Structural basis of p38α regulation by hematopoietic tyrosine phosphatase

Abstract

MAP kinases regulate essential cellular events, including cell growth, differentiation and inflammation. The solution structure of a complete MAPK–MAPK-regulatory protein complex, p38α–HePTP, was determined, enabling a comprehensive investigation of the molecular basis of specificity and fidelity in MAPK regulation. Structure determination was achieved by combining NMR spectroscopy and small-angle X-ray scattering data with a new ensemble calculation–refinement procedure. We identified 25 residues outside of the HePTP kinase interaction motif necessary for p38α recognition. The complex adopts an extended conformation in solution and rarely samples the conformation necessary for kinase deactivation. Complex formation also does not affect the N-terminal lobe, the activation loop of p38α or the catalytic domain of HePTP. Together, these results show how the downstream tyrosine phosphatase HePTP regulates p38α and provide for fundamentally new insights into MAPK regulation and specificity.

Structure and dynamics of the MKK7–JNK signaling complex

“…4B). The intensities also decrease toward the C terminus, in agreement with previous NMR studies of p38α showing that residues outside the canonical docking sites contact the MAPK surface (28).…”

Structural Basis for the Regulation of the Mitogen-activated Protein (MAP) Kinase p38α by the Dual Specificity Phosphatase 16 MAP Kinase Binding Domain in Solution

“…For example, a direct comparison of the K D values between KIM peptides derived from KIM-PTPs (17,19,39) and MAPKs shows that the interaction between p38␣ and the DUSP16 MKBD, which contains a structured KIM, is ϳ5-10 times stronger. Furthermore, we show that the interaction of a MAPK with KIMs from proteins within a single family, namely the DUSP MKBDs, is also structurally distinct.…”

“…These sequence differences, in addition to the differences in their structures, also suggest that their mode of binding to MAPKs may not be strictly conserved. Furthermore, as observed previously, solution state studies, in addition to crystallographic studies, often reveal new insights into the structure and function of key signaling complexes (17)(18)(19)24). Thus, additional studies that investigate how, at a molecular level, other DUSPs interact with MAPKs are critical for elucidating the structural basis of specificity of these key regulatory proteins.…”

“…for KIM-PTPs and MAPKKs) usually found in an unstructured N-terminal extension of the protein. The interaction of KIMs with MAPKs has been studied via multiple techniques, including x-ray crystallography as well as biomolecular NMR spectroscopy in solution (10,(13)(14)(15)(16)(17)(18)(19).…”

Bayesian ensemble refinement by replica simulations and reweighting

“…It is therefore essential that ensemble refinement methods can properly integrate data from a broad range of experiments 2,4,12 that may report on molecular size and shape (e.g., from SAXS, SANS, or hydrodynamic measurements 3,13,14 ), the proximity (e.g., from cross-links) or distance between atoms and residues [e.g., from fluorescence resonant energy transfer (FRET), NMR, [15][16][17] including nuclear Overhauser effects (NOE), or double electron-electron resonance (DEER) measurements 3,18 ], the local chemical environment and structure (e.g., from NMR chemical shifts 14 and J-couplings 10,11 or X-ray absorption spectroscopy), all the way to measures of the global structure (e.g., from X-ray crystal diffraction or electron microscopy 4,12,19 ). Taking into account the uncertainties of the different experiments 20 is critical for the construction of a properly weighted configurational ensemble.…”