| Adenylate kinase (ADK) conformations segregate naturally into open; intermediate; and closed forms with long-term residence in the intermediate state. | Fine structure of conformational ensembles in adenylate kinase.
Wang Y, Makowski L. | 02/2/2019 |
| These results are consistent with an induced-fit model in which the transition of AdK from an open state to a closed state is initiated by ATP binding. | Effects of Catalytic Action and Ligand Binding on Conformational Ensembles of Adenylate Kinase.
Onuk E, Badger J, Wang YJ, Bardhan J, Chishti Y, Akcakaya M, Brooks DH, Erdogmus D, Minh DDL, Makowski L. | 09/2/2017 |
| Fast closure of N-terminal long loops but slow formation of beta strands precedes the folding transition state of Escherichia coli adenylate kinase. | Fast closure of N-terminal long loops but slow formation of β strands precedes the folding transition state of Escherichia coli adenylate kinase.
Orevi T, Ben Ishay E, Gershanov SL, Dalak MB, Amir D, Haas E. | 07/5/2014 |
| As both open and closed states sampled a wide range of conformation transitions, our simulation strongly supported the conformational selection mechanism for Escherichia coli ADK. | Molecular dynamics studies on the conformational transitions of adenylate kinase: a computational evidence for the conformational selection mechanism.
Ping J, Hao P, Li YX, Wang JF., Free PMC Article | 03/22/2014 |
| fast subdomain folding prior to global refolding transition of adenylate kinase; applied double kinetics method to test the hypothesis that specific short native-like intramolecular distances between residues separated by long chain segments in a globular protein can be formed in the collapsed state, prior to the cooperative folding transition | Fast subdomain folding prior to the global refolding transition of E. coli adenylate kinase: a double kinetics study.
Ben Ishay E, Rahamim G, Orevi T, Hazan G, Amir D, Haas E. | 01/26/2013 |
| In Cartesian space, LID domain closure precedes NMP domain closure in the bound simulation, consistent with prior coarse-grained models of the adenylate kinase conformational transition. | Many local motions cooperate to produce the adenylate kinase conformational transition.
Daily MD, Phillips GN Jr, Cui Q., Free PMC Article | 08/2/2010 |
| Results demonstrate that the conformational ensemble of adenylate kinase is significantly populated by a locally unfolded state and that the excited-state can be manipulated through mutation, independent of perturbations of the ground-state structures. | Rational modulation of conformational fluctuations in adenylate kinase reveals a local unfolding mechanism for allostery and functional adaptation in proteins.
Schrank TP, Bolen DW, Hilser VJ., Free PMC Article | 01/21/2010 |
| Results show that the flexible subdomains of adk fold into their native structure in a noncooperative manner with respect to the CORE subdomain. | Noncooperative folding of subdomains in adenylate kinase.
Rundqvist L, Adén J, Sparrman T, Wallgren M, Olsson U, Wolf-Watz M. | 01/21/2010 |
| Results describe the atomistic mechanism of conformational transition in adenylate kinase. | The atomistic mechanism of conformational transition in adenylate kinase: a TEE-REX molecular dynamics study.
Kubitzki MB, de Groot BL. | 01/21/2010 |
| N-terminus verified by Edman degradation on complete protein | See all PubMed (4) articlesProtein identification with N and C-terminal sequence tags in proteome projects.
Wilkins MR, Gasteiger E, Tonella L, Ou K, Tyler M, Sanchez JC, Gooley AA, Walsh BJ, Bairoch A, Appel RD, Williams KL, Hochstrasser DF. Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12.
Link AJ, Robison K, Church GM. Adenylate kinase complements nucleoside diphosphate kinase deficiency in nucleotide metabolism.
Lu Q, Inouye M. Structural and catalytic characteristics of Escherichia coli adenylate kinase.
Saint Girons I, Gilles AM, Margarita D, Michelson S, Monnot M, Fermandjian S, Danchin A, Bârzu O. | 11/5/2007 |
| Data describe the plastic network model, used to generate a conformational change pathway for Escherichia coli adenylate kinase based on two crystal structures, namely that of an open and a closed conformer. | Large amplitude conformational change in proteins explored with a plastic network model: adenylate kinase.
Maragakis P, Karplus M. | 01/21/2010 |
| AK molecules undergo fast collapse to an ensemble of compact structures where the local environment of surface probes seems to be native-like but the two labeled secondary structure elements remain unfolded. | Fast collapse but slow formation of secondary structure elements in the refolding transition of E. coli adenylate kinase.
Ratner V, Amir D, Kahana E, Haas E. | 01/21/2010 |
| Adenylate kinase from E coli have two highly flexible domains which close over bound substrates. | Crystal structure of ADP/AMP complex of Escherichia coli adenylate kinase.
Berry MB, Bae E, Bilderback TR, Glaser M, Phillips GN Jr. | 01/21/2010 |
| The dynamics of adenylate kinase of Escherichia coli, and its complex with the inhibitor AP(5)A, are characterized | Escherichia coli adenylate kinase dynamics: comparison of elastic network model modes with mode-coupling (15)N-NMR relaxation data.
Temiz NA, Meirovitch E, Bahar I., Free PMC Article | 01/21/2010 |
| for adenylate kinase, the change in the number of interdomain contacting atoms upon closure showed a considerable increase, suggesting that adk undergoes closure through a hinge mechanism | Essential dynamics sampling study of adenylate kinase: comparison to citrate synthase and implication for the hinge and shear mechanisms of domain motions.
Snow C, Qi G, Hayward S. | 01/21/2010 |
| Simulation supports the hypothesis that hydrogen bonds between AMP's adenine and the protein are at the origin of the high nucleoside monophosphate (NMP) specificity of adenylate kinase | Associative mechanism for phosphoryl transfer: a molecular dynamics simulation of Escherichia coli adenylate kinase complexed with its substrates.
Krishnamurthy H, Lou H, Kimple A, Vieille C, Cukier RI. | 01/21/2010 |