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

Harini Krishnamurthy; Hongfeng Lou; Adam Kimple; Claire Vieille; Robert I. Cukier

doi:10.1002/prot.20301

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 ◽

Cited By ~ 28

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

Download Full-text

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 ◽

Reduced Model

Download Full-text

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

Download Full-text

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

Download Full-text

1P564 All-Atom Molecular Dynamics Simulation of Conformational Changes in Adenylate Kinase(27. Molecular dynamics simulation,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)

Seibutsu Butsuri ◽

10.2142/biophys.46.s287_4 ◽

2006 ◽

Vol 46 (supplement2) ◽

pp. S287

Author(s):

Sotaro Fuchigami ◽

Mitsunori Ikeguchi ◽

Akinori Kidera

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Conformational Changes ◽

Adenylate Kinase ◽

Poster Session ◽

Dynamics Simulation ◽

Meeting Program

Download Full-text

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 ◽

Ompf Porin

Download Full-text

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 ◽

Cited By ~ 36

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

Download Full-text

Effect of metal ions on the internal motions of Adenylate Kinase: A Molecular dynamics simulation study

Authorea ◽

10.22541/au.158359643.35625009 ◽

2020 ◽

Author(s):

Marzieh Allahdaneh ◽

Emran Heshmati ◽

Khosrow Khalifeh

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Metal Ions ◽

Simulation Study ◽

Adenylate Kinase ◽

Dynamics Simulation ◽

Internal Motions ◽

Kinase A

Download Full-text

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 ◽

Cited By ~ 195

Author(s):

Wonpil Im ◽

Benoı̂t Roux

Keyword(s):

Escherichia Coli ◽

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Salt Solution ◽

Aqueous Salt Solution ◽

Dynamics Simulation ◽

Ompf Porin

Download Full-text

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 ◽

Cited By ~ 51

Author(s):

Michael J. Bradley ◽

Peter T. Chivers ◽

Nathan A. Baker

Keyword(s):

Escherichia Coli ◽

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Allosteric Communication

Download Full-text

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

BIOPHYSICS ◽

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

Download Full-text