Death-Associated Protein Kinase Activity Is Regulated by Coupled Calcium/Calmodulin Binding to Two Distinct Sites

Abstract

The regulation of many protein kinases by binding to calcium/calmodulin connects two principal mechanisms in signaling processes: protein phosphorylation and responses to dose- and time-dependent calcium signals. We used the calcium/calmodulin-dependent members of the death-associated protein kinase (DAPK) family to investigate the role of a basic DAPK signature loop near the kinase active site. In DAPK2, this loop comprises a novel dimerization-regulated calcium/calmodulin-binding site, in addition to a well-established calcium/calmodulin site in the C-terminal autoregulatory domain. Unexpectedly, impairment of the basic loop interaction site completely abolishes calcium/calmodulin binding and DAPK2 activity is reduced to a residual level, indicative of coupled binding to the two sites. This contrasts with the generally accepted view that kinase calcium/calmodulin interactions are autonomous of the kinase catalytic domain. Our data establish an intricate model of multi-step kinase activation and expand our understanding of how calcium binding connects with other mechanisms involved in kinase activity regulation.

Graphical abstract

Figure 1

Structures of hDAPK1, hDAPK2, and hDAPK3 Dimers with an Identical Arrangement Upper panel, topology of CD (violet) and ARD (blue) in hDAPK1 (PDB: 2XZS), hDAPK2 (PDB: 2A2A), and hDAPK3 (PDB: 1YRP) sequences. The approximate locations of the BL (green) and the HP (yellow) are also colored. A ruler indicates approximate residue positions. For each structure, the two monomers are depicted as ribbons under transparent surface (violet, blue) showing the basic loop (green), the HP helix αG (yellow), and the ARD (blue). Each monomer is labeled. Dashed lines represent flexible regions that are not supported by electron density (for further details, see Tables S1 and S2). The common dimer arrangement found in all three kinases is equivalent to the starting state on the very left in the cartoon presentation of Figure 7.

Figure 2

The Homodimeric Assembly of hDAPK2 CD + ARD Involves Two Major Surface Areas Termed “Hydrophobic Patch Interface” and “Basic Loop Interface” The hydrophobic patch (HP) interface and basic loop (BL) interface are colored in orange/yellow and green, respectively. All other color codes are as in Figure 1. The topology scheme from Figure 1 has been included as reference for each monomer. The orientation of the DAPK2 dimer is different from Figure 1 to optimize the view into the dimeric interface. The lower panels zoom into the two interface patches, indicating key interface residues discussed in the text (cf. Figure 3 and Table S2). Interface hydrogen bonds are shown in by red dashed lines.

Figure 3

The Structurally Conserved DAPK Homodimeric Interface Overlaps with the DAPK1-Ca²⁺/CaM Interface (A and B) Multiple sequence alignment (A) and dimer surface (B) of hDAPK1 (PDB: 2XZS), hDAPK2 (PDB: 2A2A, chains A/B and C/D), and hDAPK3 (PDB: 1YRP). Secondary structural elements are indicated and labeled according to the conventions established for members of the DAPK family (Temmerman et al., 2013). Interface residues have been identified and characterized with PDBePISA (Krissinel and Henrick, 2007). Residues discussed in the text are labeled with red asterisks. DAPK homodimeric interfaces are colored from yellow to dark red, depending on the level of involvement per residue. The hDAPK1 Ca²⁺/CaM interface is colored from blue to purple. Residues that are not modeled in the respective structures due to lack of interpretable electron density are in gray. Residues that have been mutated and used for functional characterization are labeled in red. Homodimeric interface regions that overlap with the Ca²⁺/CaM-binding interface in hDAPK1 are boxed and numbered I to V. For further details, see Table S2.

Figure 4

Characterization of hDAPK2 Dimerization Properties (A) SEC analysis of DAPK2 CD + ARD WT (black) and mutants (BL, green; D220K, orange; L226R, yellow). Calculated retention volumes for dimeric and monomeric hDAPK2 are indicated. (B) SAXS experimental curves and model fitting of selected hDAPK2 mutants (for further details, see Table 2 and Table S3). Blue dashed lines, calculated monomer fit; red dashed lines, calculated dimer fit; solid lines (WT, black; D220K, orange; BL, green), calculated equilibrium fit. Y axis values have been manually offset to allow data comparison. Error bars represent the SE of the mean scattering intensities detected at each pixel by the photon counting detector. (C) Dimerization of hDAPK2 mutants by bimolecular fluorescence complementation (BiFC). Left panel: representative images; right panel: quantification of the BiFC readout normalized to protein expression (see Figure S4). Errors bars represent SDs from two independent experiments. Scattering real-space distance distributions are shown in Figure S5.

Figure 5

CD-Mediated Ca²⁺/CaM Binding in hDAPK2 (A) CaM pull-down assays of purified hDAPK2 variants monitored by SDS-PAGE Coomassie blue staining. ND, not determined. Data are normalized to the hDAPK2 S308A mutant. Error bars represent one SD from three experimental repetitions. (B) CaM pull-down assays of hDAPK2 variants HEK293T transfected cells monitored by western blot. Data are normalized to the hDAPK2 W305D mutant. I, cell input; E, EGTA-mediated elution on Sepharose 4B-CaM; C, EGTA-mediated elution on Sepharose 4B without CaM (negative control). Relative units were calculated using the average ratio between input and elution band intensities for each mutant over three replicates. Error bars represent one SD from three experimental repetitions. (C and D) In vitro fluorescence anisotropy assays of purified hDAPK2 variants titrated against Ca²⁺/CrAsH-CaM. Error bars represent one SD between the triplicates of a representative experimental curve. K_D values were estimated using a non-linear regression assuming one-site specific binding with the software Prism (version 5.0, GraphPad) for three experiments.

Figure 6

hDAPK2 Blebbing Assay in HEK293T Cells in the Absence and Presence of Thapsigargin (A) Error bars indicate one SD. All experiments were performed in triplicate. Representative images of HEK293T cells expressing hDAPK2 variants are shown below. ND, not determined. (B) Schematic representation outlining our findings on how homodimerization, Ca²⁺/CaM binding, and cellular activity of hDAPK2 are coupled. The thickness of the arrows representing the dimer/monomer equilibrium of different hDAPK2 mutants indicates shifts measured by SEC and SAXS (cf. Figure 4).

Figure 7

General Mechanism of DAPK Activity Regulation CD-mediated monomerization (step 1), micromolar-affinity CD-mediated Ca²⁺/CaM binding (step 2), and nanomolar-affinity ARD-mediated Ca²⁺/CaM binding (step 3). Step 4—release of the Ca²⁺/CaM-bound ARD module—has not yet been mechanistically investigated and is therefore labeled with a “?”. For reasons of clarity, effects on DAPK activity regulation by ARD phosphorylation are not included in this scheme. Color codes are as in Figures 1 and 2. The DAPK CD active site is indicated with a star. As extracted from available structural data the ARD helix, shown by a cylinder, is formed upon Ca²⁺/CaM binding.