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米澤 康滋 - One of the best experts on this subject based on the ideXlab platform.
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Molecular Dynamics Simulation with Principle Component Analysis Study on the Dynamics of DHFR Protein from Moritella profunda at High Pressure Condition
キンキ ダイガク センタン ギジュツ ソウゴウ ケンキュウジョ, 2015Co-Authors: 米澤 康滋, ヨネザワ ヤスシゲ, Yonezawa YasushigeAbstract:publisher近畿大学先端技術総合研究所紀要編集委員会[要旨] 高圧力下に生存する深海生物はその高圧力環境に適した進化を遂げている. その進化は細胞機能の殆どを司る蛋白質にも反映されていることが最近の研究から明らかとなって来た. 一般に常圧下（１気圧）に生存する蛋白質は高圧力下でその機能及び構造を変化させ多くの場合は機能が低下する. 従って高圧力下に暮らす生物（深海生物）の蛋白質は高圧力に対して最適な分子進化を遂げていることが予想される. このような背景のもと高圧力下での蛋白質構造機能を研究する実験及び理論的試みが世界中各地で進められている. 本研究では, 深海生物Moritella profunda のDHFR を, Escherichia coli のDHFR と比較することでその構造及び機能動態・構造揺らぎ, 及びその圧力依存性を様々な手法で解析した. その結果, 深海生物由来DHFR の構造揺らぎは高圧力下でも機能を失わないような独自な構造動態を示す進化を遂げていることを示唆する結果を得た. [Abstract] Organisms live in a variety of extreme environmental conditions such as high/low temperature, high salt concentration and also high pressure. For instance, a number of Organisms have been so far discovered at deep sea. It is believed that the deep sea Organisms have been evolved with adaptation to high pressure. In recent decades, proteins of the deep sea Organisms have been isolated like those from thermophilic Organisms. Here, in order to elucidate the adaptation mechanism to the high pressure, we have conducted extensive molecular dynamics simulation studies at high（2000 bar） and normal pressure conditions using DHFR from a deep sea Organism Moritella profunda（mpDHFR）. We also simulated DHFR from Escherichia coli（ecDHFR） for omparison. We took a trajectory from the simulations and performed several analyses involving RMSD, RMSF, Gyration and principle component analysis（PCA）. We found that high pressure does not affect overall structure of DHFRs. However, large slow fluctuations that govern the functions of DHFR are significantly different between ecDHFR and mpDHFR, while the trajectory we used is rather short to sufficiently elucidate the result. The difference is likely to be caused from the E-helix fluctuation. The fluctuation differences should be responsible for the activity change of mpDHFR at high pressure
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Molecular Dynamics Simulation with Principle Component Analysis Study on the Dynamics of DHFR Protein from Moritella profunda at High Pressure Condition
近畿大学先端技術総合研究所, 2015Co-Authors: 米澤 康滋Abstract:[要旨] 高圧力下に生存する深海生物はその高圧力環境に適した進化を遂げている. その進化は細胞機能の殆どを司る蛋白質にも反映されていることが最近の研究から明らかとなって来た. 一般に常圧下（１気圧）に生存する蛋白質は高圧力下でその機能及び構造を変化させ多くの場合は機能が低下する. 従って高圧力下に暮らす生物（深海生物）の蛋白質は高圧力に対して最適な分子進化を遂げていることが予想される. このような背景のもと高圧力下での蛋白質構造機能を研究する実験及び理論的試みが世界中各地で進められている. 本研究では, 深海生物Moritella profunda のDHFR を, Escherichia coli のDHFR と比較することでその構造及び機能動態・構造揺らぎ, 及びその圧力依存性を様々な手法で解析した. その結果, 深海生物由来DHFR の構造揺らぎは高圧力下でも機能を失わないような独自な構造動態を示す進化を遂げていることを示唆する結果を得た. [Abstract] Organisms live in a variety of extreme environmental conditions such as high/low temperature, high salt concentration and also high pressure. For instance, a number of Organisms have been so far discovered at deep sea. It is believed that the deep sea Organisms have been evolved with adaptation to high pressure. In recent decades, proteins of the deep sea Organisms have been isolated like those from thermophilic Organisms. Here, in order to elucidate the adaptation mechanism to the high pressure, we have conducted extensive molecular dynamics simulation studies at high（2000 bar） and normal pressure conditions using DHFR from a deep sea Organism Moritella profunda（mpDHFR）. We also simulated DHFR from Escherichia coli（ecDHFR） for omparison. We took a trajectory from the simulations and performed several analyses involving RMSD, RMSF, Gyration and principle component analysis（PCA）. We found that high pressure does not affect overall structure of DHFRs. However, large slow fluctuations that govern the functions of DHFR are significantly different between ecDHFR and mpDHFR, while the trajectory we used is rather short to sufficiently elucidate the result. The difference is likely to be caused from the E-helix fluctuation. The fluctuation differences should be responsible for the activity change of mpDHFR at high pressure.近畿大学先端技術総合研究所紀要編集委員
Yonezawa Yasushige - One of the best experts on this subject based on the ideXlab platform.
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Molecular Dynamics Simulation with Principle Component Analysis Study on the Dynamics of DHFR Protein from Moritella profunda at High Pressure Condition
キンキ ダイガク センタン ギジュツ ソウゴウ ケンキュウジョ, 2015Co-Authors: 米澤 康滋, ヨネザワ ヤスシゲ, Yonezawa YasushigeAbstract:publisher近畿大学先端技術総合研究所紀要編集委員会[要旨] 高圧力下に生存する深海生物はその高圧力環境に適した進化を遂げている. その進化は細胞機能の殆どを司る蛋白質にも反映されていることが最近の研究から明らかとなって来た. 一般に常圧下（１気圧）に生存する蛋白質は高圧力下でその機能及び構造を変化させ多くの場合は機能が低下する. 従って高圧力下に暮らす生物（深海生物）の蛋白質は高圧力に対して最適な分子進化を遂げていることが予想される. このような背景のもと高圧力下での蛋白質構造機能を研究する実験及び理論的試みが世界中各地で進められている. 本研究では, 深海生物Moritella profunda のDHFR を, Escherichia coli のDHFR と比較することでその構造及び機能動態・構造揺らぎ, 及びその圧力依存性を様々な手法で解析した. その結果, 深海生物由来DHFR の構造揺らぎは高圧力下でも機能を失わないような独自な構造動態を示す進化を遂げていることを示唆する結果を得た. [Abstract] Organisms live in a variety of extreme environmental conditions such as high/low temperature, high salt concentration and also high pressure. For instance, a number of Organisms have been so far discovered at deep sea. It is believed that the deep sea Organisms have been evolved with adaptation to high pressure. In recent decades, proteins of the deep sea Organisms have been isolated like those from thermophilic Organisms. Here, in order to elucidate the adaptation mechanism to the high pressure, we have conducted extensive molecular dynamics simulation studies at high（2000 bar） and normal pressure conditions using DHFR from a deep sea Organism Moritella profunda（mpDHFR）. We also simulated DHFR from Escherichia coli（ecDHFR） for omparison. We took a trajectory from the simulations and performed several analyses involving RMSD, RMSF, Gyration and principle component analysis（PCA）. We found that high pressure does not affect overall structure of DHFRs. However, large slow fluctuations that govern the functions of DHFR are significantly different between ecDHFR and mpDHFR, while the trajectory we used is rather short to sufficiently elucidate the result. The difference is likely to be caused from the E-helix fluctuation. The fluctuation differences should be responsible for the activity change of mpDHFR at high pressure
Christoph Gelhaus - One of the best experts on this subject based on the ideXlab platform.
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Characterization and Function of the First Antibiotic Isolated from a Vent Organism: The Extremophile Metazoan Alvinella pompejana
PLoS ONE, 2014Co-Authors: Aurélie Tasiemski, Sascha Jung, Céline Boidin-wichlacz, Didier Jollivet, Virginie Cuvillier-hot, Florence Pradillon, Costantino Vetriani, Oliver Hecht, Frank D. Sönnichsen, Christoph GelhausAbstract:The emblematic hydrothermal worm Alvinella pompejana is one of the most thermo tolerant animal known on Earth. It relies on a symbiotic association offering a unique opportunity to discover biochemical adaptations that allow animals to thrive in such a hostile habitat. Here, by studying the Pompeii worm, we report on the discovery of the first antibiotic peptide from a Deep-Sea Organism, namely alvinellacin. After purification and peptide sequencing, both the gene and the peptide tertiary structures were elucidated. As epibionts are not cultivated so far and because of lethal decompression effects upon Alvinella sampling, we developed shipboard biological assays to demonstrate that in addition to act in the first line of defense against microbial invasion, alvinellacin shapes and controls the worm's epibiotic microflora. Our results provide insights into the nature of an abyssal antimicrobial peptide (AMP) and into the manner in which an extremophile eukaryote uses it to interact with the particular microbial community of the hydrothermal vent ecosystem. Unlike earlier studies done on hydrothermal vents that all focused on the microbial side of the symbiosis, our work gives a view of this interaction from the host side.
ヨネザワ ヤスシゲ - One of the best experts on this subject based on the ideXlab platform.
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Molecular Dynamics Simulation with Principle Component Analysis Study on the Dynamics of DHFR Protein from Moritella profunda at High Pressure Condition
キンキ ダイガク センタン ギジュツ ソウゴウ ケンキュウジョ, 2015Co-Authors: 米澤 康滋, ヨネザワ ヤスシゲ, Yonezawa YasushigeAbstract:publisher近畿大学先端技術総合研究所紀要編集委員会[要旨] 高圧力下に生存する深海生物はその高圧力環境に適した進化を遂げている. その進化は細胞機能の殆どを司る蛋白質にも反映されていることが最近の研究から明らかとなって来た. 一般に常圧下（１気圧）に生存する蛋白質は高圧力下でその機能及び構造を変化させ多くの場合は機能が低下する. 従って高圧力下に暮らす生物（深海生物）の蛋白質は高圧力に対して最適な分子進化を遂げていることが予想される. このような背景のもと高圧力下での蛋白質構造機能を研究する実験及び理論的試みが世界中各地で進められている. 本研究では, 深海生物Moritella profunda のDHFR を, Escherichia coli のDHFR と比較することでその構造及び機能動態・構造揺らぎ, 及びその圧力依存性を様々な手法で解析した. その結果, 深海生物由来DHFR の構造揺らぎは高圧力下でも機能を失わないような独自な構造動態を示す進化を遂げていることを示唆する結果を得た. [Abstract] Organisms live in a variety of extreme environmental conditions such as high/low temperature, high salt concentration and also high pressure. For instance, a number of Organisms have been so far discovered at deep sea. It is believed that the deep sea Organisms have been evolved with adaptation to high pressure. In recent decades, proteins of the deep sea Organisms have been isolated like those from thermophilic Organisms. Here, in order to elucidate the adaptation mechanism to the high pressure, we have conducted extensive molecular dynamics simulation studies at high（2000 bar） and normal pressure conditions using DHFR from a deep sea Organism Moritella profunda（mpDHFR）. We also simulated DHFR from Escherichia coli（ecDHFR） for omparison. We took a trajectory from the simulations and performed several analyses involving RMSD, RMSF, Gyration and principle component analysis（PCA）. We found that high pressure does not affect overall structure of DHFRs. However, large slow fluctuations that govern the functions of DHFR are significantly different between ecDHFR and mpDHFR, while the trajectory we used is rather short to sufficiently elucidate the result. The difference is likely to be caused from the E-helix fluctuation. The fluctuation differences should be responsible for the activity change of mpDHFR at high pressure
Aurélie Tasiemski - One of the best experts on this subject based on the ideXlab platform.
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Characterization and Function of the First Antibiotic Isolated from a Vent Organism: The Extremophile Metazoan Alvinella pompejana
PLoS ONE, 2014Co-Authors: Aurélie Tasiemski, Sascha Jung, Céline Boidin-wichlacz, Didier Jollivet, Virginie Cuvillier-hot, Florence Pradillon, Costantino Vetriani, Oliver Hecht, Frank D. Sönnichsen, Christoph GelhausAbstract:The emblematic hydrothermal worm Alvinella pompejana is one of the most thermo tolerant animal known on Earth. It relies on a symbiotic association offering a unique opportunity to discover biochemical adaptations that allow animals to thrive in such a hostile habitat. Here, by studying the Pompeii worm, we report on the discovery of the first antibiotic peptide from a Deep-Sea Organism, namely alvinellacin. After purification and peptide sequencing, both the gene and the peptide tertiary structures were elucidated. As epibionts are not cultivated so far and because of lethal decompression effects upon Alvinella sampling, we developed shipboard biological assays to demonstrate that in addition to act in the first line of defense against microbial invasion, alvinellacin shapes and controls the worm's epibiotic microflora. Our results provide insights into the nature of an abyssal antimicrobial peptide (AMP) and into the manner in which an extremophile eukaryote uses it to interact with the particular microbial community of the hydrothermal vent ecosystem. Unlike earlier studies done on hydrothermal vents that all focused on the microbial side of the symbiosis, our work gives a view of this interaction from the host side.
