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Dynamic Allostery of the Catabolite Activator Protein Revealed by Interatomic Forces.

Louet M, Seifert C, Hensen U, Gräter F - PLoS Comput. Biol. (2015)

Bottom Line: We recover the experimentally observed entropic penalty for the second cAMP binding event with our recently developed force covariance entropy estimator and reveal allosteric communication pathways with Force Distribution Analyses (FDA).We identified crucial relays in the mostly symmetric allosteric activation network, and suggest point mutants to test this mechanism.Our study suggests inter-residue forces, as opposed to coordinates, as a highly sensitive measure for structural adaptations that, even though minute, can very effectively propagate allosteric signals.

View Article: PubMed Central - PubMed

Affiliation: Heidelberg Institutes for Theoretical Studies gGmbH, Heidelberg, Germany.

ABSTRACT
The Catabolite Activator Protein (CAP) is a showcase example for entropic allostery. For full activation and DNA binding, the homodimeric protein requires the binding of two cyclic AMP (cAMP) molecules in an anti-cooperative manner, the source of which appears to be largely of entropic nature according to previous experimental studies. We here study at atomic detail the allosteric regulation of CAP with Molecular dynamics (MD) simulations. We recover the experimentally observed entropic penalty for the second cAMP binding event with our recently developed force covariance entropy estimator and reveal allosteric communication pathways with Force Distribution Analyses (FDA). Our observations show that CAP binding results in characteristic changes in the interaction pathways connecting the two cAMP allosteric binding sites with each other, as well as with the DNA binding domains. We identified crucial relays in the mostly symmetric allosteric activation network, and suggest point mutants to test this mechanism. Our study suggests inter-residue forces, as opposed to coordinates, as a highly sensitive measure for structural adaptations that, even though minute, can very effectively propagate allosteric signals.

No MeSH data available.


Glu58 and Arg87 minimal distance decreases upon activation.Probability distribution of the minimal distance between Glu68 and Arg87 for apo (black), cap1 (blue) and cap2 (orange) states. Both protomers were taken into account. Vertical dashed lines represent the respective values as observed in the cap2 X-ray structure (1G6N) and the range covered in the apo NMR structures (2WC2 [25]). The integration limits used in the inset for the three states (activated, intermediate and deactivated) have been determined by the two inflection points of the cap2 distribution (2.71 and 5.11 for intermediate and deactivated respectively).
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pcbi.1004358.g006: Glu58 and Arg87 minimal distance decreases upon activation.Probability distribution of the minimal distance between Glu68 and Arg87 for apo (black), cap1 (blue) and cap2 (orange) states. Both protomers were taken into account. Vertical dashed lines represent the respective values as observed in the cap2 X-ray structure (1G6N) and the range covered in the apo NMR structures (2WC2 [25]). The integration limits used in the inset for the three states (activated, intermediate and deactivated) have been determined by the two inflection points of the cap2 distribution (2.71 and 5.11 for intermediate and deactivated respectively).

Mentions: Interestingly, Asp68, which played a key role in the first binding event, is also important after the binding of the second nucleotide. Asp68 propagated the perturbation due to cAMP binding symmetrically to the anti-parallel β-sheet core and then reach the β4/β5-hairpin in close contact with the DBD This symmetric pathway, bridging Asp68 to Glu58, involves sequentially Leu64, Val47, Ser46, Lys89, Ala88 and Arg87. In this network, main chains play an important role. The β-bundle which connect the cAMP pocket with the NBD-DBD interface acts as a good signal propagator through H-bond interactions. We observed in both protomers a significant change in the interaction between Glu58 (β-hairpin) and Arg87 (β-strand 2, Fig 5D) side chains, the last residue pair of this network. Structural data has suggested the distance Glu58-Arg87 to critically change as a function of the activation state [9,25], namely to decrease by about 5 Å upon CAP activation. We observed the same trend in our MD simulations: the Glu58-Arg87 minimal distance was larger in the apo and cap1 states in comparison to the cap2 state, for both protomers (Fig 6). Interestingly, the network further reaches Gln174 located on the DBD in the second protomer. We computed dihedral order parameter difference for each residue from the cap1 and the cap2 simulations (S6 Fig), and obtained significant changes for some of the key residues highlighted by FDA. We observed stiffening of Glu77’, Glu78’, Gly79’ and Gln80’, due to their enhanced interaction with Arg122.


Dynamic Allostery of the Catabolite Activator Protein Revealed by Interatomic Forces.

Louet M, Seifert C, Hensen U, Gräter F - PLoS Comput. Biol. (2015)

Glu58 and Arg87 minimal distance decreases upon activation.Probability distribution of the minimal distance between Glu68 and Arg87 for apo (black), cap1 (blue) and cap2 (orange) states. Both protomers were taken into account. Vertical dashed lines represent the respective values as observed in the cap2 X-ray structure (1G6N) and the range covered in the apo NMR structures (2WC2 [25]). The integration limits used in the inset for the three states (activated, intermediate and deactivated) have been determined by the two inflection points of the cap2 distribution (2.71 and 5.11 for intermediate and deactivated respectively).
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4526232&req=5

pcbi.1004358.g006: Glu58 and Arg87 minimal distance decreases upon activation.Probability distribution of the minimal distance between Glu68 and Arg87 for apo (black), cap1 (blue) and cap2 (orange) states. Both protomers were taken into account. Vertical dashed lines represent the respective values as observed in the cap2 X-ray structure (1G6N) and the range covered in the apo NMR structures (2WC2 [25]). The integration limits used in the inset for the three states (activated, intermediate and deactivated) have been determined by the two inflection points of the cap2 distribution (2.71 and 5.11 for intermediate and deactivated respectively).
Mentions: Interestingly, Asp68, which played a key role in the first binding event, is also important after the binding of the second nucleotide. Asp68 propagated the perturbation due to cAMP binding symmetrically to the anti-parallel β-sheet core and then reach the β4/β5-hairpin in close contact with the DBD This symmetric pathway, bridging Asp68 to Glu58, involves sequentially Leu64, Val47, Ser46, Lys89, Ala88 and Arg87. In this network, main chains play an important role. The β-bundle which connect the cAMP pocket with the NBD-DBD interface acts as a good signal propagator through H-bond interactions. We observed in both protomers a significant change in the interaction between Glu58 (β-hairpin) and Arg87 (β-strand 2, Fig 5D) side chains, the last residue pair of this network. Structural data has suggested the distance Glu58-Arg87 to critically change as a function of the activation state [9,25], namely to decrease by about 5 Å upon CAP activation. We observed the same trend in our MD simulations: the Glu58-Arg87 minimal distance was larger in the apo and cap1 states in comparison to the cap2 state, for both protomers (Fig 6). Interestingly, the network further reaches Gln174 located on the DBD in the second protomer. We computed dihedral order parameter difference for each residue from the cap1 and the cap2 simulations (S6 Fig), and obtained significant changes for some of the key residues highlighted by FDA. We observed stiffening of Glu77’, Glu78’, Gly79’ and Gln80’, due to their enhanced interaction with Arg122.

Bottom Line: We recover the experimentally observed entropic penalty for the second cAMP binding event with our recently developed force covariance entropy estimator and reveal allosteric communication pathways with Force Distribution Analyses (FDA).We identified crucial relays in the mostly symmetric allosteric activation network, and suggest point mutants to test this mechanism.Our study suggests inter-residue forces, as opposed to coordinates, as a highly sensitive measure for structural adaptations that, even though minute, can very effectively propagate allosteric signals.

View Article: PubMed Central - PubMed

Affiliation: Heidelberg Institutes for Theoretical Studies gGmbH, Heidelberg, Germany.

ABSTRACT
The Catabolite Activator Protein (CAP) is a showcase example for entropic allostery. For full activation and DNA binding, the homodimeric protein requires the binding of two cyclic AMP (cAMP) molecules in an anti-cooperative manner, the source of which appears to be largely of entropic nature according to previous experimental studies. We here study at atomic detail the allosteric regulation of CAP with Molecular dynamics (MD) simulations. We recover the experimentally observed entropic penalty for the second cAMP binding event with our recently developed force covariance entropy estimator and reveal allosteric communication pathways with Force Distribution Analyses (FDA). Our observations show that CAP binding results in characteristic changes in the interaction pathways connecting the two cAMP allosteric binding sites with each other, as well as with the DNA binding domains. We identified crucial relays in the mostly symmetric allosteric activation network, and suggest point mutants to test this mechanism. Our study suggests inter-residue forces, as opposed to coordinates, as a highly sensitive measure for structural adaptations that, even though minute, can very effectively propagate allosteric signals.

No MeSH data available.