Thermodynamics, Protein Modification, and Molecular Dynamics in Characterizing Lactose Repressor Protein: Strategies for Complex Analyses of Protein Structure–Function

Methods in Enzymology - Energetics of Biological Macromolecules, Part D ◽

10.1016/s0076-6879(04)79011-4 ◽

2004 ◽

pp. 188-209 ◽

Cited By ~ 8

Author(s):

Liskin Swint-Kruse ◽

Kathleen S Matthews

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Structure Function ◽

Protein Modification ◽

Repressor Protein ◽

Lactose Repressor

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1P026 MD and ab initio MO simulations on transcriptional mechanism controlled by lactose repressor protein and ligand(Protein: Structure & Function,Poster,The 52th Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Seibutsu Butsuri ◽

10.2142/biophys.54.s145_2 ◽

2014 ◽

Vol 54 (supplement1-2) ◽

pp. S145

Author(s):

Matsushita Yuki ◽

Shimamura Kanako ◽

Oishi Masato ◽

Ohyama Tatsuya ◽

Kurita Noriyuki

Keyword(s):

Protein Structure ◽

Structure Function ◽

Ab Initio ◽

Annual Meeting ◽

Repressor Protein ◽

Lactose Repressor ◽

Biophysical Society ◽

Ab Initio Mo

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3D0936 Prediction of dynamical conformation of biantennary complex-type N-glycan in water by replica-exchange molecular dynamics simulations(3D Protein: Structure & Function 2,The 49th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.51.s117_3 ◽

2011 ◽

Vol 51 (supplement) ◽

pp. S117

Author(s):

Suyong Re ◽

Naoyuki Miyashita ◽

Yoshiki Yamaguchi ◽

Yuji Sugita

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Structure Function ◽

Molecular Dynamics Simulations ◽

Replica Exchange ◽

Complex Type ◽

3D Protein Structure ◽

Replica Exchange Molecular Dynamics ◽

Biophysical Society ◽

Dynamics Simulations

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2P037 Molecular dynamics study on dynamics of allosteric conformational change of Catabolite activator protein induced by cAMP binding(01B. Protein: Structure & Function,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Seibutsu Butsuri ◽

10.2142/biophys.54.s201_1 ◽

2014 ◽

Vol 54 (supplement1-2) ◽

pp. S201

Author(s):

Mayuka Ojima ◽

Yoshifumi Fukunishi ◽

Masami Lintuluoto

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Structure Function ◽

Annual Meeting ◽

Conformational Change ◽

Catabolite Activator Protein ◽

Activator Protein ◽

Biophysical Society

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2P046 Screening for Mechanical Communication in Proteins by Coarse-Grained Molecular Dynamics(01B. Protein: Structure & Function,Poster)

Seibutsu Butsuri ◽

10.2142/biophys.53.s166_4 ◽

2013 ◽

Vol 53 (supplement1-2) ◽

pp. S166

Author(s):

Yuichi Togashi

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Structure Function ◽

Coarse Grained ◽

Coarse Grained Molecular Dynamics

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3P044 The development of multi-dimensional replica-exchange molecular dynamics program (REIN)(Protein: Structure & Function,The 48th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.50.s152_5 ◽

2010 ◽

Vol 50 (supplement2) ◽

pp. S152-S153

Author(s):

Naoyuki Miyashita ◽

Mitsunori Ikeguchi ◽

Yuji Sugita

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Structure Function ◽

Annual Meeting ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Biophysical Society

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The influence of cholesterol on membrane protein structure, function, and dynamics studied by molecular dynamics simulations

Biochimica et Biophysica Acta (BBA) - Biomembranes ◽

10.1016/j.bbamem.2015.03.029 ◽

2015 ◽

Vol 1848 (9) ◽

pp. 1783-1795 ◽

Cited By ~ 76

Author(s):

Julie Grouleff ◽

Sheeba Jem Irudayam ◽

Katrine K. Skeby ◽

Birgit Schiøtt

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Membrane Protein ◽

Structure Function ◽

Molecular Dynamics Simulations ◽

Membrane Protein Structure ◽

Dynamics Simulations

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3P042 Applications of the Hamiltonian replica-permutation molecular dynamics simulations to Aβ fragments(01B. Protein: Structure & Function,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Seibutsu Butsuri ◽

10.2142/biophys.54.s255_6 ◽

2014 ◽

Vol 54 (supplement1-2) ◽

pp. S255

Author(s):

Satoru G. Itoh ◽

OkumuraHisashi

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Structure Function ◽

Molecular Dynamics Simulations ◽

Annual Meeting ◽

Biophysical Society ◽

Dynamics Simulations

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3P043 Relaxation Mode Analysis of a protein using a Molecular Dynamics Simulation(Protein: Structure & Function,The 48th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.50.s152_4 ◽

2010 ◽

Vol 50 (supplement2) ◽

pp. S152

Author(s):

Toshiki Nagai ◽

Ayori Mitsutake ◽

Hiroshi Takano

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Molecular Dynamics Simulation ◽

Structure Function ◽

Annual Meeting ◽

Dynamics Simulation ◽

Mode Analysis ◽

Relaxation Mode ◽

Biophysical Society

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Change in specific interactions between lactose repressor protein and DNA induced by ligand binding: molecular dynamics and molecular orbital calculations

Molecular Simulation ◽

10.1080/08927022.2015.1036265 ◽

2015 ◽

Vol 42 (3) ◽

pp. 242-256 ◽

Cited By ~ 5

Author(s):

Yuki Matsushita ◽

Takeru Murakawa ◽

Kanako Shimamura ◽

Tatsuya Ohyama ◽

Masato Oishi ◽

...

Keyword(s):

Molecular Dynamics ◽

Ligand Binding ◽

Molecular Orbital ◽

Molecular Orbital Calculations ◽

Specific Interactions ◽

Repressor Protein ◽

Lactose Repressor

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3D1136 Molecular dynamics simulation study of diubiquitins : Analysis of ubiquitin-ubiquitin interactions(3D Protein: Structure & Function 2,The 49th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.51.s118_6 ◽

2011 ◽

Vol 51 (supplement) ◽

pp. S118-S119

Author(s):

Sotaro Fuchigami ◽

Mitsunori Ikeguchi ◽

Akinori Kidera

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Molecular Dynamics Simulation ◽

Structure Function ◽

Annual Meeting ◽

Simulation Study ◽

Dynamics Simulation ◽

3D Protein Structure ◽

Biophysical Society

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