Simulations of PKA RIα Homodimer Reveal cAMP-coupled Conformational Dynamics of Each Protomer and the Dimer Interface with Functional Implications

<p>Protein kinase A (PKA) is a ubiquitous cAMP-dependent enzyme in mammalian tissues. The inactive PKA holoenzyme disassociates into a homodimer of regulatory (R) subunits and two active catalytic (C) subunits upon cAMP binding to two tandem domains (termed <span>CBD-A</span>&nbsp;<span>and</span>&nbsp;<span>CBD</span>-<span>B</span>) in R subunits. The release of cAMP facilitates reassociation of R and C subunits<span>,</span>&nbsp;resetting PKA to its basal state. The cAMP-mediated structural changes in the activation-termination cycle <span>remain</span>&nbsp;<span>partially</span>&nbsp;<span>understood</span>. The multimeric states of PKA complicate the issue and are particularly <span>less</span>&nbsp;<span>studied</span>. Therefore, we computationally investigate the conformational dynamics of PKA <span>RI</span>a&nbsp;homodimer in different cAMP-bound states. The absence of cAMP in two CBDs affect differently the <span>conformational</span>&nbsp;<span>dynamics</span>&nbsp;of protomers.&nbsp;Moreover, <span>such</span>&nbsp;disparate <span>responses</span>&nbsp;are extended to the dimer interface <span>constituted</span>&nbsp;<span>by</span>&nbsp;<span>the</span>&nbsp;<span>N</span>-<span>terminal</span>&nbsp;<span>helical</span>&nbsp;<span>sub-domains</span>&nbsp;termed N3A motifs.&nbsp;T<span>he removal of cAMP from CBD-A induces large-scale structure</span>&nbsp;changes <span>of individual </span>R subunits&nbsp;<span>towards the holoenzyme state,</span>&nbsp;consist with previous simulations of a single R subunit. <span>Meanwhile</span>&nbsp;<span>it</span>&nbsp;<span>keeps the structural heterogeneity of the </span>N3A-N3A'&nbsp;<span>dimer interface observed in the fully bound state.</span>&nbsp;By contrast, the removal of cAMP from CBD-B does not affect <span>individual </span>R subunits&nbsp;but alters the conformational space of the N3A-N3A'&nbsp;dimer interface. The cAMP-coupled s<span>tructural</span>&nbsp;<span>changes</span>&nbsp;<span>of</span>&nbsp;<span>each</span>&nbsp;<span>protomer</span>&nbsp;<span>and</span>&nbsp;conserved conformational space of <span>the</span>&nbsp;N3A-N3A'&nbsp;<span>dimer</span>&nbsp;<span>interface</span>&nbsp;are essential for t<span>he</span>&nbsp;<span>transition</span>&nbsp;<span>between</span>&nbsp;the fully cAMP-bound R₂&nbsp;homodimer and the R₂C₂&nbsp;holoenzyme as suggested by their crystal structures. Our work provides structural insights into <span>the</span> regulatory mechanism of cAMP in PKA signaling. &nbsp;</p>