Protein kinase Iα (PKGIα) is a pivotal cyclic guanosine monophosphate (cGMP) signalling protein. Major steps related to the structural plasticity of PKGIα have been inferred but the structural aspects of the auto-inhibition and multidomain tertiary organization of human PKGIα in active and inactive form are not clear. Here we combine computational comparative modelling, protein–protein docking and molecular dynamics (MD) simulations to investigate structural details of the repressed state of the catalytic domain of PKGIα. Exploration of the potential inhibitory conformation of the auto-inhibitory domain (AI) within the catalytic cleft reveals that the pseudo-substrate motif binds with residues of the glycine rich loop and substrate-binding lobe. Dynamic changes as a result of coupling of the catalytic and AI domains are also investigated. The three-dimensional homodimeric models of PKGIα in the active and inactive state indicate that PKGIα in its inactive-state attains a compact globular structure where cyclic nucleotide binding (CNB-A/B) domains are buried, whereas the catalytic domains are inaccessible with their substrate-binding pockets facing the N-terminal of CNB-A. Contrary to this, the active-state model of PKGIα shows an extended conformation where CNB-A/B domains are slightly rearranged and the catalytic domains of homodimer flanking the C-terminal with their substrate binding lobes free to entrap downstream proteins. These findings are consistent with previously reported static images of the multidomain organization of PKGIα. Structural insights pertaining to the conformational heterogeneity and auto-inhibition of PKGIα provided in this study may help to understand the dynamics-driven effective regulation of PKGIα.

蛋白激酶 Iα (PKGIα) 是一种关键的环磷酸鸟苷 (cGMP) 信号蛋白。与 PKGIα 结构可塑性相关的主要步骤已被推断出来，但活性和非活性形式的人类 PKGIα 的自动抑制和多域三级组织的结构方面尚不清楚。在这里，我们结合计算比较模型、蛋白质-蛋白质对接和分子动力学 (MD) 模拟来研究 PKGIα 催化结构域抑制状态的结构细节。对催化裂隙内自抑制结构域 (AI) 的潜在抑制构象的探索表明，假底物基序与富含甘氨酸的环和底物结合叶的残基结合。还研究了催化域和人工智能域耦合导致的动态变化。活性和非活性状态下 PKGIα 的三维同二聚体模型表明，非活性状态下的 PKGIα 获得了紧凑的球状结构，其中环核苷酸结合（CNB-A/B）结构域被掩埋，而催化结构域则无法通过其催化结构域进入。面向 CNB-A N 端的底物结合口袋。与此相反，PKGIα 的活性状态模型显示出扩展的构象，其中 CNB-A/B 结构域稍微重排，C 端侧翼的同型二聚体催化结构域及其底物结合叶可以自由捕获下游蛋白质。这些发现与之前报道的 PKGIα 多域组织的静态图像一致。本研究提供的有关 PKGIα 构象异质性和自动抑制的结构见解可能有助于理解 PKGIα 的动力学驱动的有效调节。