Conformational coupling by trans-phosphorylation in calcium calmodulin dependent kinase II

Abstract

31The calcium calmodulin dependent protein kinase II (CaMKII) is a dodecameric holoenzyme 32 important for encoding memory. Its activation, triggered by binding of calcium calmodulin, persists 33 autonomously after calmodulin dissociation. One (receiver) kinase captures and subsequently phos-34 phorylates the regulatory domain peptide of a donor kinase forming a chained dimer as a first stage 35 of autonomous activation. Protein dynamics simulations examined the conformational changes trig-36 gered by dimer formation and phosphorylation, aimed to provide a molecular rationale for human 37 mutations that result in learning disabilities. Ensembles generated from X-ray crystal structures were 38 characterized by network centrality and community analysis. Mutual information related collective 39 motions to local fragment dynamics encoded with a structural alphabet. Implicit solvent tCONCOORD 40 conformational ensembles revealed the dynamic architecture of Inactive kinase domains was co-opted 41 in the activated dimer but the network hub shifted from the nucleotide binding cleft to the captured 42 peptide. Explicit solvent molecular dynamics (MD) showed nucleotide and substrate binding determi-43 nants formed coupled nodes in long-range signal relays between regulatory peptides in the dimer. 44Strain in the extended captured peptide was balanced by reduced flexibility of the receiver kinase C-45 lobe core. The relays were organized around a hydrophobic patch between the captured peptide and 46a key binding helix. The human mutations aligned along the relays. Thus, these mutations could disrupt 47 Author Summary 58Protein kinases play central roles in intracellular signalling. Auto-phosphorylation by bound 59 nucleotide typically precedes phosphate transfer to multiple substrates. Protein conformational 60 changes are central to kinase function, altering binding affinities to change cellular location and shunt 61 from one signal pathway to another. In the brain, the multi-subunit kinase, CaMKII is activated by cal-62 cium calmodulin upon calcium jumps produced by synaptic stimulation. Auto-transphosphorylation of 63 a regulatory peptide enables the kinase to remain activated and mediate long-term behavioural effects 64 after return to basal calcium levels. A database of mutated residues responsible for these effects is 65 difficult to reconcile solely with impaired nucleotide or substrate binding. Therefore, we have compu-66 tationally generated interaction networks to map the conformational plasticity of the kinase domains 67where most mutations localize. The network generated from the atomic structure of a phosphorylated 68 dimer resolves protein sectors based on their collective motions. The sectors link nucleotide and sub-69 strate binding sites in self-reinforcing relays between regulatory peptides. The self-reinforcement is 70 strengthened by phosphorylation consistent with the reported positive cooperativity of kinase activity 71 with calcium-calmodulin concentration. The network gives a better match with the mu...