Dynamic allostery-based molecular workings of kinase peptide complexes

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 116; no. 30; pp. 15052 - 15061
• Main Authors: Ahuja, Lalima G., Aoto, Phillip C., Kornev, Alexandr P., Veglia, Gianluigi, Taylor, Susan S.
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 23.07.2019
• Series: PNAS Plus
• Subjects: Adenosine Triphosphate - chemistry; Adenosine Triphosphate - metabolism; Allosteric properties; Allosteric Regulation; Allosteric Site; Amino Acid Sequence; Amino acids; Binding; Biological Sciences; Catalysis; Catalytic Domain; Computer simulation; Coupling (molecular); Cyclic AMP-Dependent Protein Kinases - chemistry; Cyclic AMP-Dependent Protein Kinases - metabolism; Entropy; Enzyme Inhibitors - chemistry; Enzyme Inhibitors - metabolism; Enzymes; Exploration; Kinases; Kinetics; Magnesium - chemistry; Magnesium - metabolism; Molecular Dynamics Simulation; Molecular machines; Nucleotides; Peptide mapping; Peptides; Peptides - chemistry; Peptides - metabolism; PNAS Plus; Protein Binding; Protein Conformation, alpha-Helical; Protein Conformation, beta-Strand; Protein Interaction Domains and Motifs; Protein kinase A; Protein Structure, Tertiary; Proteins; Structural members; Substrate inhibition; Substrate Specificity; Substrates; Switches; Switching theory; Thermodynamics; violin model; community maps; dynamics; protein kinase; allostery
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1900163116

A dense interplay between structure and dynamics underlies the working of proteins, especially enzymes. Protein kinases are molecular switches that are optimized for their regulation rather than catalytic turnover rates. Using long-simulations dynamic allostery analysis, this study describes an exploration of the dynamic kinase:peptide complex. We have used protein kinase A (PKA) as a model system as a generic prototype of the protein kinase superfamily of signaling enzymes. Our results explain the role of dynamic coupling of active-site residues that must work in coherence to provide for a successful activation or inhibition response from the kinase. Amino acid networks-based community analysis allows us to ponder the conformational entropy of the kinase:nucleotide:peptide ternary complex. We use a combination of 7 peptides that include 3 types of PKA-binding partners: Substrates, products, and inhibitors. The substrate peptides provide for dynamic insights into the enzyme:substrate complex, while the product phospho-peptide allows for accessing modes of enzyme: product release. Mapping of allosteric communities onto the PKA structure allows us to locate the more unvarying and flexible dynamic regions of the kinase. These distributions, when correlated with the structural elements of the kinase core, allow for a detailed exploration of key dynamics-based signatures that could affect peptide recognition and binding at the kinase active site. These studies provide a unique dynamic allostery-based perspective to kinase:peptide complexes that have previously been explored only in a structural or thermodynamic context.