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Article: Structural changes induced by ligand binding drastically increase the thermostability of the Ser/Thr protein kinase TpkD from Thermus thermophilus HB8

Fujino, Yusuke / Miyagawa, Takero / Torii, Masayuki / Inoue, Masao / Fujii, Yuki / Okanishi, Hiroki / Kanai, Yoshikatsu / Masui, Ryoji

FEBS letters. 2021 Jan., v. 595, no. 2

2021

Abstract: Thermophilic proteins maintain their structure at high temperatures through a combination of various factors. Here, we report the ligand‐induced stabilization of a thermophilic Ser/Thr protein kinase. Thermus thermophilus TpkD unfolds completely at 55 °C ...

Abstract	Thermophilic proteins maintain their structure at high temperatures through a combination of various factors. Here, we report the ligand‐induced stabilization of a thermophilic Ser/Thr protein kinase. Thermus thermophilus TpkD unfolds completely at 55 °C despite the optimum growth temperature of 75 °C. Unexpectedly, we found that the TpkD structure is drastically stabilized by its natural ligands ATP and ADP, as evidenced by the increase in the melting temperature to 80 °C. Such a striking effect of a substrate on thermostability has not been reported for other protein kinases. Conformational changes upon ATP binding were observed in fluorescence quenching and limited proteolysis experiments. Urea denaturation of Trp mutants suggested that ATP binding affects not only the ATP‐binding site, but also the remote regions. Our findings shed light on thermoadaptation of thermophilic proteins.
Keywords	Thermus thermophilus ; binding sites ; denaturation ; fluorescence ; ligands ; protein kinases ; proteolysis ; temperature ; thermal stability ; urea
Language	English
Dates of publication	2021-01
Size	p. 264-274.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	212746-5
ISSN	1873-3468 ; 0014-5793
ISSN (online)	1873-3468
ISSN	0014-5793
DOI	10.1002/1873-3468.13996
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Successful closure of refractory esophago-pulmonary fistula after esophagectomy using a vascular embolization plug under endoscopy: A case report.

Tsuji, Toshikatsu / Okamoto, Koichi / Torii, Masayuki / Saito, Hiroto / Shimada, Mari / Moriyama, Hideki / Nakamura, Keishi / Kinoshita, Jun / Inaki, Noriyuki

Asian journal of endoscopic surgery

2022

Abstract: Esophago-pulmonary fistula after esophagectomy is a fatal complication of severe respiratory distress. Minimally invasive treatments, such as esophageal stent placement, have been developed to treat esophago-pulmonary fistulae; however refractory ... ...

Abstract	Esophago-pulmonary fistula after esophagectomy is a fatal complication of severe respiratory distress. Minimally invasive treatments, such as esophageal stent placement, have been developed to treat esophago-pulmonary fistulae; however refractory fistulae may not be cured by this mode of treatment. We encountered a case in which the esophago-pulmonary fistula did not close even though sealing of polyglycolic acid sheets and fibrin glue was administered three times over 4 mo while the esophageal stent was in place. We successfully closed this refractory esophago-pulmonary fistula using a vascular embolization plug under endoscopy. Our procedure can thus be an effective and less invasive treatment for refractory esophago-pulmonary fistula after esophagectomy.
Language	English
Publishing date	2022-08-10
Publishing country	Japan
Document type	Case Reports
ZDB-ID	2503256-2
ISSN	1758-5910 ; 1758-5902
ISSN (online)	1758-5910
ISSN	1758-5902
DOI	10.1111/ases.13117
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Article ; Online: Structural changes induced by ligand binding drastically increase the thermostability of the Ser/Thr protein kinase TpkD from Thermus thermophilus HB8.

Fujino, Yusuke / Miyagawa, Takero / Torii, Masayuki / Inoue, Masao / Fujii, Yuki / Okanishi, Hiroki / Kanai, Yoshikatsu / Masui, Ryoji

FEBS letters

2020 Volume 595, Issue 2, Page(s) 264–274

Abstract: Thermophilic proteins maintain their structure at high temperatures through a combination of various factors. Here, we report the ligand-induced stabilization of a thermophilic Ser/Thr protein kinase. Thermus thermophilus TpkD unfolds completely at 55 °C ...

Abstract	Thermophilic proteins maintain their structure at high temperatures through a combination of various factors. Here, we report the ligand-induced stabilization of a thermophilic Ser/Thr protein kinase. Thermus thermophilus TpkD unfolds completely at 55 °C despite the optimum growth temperature of 75 °C. Unexpectedly, we found that the TpkD structure is drastically stabilized by its natural ligands ATP and ADP, as evidenced by the increase in the melting temperature to 80 °C. Such a striking effect of a substrate on thermostability has not been reported for other protein kinases. Conformational changes upon ATP binding were observed in fluorescence quenching and limited proteolysis experiments. Urea denaturation of Trp mutants suggested that ATP binding affects not only the ATP-binding site, but also the remote regions. Our findings shed light on thermoadaptation of thermophilic proteins.
MeSH term(s)	Adenosine Triphosphate/metabolism ; Bacterial Proteins/chemistry ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Circular Dichroism ; Enzyme Stability ; Ligands ; Mutation ; Protein Binding ; Protein Structure, Tertiary ; Protein-Serine-Threonine Kinases/chemistry ; Protein-Serine-Threonine Kinases/genetics ; Protein-Serine-Threonine Kinases/metabolism ; Proteolysis ; Thermus thermophilus/enzymology ; Thermus thermophilus/genetics ; Transition Temperature
Chemical Substances	Bacterial Proteins ; Ligands ; Adenosine Triphosphate (8L70Q75FXE) ; Protein-Serine-Threonine Kinases (EC 2.7.11.1)
Language	English
Publishing date	2020-11-28
Publishing country	England
Document type	Journal Article
ZDB-ID	212746-5
ISSN	1873-3468 ; 0014-5793
ISSN (online)	1873-3468
ISSN	0014-5793
DOI	10.1002/1873-3468.13996
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Article ; Online: Instrumentation of a PLC-regulated temperature cycler with a PID control unit and its use for miniaturized PCR systems with reduced volumes of aqueous sample droplets isolated in oil phase in a microwell.

Hashimoto, Masahiko / Torii, Masayuki / Yoshida, Kazuma / Noda, Keiichi / Tsukagoshi, Kazuhiko

Analytical sciences : the international journal of the Japan Society for Analytical Chemistry

2011 Volume 27, Issue 12, Page(s) 1191–1196

Abstract: We have developed a temperature cycler for polymerase chain reaction (PCR) in a microwell fabricated on a polymer/glass chip. The entire system consisted of three subsystems, which included (1) a thermal conditioner, (2) a proportional-integral- ... ...

Abstract	We have developed a temperature cycler for polymerase chain reaction (PCR) in a microwell fabricated on a polymer/glass chip. The entire system consisted of three subsystems, which included (1) a thermal conditioner, (2) a proportional-integral-derivative (PID) control signal conditioner and (3) a data acquisition subsystem. The subsystems were regulated coordinately by a ladder logic program written for the programmable logic control (PLC) so that an actual sample temperature could be timed, changed and maintained according to the programmed temperature cycles. The present temperature control system showed high accuracy, stability and minimum overshoot with reduced heating and cooling transition rates. Applicability of the temperature controller to the miniaturized PCR system with reduced volumes of aqueous sample droplets isolated in an oil phase was confirmed by successful amplifications of a target DNA sequence in the microwell.
MeSH term(s)	Base Sequence ; DNA Primers ; Miniaturization ; Oils ; Reproducibility of Results ; Reverse Transcriptase Polymerase Chain Reaction/instrumentation ; Temperature ; Water
Chemical Substances	DNA Primers ; Oils ; Water (059QF0KO0R)
Language	English
Publishing date	2011-11-25
Publishing country	Japan
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1483376-1
ISSN	1348-2246 ; 0910-6340
ISSN (online)	1348-2246
ISSN	0910-6340
DOI	10.2116/analsci.27.1191
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Book ; Conference proceedings ; Online: (Table T1) Magnetic properties of MORB from ODP Leg 187 sites, supplementary data to: Shau, Yen-Hong; Torii, Masayuki; Horng, Chorng-Shern; Liang, Wen-Tzong (2004): Magnetic properties of mid-ocean-ridge basalts from Ocean Drilling Program Leg 187. In: Pedersen, RB; Christie, DM; Miller, DJ (eds.) Proceedings of the Ocean Drilling Program, Scientific Results, College Station, TX (Ocean Drilling Program), 187, 1-25

Shau, Yen-Hong / Horng, Chorng-Shern / Liang, Wen-Tzong / Torii, Masayuki

2004

Abstract: The core samples of mid-ocean-ridge basalts (including Indian and Pacific type) recovered from the Southeast Indian Ridge (SEIR) area near the Australian Antarctic Discordance during Ocean Drilling Program Leg 187 were studied using rock magnetism, ... ...

Abstract	The core samples of mid-ocean-ridge basalts (including Indian and Pacific type) recovered from the Southeast Indian Ridge (SEIR) area near the Australian Antarctic Discordance during Ocean Drilling Program Leg 187 were studied using rock magnetism, mineralogy, and petrography methods. On the basis of thermomagnetic analyses and low-temperature magnetometry, the dominant magnetic carrier in most of the basalt samples (pillow basalts) is characterized as titanomaghemite, which presumably formed by low-temperature oxidation of primary titanomagnetite. Some samples from unaltered massive basalts contain nearly unoxidized titanomagnetite as the main magnetic mineral. A metadiabase sample showing greenschist facies metamorphism contains magnetic minerals dominated by magnetite. The pillow basalts contain titanomaghemite ranging from stable single-domain to pseudosingle-domain (PSD) grains, and the majority are characterized by a single stable component of remanence. The massive basalts show hysteresis features of larger PSD grains and contain a very low coercivity remanence. The values of natural remanent magnetization (NRM) of the samples in this SEIR area are on the same order as those of other oceanic ridge basalts. They show a general decreasing trend of NRM with increasing crust age. However, the values of NRM show no correlation either with the tectonic zonations (Zone A vs. Zone B) or with the mantle provinces (Pacific vs. Indian types).
Language	English
Dates of publication	2004-9999
Size	Online-Ressource
Publisher	PANGAEA - Data Publisher for Earth & Environmental Science
Publishing place	Bremen/Bremerhaven
Document type	Book ; Conference proceedings ; Online
Note	This dataset is supplement to doi:10.2973/odp.proc.sr.187.204.2004
DOI	10.1594/PANGAEA.780754
Database	Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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Book ; Online: Benthic foraminiferal abundances from eight sites of the Northwest Australian shelf, supplementary data to: Gallagher, Stephen J; Wallace, Malcolm W; Li, Chung Leong; Kinna, Belinda; Bye, John A T; Akimoto, Kazumi; Torii, Masayuki (2009): Neogene history of the West Pacific Warm Pool, Kuroshio and Leeuwin currents. Paleoceanography, 24, PA1206

Gallagher, Stephen J / Akimoto, Kazumi / Bye, John A T / Kinna, Belinda / Li, Chung Leong / Torii, Masayuki / Wallace, Malcolm W

2009

Abstract: Foraminiferal analysis of Miocene to recent strata of the Northwest Shelf of Australia is used to chart West Pacific Warm Pool (WPWP) influence. The assemblage is typified by "larger" foraminifera with ingressions of the Indo-Pacific "smaller" taxa ... ...

Abstract	Foraminiferal analysis of Miocene to recent strata of the Northwest Shelf of Australia is used to chart West Pacific Warm Pool (WPWP) influence. The assemblage is typified by "larger" foraminifera with ingressions of the Indo-Pacific "smaller" taxa Asterorotalia and Pseudorotalia at around 4 Ma and from 1.6 to 0.8 Ma. A review of recent and fossil biogeography of these taxa suggests their stratigraphic distribution can be used to document WPWP evolution. From 10 to 4.4 Ma a lack of biogeographic connectivity between the Pacific and Indian Ocean suggests Indonesian Throughflow (ITF) restriction. During this period, the collision of Australia and Asia trapped warmer waters in the Pacific, creating a central WPWP biogeographic province from the equator to 26°N. By 3 Ma Indo-Pacific species migrated to Japan with the initiation of the "modern" Kuroshio Current coinciding with the intensification of the North Pacific Gyre and Northern Hemisphere ice sheet expansion. Indo-Pacific taxa migrated to the northwest Australia from 4.4 to 4 Ma possibly because of limited ITF. The absence of Indo-Pacific taxa in northwest Australia indicates possible ITF restriction from 4 to 1.6 Ma. Full northwest Australian biogeographic connectivity with the WPWP from 1.6 to 0.8 Ma suggests an unrestricted stronger ITF (compared to today) and the initiation of the modern Leeuwin Current. The extinction of some Indo-Pacific species in northwest Australia after 0.8 Ma may be related to the effects of large glacial/interglacial oscillations and uplift of the Indonesian Archipelago causing Indonesian seaway restriction.
Language	English
Dates of publication	2009-9999
Size	Online-Ressource
Publisher	PANGAEA - Data Publisher for Earth & Environmental Science
Publishing place	Bremen/Bremerhaven
Document type	Book ; Online
Note	This dataset is supplement to doi:10.1029/2008PA001660
DOI	10.1594/PANGAEA.758377
Database	Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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Book ; Conference proceedings ; Online: Magnetostratigraphy of ODP Leg 107 holes, supplementary data to: Channell, James ET; Torii, Masayuki; Hawthorne, Teresa B (1990): Magnetostratigraphy of sediments recovered at sites 650, 651, 652 and 654 (Leg 107 in the Tyrrhenian Sea). In: Kastens, KA; Mascle, J; et al. (eds.), Proceedings of the Ocean Drilling Program, Scientific Results, College Station, TX (Ocean Drilling Program), 107, 335-346

Channell, James ET / Hawthorne, Teresa B / Torii, Masayuki

1990

Abstract: Apart from Site 650, core disturbance due to rotary drilling severely compromised the quality of the magnetostratigraphic data obtained from Leg 107 sediments. The correlation of polarity zones to the geomagnetic polarity time scale cannot be made solely ...

Abstract	Apart from Site 650, core disturbance due to rotary drilling severely compromised the quality of the magnetostratigraphic data obtained from Leg 107 sediments. The correlation of polarity zones to the geomagnetic polarity time scale cannot be made solely on the basis of pattern fit. The proposed correlations are consistent between sites, and this consistency is constrained by the biostratigraphic datums. The resulting biomagnetostratigraphic correlations are reviewed in the synthesis section of this volume. The purpose of this paper is to document the magnetic stratigraphies, and present the preferred correlation to the geomagnetic reversal time scale. Four implications of the proposed correlations are: (1) The Mio-Pliocene boundary occurs in the lowest reversed interval of the Gilbert (Chron 3r) at about 4.9 Ma. (2) The thick pre-Pliocene lacustrine sequence recovered at Site 652 appears to have been deposited entirely within a single reversed polarity chron (Chron 3r). (3) The balatino-type gypsum recovered at Site 654 was also deposited entirely within this polarity chron (Chron 3r). (4) The Tortonian-Messinian boundary occurs within a normal polarity zone which is probably correlative to Chron 6 (Chron 3B) giving a boundary age of about 6.4 Ma.
Language	English
Dates of publication	1990-9999
Size	Online-Ressource
Publisher	PANGAEA - Data Publisher for Earth & Environmental Science
Publishing place	Bremen/Bremerhaven
Document type	Book ; Conference proceedings ; Online
Note	This dataset is supplement to doi:10.2973/odp.proc.sr.107.167.1990
DOI	10.1594/PANGAEA.745981
Database	Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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Book ; Conference proceedings ; Online: Magnetic properties and paleomagnetism of basalts from ODP Leg 107 basalts, supplementary data to: Vigliotti, Luigi; Torii, Masayuki; Channell, James ET (1990): Magnetic properties and paleomagnetism of basalts from Leg 107 (Holes 651A and 655B). In: Kastens, KA; Mascle, J; et al. (eds.), Proceedings of the Ocean Drilling Program, Scientific Results, College Station, TX (Ocean Drilling Program), 107, 99-110

Vigliotti, Luigi / Channell, James ET / Torii, Masayuki

1990

Abstract: The basalts recovered at Holes 651A and 655B appear to carry a single component remanent magnetization, which is generally of reversed polarity. These magnetizations are consistent with eruption during the Matuyama (651A) and Gilbert (655B) polarity ... ...

Abstract	The basalts recovered at Holes 651A and 655B appear to carry a single component remanent magnetization, which is generally of reversed polarity. These magnetizations are consistent with eruption during the Matuyama (651A) and Gilbert (655B) polarity epochs. The blocking temperature spectra and the Js/T curves indicate that titanomaghemite is the principal remanence carrier. The lower mean destructive field (MDF) and higher susceptibility at 651A probably indicates a lower mean oxidation state at this hole relative to 655B, which may simply reflect the age difference between the two basalt sequences. At both holes, a decreasing downcore trend both in natural remanent magnetization (NRM) and susceptibility probably indicates that maghemitization (from primary titanomagnetite) increases downcore. An interval of high coercivity at hole 655B (119.80-151.45 mbsf) appears to define a magnetically distinct unit within the basalt sequence.
Language	English
Dates of publication	1990-9999
Size	Online-Ressource
Publisher	PANGAEA - Data Publisher for Earth & Environmental Science
Publishing place	Bremen/Bremerhaven
Document type	Book ; Conference proceedings ; Online
Note	This dataset is supplement to doi:10.2973/odp.proc.sr.107.165.1990
DOI	10.1594/PANGAEA.745793
Database	Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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Book ; Conference proceedings ; Online: (Table 1) Polarity boundaries observed in ODP Leg 127/128 sites, supplementary data to: Torii, Masayuki; Hayashida, Akira; Vigliotti, Luigi; Wippern, Jobst JM (1992): Rock magnetic properties of sediments from Site 797, Japan Sea. In: Tamaki, K; Suychiro, K; Allan, J; McWilliams, M; et al. (eds.), Proceedings of the Ocean Drilling Program, Scientific Results, College Station, TX (Ocean Drilling Program), 127/128(2), 947-957

Torii, Masayuki / Hayashida, Akira / Vigliotti, Luigi / Wippern, Jobst JM

1992

Abstract: We present the magnetostratigraphic data for Sites 794, 795, 797, 798, and 799 in the Japan Sea. APC cores from these sites record the polarity sequence for the Pliocene-Pleistocene period. The intensity of the magnetization decreases with depth by more ... ...

Abstract	We present the magnetostratigraphic data for Sites 794, 795, 797, 798, and 799 in the Japan Sea. APC cores from these sites record the polarity sequence for the Pliocene-Pleistocene period. The intensity of the magnetization decreases with depth by more than an order of magnitude, and the low intensity samples tend to give scattered directional data. The cause of these phenomena is examined based on the correlation of the intensity with the bulk magnetic susceptibility.
Language	English
Dates of publication	1992-9999
Size	Online-Ressource
Publisher	PANGAEA - Data Publisher for Earth & Environmental Science
Publishing place	Bremen/Bremerhaven
Document type	Book ; Conference proceedings ; Online
Note	This dataset is supplement to doi:10.2973/odp.proc.sr.127128-2.213.1992
DOI	10.1594/PANGAEA.777663
Database	Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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Book ; Conference proceedings ; Online: (Table 1) Rock magnetic properties of the sediment samples from ODP Hole 127-797B, supplementary data to: Torii, Masayuki; Hayashida, Akira; Vigliotti, Luigi; Wippern, Jobst JM (1992): Rock magnetic properties of sediments from Site 797, Japan Sea. In: Tamaki, K; Suychiro, K; Allan, J; McWilliams, M; et al. (eds.), Proceedings of the Ocean Drilling Program, Scientific Results, College Station, TX (Ocean Drilling Program), 127/128(2), 947-957

Torii, Masayuki / Hayashida, Akira / Vigliotti, Luigi / Wippern, Jobst JM

1992

Abstract: Paleomagnetic and rock magnetic studies of the sediment samples from Site 797 were carried out. Thermal demagnetization was found to be more effective in removing secondary overprinting than alternating field demagnetization. Production of new magnetic ... ...

Abstract	Paleomagnetic and rock magnetic studies of the sediment samples from Site 797 were carried out. Thermal demagnetization was found to be more effective in removing secondary overprinting than alternating field demagnetization. Production of new magnetic minerals during the thermal treatment was frequently observed and made thorough demagnetization difficult, however. Thermal demagnetization of orthogonal IRM's suggests that magnetite and pyrrhotite are common magnetic minerals in these sediments. The Lowrie-Fuller test and xARM/x ratio show apparent grain size of the magnetic minerals to be that of single-domain to small multi-domain state. A downcore decrease of rock magnetic parameters such as ARM, IRM, and xARM/x ratio in the upper half of the hole indicates progressive diagenetic dissolution of finer magnetic minerals. In the lower part where igneous rocks intruded, production of magnetic minerals is suggested by discontinuous change of the downcore trend, which may have brought remagnetization of the sediment samples.
Language	English
Dates of publication	1992-9999
Size	Online-Ressource
Publisher	PANGAEA - Data Publisher for Earth & Environmental Science
Publishing place	Bremen/Bremerhaven
Document type	Book ; Conference proceedings ; Online
Note	This dataset is supplement to doi:10.2973/odp.proc.sr.127128-2.213.1992
DOI	10.1594/PANGAEA.777652
Database	Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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