51
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Deshpande MS, Parui PP, Kamikubo H, Yamanaka M, Nagao S, Komori H, Kataoka M, Higuchi Y, Hirota S. Formation of Domain-Swapped Oligomer of Cytochrome c from Its Molten Globule State Oligomer. Biochemistry 2014; 53:4696-703. [DOI: 10.1021/bi500497s] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Megha Subhash Deshpande
- Graduate
School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Partha Pratim Parui
- Graduate
School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
- Department
of Chemistry, Jadavpur University, Kolkata 700032, India
| | - Hironari Kamikubo
- Graduate
School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Masaru Yamanaka
- Graduate
School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Satoshi Nagao
- Graduate
School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Hirofumi Komori
- Faculty
of Education, Kagawa University, 1-1 Saiwai, Takamatsu, Kagawa 760-8522, Japan
| | - Mikio Kataoka
- Graduate
School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Yoshiki Higuchi
- Department
of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1
Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Shun Hirota
- Graduate
School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
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52
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Structure of a mitochondrial cytochrome c conformer competent for peroxidase activity. Proc Natl Acad Sci U S A 2014; 111:6648-53. [PMID: 24760830 DOI: 10.1073/pnas.1323828111] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
At the onset of apoptosis, the peroxidation of cardiolipin at the inner mitochondrial membrane by cytochrome c requires an open coordination site on the heme. We report a 1.45-Å resolution structure of yeast iso-1-cytochrome c with the Met80 heme ligand swung out of the heme crevice and replaced by a water molecule. This conformational change requires modest adjustments to the main chain of the heme crevice loop and is facilitated by a trimethyllysine 72-to-alanine mutation. This mutation also enhances the peroxidase activity of iso-1-cytochrome c. The structure shows a buried water channel capable of facilitating peroxide access to the active site and of moving protons produced during peroxidase activity to the protein surface. Alternate positions of the side chain of Arg38 appear to mediate opening and closing of the buried water channel. In addition, two buried water molecules can adopt alternate positions that change the network of hydrogen bonds in the buried water channel. Taken together, these observations suggest that low and high proton conductivity states may mediate peroxidase function. Comparison of yeast and mammalian cytochrome c sequences, in the context of the steric factors that permit opening of the heme crevice, suggests that higher organisms have evolved to inhibit peroxidase activity, providing a more stringent barrier to the onset of apoptosis.
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53
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Sun MH, Liu SQ, Du KJ, Nie CM, Lin YW. A spectroscopic study of uranyl-cytochrome b5/cytochrome c interactions. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 118:130-137. [PMID: 24051281 DOI: 10.1016/j.saa.2013.08.112] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 08/28/2013] [Accepted: 08/28/2013] [Indexed: 06/02/2023]
Abstract
Uranium is harmful to human health due to its radiation damage and the ability of uranyl ion (UO2(2+)) to interact with various proteins and disturb their biological functions. Cytochrome b5 (cyt b5) is a highly negatively charged heme protein and plays a key role in mediating cytochrome c (cyt c) signaling in apoptosis by forming a dynamic cyt b5-cyt c complex. In previous molecular modeling study in combination with UV-Vis studies, we found that UO2(2+) is capable of binding to cyt b5 at surface residues, Glu37 and Glu43. In this study, we further investigated the structural consequences of cyt b5 and cyt c, as well as cyt b5-cyt c complex, upon uranyl binding, by fluorescence spectroscopic and circular dichroism techniques. Moreover, we proposed a uranyl binding site for cyt c at surface residues, Glu66 and Glu69, by performing a molecular modeling study. It was shown that uranyl binds to cyt b5 (KD=10 μM), cyt c (KD=87 μM), and cyt b5-cyt c complex (KD=30 μM) with a different affinity, which slightly alters the protein conformation and disturbs the interaction of cyt b5-cyt c complex. Additionally, we investigated the functional consequences of uranyl binding to the protein surface, which decreases the inherent peroxidase activity of cyt c. The information of uranyl-cyt b5/cyt c interactions gained in this study likely provides a clue for the mechanism of uranyl toxicity.
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Affiliation(s)
- Mei-Hui Sun
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
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54
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Junedi S, Yasuhara K, Nagao S, Kikuchi JI, Hirota S. Morphological Change of Cell Membrane by Interaction with Domain-Swapped CytochromecOligomers. Chembiochem 2014; 15:517-21. [DOI: 10.1002/cbic.201300728] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Indexed: 01/17/2023]
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55
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Ariga K, Ji Q, Mori T, Naito M, Yamauchi Y, Abe H, Hill JP. Enzyme nanoarchitectonics: organization and device application. Chem Soc Rev 2014; 42:6322-45. [PMID: 23348617 DOI: 10.1039/c2cs35475f] [Citation(s) in RCA: 270] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Fabrication of ultrasmall functional machines and their integration within ultrasmall areas or volumes can be useful for creation of novel technologies. The ultimate goal of the development of ultrasmall machines and device systems is to construct functional structures where independent molecules operate as independent device components. To realize exotic functions, use of enzymes in device structures is an attractive solution because enzymes can be regarded as efficient machines possessing high reaction efficiencies and specificities and can operate even under ambient conditions. In this review, recent developments in enzyme immobilization for advanced functions including device applications are summarized from the viewpoint of micro/nano-level structural control, or nanoarchitectonics. Examples are roughly classified as organic soft matter, inorganic soft materials or integrated/organized media. Soft matter such as polymers and their hybrids provide a medium appropriate for entrapment and encapsulation of enzymes. In addition, self-immobilization based on self-assembly and array formation results in enzyme nanoarchitectures with soft functions. For the confinement of enzymes in nanospaces, hard inorganic mesoporous materials containing well-defined channels play an important role. Enzymes that are confined exhibit improved stability and controllable arrangement, which are useful for formation of functional relays and for their integration into artificial devices. Layer-by-layer assemblies as well as organized lipid assemblies such as Langmuir-Blodgett films are some of the best media for architecting controllable enzyme arrangements. The ultrathin forms of these films facilitate their connection with external devices such as electrodes and transistors. Artificial enzymes and enzyme-mimicking catalysts are finally briefly described as examples of enzyme functions involving non-biological materials. These systems may compensate for the drawbacks of natural enzymes, such as their instabilities under harsh conditions. We believe that enzymes and their mimics will be freely coupled, organized and integrated upon demand in near future technologies.
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Affiliation(s)
- Katsuhiko Ariga
- World Premier International (WPI) Research Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba 305-0044, Japan.
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56
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Parui PP, Deshpande MS, Nagao S, Kamikubo H, Komori H, Higuchi Y, Kataoka M, Hirota S. Formation of Oligomeric Cytochrome c during Folding by Intermolecular Hydrophobic Interaction between N- and C-Terminal α-Helices. Biochemistry 2013; 52:8732-44. [DOI: 10.1021/bi400986g] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Partha Pratim Parui
- Graduate
School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
- Department
of Chemistry, Jadavpur University, Kolkata 700032, India
| | - Megha Subhash Deshpande
- Graduate
School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Satoshi Nagao
- Graduate
School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Hironari Kamikubo
- Graduate
School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Hirofumi Komori
- Department
of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1
Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yoshiki Higuchi
- Department
of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1
Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Mikio Kataoka
- Graduate
School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Shun Hirota
- Graduate
School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
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57
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Lin YW, Wang J. Structure and function of heme proteins in non-native states: a mini-review. J Inorg Biochem 2013; 129:162-71. [PMID: 23916118 DOI: 10.1016/j.jinorgbio.2013.07.023] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 07/11/2013] [Accepted: 07/13/2013] [Indexed: 12/12/2022]
Abstract
Heme proteins perform various biological functions ranging from electron transfer, oxygen binding and transport, catalysis, to signaling. Although adopting proper native states is very important for these functions, progresses in representative heme proteins, including cytochrome c (cyt c), cytochrome b5 (cyt b5), myoglobin (Mb), neuroglobin (Ngb), cytochrome P450 (CYP) and heme-based sensor proteins such as CO sensor CooA, showed that various native functions, or new functions evolved, are also closely associated with non-native states. The structure and function relationship of heme proteins in non-native states is thus as important as that in native states for elucidating the precise roles of heme proteins in biological systems.
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Affiliation(s)
- Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
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58
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Patila M, Pavlidis IV, Diamanti EK, Katapodis P, Gournis D, Stamatis H. Enhancement of cytochrome c catalytic behaviour by affecting the heme environment using functionalized carbon-based nanomaterials. Process Biochem 2013. [DOI: 10.1016/j.procbio.2013.04.021] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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59
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Peroxidase activity of a myoglobin mutant with three distal histidines forming a metal-binding site: Implications for the cross-reactivity of cytochrome c oxidase. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcatb.2013.02.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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60
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Lin YW, Sawyer EB, Wang J. Rational heme protein design: all roads lead to Rome. Chem Asian J 2013; 8:2534-44. [PMID: 23704071 DOI: 10.1002/asia.201300291] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Indexed: 01/03/2023]
Abstract
Heme proteins are among the most abundant and important metalloproteins, exerting diverse biological functions including oxygen transport, small molecule sensing, selective C-H bond activation, nitrite reduction, and electron transfer. Rational heme protein designs focus on the modification of the heme-binding active site and the heme group, protein hybridization and domain swapping, and de novo design. These strategies not only provide us with unique advantages for illustrating the structure-property-reactivity-function (SPRF) relationship of heme proteins in nature but also endow us with the ability to create novel biocatalysts and biosensors.
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Affiliation(s)
- Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001 (China)
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61
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Kimata-Ariga Y, Kubota-Kawai H, Lee YH, Muraki N, Ikegami T, Kurisu G, Hase T. Concentration-dependent oligomerization of cross-linked complexes between ferredoxin and ferredoxin-NADP+ reductase. Biochem Biophys Res Commun 2013; 434:867-72. [PMID: 23618857 DOI: 10.1016/j.bbrc.2013.04.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 04/03/2013] [Indexed: 01/17/2023]
Abstract
Ferredoxin-NADP(+) reductase (FNR) forms a 1:1 complex with ferredoxin (Fd), and catalyzes the electron transfer between Fd and NADP(+). In our previous study, we prepared a series of site-specifically cross-linked complexes of Fd and FNR, which showed diverse electron transfer properties. Here, we show that X-ray crystal structures of the two different Fd-FNR cross-linked complexes form oligomers by swapping Fd and FNR moieties across the molecules; one complex is a dimer from, and the other is a successive multimeric form. In order to verify whether these oligomeric structures are formed only in crystal, we investigated the possibility of the oligomerization of these complexes in solution. The mean values of the particle size of these cross-linked complexes were shown to increase with the rise of protein concentration at sub-milimolar order, whereas the size of dissociable wild-type Fd:FNR complex was unchanged as analyzed by dynamic light scattering measurement. The oligomerization products were detected by SDS-PAGE after chemical cross-linking of these complexes at the sub-milimolar concentrations. The extent and concentration-dependent profile of the oligomerizaion were differentiated between the two cross-linked complexes. These results show that these Fd-FNR cross-linked complexes exhibit concentration-dependent oligomerization, possibly through swapping of Fd and FNR moieties also in solution. These findings lead to the possibility that some native multi-domain proteins may present similar phenomenon in vivo.
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Affiliation(s)
- Yoko Kimata-Ariga
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
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62
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Nugraheni AD, Nagao S, Yanagisawa S, Ogura T, Hirota S. Interaction of dimeric horse cytochrome c with cyanide ion. J Biol Inorg Chem 2013; 18:383-90. [DOI: 10.1007/s00775-013-0982-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 01/29/2013] [Indexed: 01/19/2023]
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63
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Hayashi Y, Nagao S, Osuka H, Komori H, Higuchi Y, Hirota S. Domain Swapping of the Heme and N-Terminal α-Helix in Hydrogenobacter thermophilus Cytochrome c552 Dimer. Biochemistry 2012; 51:8608-16. [DOI: 10.1021/bi3011303] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Yugo Hayashi
- Graduate School
of Materials
Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Satoshi Nagao
- Graduate School
of Materials
Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Hisao Osuka
- Department of Life Science,
Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Hirofumi Komori
- Department of Life Science,
Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yoshiki Higuchi
- Department of Life Science,
Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Shun Hirota
- Graduate School
of Materials
Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
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64
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Maiti S, Das K, Dutta S, Das PK. Striking Improvement in Peroxidase Activity of Cytochrome c by Modulating Hydrophobicity of Surface-Functionalized Gold Nanoparticles within Cationic Reverse Micelles. Chemistry 2012; 18:15021-30. [DOI: 10.1002/chem.201202398] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Indexed: 01/07/2023]
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65
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Hirota S, Ueda M, Hayashi Y, Nagao S, Kamikubo H, Kataoka M. Maintenance of the secondary structure of horse cytochrome c during the conversion process of monomers to oligomers by addition of ethanol. ACTA ACUST UNITED AC 2012; 152:521-9. [DOI: 10.1093/jb/mvs098] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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66
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Nagao S, Osuka H, Yamada T, Uni T, Shomura Y, Imai K, Higuchi Y, Hirota S. Structural and oxygen binding properties of dimeric horse myoglobin. Dalton Trans 2012; 41:11378-85. [DOI: 10.1039/c2dt30893b] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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