2P040 Molecular dynamics simurations of the ligand-binding core of the inositol 1,4,5-trisphosphate receptor in the ligand-free state(The 48th Annual Meeting of the Biophysical Society of Japan)

Yoichi Ida; Sotaro Fuchigami; mitsunori ikeguchi; akinori kidera

doi:10.2142/biophys.50.s89_1

2P040 Molecular dynamics simurations of the ligand-binding core of the inositol 1,4,5-trisphosphate receptor in the ligand-free state(The 48th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.50.s89_1 ◽

2010 ◽

Vol 50 (supplement2) ◽

pp. S89

Author(s):

Yoichi Ida ◽

Sotaro Fuchigami ◽

mitsunori ikeguchi ◽

akinori kidera

Keyword(s):

Molecular Dynamics ◽

Ligand Binding ◽

Annual Meeting ◽

Free State ◽

Ligand Free ◽

Inositol 1,4,5 Trisphosphate ◽

Biophysical Society ◽

Binding Core ◽

Trisphosphate Receptor

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1P-058 Molecular dynamics simulations of the ligand-binding core of inositol 1, 4, 5-trisphosphate receptor and its mutant in the ligand-free state(The 46th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.48.s30_1 ◽

2008 ◽

Vol 48 (supplement) ◽

pp. S30

Author(s):

Yoichi Ida ◽

Sotaro Fuchigamai ◽

Mitsunori Ikeguchi ◽

Akainori Kidera

Keyword(s):

Molecular Dynamics ◽

Ligand Binding ◽

Molecular Dynamics Simulations ◽

Annual Meeting ◽

Inositol 1 ◽

Ligand Free ◽

Biophysical Society ◽

Binding Core ◽

Dynamics Simulations ◽

Trisphosphate Receptor

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1P003 Molecular dynamics simulations of the ligand-binding core of the inositol 1,4,5-trisphosphate receptor in the ligand-free slate(Proteins-structure and structure-function relationship,Oral Presentations)

Seibutsu Butsuri ◽

10.2142/biophys.47.s24_2 ◽

2007 ◽

Vol 47 (supplement) ◽

pp. S24

Author(s):

Yoichi Ida ◽

Sotaro Fuchigami ◽

Mitsunori Ikeguchi ◽

Akinori Kidera

Keyword(s):

Molecular Dynamics ◽

Ligand Binding ◽

Structure Function ◽

Ligand Free ◽

Inositol 1,4,5 Trisphosphate ◽

Binding Core ◽

Function Relationship ◽

Dynamics Simulations ◽

Trisphosphate Receptor ◽

Oral Presentations

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The conserved Arg241-Glu439 salt bridge determines flexibility of the inositol 1,4,5-trisphosphate receptor binding core in the ligand-free state

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.24304 ◽

2013 ◽

Vol 81 (10) ◽

pp. 1699-1708 ◽

Cited By ~ 4

Author(s):

Yoichi Ida ◽

Akinori Kidera

Keyword(s):

Receptor Binding ◽

Salt Bridge ◽

Free State ◽

Ligand Free ◽

Inositol 1,4,5 Trisphosphate ◽

Binding Core ◽

Trisphosphate Receptor

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2SCP-05 Protein-ligand binding processes studied by coarse-grained molecular dynamics simulations(Prediction and analysis of protein functions from structural bioinformatics,Symposium,The 52th Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Seibutsu Butsuri ◽

10.2142/biophys.54.s133_1 ◽

2014 ◽

Vol 54 (supplement1-2) ◽

pp. S133

Author(s):

Tohru Terada ◽

Tatsuki Negami ◽

Kentaro Shimizu

Keyword(s):

Molecular Dynamics ◽

Ligand Binding ◽

Molecular Dynamics Simulations ◽

Annual Meeting ◽

Structural Bioinformatics ◽

Coarse Grained ◽

Biophysical Society ◽

Protein Functions ◽

Dynamics Simulations ◽

Coarse Grained Molecular Dynamics

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3P-134 Estimation of ligand binding free energies of F-ATPase by using molecular dynamics/free energy calculation(The 46th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.48.s148_3 ◽

2008 ◽

Vol 48 (supplement) ◽

pp. S148

Author(s):

Atsushi Suenaga ◽

Osamu Umezu ◽

Tadashi Ando ◽

Ichiro Yamato ◽

Takeshi Murata ◽

...

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Ligand Binding ◽

Annual Meeting ◽

Free Energy Calculation ◽

Energy Calculation ◽

Free Energies ◽

Biophysical Society ◽

Binding Free Energies

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3C1024 Molecular dynamics simulations for glutamate-binding and cleft-closing processes of the ligand-binding domain of GluR2(3C Protein: Funcrion 2,The 49th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.51.s113_3 ◽

2011 ◽

Vol 51 (supplement) ◽

pp. S113

Author(s):

Okimasa Okada ◽

Kei Odai ◽

Tohru Sugimoto ◽

Etsuro Ito

Keyword(s):

Molecular Dynamics ◽

Ligand Binding ◽

Molecular Dynamics Simulations ◽

Annual Meeting ◽

Binding Domain ◽

Ligand Binding Domain ◽

Glutamate Binding ◽

Biophysical Society ◽

Dynamics Simulations

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1P058 Molecular dynamics simulations for structure changes of PRSet7 by ligand binding(01C. Protein : Property,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Seibutsu Butsuri ◽

10.2142/biophys.54.s150_4 ◽

2014 ◽

Vol 54 (supplement1-2) ◽

pp. S150

Author(s):

Takako Sakano ◽

Hideaki Fujitani

Keyword(s):

Molecular Dynamics ◽

Ligand Binding ◽

Molecular Dynamics Simulations ◽

Annual Meeting ◽

Structure Changes ◽

Protein Property ◽

Biophysical Society ◽

Dynamics Simulations

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1P242 1I1435 Analysis of the effect of water molecules on lipid bilayer dynamics in aqueous salt solutions using molecular dynamics simulations(Biol & Artifi memb.:Dynamics,Oral Presentations,The 48th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.50.s62_2 ◽

2010 ◽

Vol 50 (supplement2) ◽

pp. S62

Author(s):

Rina Kagawa ◽

Yoshinori Hirano ◽

Kenji Yasuoka ◽

Masato Yasui

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Annual Meeting ◽

Lipid Bilayer ◽

Water Molecules ◽

Salt Solutions ◽

Aqueous Salt Solutions ◽

Biophysical Society ◽

Dynamics Simulations ◽

Oral Presentations

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1E1636 PSCDB : a database for protein structural change upon ligand binding(Genome biology, Bioinformatics,The 49th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.51.s42_1 ◽

2011 ◽

Vol 51 (supplement) ◽

pp. S42

Author(s):

Takayuki Amemiya ◽

Ryotaro Koike ◽

Akinori Kidera ◽

Motonori Ota

Keyword(s):

Structural Change ◽

Ligand Binding ◽

Annual Meeting ◽

Genome Biology ◽

Biophysical Society

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1N1348 Quantitation of molecular dynamics and interactions in T cell activation by single-molecule microscopy with a lipid bilayer system(Bioimaging 1,The 49th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.51.s66_5 ◽

2011 ◽

Vol 51 (supplement) ◽

pp. S66-S67

Author(s):

Yuma Ito ◽

Kumiko Sakata-Sogawa ◽

Makio Tokunaga

Keyword(s):

Molecular Dynamics ◽

T Cell ◽

Annual Meeting ◽

Lipid Bilayer ◽

T Cell Activation ◽

Single Molecule ◽

Cell Activation ◽

Single Molecule Microscopy ◽

Bilayer System ◽

Biophysical Society

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