodide complexes, one of the two triiodides bound to ARP was located at the distal side of the heme. When triiodide bound to ARP, unlike the rearrangement of the distal arginine of cytochrome c peroxidase that occurs on formation of the fluoride complex or compound I, the side chain of Arg-52 moved little. The conformation of the side chain of His-56, however, changed markedly. Conformational flexibility of His-56 appears to be a requisite for proton translocation from one oxygen atom to the other of HOO- by acid-base catalysis to produce compound I. The iron atom in each cyanide complex (low-spin ferric) is located in the heme plane, whereas in each triiodide complex (high-spin ferric) the iron atom is displaced from the plane about 0.2 A toward the proximal side.
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Affiliation(s)
- K Fukuyama
- Department of Biology, Faculty of Science, Osaka University, Japan
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Neya S, Kaku T, Funasaki N, Shiro Y, Iizuka T, Imai K, Hori H. Novel ligand binding properties of the myoglobin substituted with monoazahemin. J Biol Chem 1995; 270:13118-23. [PMID: 7768907 DOI: 10.1074/jbc.270.22.13118] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The iron complex of alpha-azamesoporphyrin XIII was combined with apomyoglobin to investigate influence of the meso nitrogen on ligand binding properties in the reconstituted protein. Stoichiometric complex formation between the two components was confirmed, and conservation of the native coordination structures in the resultant myoglobin was established with spectroscopic criteria and apparently normal ligand binding. The visible absorption spectra of various ferric and ferrous derivatives are characteristic with less intense Soret peaks and enhanced visible bands. The electron paramagnetic resonance spectrum with g = 5.2 suggests an anomalous intermediate spin (S = 3/2) character for the aquomet protein. The oxygen affinity of reduced azaheme myoglobin, 0.010 mm Hg, is 50 times larger than that of the native myoglobin. In addition, azaheme myoglobin forms stable complexes with imidazole, pyridine, or cyanide in ferrous state. All of these new properties were consistently explained in terms of stronger equatorial ligand field of the heme iron in a narrower coordination cavity. Similarities of azaheme to verdoheme were also pointed out.
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Affiliation(s)
- S Neya
- Department of Physical Chemistry, Kyoto Pharmaceutical University, Japan
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Neya S, Funasaki N, Shiro Y, Iizuka T, Imai K. Consequence of rapid heme rotation to the oxygen binding of myoglobin. BIOCHIMICA ET BIOPHYSICA ACTA 1994; 1208:31-7. [PMID: 8086436 DOI: 10.1016/0167-4838(94)90156-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The myoglobin complexed with octamethylhemin was prepared. The visible absorption profiles are typical of general alkylhemin-substituted myoglobins, suggesting normal insertion of the hemin into the hydrophobic cavity. The NMR spectra of various ferric proteins were anomalous, without clearly resolved signals from the prosthetic group, most probably reflecting rapid heme rotation about the iron-histidine bond. The equilibrium and kinetic oxygen bindings were measured to examine the functional significance of the heme motion. Functional comparison with the myoglobin having immobile hemin indicates that rotation of the octamethylheme negligibly affects the myoglobin function. The results suggest that neither the heme peripheral contacts nor the proximal imidazole orientation about the heme normal is the dominant factor to control myoglobin function.
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Affiliation(s)
- S Neya
- Department of Physical Chemistry, Kyoto Pharmaceutical University, Japan
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