An Allosteric Cross-Talk Between the Activation Loop and the ATP Binding Site Regulates the Activation of Src Kinase

Pucheta-Martinez, Encarna; Saladino, Giorgio; Morando, Maria; Martı́nez-Torrecuadrada, Jorge L.; Lelli, Moreno; Sutto, Ludovico; D’Amelio, Nicola; Gervasio, Francesco Luigi

doi:10.1038/srep24235

Cited by 42 publications

(42 citation statements)

References 34 publications

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“…Similar to previous experimental work on protein kinase A 62 , ERK2 61 , p38 62 , and Src 63 , the concerted conformational change predicted by our simulations is likely to display NMR signature. In particular, our MSM is highly consistent with the Src study 63 where the authors experimentally showed that Src's catalytic domain exists in at least two conformational states in solution. The major and minor conformational state exchange on the micro to millisecond timescales and are related via hinge motion.…”

Section: Active and Inactive States Are Similarly Populatedsupporting

confidence: 88%

Towards simple kinetic models of functional dynamics for a kinase subfamily

Sultan

Kiss

Pande

2017

Preprint

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Kinases are ubiquitous enzymes involved in the regulation of critical cellular pathways and have been implicated in several cancers. Consequently, the kinetics and thermodynamics of prototypical kinases are of interest and have been the subject of numerous experimental studies. In-silico modeling of the conformational ensembles of these enzymes, on the other hand, is lacking due to inherent computational limitations. Recent algorithmic advances combined with homology modeling and parallel simulations allow us to address this computational sampling bottleneck. Here, we present the results of molecular dynamics (MD) studies for seven Src family kinase (SFK) members Fyn, Lyn, Lck, Hck, Fgr, Yes, and Blk. We present a sequence invariant extension to Markov state models (MSMs), which allows us to quantitatively compare the structural ensembles of the seven kinases. Our findings indicate that in the absence of their regulatory partners, SFK members have similar in-silico dynamics with active state populations ranging from 4-40% and activation timescales in the hundreds of microseconds. Furthermore, we observe several potentially druggable intermediate states, including a pocket next to the ATP binding site that could be potentially targeted via a small molecule inhibitors. These results establish the utility of MSMs for studying protein families.

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Section: Active and Inactive States Are Similarly Populatedsupporting

confidence: 88%

Towards simple kinetic models of functional dynamics for a kinase subfamily

Sultan

Kiss

Pande

2017

Preprint

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“…MD simulations have been successfully used for the identification of intermediate structures during the activation pathway of various kinases 19 , 31 . Conventional MD 32 – 34 or biased, enhanced sampling methodologies 35 – 37 have been extensively used to study the mechanism of constitutive activation of various protein kinases as well as the mechanism of action of anti-cancer drugs 35 , 37 , 38 . A recent MD study of oncogenic mutations of PI3Kα suggests that all tumor-associated mutants weaken p110α-p85α interactions by increasing positional fluctuations of nSH2 (p85α) domain 39 .…”

Section: Introductionmentioning

confidence: 99%

Insights into the mechanism of the PIK3CA E545K activating mutation using MD simulations

Leontiadou

Galdadas

Athanasiou

et al. 2018

Sci Rep

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Phosphoinositide 3-kinase alpha (PI3Kα) is involved in fundamental cellular processes including cell proliferation and differentiation and is frequently mutated in human malignancies. One of the most common mutations is E545K, which results in an amino acid substitution of opposite charge. It has been recently proposed that in this oncogenic charge-reversal mutation, the interactions between the protein catalytic and regulatory subunits are abrogated, resulting in loss of regulation and constitutive PI3Kα activity, which can lead to oncogenesis. To assess the mechanism of the PI3Kα E545K activating mutation, extensive Molecular Dynamics simulations were performed to examine conformational changes differing between the wild type (WT) and mutant proteins as they occur in microsecond simulations. In the E545K mutant PI3Kα, we observe a spontaneous detachment of the nSH2 PI3Kα domain (regulatory subunit, p85α) from the helical domain (catalytic subunit, p110α) causing significant loss of communication between the regulatory and catalytic subunits. We examine the allosteric network of the two proteins and show that a cluster of residues around the mutation is important for delivering communication signals between the catalytic and regulatory subunits. Our results demonstrate the dynamical and structural effects induced by the p110α E545K mutation in atomic level detail and indicate a possible mechanism for the loss of regulation that E545K confers on PI3Kα.

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“…As such, during the evolution process, kinases traded their enzymatic efficiency for the ability to unambiguously switch between "on" and "off" states and to select protein substrates with high specificity (2). Since the tuning of kinase function relies on a complex network of interactions with cofactors and regulatory subunits, it inherently involves an array of subtle allosteric effects (3)(4)(5)(6)(7)(8)(9). Malfunction of this regulatory mechanism is associated with a variety of diseases ranging from cancer to immunological and metabolic disorders, motivating the need for its thorough investigation not only to uncover general principles of protein mechanics but also to guide therapeutic and drug design strategies (10).…”

mentioning

confidence: 99%

Water-mediated conformational preselection mechanism in substrate binding cooperativity to protein kinase A

Setny

Wiśniewska

2018

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

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Substrate binding cooperativity in protein kinase A (PKA) seems to involve allosteric coupling between the two binding sites. It received significant attention, but its molecular basis still remains not entirely clear. Based on long molecular dynamics of PKA and its complexes, we characterized an allosteric pathway that links ATP binding to the redistribution of states adopted by a protein substrate positioning segment in favor of those that warrant correct binding. We demonstrate that the cooperativity mechanism critically depends on the presence of water in two distinct, buried hydration sites. One holds just a single water molecule, which acts as a switchable hydrogen bond bridge along the allosteric pathway. The second, filled with partially disordered solvent, is essential for providing a smooth free energy landscape underlying conformational transitions of the peptide binding region. Our findings remain in agreement with experimental data, also concerning the cooperativity abolishing effect of the Y204A mutation, and indicate a plausible molecular mechanism contributing to experimentally observed binding cooperativity of the two substrates.

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An Allosteric Cross-Talk Between the Activation Loop and the ATP Binding Site Regulates the Activation of Src Kinase

Cited by 42 publications

References 34 publications

Towards simple kinetic models of functional dynamics for a kinase subfamily

Towards simple kinetic models of functional dynamics for a kinase subfamily

Insights into the mechanism of the PIK3CA E545K activating mutation using MD simulations

Water-mediated conformational preselection mechanism in substrate binding cooperativity to protein kinase A

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