Sequence determinants of a specific inactive protein kinase conformation

Abstract

Only a small percentage of protein kinases have been shown to adopt a distinct inactive ATP-binding site conformation, called the Asp-Phe-Gly-out (DFG-out) conformation. Given the high degree of homology within this enzyme family, we sought to understand the basis of this disparity on a sequence level. We identified two residue positions that sensitize mitogen-activated protein kinases (MAPKs) to inhibitors that stabilize the DFG-out inactive conformation. After characterizing the structure and dynamics of an inhibitor-sensitive MAPK mutant, we demonstrated the generality of this strategy by sensitizing a kinase (apoptosis signal-regulating kinase 1) not in the MAPK family to several DFG-out stabilizing ligands, using the same residue positions. The use of specific inactive conformations may aid the study of noncatalytic roles of protein kinases, such as binding partner interactions and scaffolding effects.

FIGURE 1. A probe for type II ligand sensitivity

A. General properties of a type II ligand, which spans a kinase active site from beyond the adenosine pocket through a hydrophobic pocket that would otherwise be occupied by the DFG motif phenylalanine. B. Structure of probe F. C. Titration of MAPKs in the presence of probe F shows the most change in fluorescence for p38α (blue triangles, K_d = 15 nM). D. Active site dissociation of probe F from p38α. The slow dissociation rate (t_1/2 = 80 min) is indicative of the large conformational change required to accommodate a type II inhibitor. E. The hydrophobic spines of protein kinase A (C-spine: yellow; N-spine: blue), connected by the gatekeeper (cyan) and xDFG (green) residues (PDB ID: 1ATP). F. Sequence alignments of MAPK hydrophobic spines shows that most of the residues are conserved within the MAPK family. The gatekeeper (cyan boxed) and xDFG (green boxed) residues are the only positions with significant variability. G. Active site dissociation of probe F from MAPKs. A gatekeeper/xDFG double mutant of Erk2 (Q103T/C164L, black squares) dissociates from probe F at a similar rate to p38α (blue triangles). See also Figure S1.

FIGURE 2. Structures of L1-4 and probe F

Despite varied structures, all of these inhibitors stabilize the DFG-out inactive conformation. Polar contacts are shown with dotted lines

FIGURE 3. L2-bound Erk2 Q103A/C164L adopts the DFG-out inactive conformation

A. Erk2 Q103A/C164L with L2 (cyan) and Phe-166 (salmon) contoured at 1.0σ. Part of the N-lobe beta sheet is hidden for clarity. B. Interaction map of L2 in the active site of Erk2 Q103A/C164L. Map generated by LigPlot⁺ (Laskowski and Swindells, 2011). C. Superimposition of L2-bound Erk2 Q103A/C164L (green) with apo inactive Erk2 (orange, activation loop shown only) (PDB ID: 1ERK) reveals a large activation loop translocation. D. Superimposition of L2-bound Erk2 Q103A/C164L (green) with L4-bound p38α (magenta, activation loop shown only) (PDB ID: 2BAJ). No pi-stacking is observed between Phe-169 and Tyr-182 in p38α. See also Table S1.

FIGURE 4. ICAT footprinting of inhibitor-sensitive and inhibitor-insensitive Erk2

A. Residue positions studied (black, sticks). The hinge region (yellow), activation loop (cyan), DFG motif (magenta, sticks), and gatekeeper residue (spheres) are also shown (PDB ID: 1ERK). B. Footprinting timecourses. The proximity of position 82 to the gatekeeper provides the explanation that a smaller gatekeeper residue, as in the case of Erk2 Q103T/C164L, would provide greater solvent accessibility and a faster alkylation rate. Position 172, however, is far from the gatekeeper and still shows altered rates for both Erk Q103T/C164L and Q103A/C164L. See also Figures S2 and S3.

FIGURE 5. The gatekeeper/xDFG sensitization strategy is general

A. Kinome dendrogram with the S/T kinases p38α (black) and Stk10 (red) circled illustrates the distant relationship between the two kinases. Kinome illustration reproduced courtesy of Cell Signaling Technology, Inc (www.cellsignal.com). B. Stk10 bound to L3 (magenta) in the DFG-out conformation with activation loop (yellow, F176 in sticks) highlighted (PDB ID: 4EQU). C. Inhibition data of STE group kinases against inhibitors L1-4 and binding and dissociation data of probe F. The ASK1 gatekeeper/xDFG double mutant (M754T/S821C) is inhibited at nanomolar levels for all inhibitors tested and binds to probe F with nanomolar affinity. n/d: not determined.