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Article ; Online: Sargassum horneri C. Agardh space capacity estimation reveals that thallus surface area varies with wet weight.

Xu, Min / Sasa, Shuji / Komatsu, Teruhisa

2018 Volume 13, Issue 6, Page(s) e0199103

Abstract: ... Chinese and Japanese fisherman rely on S. horneri beds as productive fish harvest areas. The Zhejiang ... a marine protected area. In this study we analysed the association between weight and one-sided surface area of S. horneri ... We collected samples from December 2014 to May 2015. Approximately 1 g of S. horneri biomass provided ~15 cm2 ...

Abstract	Sargassum horneri C. Agardh is an important commercial edible seaweed species in east Asia. Benthic beds and floating rafts in coastal areas make excellent habitats for marine organisms to feed, hide, and spawn. Many commercially important fish species such as Japanese anchovy (Engraulis japonicus), yellowtail (Seriola quinqueradiata), and Japanese horse mackerel (Trachurus japonicus) live in seaweed beds. Chinese and Japanese fisherman rely on S. horneri beds as productive fish harvest areas. The Zhejiang government in China set a total allowable catch standard, to preserve the Ma'an Islands ecosystem, which is a marine protected area. In this study we analysed the association between weight and one-sided surface area of S. horneri beds, and calculated the ratio of one-sided surface area to change in wet weight over time. We collected samples from December 2014 to May 2015. Approximately 1 g of S. horneri biomass provided ~15 cm2 of one-sided surface area available to marine organisms. These calculations can be used as a reference regarding potential space to improve total allowable catch standard management in S. horneri beds, through the estimation of space capacity of seaweed beds.
MeSH term(s)	Aquatic Organisms ; Biometry ; China ; Ecosystem ; Fisheries/legislation & jurisprudence ; Japan ; Sargassum/growth & development ; Sargassum/ultrastructure ; Seasons
Language	English
Publishing date	2018-06-19
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0199103
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Drug binding dynamics of the dimeric SARS-CoV-2 main protease, determined by molecular dynamics simulation.

Komatsu, Teruhisa S / Okimoto, Noriaki / Koyama, Yohei M / Hirano, Yoshinori / Morimoto, Gentaro / Ohno, Yousuke / Taiji, Makoto

Scientific reports

2020 Volume 10, Issue 1, Page(s) 16986

Abstract: We performed molecular dynamics simulation of the dimeric SARS-CoV-2 (severe acute respiratory syndrome corona virus 2) main protease ( ... ...

Abstract	We performed molecular dynamics simulation of the dimeric SARS-CoV-2 (severe acute respiratory syndrome corona virus 2) main protease (M
MeSH term(s)	Betacoronavirus/drug effects ; Betacoronavirus/metabolism ; Binding Sites/drug effects ; Biophysical Phenomena ; COVID-19 ; Catalytic Domain/drug effects ; Computational Biology ; Coronavirus 3C Proteases ; Coronavirus Infections/drug therapy ; Cysteine Endopeptidases/metabolism ; Darunavir/metabolism ; Darunavir/pharmacology ; Drug Repositioning/methods ; HIV Protease Inhibitors/metabolism ; HIV Protease Inhibitors/pharmacology ; Humans ; Indinavir/metabolism ; Indinavir/pharmacology ; Lopinavir/metabolism ; Lopinavir/pharmacology ; Molecular Dynamics Simulation ; Nelfinavir/metabolism ; Nelfinavir/pharmacology ; Pandemics ; Pneumonia, Viral/drug therapy ; Ritonavir/metabolism ; Ritonavir/pharmacology ; SARS-CoV-2 ; Saquinavir/metabolism ; Saquinavir/pharmacology ; Viral Nonstructural Proteins/metabolism
Chemical Substances	HIV Protease Inhibitors ; Viral Nonstructural Proteins ; Lopinavir (2494G1JF75) ; Indinavir (5W6YA9PKKH) ; Cysteine Endopeptidases (EC 3.4.22.-) ; Coronavirus 3C Proteases (EC 3.4.22.28) ; Nelfinavir (HO3OGH5D7I) ; Saquinavir (L3JE09KZ2F) ; Ritonavir (O3J8G9O825) ; Darunavir (YO603Y8113)
Keywords	covid19
Language	English
Publishing date	2020-10-12
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-020-74099-5
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Drug binding dynamics of the dimeric SARS-CoV-2 main protease, determined by molecular dynamics simulation

Teruhisa S. Komatsu / Noriaki Okimoto / Yohei M. Koyama / Yoshinori Hirano / Gentaro Morimoto / Yousuke Ohno / Makoto Taiji

Scientific Reports, Vol 10, Iss 1, Pp 1-

2020 Volume 11

Abstract: Abstract We performed molecular dynamics simulation of the dimeric SARS-CoV-2 (severe acute respiratory syndrome corona virus 2) main protease (Mpro) to examine the binding dynamics of small molecular ligands. Seven HIV inhibitors, darunavir, indinavir, ... ...

Abstract	Abstract We performed molecular dynamics simulation of the dimeric SARS-CoV-2 (severe acute respiratory syndrome corona virus 2) main protease (Mpro) to examine the binding dynamics of small molecular ligands. Seven HIV inhibitors, darunavir, indinavir, lopinavir, nelfinavir, ritonavir, saquinavir, and tipranavir, were used as the potential lead drugs to investigate access to the drug binding sites in Mpro. The frequently accessed sites on Mpro were classified based on contacts between the ligands and the protein, and the differences in site distributions of the encounter complex were observed among the ligands. All seven ligands showed binding to the active site at least twice in 28 simulations of 200 ns each. We further investigated the variations in the complex structure of the active site with the ligands, using microsecond order simulations. Results revealed a wide variation in the shapes of the binding sites and binding poses of the ligands. Additionally, the C-terminal region of the other chain often interacted with the ligands and the active site. Collectively, these findings indicate the importance of dynamic sampling of protein–ligand complexes and suggest the possibilities of further drug optimisations.
Keywords	Medicine ; R ; Science ; Q ; covid19
Subject code	540
Language	English
Publishing date	2020-10-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: Drug Binding Dynamics of the Dimeric SARS-CoV-2 Main Protease, Determined by Molecular Dynamics Simulation

Teruhisa S. KOMATSU / Noriaki Okimoto / Yohei M. KOYAMA / Yoshinori HIRANO / Gentaro MORIMOTO / Yousuke OHNO / Makoto Taiji

2020

Abstract: We performed molecular dynamics simulation of the dimeric SARS-CoV-2 (severe acute respiratory syndrome corona virus 2) main protease (Mpro) to examine the binding dynamics of small molecular ligands. Seven HIV inhibitors, darunavir, indinavir, lopinavir, ...

Abstract	We performed molecular dynamics simulation of the dimeric SARS-CoV-2 (severe acute respiratory syndrome corona virus 2) main protease (Mpro) to examine the binding dynamics of small molecular ligands. Seven HIV inhibitors, darunavir, indinavir, lopinavir, nelfinavir, ritonavir, saquinavir, and tipranavir, were used as the potential lead drugs to investigate access to the drug binding sites in Mpro. The frequently accessed sites on Mpro were classified based on contacts between the ligands and the protein, and the differences in site distributions of the encounter complex were observed among the ligands. All seven ligands showed binding to the active site at least twice in 28 simulations of 200 ns each. We further investigated the variations in the complex structure of the active site with the ligands, using microsecond order simulations. Results revealed a wide variation in the shapes of the binding sites and binding poses of the ligands. Additionally, the C-terminal region of the other chain often interacted with the ligands and the active site. Collectively, these findings indicate the importance of dynamic sampling of protein- ligand complexes and suggest the possibilities of further drug optimisations. Raw trajectory data analysed in this paper and movie examples are available at the zenodo repository.
Keywords	Bioinformatics and Computational Biology ; Biophysics ; Drug Discovery and Drug Delivery Systems ; COVID-19 virus (SARS-CoV-2) ; Main Protease Mpro ; 3CLpro ; Molecular Dynamics Simulation Study ; Drug Binding ; microsecond dynamics simulations ; covid19
Subject code	540
Publishing date	2020-05-27T09:55:37Z
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: Molecular dynamics trajectories for SARS-CoV-2 Mpro with 7 HIV inhibitors

KOMATSU Teruhisa S. / OKIMOTO Noriaki / KOYAMA Yohei M. / HIRANO Yoshinori / MORIMOTO Gentaro / OHNO Yousuke / TAIJI Makoto

2020

Abstract: Raw trajectory data (GROMACS format) of all atom molecular dynamics simulation of COVID-19 related SARS-CoV-2 dimeric main protease (based on PDB 6LU7) with 7 kinds of HIV inhibitors (darunavir, indinavir, lopinavir, nelfinavir, ritonavir, saquinavir, ... ...

Abstract	Raw trajectory data (GROMACS format) of all atom molecular dynamics simulation of COVID-19 related SARS-CoV-2 dimeric main protease (based on PDB 6LU7) with 7 kinds of HIV inhibitors (darunavir, indinavir, lopinavir, nelfinavir, ritonavir, saquinavir, and tipranavir) were calculated on massively parallel supercomputer HOKUSAI Big Waterfall at RIKEN ISC, and a special-purpose computer, MDGRAPE-4A, at RIKEN BDR, JAPAN. For each ligand, 200ns length 28 trajectories were calculated. Some of these trajectories were calculated further longer. We can observe formation of encounter complex and investigate potential binding sites on the surface of the dimeric protease. We hope that these raw data are valuable for further drug repurposing/development research targeting the SARS-CoV-2 main protease. We will submit analysis of these data to refereed journal. Molecular dynamics simulations were performed under NVT at 310K, with the time step 2.5fs. The starting structure was prepared based on PDB 6LU7, with amber14sb force field in about 10nm cubic box with periodic boundary conditions. The ligands were initially placed apart from the active sites of the dimeric main protease. We have also already deposited 10 microseconds trajectories of the dimeric protease without ligand (with amber99sb-ildn force field) in the repository https://data.mendeley.com/datasets/vpps4vhryg/1 (DOI:10.17632/vpps4vhryg.1). Files: LIG_28traj200ns_every200ps.zip (28trajectories for each ligand) traj200ns_every200ps/LIG/a/traj200ns_every200ps_LIG-a-n.xtc (trajectory in GROMACS XTC) traj200ns_every200ps/LIG/a/conf.gro (initial condition in GROMACS GRO) traj200ns_every200ps/LIG/topology/ (contains topology files) traj200ns_every200ps/LIG/mdp/ (contains run paramter files) ZZZ_20traj1us_every200ps.zip (20trajectories extended to 1microsecond) traj1us_every200ps/traj1us_every200ps_LIG-a-n.xtc DAR-C-06, DAR-D-07 IND-C-05, IND-C-06, IND-D-06 LOP-A-02, LOP-D-03 NEL-B-01, NEL-C-07, NEL-D-02 RIT-B-07, RIT-C-07 SAQ-B-01, SAQ-C-04, SAQ-D-03 TPR-A-07, TPR-B-04, TPR-B-06, TPR-C-05, TPR-D-02 ZZZ_3traj6us_every1ns.zip (3trajectories extended to 6microseconds or more) traj6us_every1ns/traj6us_every1ns_LIG-a-n.xtc IND-D-06, NEL-B-01, TPR-B-04 ZZZ_LigandBindingPosePDBs.zip (pickup 3 snapshots for each ligand) LigandBindingPosePDBs/LIG-a-n_frame.pdb movies_overlooking_28traj200ns.zip (7x2movies) movies_28traj200ns/movie_overlooking_LIG_28traj200ns-viewA.mp4 inspecting 28traj at once movies_28traj200ns/movie_overlooking_LIG_28traj200ns-viewB.mp4 from the opposite angle movies_1us.zip (17movies) movies_1us/movie_LIG-a-n_1us.mp4 movies_6us.zip (3movies) movies_6us/movie_LIG-a-n_6us.mp4 where LIG={DAR,IND,LOP,NEL,RIT,SAQ,TPR} DAR:darunavir IND:indinavir NEL:nelfinavir RIT:ritonavir SAQ:saquinavir TPR:tipranavir a={A,B,C,D} n={01,02,03,04,05,06,07}
Keywords	COVID-19 ; SARS-CoV-2 ; molecular dynamics ; all atom molecular dynamics simulation ; drug repurposing ; ligand binding ; HIV inhibitor ; Virus ; covid19
Subject code	540
Publishing date	2020-05-13
Publishing country	eu
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Thermal transistor utilizing gas-liquid transition.

Komatsu, Teruhisa S / Ito, Nobuyasu

Physical review. E, Statistical, nonlinear, and soft matter physics

2011 Volume 83, Issue 1 Pt 1, Page(s) 12104

Abstract: We propose a simple thermal transistor, a device to control heat current. In order to effectively change the current, we utilize the gas-liquid transition of the heat-conducting medium (fluid) because the gas region can act as a good thermal insulator. ... ...

Abstract	We propose a simple thermal transistor, a device to control heat current. In order to effectively change the current, we utilize the gas-liquid transition of the heat-conducting medium (fluid) because the gas region can act as a good thermal insulator. The three terminals of the transistor are located at both ends and the center of the system, and are put into contact with distinct heat baths. The key idea is a special arrangement of the three terminals. The temperature at one end (the gate temperature) is used as an input signal to control the heat current between the center (source, hot) and another end (drain, cold). Simulating the nanoscale systems of this transistor, control of heat current is demonstrated. The heat current is effectively cut off when the gate temperature is cold and it flows normally when it is hot. By using an extended version of this transistor, we also simulate a primitive application for an inverter.
Language	English
Publishing date	2011-01
Publishing country	United States
Document type	Journal Article
ISSN	1550-2376
ISSN (online)	1550-2376
DOI	10.1103/PhysRevE.83.012104
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Book ; Online: Molecular dynamics trajectories for SARS-CoV-2 Mpro with 7 HIV inhibitors

KOMATSU Teruhisa S. / OKIMOTO Noriaki / KOYAMA Yohei M. / HIRANO Yoshinori / MORIMOTO Gentaro / OHNO Yousuke / TAIJI Makoto

2020

Abstract	Raw trajectory data (GROMACS format) of all atom molecular dynamics simulation of COVID-19 related SARS-CoV-2 dimeric main protease (based on PDB 6LU7) with 7 kinds of HIV inhibitors (darunavir, indinavir, lopinavir, nelfinavir, ritonavir, saquinavir, and tipranavir) were calculated on massively parallel supercomputer HOKUSAI Big Waterfall at RIKEN ISC, and a special-purpose computer, MDGRAPE-4A, at RIKEN BDR, JAPAN. For each ligand, 200ns length 28 trajectories were calculated. Some of these trajectories were calculated further longer. We can observe formation of encounter complex and investigate potential binding sites on the surface of the dimeric protease. We hope that these raw data are valuable for further drug repurposing/development research targeting the SARS-CoV-2 main protease. We will submit analysis of these data to refereed journal. Molecular dynamics simulations were performed under NVT at 310K, with the time step 2.5fs. The starting structure was prepared based on PDB 6LU7, with amber14sb force field in about 10nm cubic box with periodic boundary conditions. The ligands were initially placed apart from the active sites of the dimeric main protease. We have also already deposited 10 microseconds trajectories of the dimeric protease without ligand (with amber99sb-ildn force field) in the repository https://data.mendeley.com/datasets/vpps4vhryg/1 (DOI:10.17632/vpps4vhryg.1). Files: LIG_28traj200ns_every200ps.zip (28trajectories for each ligand) traj200ns_every200ps/LIG/a/traj200ns_every200ps_LIG-a-n.xtc (trajectory in GROMACS XTC) traj200ns_every200ps/LIG/a/conf.gro (initial condition in GROMACS GRO) traj200ns_every200ps/LIG/topology/ (contains topology files) traj200ns_every200ps/LIG/mdp/ (contains run paramter files) ZZZ_20traj1us_every200ps.zip (20trajectories extended to 1microsecond) traj1us_every200ps/traj1us_every200ps_LIG-a-n.xtc DAR-C-06, DAR-D-07 IND-C-05, IND-C-06, IND-D-06 LOP-A-02, LOP-D-03 NEL-B-01, NEL-C-07, NEL-D-02 RIT-B-07, RIT-C-07 SAQ-B-01, SAQ-C-04, SAQ-D-03 TPR-A-07, TPR-B-04, TPR-B-06, TPR-C-05, TPR-D-02 ZZZ_3traj6us_every1ns.zip (3trajectories extended to 6microseconds or more) traj6us_every1ns/traj6us_every1ns_LIG-a-n.xtc IND-D-06, NEL-B-01, TPR-B-04 ZZZ_LigandBindingPosePDBs.zip (pickup 3 snapshots for each ligand) LigandBindingPosePDBs/LIG-a-n_frame.pdb movies_overlooking_28traj200ns.zip (7x2movies) movies_28traj200ns/movie_overlooking_LIG_28traj200ns-viewA.mp4 inspecting 28traj at once movies_28traj200ns/movie_overlooking_LIG_28traj200ns-viewB.mp4 from the opposite angle movies_1us.zip (17movies) movies_1us/movie_LIG-a-n_1us.mp4 movies_6us.zip (3movies) movies_6us/movie_LIG-a-n_6us.mp4 where LIG={DAR,IND,LOP,NEL,RIT,SAQ,TPR} DAR:darunavir IND:indinavir NEL:nelfinavir RIT:ritonavir SAQ:saquinavir TPR:tipranavir a={A,B,C,D} n={01,02,03,04,05,06,07} ZZZz_3traj1us_every200ps_unbinding.zip (3trajectories extended to 1microsecond exhibiting unbinding) ZZZz_56traj200ns_every200ps_negative_control.zip (56trajectories as a negative control) ZZZz_LigandBindingPosePDBsRevised.zip (pickuped 3 snapshots for each ligand)
Keywords	COVID-19 ; SARS-CoV-2 ; molecular dynamics ; all atom molecular dynamics simulation ; drug repurposing ; ligand binding ; HIV inhibitor ; Virus ; covid19
Subject code	540
Publishing date	2020-05-13
Publishing country	eu
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Thermal diode utilizing asymmetric contacts to heat baths.

Komatsu, Teruhisa S / Ito, Nobuyasu

Physical review. E, Statistical, nonlinear, and soft matter physics

2010 Volume 81, Issue 1 Pt 1, Page(s) 10103

Abstract: We propose a simple thermal diode passively acting as a rectifier of heat current. The key design of the diode is the size asymmetry of the areas in contact with two distinct heat baths. The heat-conducting medium is liquid, inside of which gaslike ... ...

Abstract	We propose a simple thermal diode passively acting as a rectifier of heat current. The key design of the diode is the size asymmetry of the areas in contact with two distinct heat baths. The heat-conducting medium is liquid, inside of which gaslike regions are induced depending on the applied conditions. Simulating nanoscale systems of this diode, the rectification of heat current is demonstrated. If the packing density of the medium and the working regime of temperature are properly chosen, the heat current is effectively cut off when the heat bath with narrow contact is hotter, but it flows normally under opposite temperature conditions. In the former case, the gaslike region is induced in the system and it acts as a thermal insulator because it covers the entire narrow area of contact with the bath.
Language	English
Publishing date	2010-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1550-2376
ISSN (online)	1550-2376
DOI	10.1103/PhysRevE.81.010103
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Drug binding dynamics of the dimeric SARS-CoV-2 main protease, determined by molecular dynamics simulation

Komatsu, Teruhisa S / Okimoto, Noriaki / Koyama, Yohei M / Hirano, Yoshinori / Morimoto, Gentaro / Ohno, Yousuke / Taiji, Makoto

Sci Rep

Abstract	We performed molecular dynamics simulation of the dimeric SARS-CoV-2 (severe acute respiratory syndrome corona virus 2) main protease (Mpro) to examine the binding dynamics of small molecular ligands. Seven HIV inhibitors, darunavir, indinavir, lopinavir, nelfinavir, ritonavir, saquinavir, and tipranavir, were used as the potential lead drugs to investigate access to the drug binding sites in Mpro. The frequently accessed sites on Mpro were classified based on contacts between the ligands and the protein, and the differences in site distributions of the encounter complex were observed among the ligands. All seven ligands showed binding to the active site at least twice in 28 simulations of 200 ns each. We further investigated the variations in the complex structure of the active site with the ligands, using microsecond order simulations. Results revealed a wide variation in the shapes of the binding sites and binding poses of the ligands. Additionally, the C-terminal region of the other chain often interacted with the ligands and the active site. Collectively, these findings indicate the importance of dynamic sampling of protein-ligand complexes and suggest the possibilities of further drug optimisations.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #851312
Database	COVID19

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Article: Morphological and behavioral ontogeny in larval and early juvenile discus fish Symphysodon aequifasciatus

Satoh, Shun / Hideaki Tanoue / Sandrine Ruitton / Masahiko Mohri / Teruhisa Komatsu

Ichthyological research. 2017 Jan., v. 64, no. 1

2017

Abstract: ... and early juvenile S. aequifasciatus exhibit adaptations for mucus provisioning. ...

Abstract	We observed the growth, morphological changes, and behavior of larvae and juveniles of the Amazonian substrate-brooding cichlid discus fish Symphysodon aequifasciatus under laboratory conditions. The mean body length (BL) of newly hatched larvae was 3.4â3.5Â mm, and the yolksac extended to approximately 42Â % of their BL. Larvae detached from the substrate on day 4 began swimming and immediately displayed biting behavior on the body surface of the parents. Larvae had completely consumed their yolksacs by day 7. They began swimming at an earlier developmental stage compared with other cichlid species. Their thick lips may be advantageous for removing mucus from the bodies of the parent fish. Juveniles actively fed on Artemia spp. by day 30, and the frequency of biting behavior toward the parents decreased between days 20 and 35. Bone ossification was essentially complete in juveniles by day 32. Juveniles reached 16.0Â Â±Â 1.1Â mm BL by day 35. These results indicate that the morphology and behavior of larval and early juvenile S. aequifasciatus exhibit adaptations for mucus provisioning.
Keywords	Artemia ; Symphysodon aequifasciatus ; body length ; bone formation ; fish ; juveniles ; larvae ; lips ; mucus ; ontogeny ; parents ; swimming
Language	English
Dates of publication	2017-01
Size	p. 37-44.
Publishing place	Springer Japan
Document type	Article
ZDB-ID	2048252-8
ISSN	1616-3915 ; 1341-8998
ISSN (online)	1616-3915
ISSN	1341-8998
DOI	10.1007/s10228-016-0530-y
Database	NAL-Catalogue (AGRICOLA)

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