{"@context":{"@vocab":"https://cir.nii.ac.jp/schema/1.0/","rdfs":"http://www.w3.org/2000/01/rdf-schema#","dc":"http://purl.org/dc/elements/1.1/","dcterms":"http://purl.org/dc/terms/","foaf":"http://xmlns.com/foaf/0.1/","prism":"http://prismstandard.org/namespaces/basic/2.0/","cinii":"http://ci.nii.ac.jp/ns/1.0/","datacite":"https://schema.datacite.org/meta/kernel-4/","ndl":"http://ndl.go.jp/dcndl/terms/","jpcoar":"https://github.com/JPCOAR/schema/blob/master/2.0/"},"@id":"https://cir.nii.ac.jp/crid/1361418519772015232.json","@type":"Article","productIdentifier":[{"identifier":{"@type":"DOI","@value":"10.1021/bi0520131"}},{"identifier":{"@type":"URI","@value":"https://pubs.acs.org/doi/pdf/10.1021/bi0520131"}},{"identifier":{"@type":"PMID","@value":"16681384"}}],"dc:title":[{"@value":"Structure of Cytochrome <i>c</i>552 from a Moderate Thermophilic Bacterium, <i>Hydrogenophilus thermoluteolus</i>:  Comparative Study on the Thermostability of Cytochrome <i>c</i>"}],"description":[{"notation":[{"@value":"We have studied the structure-thermostability relationship using cytochromes c from mesophilic and thermophilic bacteria; Pseudomonas aeruginosa (PAc(551)) growing at 37 degrees C and Hydrogenobacter thermophilus (HTc(552)) at 72 degrees C and showed that only five residues primarily differentiate their stabilities. For a more comprehensive study, we found Hydrogenophilus thermoluteolus (Pseudomonas hydrogenothermophila) growing at 52 degrees C and showed the moderate stability of the cytochrome c from this bacterium (PHc(552)). To explore the stabilization mechanisms, the crystal structure of PHc(552) was determined by X-ray analysis. The solution structure of HTc(552) elucidated previously by NMR was refined using distributed computational implementation. Furthermore, the recently reported crystal structure of HTc(552) has become available [Travaglini-Allocatelli, C. et al. (2005) J. Biol. Chem. 280, 25729-25734]. When the structures of these three cytochromes c were combined, this revealed that the five residues, corresponding to those mentioned above, determine the difference of stabilities among them as well. These facts suggested the stabilization mechanisms as follows: (1) improved van der Waals interactions by packing optimization at the N-terminal helix, (2) attractive electrostatic interactions with the heme propionate group, and (3) favorable van der Waals interaction with the heme. This comparative study, by supplementing the structural information of PHc(552) with its complementary feature, demonstrates that just a small number of amino acid residues determine the overall molecular stability by means of additivity of the effects of their substitutions. It is interesting that, in naturally occurring proteins, these adaptation strategies are accommodated by these bacteria to survive in the wide range of thermal conditions."}]}],"creator":[{"@id":"https://cir.nii.ac.jp/crid/1381418519772015237","@type":"Researcher","foaf:name":[{"@value":"Shota Nakamura"}],"jpcoar:affiliationName":[{"@value":"Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan, Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan, Daiichi Pharmaceutical Co., Ltd., Edogawa-ku, Tokyo 134-8630, Japan, and Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka 569-1094, Japan"}]},{"@id":"https://cir.nii.ac.jp/crid/1381418519772015238","@type":"Researcher","foaf:name":[{"@value":"Shin-ichi Ichiki"}],"jpcoar:affiliationName":[{"@value":"Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan, Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan, Daiichi Pharmaceutical Co., Ltd., Edogawa-ku, Tokyo 134-8630, Japan, and Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka 569-1094, Japan"}]},{"@id":"https://cir.nii.ac.jp/crid/1381418519772015236","@type":"Researcher","foaf:name":[{"@value":"Hiroyuki Takashima"}],"jpcoar:affiliationName":[{"@value":"Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan, Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan, Daiichi Pharmaceutical Co., Ltd., Edogawa-ku, Tokyo 134-8630, Japan, and Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka 569-1094, Japan"}]},{"@id":"https://cir.nii.ac.jp/crid/1381418519772015232","@type":"Researcher","foaf:name":[{"@value":"Susumu Uchiyama"}],"jpcoar:affiliationName":[{"@value":"Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan, Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan, Daiichi Pharmaceutical Co., Ltd., Edogawa-ku, Tokyo 134-8630, Japan, and Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka 569-1094, Japan"}]},{"@id":"https://cir.nii.ac.jp/crid/1381418519772015239","@type":"Researcher","foaf:name":[{"@value":"Jun Hasegawa"}],"jpcoar:affiliationName":[{"@value":"Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan, Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan, Daiichi Pharmaceutical Co., Ltd., Edogawa-ku, Tokyo 134-8630, Japan, and Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka 569-1094, Japan"}]},{"@id":"https://cir.nii.ac.jp/crid/1381418519772015235","@type":"Researcher","foaf:name":[{"@value":"Yuji Kobayashi"}],"jpcoar:affiliationName":[{"@value":"Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan, Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan, Daiichi Pharmaceutical Co., Ltd., Edogawa-ku, Tokyo 134-8630, Japan, and Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka 569-1094, Japan"}]},{"@id":"https://cir.nii.ac.jp/crid/1381418519772015233","@type":"Researcher","foaf:name":[{"@value":"Yoshihiro Sambongi"}],"jpcoar:affiliationName":[{"@value":"Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan, Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan, Daiichi Pharmaceutical Co., Ltd., Edogawa-ku, Tokyo 134-8630, Japan, and Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka 569-1094, Japan"}]},{"@id":"https://cir.nii.ac.jp/crid/1381418519772015234","@type":"Researcher","foaf:name":[{"@value":"Tadayasu Ohkubo"}],"jpcoar:affiliationName":[{"@value":"Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan, Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan, Daiichi Pharmaceutical Co., Ltd., Edogawa-ku, Tokyo 134-8630, Japan, and Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka 569-1094, Japan"}]}],"publication":{"publicationIdentifier":[{"@type":"PISSN","@value":"00062960"},{"@type":"EISSN","@value":"15204995"}],"prism:publicationName":[{"@value":"Biochemistry"}],"dc:publisher":[{"@value":"American Chemical Society (ACS)"}],"prism:publicationDate":"2006-04-20","prism:volume":"45","prism:number":"19","prism:startingPage":"6115","prism:endingPage":"6123"},"reviewed":"false","url":[{"@id":"https://pubs.acs.org/doi/pdf/10.1021/bi0520131"}],"createdAt":"2006-05-09","modifiedAt":"2021-10-17","foaf:topic":[{"@id":"https://cir.nii.ac.jp/all?q=Models,%20Molecular","dc:title":"Models, Molecular"},{"@id":"https://cir.nii.ac.jp/all?q=Sequence%20Homology,%20Amino%20Acid","dc:title":"Sequence Homology, Amino Acid"},{"@id":"https://cir.nii.ac.jp/all?q=Protein%20Conformation","dc:title":"Protein Conformation"},{"@id":"https://cir.nii.ac.jp/all?q=Molecular%20Sequence%20Data","dc:title":"Molecular Sequence Data"},{"@id":"https://cir.nii.ac.jp/all?q=Static%20Electricity","dc:title":"Static Electricity"},{"@id":"https://cir.nii.ac.jp/all?q=Cytochrome%20c%20Group","dc:title":"Cytochrome c Group"},{"@id":"https://cir.nii.ac.jp/all?q=Pseudomonas","dc:title":"Pseudomonas"},{"@id":"https://cir.nii.ac.jp/all?q=Enzyme%20Stability","dc:title":"Enzyme Stability"},{"@id":"https://cir.nii.ac.jp/all?q=Thermodynamics","dc:title":"Thermodynamics"},{"@id":"https://cir.nii.ac.jp/all?q=Amino%20Acid%20Sequence","dc:title":"Amino Acid Sequence"},{"@id":"https://cir.nii.ac.jp/all?q=Crystallization","dc:title":"Crystallization"}],"relatedProduct":[{"@id":"https://cir.nii.ac.jp/crid/1050585039689027968","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@language":"en","@value":"Structural and functional insights into thermally stable cytochrome c' from a thermophile"},{"@value":"Structural and functional insights into thermally stable cytochrome <i>c</i>′ from a thermophile"},{"@value":"Structural and functional insights into thermally stable cytochrome c′ from a thermophile"},{"@value":"Structural and functional insights into thermally stable cytochrome c"}]},{"@id":"https://cir.nii.ac.jp/crid/1360002217278850688","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Comparative study on stabilization mechanism of monomeric cytochrome <i>c</i>5 from deep-sea piezophilic <i>Shewanella violacea</i>"}]},{"@id":"https://cir.nii.ac.jp/crid/1360283690314879232","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Correlation between the optimal growth pressures of four Shewanella species and the stabilities of their cytochromes c 5"}]},{"@id":"https://cir.nii.ac.jp/crid/1360285709149679232","@type":"Article","resourceType":"学術雑誌論文(journal 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<i>Pseudomonas</i>"}]},{"@id":"https://cir.nii.ac.jp/crid/1390001206476973440","@type":"Article","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@language":"en","@value":"Effects of Cysteine Introduction into Three Homologous Cytochromes c"},{"@value":"Effects of Cysteine Introduction into Three Homologous Cytochromes<i>c</i>"}]},{"@id":"https://cir.nii.ac.jp/crid/1390001206478679552","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@language":"en","@value":"High Thermal Stability and Unique Trimer Formation of Cytochrome <i>c</i>′ from Thermophilic <i>Hydrogenophilus thermoluteolus</i>"},{"@value":"High Thermal Stability and Unique Trimer Formation of Cytochrome c' from Thermophilic Hydrogenophilus thermoluteolus"},{"@value":"High thermal stability and unique trimer formation of cytochrome c′ from thermophilic Hydrogenophilus thermoluteolus"},{"@value":"High thermal stability and unique trimer formation of cytochrome c"}]},{"@id":"https://cir.nii.ac.jp/crid/1390001206479726848","@type":"Article","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@language":"en","@value":"Stabilization Mechanism of Cytochrome c552 from a Moderately Thermophilic Bacterium, Hydrogenophilus thermoluteolus"},{"@value":"Stabilization Mechanism of Cytochrome<i>c</i><sub>552</sub>from a Moderately Thermophilic Bacterium,<i>Hydrogenophilus thermoluteolus</i>"}]},{"@id":"https://cir.nii.ac.jp/crid/1390581148791663360","@type":"Article","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@language":"en","@value":"Stability of Cytochrome <i>c</i><sub>5</sub> from <i>Shewanella </i>Species Isolated from Deep-Sea and Shallow-Water Areas"},{"@language":"ja","@value":"深海および浅瀬環境由来<i>Shewanella</i>属細菌のシトクロム<i>c</i><sub>5</sub>の構造安定性"},{"@value":"深海および浅瀬環境由来Shewanella属細菌のシトクロムc₅の構造安定性"},{"@language":"ja-Kana","@value":"シンカイ オヨビ アサセ カンキョウ ユライ Shewanellaゾク サイキン ノ シトクロム c ₅ ノ コウゾウ 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