Maryam Arooma, Khalid Rana Rehan, Vedithi Sundeep Chaitanya, Ece Abdulilah, Çınaroğlu Suleyman Selim, Siddiqi Abdul Rauf, Blundell Tom L
Department of Biosciences, COMSATS University Islamabad (CUI), Park Road, Islamabad 4550, Pakistan.
Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd., Cambridge CB2 1GA, UK.
Comput Struct Biotechnol J. 2020 Jun 12;18:1625-1638. doi: 10.1016/j.csbj.2020.06.016. eCollection 2020.
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，但人类PKGIα在活性和非活性形式下的自抑制和多结构域三级组织的结构方面尚不清楚。在这里，我们结合计算比较建模、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）潜在抑制构象的探索表明，假底物基序与富含甘氨酸环和底物结合叶的残基结合。还研究了催化结构域和AI结构域偶联导致的动态变化。活性和非活性状态下PKGIα的三维同二聚体模型表明，处于非活性状态的PKGIα获得了一种紧凑的球状结构，其中环核苷酸结合（CNB-A/B）结构域被掩埋，而催化结构域无法接近，其底物结合口袋面向CNB-A的N端。与此相反，PKGIα的活性状态模型显示出一种伸展构象，其中CNB-A/B结构域略有重排，同二聚体的催化结构域位于C端两侧，其底物结合叶可自由捕获下游蛋白质。这些发现与先前报道的PKGIα多结构域组织的静态图像一致。本研究中提供的关于PKGIα构象异质性和自抑制的结构见解可能有助于理解PKGIα由动力学驱动的有效调节。
