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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.


Conformational ensemble of Leu73 (A) and Arg123’ (B), involved in pathway A, for the apo (black), the cap1 (blue) and the cap2 (orange) states.The protein is represented as cartoon in white (first protomer) and yellow (second protomer). Key residues are represented as cyan sticks. Histograms of local RMSDs are shown. The average structure of all CAP simulations was used as reference structure for the fitting and RMSD calculation, allowing to directly compare conformations of different states. Only residues around a 6Å cut-off were used for the fitting to track local rearrangements without including global motions.
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pcbi.1004358.g004: Conformational ensemble of Leu73 (A) and Arg123’ (B), involved in pathway A, for the apo (black), the cap1 (blue) and the cap2 (orange) states.The protein is represented as cartoon in white (first protomer) and yellow (second protomer). Key residues are represented as cyan sticks. Histograms of local RMSDs are shown. The average structure of all CAP simulations was used as reference structure for the fitting and RMSD calculation, allowing to directly compare conformations of different states. Only residues around a 6Å cut-off were used for the fitting to track local rearrangements without including global motions.

Mentions: Pathway A is composed of only three specific residue pairs: Leu73-Leu124’, Leu124’-Arg123’ and Arg123’-Glu72’. The presence of the ligand in the binding pocket results in a stronger hydrophobic packing interaction between Leu73 and Leu124’ (Fig 4A). The signal is then propagating through backbone interactions from Leu124’ to Arg123’. Finally, the Arg123’ side-chain gains flexibility upon binding of the first cAMP (Fig 4B), leading to altered pairwise interactions between Arg123’ and Glu72’. Arg123’ is in close contact with the cAMP molecule in the second protomer, and mutation of this residue drastically decreases CAP activity [32]. Likewise, Glu72’ interacts directly with the second cAMP in the 2 cAMP-bound X-ray structure (the starting structure of our MD simulations) through a hydrogen bond with the sugar moiety. Also this residue has been shown to be crucial for nucleotide binding and CAP activity, as shown in site-directed mutagenesis studies [33]. Pathway A as revealed by FDA now suggests these two residues to be directly involved in the allosteric communication for anticooperative binding of cAMP.


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

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

Conformational ensemble of Leu73 (A) and Arg123’ (B), involved in pathway A, for the apo (black), the cap1 (blue) and the cap2 (orange) states.The protein is represented as cartoon in white (first protomer) and yellow (second protomer). Key residues are represented as cyan sticks. Histograms of local RMSDs are shown. The average structure of all CAP simulations was used as reference structure for the fitting and RMSD calculation, allowing to directly compare conformations of different states. Only residues around a 6Å cut-off were used for the fitting to track local rearrangements without including global motions.
© Copyright Policy
Related In: Results  -  Collection

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

pcbi.1004358.g004: Conformational ensemble of Leu73 (A) and Arg123’ (B), involved in pathway A, for the apo (black), the cap1 (blue) and the cap2 (orange) states.The protein is represented as cartoon in white (first protomer) and yellow (second protomer). Key residues are represented as cyan sticks. Histograms of local RMSDs are shown. The average structure of all CAP simulations was used as reference structure for the fitting and RMSD calculation, allowing to directly compare conformations of different states. Only residues around a 6Å cut-off were used for the fitting to track local rearrangements without including global motions.
Mentions: Pathway A is composed of only three specific residue pairs: Leu73-Leu124’, Leu124’-Arg123’ and Arg123’-Glu72’. The presence of the ligand in the binding pocket results in a stronger hydrophobic packing interaction between Leu73 and Leu124’ (Fig 4A). The signal is then propagating through backbone interactions from Leu124’ to Arg123’. Finally, the Arg123’ side-chain gains flexibility upon binding of the first cAMP (Fig 4B), leading to altered pairwise interactions between Arg123’ and Glu72’. Arg123’ is in close contact with the cAMP molecule in the second protomer, and mutation of this residue drastically decreases CAP activity [32]. Likewise, Glu72’ interacts directly with the second cAMP in the 2 cAMP-bound X-ray structure (the starting structure of our MD simulations) through a hydrogen bond with the sugar moiety. Also this residue has been shown to be crucial for nucleotide binding and CAP activity, as shown in site-directed mutagenesis studies [33]. Pathway A as revealed by FDA now suggests these two residues to be directly involved in the allosteric communication for anticooperative binding of cAMP.

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.