NMR Characterization of Kinase p38 Dynamics in Free and Ligand‐Bound Forms

Vogtherr, Martin; Saxena, Krishna; Hoelder, Swen; Grimme, Susanne; Betz, Marco; Schieborr, Ulrich; Pescatore, Barbara; Robin, Michel; Delarbre, Laure; Langer, Thomas; Wendt, K. Ulrich; Schwalbe, Harald

doi:10.1002/anie.200502770

Cited by 145 publications

(170 citation statements)

References 27 publications

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“…This suggestion is supported by the recent results showing that unphosphorylated Abl kinase can be crystallized in both ''DFG in'' and ''DFG out'' forms (20), suggesting that the inactive ''DFG in'' conformation is an intermediate state between the active and the ''DFG out'' conformation. NMR study of the p38 kinase apo form in its dephosphorylated state has also demonstrated that it dynamically changes its conformation between ''DFG in'' and ''DFG out'' configurations, proving that the magnesium-binding loop in inactive kinases can be remarkably flexible (21).…”

Section: Resultsmentioning

confidence: 99%

“…Recent studies (20,21) have demonstrated that, in inactive Abl and p38 kinases, the DFG motif was extremely flexible, flipping between ''DFG in'' and ''DFG out'' conformations. Our model is in a good correspondence with these facts because it suggests not only relaxation of the magnesium-binding loop, but also disruption of a connection between the lobes, that has to facilitate such conformational changes.…”

Section: Discussionmentioning

confidence: 99%

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Surface comparison of active and inactive protein kinases identifies a conserved activation mechanism

Kornev

Haste²,

Taylor³

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

674

746

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The surface comparison of different serine-threonine and tyrosine kinases reveals a set of 30 residues whose spatial positions are highly conserved. The comparison between active and inactive conformations identified the residues whose positions are the most sensitive to activation. Based on these results, we propose a model of protein kinase activation. This model explains how the presence of a phosphate group in the activation loop determines the position of the catalytically important aspartate in the AspPhe-Gly motif. According to the model, the most important feature of the activation is a ''spine'' formation that is dynamically assembled in all active kinases. The spine is comprised of four hydrophobic residues that we detected in a set of 23 eukaryotic and prokaryotic kinases. It spans the molecule and plays a coordinating role in activated kinases. The spine is disordered in the inactive kinases and can explain how stabilization of the whole molecule is achieved upon phosphorylation.protein surface ͉ graph theory

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Surface comparison of active and inactive protein kinases identifies a conserved activation mechanism

Kornev

Haste²,

Taylor³

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

674

746

View full text Add to dashboard Cite

show abstract

“…As a negative control, we have also performed fluorescence experiments using the DFG-in binder dasatinib (38,39). It is thought that so-called DFG-in binders typically bind to both DFG-in and DFG-out conformations (13). We find only a very weak pH dependence for dasatinib binding (Fig.…”

Section: Probing the Dfg-out Conformation By Using Abl-imatinib Bindingmentioning

confidence: 94%

“…However, it is very challenging to directly probe the dynamics of this motif experimentally (13). Molecular dynamics (MD) simulation provides an alternative means to study kinase dynamics (14)(15)(16), but the time scale accessible to such studies has typically been restricted to between 100 ps and 10 ns.…”

mentioning

confidence: 99%

A conserved protonation-dependent switch controls drug binding in the Abl kinase

Shan

Seeliger

Eastwood

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

239

314

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In many protein kinases, a characteristic conformational change (the ''DFG flip'') connects catalytically active and inactive conformations. Many kinase inhibitors-including the cancer drug imatinib-selectively target a specific DFG conformation, but the function and mechanism of the flip remain unclear. Using long molecular dynamics simulations of the Abl kinase, we visualized the DFG flip in atomiclevel detail and formulated an energetic model predicting that protonation of the DFG aspartate controls the flip. Consistent with our model's predictions, we demonstrated experimentally that the kinetics of imatinib binding to Abl kinase have a pH dependence that disappears when the DFG aspartate is mutated. Our model suggests a possible explanation for the high degree of conservation of the DFG motif: that the flip, modulated by electrostatic changes inherent to the catalytic cycle, allows the kinase to access flexible conformations facilitating nucleotide binding and release.conformational change ͉ DFG motif ͉ imatinib ͉ molecular dynamics simulation ͉ pH dependence

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“…Similarly, this suggests that imatinib could also temporarily bind in an ATP-competitive manner to Abl and uses the opportunity provided by spontaneous conformational changes to switch to its known Type II binding mode. The observation of two alternative binding modes for the Type I inhibitor BIM-2 in PKC [92], and of two different binding modes for a imidazole-pyridine inhibitor to the active and inactive conformations of p38a further supports this hypothesis of temporary binding modes [93]. Such a mechanism could explain the observation that a drug-resistant gatekeeper mutant of Src can be bound by certain irreversible 4-aminoquinazoline-based inhibitors, but not by their reversible counterparts [94].…”

Section: Kinase Inhibitors and Conformational Changesmentioning

confidence: 61%

Proteus in the World of Proteins: Conformational Changes in Protein Kinases

Rabiller

Getlik

Klüter

et al. 2010

Archiv der Pharmazie

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The 512 protein kinases encoded by the human genome are a prime example of nature's ability to create diversity by introducing variations to a highly conserved theme. The activity of each kinase domain is controlled by layers of regulatory mechanisms involving different combinations of post-translational modifications, intramolecular contacts, and intermolecular interactions. Ultimately, they all achieve their effect by favoring particular conformations that promote or prevent the kinase domain from catalyzing protein phosphorylation. The central role of kinases in various diseases has encouraged extensive investigations of their biological function and three-dimensional structures, yielding a more detailed understanding of the mechanisms that regulate protein kinase activity by conformational changes. In the present review, we discuss these regulatory mechanisms and show how conformational changes can be exploited for the design of specific inhibitors that lock protein kinases in inactive conformations. In addition, we highlight recent developments to monitor ligand-induced structural changes in protein kinases and for screening and identifying inhibitors that stabilize enzymatically incompetent kinase conformations.

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NMR Characterization of Kinase p38 Dynamics in Free and Ligand‐Bound Forms

Cited by 145 publications

References 27 publications

Surface comparison of active and inactive protein kinases identifies a conserved activation mechanism

Surface comparison of active and inactive protein kinases identifies a conserved activation mechanism

A conserved protonation-dependent switch controls drug binding in the Abl kinase

Proteus in the World of Proteins: Conformational Changes in Protein Kinases

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