Crystal Structures Reveal Hidden Domain Mechanics in Protein Kinase A (PKA)

SIMPLE SUMMARY: Understanding the changes that occur in proteins as they perform their cellular function is critical to understanding our biology. Here, we investigated PKA, a protein partially responsible for processing signals that allows cells to respond to their environment, as well as how the shape of this protein changes as it performs its role by chemically altering other proteins. We analyzed a repertoire of publicly available crystal structures of PKA and identified regions of PKA that change shape based on its physical interactions with its ligands, or other signaling proteins. Studies of these shape changes allow researchers to better explore PKA for making advances in improving existing pharmacological therapies and gaining a deeper understanding of disease biology. ABSTRACT: 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.