Dynamic Allostery of the Catabolite Activator Protein Revealed by Interatomic Forces

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.

Transient association between proteins elicits alteration of dynamics at sites far away from interfaces

“…This changing view of allostery has been appreciated in the last decade with popularization of nuclear magnetic resonance methods to study protein motions. Proteins such as catabolite activator protein have been shown to exhibit dynamic allostery, arising from changes in intrinsic dynamics of the structure upon cyclic AMP binding (Louet et al, 2015;Popovych et al, 2006). Similar observations have been made for a few small molecule-protein and peptide-protein interactions (Kern and Zuiderweg, 2003;Mercier et al, 2001;Olejniczak et al, 1997;Wang et al, 2001;Zidek et al, 1999).…”

Oncogenic Mutations Differentially Affect Bax Monomer, Dimer, and Oligomeric Pore Formation in the Membrane

“…Allostery is an intrinsic property of many proteins 49 50 51 52 . Constitutive allosteric activation by oncogenic mutations is at play in virtually all biological processes in the living cells 53 54 55 .…”

Entropic allostery dominates the phosphorylation‐dependent regulation of Syk tyrosine kinase release from immunoreceptor tyrosine‐based activation motifs

“…Because Y130 is distant to the two binding sites of the SH2 domains, the negative regulation of Syk‐receptor association by Y130 phosphorylation is allosteric. Entropically driven allostery (sometimes imprecisely referred to as dynamic allostery) has been increasingly recognized and discussed . As shown in Figure (D), an entropic basis for reducing the equilibrium for isomerization in the forward direction is that Y130 phosphorylation increases the entropy of the unligated and singly bound forms of tSH2 relative to the bifunctional complex, resulting in a higher entropy penalty for the isomerization step.…”