Dynamic architecture of a protein kinase

Abstract

To better understand the mechanism of long distance allosteric signaling inside the protein kinase core using protein kinase A (PKA) as a prototype, we obtained 5μs molecular dynamics trajectories in different liganded and conformational states using the Anton supercomputer, providing for the first time an opportunity to observe intermediate‐timescale conformational transitions in the study of the dynamics of this stable kinase. We used community analysis to identify structurally‐contiguous groups of residues exhibiting correlated motions in the kinase catalytic domain. This dynamic partitioning of the kinase into communities provides a framework for analyzing the local vs. long‐range effects of mutations, binding, phosphorylation, etc. We hypothesize that perturbations will be readily felt within these communities and then propagated possibly to a lesser extent to other elements through correlated motions. Moreover, using a wealth of published mutational data, we can annotate these communities with functions. Our functional annotation of kinase communities provides an extremely valuable framework for viewing a signaling enzyme in terms of functional substructures rather than isolated linear motifs such as secondary structure elements and short three or four residue motifs. Figure 1. Functional annotation of the kinase communitiy map. Each community is shown in red on the structure of PKA. Grant Funding Source: Supported by NIH F32 GM099197, R01 GM19301

Mutation of a kinase allosteric node uncouples dynamics linked to phosphotransfer

“…Our mechanistic understanding of these enzymes is limited by simplification of these structures as rigid bodies that do not allow for molecular explanations of subtleties in kinase function. In an effort to understand the internal allosteric networks that weave a kinase into a functional module, we have recently used a community analysis that clusters the PKA residues into functionally distinct groups called communities (22). These community maps, coupled with crystal structures and NMR analyses, provide a more comprehensive perspective for understanding the protein kinase core as an ensemble of communities that must work coherently with each other to yield the required function.…”

“…This forms the first step of the catalytic cycle when the kinase binds the nucleotide and first metal ion. Our previously presented work has suggested this closed ATP-1Mg 2+ -bound form of PKA to be most allosterically coupled and having fewer communities compared with the open ATP-1Mg 2+ -bound form or the ATP-2Mg 2+ -bound form (22).…”

“…These biochemical studies then provide a framework for analysis of conformational entropy in PKA's catalytic cycle. Conformational entropy is studied for both wtPKA and the Y204A mutant using community analysis (22) where the Girvan Newman algorithm is used to identify functional ensembles called "communities" in the protein microsecond simulations based on the mutual informational matrices obtained for the structures' internal dynamics. This community network model can reflect the conformational entropy of the molecule and has been recently gaining appreciation as a way to understand dynamics-based protein allostery in various proteins including thrombin (23), Tec kinases (24), and also PKA (22).…”

“…Conformational entropy is studied for both wtPKA and the Y204A mutant using community analysis (22) where the Girvan Newman algorithm is used to identify functional ensembles called "communities" in the protein microsecond simulations based on the mutual informational matrices obtained for the structures' internal dynamics. This community network model can reflect the conformational entropy of the molecule and has been recently gaining appreciation as a way to understand dynamics-based protein allostery in various proteins including thrombin (23), Tec kinases (24), and also PKA (22). By building on our earlier models for community-based networks for the wtPKA (22,25), we provide a dynamic conformational entropy-based explanation for the disruption of catalytic activity in PKA by a single point mutation that lies far from the active site.…”

“…This community network model can reflect the conformational entropy of the molecule and has been recently gaining appreciation as a way to understand dynamics-based protein allostery in various proteins including thrombin (23), Tec kinases (24), and also PKA (22). By building on our earlier models for community-based networks for the wtPKA (22,25), we provide a dynamic conformational entropy-based explanation for the disruption of catalytic activity in PKA by a single point mutation that lies far from the active site. We carry out this comparison for the catalytically competent ATP-bound states of both wild-type and Y204A structures.…”