Welsh Colin L, Conklin Abigail E, Madan Lalima K
Department of Cellular and Molecular Pharmacology and Experimental Therapeutics, College of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA.
Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA.
Biology (Basel). 2023 Oct 26;12(11):1370. doi: 10.3390/biology12111370.
Cyclic-AMP-dependent protein kinase A (PKA) is a critical enzyme involved in various signaling pathways that plays a crucial role in regulating cellular processes including metabolism, gene transcription, cell proliferation, and differentiation. In this study, the mechanisms of allostery in PKA were investigated by analyzing the vast repertoire of crystal structures available in the RCSB database. From existing structures of murine and human PKA, we elucidated the conformational ensembles and protein dynamics that are altered in a ligand-dependent manner. Distance metrics to analyze conformations of the G-loop were proposed to delineate different states of PKA and were compared to existing structural metrics. Furthermore, ligand-dependent flexibility was investigated through normalized B'-factors to better understand the inherent dynamics in PKA. The presented study provides a contemporary approach to traditional methods in engaging the use of crystal structures for understanding protein dynamics. Importantly, our studies provide a deeper understanding into the conformational ensemble of PKA as the enzyme progresses through its catalytic cycle. These studies provide insights into kinase regulation that can be applied to both PKA individually and protein kinases as a class.
环磷酸腺苷依赖性蛋白激酶A（PKA）是一种参与多种信号通路的关键酶，在调节包括代谢、基因转录、细胞增殖和分化在内的细胞过程中发挥着至关重要的作用。在本研究中，通过分析RCSB数据库中大量可用的晶体结构，对PKA的变构机制进行了研究。从鼠源和人源PKA的现有结构中，我们阐明了以配体依赖方式改变的构象集合和蛋白质动力学。提出了用于分析G环构象的距离度量，以描绘PKA的不同状态，并与现有的结构度量进行比较。此外，通过归一化的B因子研究了配体依赖性灵活性，以更好地理解PKA的内在动力学。本研究提供了一种当代方法，用于采用晶体结构来理解蛋白质动力学的传统方法。重要的是，我们的研究随着酶通过其催化循环的进程，对PKA的构象集合有了更深入的理解。这些研究为激酶调节提供了见解，这些见解既可以应用于单个PKA，也可以应用于作为一类的蛋白激酶。
