Journal Article

Dynamic architecture of a protein kinase

Christopher L. McClendon, Alexandr P. Kornev, Susan S. Taylor, Michael K. Gilson

2014

Overview

Significance Protein kinases represent a critically important family of regulatory enzymes. Their activity can be altered by mutations and binding events distant from the active site. To understand the nature of these long-distance effects, we used microsecond-timescale molecular dynamic simulation to subdivide a prototypical kinase, protein kinase A, into contiguous communities that exhibit internally correlated motions. Surprisingly, most of these unconventional structural entities were centered around known protein kinase functions. We thus propose a new framework for analysis of protein kinase structure and function that differs from traditional representations based simply on sequence motifs and secondary structure elements. These results extend our view on the dynamic nature of protein kinases and open a door to understanding of allosteric signaling in these enzymes. Protein kinases are dynamically regulated signaling proteins that act as switches in the cell by phosphorylating target proteins. To establish a framework for analyzing linkages between structure, function, dynamics, and allostery in protein kinases, we carried out multiple microsecond-scale molecular-dynamics simulations of protein kinase A (PKA), an exemplar active kinase. We identified residue–residue correlated motions based on the concept of mutual information and used the Girvan–Newman method to partition PKA into structurally contiguous “communities.” Most of these communities included 40–60 residues and were associated with a particular protein kinase function or a regulatory mechanism, and well-known motifs based on sequence and secondary structure were often split into different communities. The observed community maps were sensitive to the presence of different ligands and provide a new framework for interpreting long-distance allosteric coupling. Communication between different communities was also in agreement with the previously defined architecture of the protein kinase core based on the “hydrophobic spine” network. This finding gives us confidence in suggesting that community analyses can be used for other protein kinases and will provide an efficient tool for structural biologists. The communities also allow us to think about allosteric consequences of mutations that are linked to disease.

• Publisher: National Academy of Sciences,National Acad Sciences
• Subject: active sites / Adenosine Triphosphate - metabolism / Allosteric Regulation / Biological Sciences / cAMP-dependent protein kinase / Catalytic Domain / Kinases / Ligands / Magnesium - metabolism / Molecular Dynamics Simulation / Molecular structure / Mutagenesis / Mutation / Phosphorylation / PNAS Plus / Protein Kinases - chemistry / Reproducibility of Results / Signal transduction / Spine / Templates, Genetic