Molecular Dynamics Simulation of the Escherichia coli NikR Protein: Equilibrium Conformational Fluctuations Reveal Interdomain Allosteric Communication Pathways

Journal of Molecular Biology ◽

10.1016/j.jmb.2008.03.010 ◽

2008 ◽

Vol 378 (5) ◽

pp. 1155-1173 ◽

Author(s):

Michael J. Bradley ◽

Peter T. Chivers ◽

Nathan A. Baker

Keyword(s):

Escherichia Coli ◽

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Allosteric Communication

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Faculty Opinions recommendation of Molecular dynamics simulation of the Escherichia coli NikR protein: equilibrium conformational fluctuations reveal interdomain allosteric communication pathways.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1108774.564895 ◽

2008 ◽

Author(s):

Michael Maroney

Keyword(s):

Escherichia Coli ◽

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Allosteric Communication

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Changes in the level of poly(Phe) synthesis in Escherichia coli ribosomes containing mutants of L4 ribosomal protein from Thermus thermophilus can be explained by structural changes in the peptidyltransferase center: a molecular dynamics simulation analysis

European Biophysics Journal ◽

10.1007/s00249-006-0076-4 ◽

2006 ◽

Vol 35 (8) ◽

pp. 675-683

Author(s):

G. Papadopoulos ◽

S. Grudinin ◽

D. L. Kalpaxis ◽

T. Choli-Papadopoulou

Keyword(s):

Escherichia Coli ◽

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Ribosomal Protein ◽

Structural Changes ◽

Simulation Analysis ◽

Thermus Thermophilus ◽

Dynamics Simulation ◽

Peptidyltransferase Center

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Ion Selectivity Mechanism of Escherichia Coli OmpF Porin: a Molecular Dynamics Simulation/ free Energy Calculation Study

Journal of Computer Chemistry Japan ◽

10.2477/jccj.2014-0040 ◽

2014 ◽

Vol 13 (5) ◽

pp. 278-291

Author(s):

Yasuhiro MATSUURA ◽

Ichiro YAMATO ◽

Tadashi ANDO ◽

Atsushi SUENAGA

Keyword(s):

Escherichia Coli ◽

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Ion Selectivity ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

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Characterization of the internal motions of Escherichia coli ribonuclease HI by a combination of 15N-NMR relaxation analysis and molecular dynamics simulation: examination of dynamic models

Biochemistry ◽

10.1021/bi00020a003 ◽

1995 ◽

Vol 34 (20) ◽

pp. 6587-6601 ◽

Author(s):

Kazuhiko Yamasaki ◽

Minoru Saito ◽

Motohisa Oobatake ◽

Shigenori Kanaya

Keyword(s):

Escherichia Coli ◽

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Dynamic Models ◽

Nmr Relaxation ◽

Dynamics Simulation ◽

15N Nmr ◽

Internal Motions ◽

15N Nmr Relaxation

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Ions and Counterions in a Biological Channel: A Molecular Dynamics Simulation of OmpF Porin from Escherichia coli in an Explicit Membrane with 1M KCl Aqueous Salt Solution

Journal of Molecular Biology ◽

10.1016/s0022-2836(02)00380-7 ◽

2002 ◽

Vol 319 (5) ◽

pp. 1177-1197 ◽

Author(s):

Wonpil Im ◽

Benoı̂t Roux

Keyword(s):

Escherichia Coli ◽

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Salt Solution ◽

Aqueous Salt Solution ◽

Dynamics Simulation ◽

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Associative mechanism for phosphoryl transfer: A molecular dynamics simulation of Escherichia coli adenylate kinase complexed with its substrates

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.20301 ◽

2004 ◽

Vol 58 (1) ◽

pp. 88-100 ◽

Author(s):

Harini Krishnamurthy ◽

Hongfeng Lou ◽

Adam Kimple ◽

Claire Vieille ◽

Robert I. Cukier

Keyword(s):

Escherichia Coli ◽

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Adenylate Kinase ◽

Dynamics Simulation ◽

Phosphoryl Transfer ◽

Associative Mechanism

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Investigation of σ70 subunit structure dependence in Escherichia coli RNA polymerase on ionic strength by the molecular dynamics simulation method

10.1134/s0006350915060251 ◽

2015 ◽

Vol 60 (6) ◽

pp. 865-869

Author(s):

A. P. Tolstova ◽

E. V. Dubrovin ◽

O. N. Koroleva

Keyword(s):

Escherichia Coli ◽

Molecular Dynamics ◽

Ionic Strength ◽

Molecular Dynamics Simulation ◽

Rna Polymerase ◽

Simulation Method ◽

Dynamics Simulation ◽

Subunit Structure ◽

Structure Dependence

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Molecular dynamics simulation of an active site-reduced model of the adenylate kinase from escherichia coli

Journal of Molecular Graphics ◽

10.1016/0263-7855(93)80050-2 ◽

1993 ◽

Vol 11 (4) ◽

pp. 277

Author(s):

Petra Kern ◽

Gerd Folkers

Keyword(s):

Escherichia Coli ◽

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Active Site ◽

Adenylate Kinase ◽

Dynamics Simulation ◽

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Molecular dynamics simulation of the NikR protein: Equilibrium conformational fluctuations reveal inter‐domain allosteric communication pathways

The FASEB Journal ◽

10.1096/fasebj.22.1_supplement.612.2 ◽

2008 ◽

Vol 22 (S1) ◽

Author(s):

Michael John Bradley ◽

Peter Chivers ◽

Nathan Baker

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Allosteric Communication

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Synthesis of the tetrasaccharide repeating unit of the O-antigen of the Escherichia coli O69 strain and its conformational analysis

RSC Advances ◽

10.1039/c4ra06989g ◽

2014 ◽

Vol 4 (70) ◽

pp. 37079-37084 ◽

Author(s):

Manas Jana ◽

Rajiv Kumar Kar ◽

Anirban Bhunia ◽

Anup Kumar Misra

Keyword(s):

Escherichia Coli ◽

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Conformational Analysis ◽

Dynamics Simulation ◽

Two Dimensional ◽

Simulation Studies ◽

One Pot ◽

E Coli ◽

A tetrasaccharide corresponding to theO-antigen of theE. coliO69 strain has been synthesized using iterative glycosylations in one pot. The conformational analysis of the tetrasaccharide was carried out using two-dimensional ROESY spectroscopy and molecular dynamics simulation studies.

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