Nucleotide-binding properties of adenylate kinase from Escherichia coli: A molecular dynamics study in aqueous and vacuum environments

1994 ◽  
Vol 8 (4) ◽  
pp. 367-388 ◽  
Author(s):  
Petra Kern ◽  
Roger M. Brunne ◽  
Gerd Folkers
Keyword(s):  
Escherichia Coli ◽  
Molecular Dynamics ◽  
Adenylate Kinase ◽  
Nucleotide Binding ◽  
Binding Properties

scholarly journals Molecular Dynamics Studies on the Conformational Transitions of Adenylate Kinase: A Computational Evidence for the Conformational Selection Mechanism

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Jie Ping ◽  
Pei Hao ◽  
Yi-Xue Li ◽  
Jing-Fang Wang
Keyword(s):  
Escherichia Coli ◽  
Molecular Dynamics ◽  
Adenylate Kinase ◽  
Large Scale ◽  
Conformational Transition ◽  
Conformational Transitions ◽  
Selection Mechanism ◽  
Conformational Selection ◽  
Domain Motion ◽  
Lid Domain

Escherichia coliadenylate kinase (ADK) is a monomeric phosphotransferase enzyme that catalyzes reversible transfer of phosphoryl group from ATP to AMP with a large-scale domain motion. The detailed mechanism for this conformational transition remains unknown. In the current study, we performed long time-scale molecular dynamics simulations on both open and closed states of ADK. Based on the structural analyses of the simulation trajectories, we detected over 20 times conformational transitions between the open and closed states of ADK and identified two novel conformations as intermediate states in the catalytic processes. With these findings, we proposed a possible mechanism for the large-scale domain motion ofEscherichia coliADK and its catalytic process: (1) the substrate free ADK adopted an open conformation; (2) ATP bound with LID domain closure; (3) AMP bound with NMP domain closure; (4) phosphoryl transfer occurred with ATP, and AMP converted into two ADPs, and no conformational transition was detected in the enzyme; (5) LID domain opened with one ADP released; (6) another ADP released with NMP domain open. As both open and closed states sampled a wide range of conformation transitions, our simulation strongly supported the conformational selection mechanism forEscherichia coliADK.

scholarly journals Structural and nucleotide-binding properties of YajQ and YnaF, two Escherichia coli proteins of unknown function

2008 ◽  
Vol 11 (11) ◽  
pp. 2551-2560 ◽  
Author(s):  
Cosmin Saveanu ◽  
Simona Miron ◽  
Tudor Borza ◽  
Constantin T. Craescu ◽  
Gilles Labesse ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Unknown Function ◽  
Nucleotide Binding ◽  
Binding Properties

Mutations in the nucleotide binding loop of adenylate kinase of Escherichia coli

Biochemistry ◽  
1988 ◽  
Vol 27 (13) ◽  
pp. 4712-4720 ◽  
Author(s):  
Jochen Reinstein ◽  
Martin Brune ◽  
Alfred Wittinghofer
Keyword(s):  
Escherichia Coli ◽  
Adenylate Kinase ◽  
Nucleotide Binding ◽  
Binding Loop
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