Dual-specific autophosphorylation of kinase IKK2 enables phosphorylation of substrate I-kappaBalpha through a phosphoenzyme intermediate

This repository contains data and findings from the study titled "Dual-specific autophosphorylation of kinase IKK2 enables phosphorylation of substrate IkBa through a phosphoenzyme intermediate". It includes the following datasets:

Molecular Dynamics Simulation Data:

GROMACS input files (topology files, coordinate files, parameter files)
Energy minimization and equilibration configuration files
Production MD run parameters
Analysis data including RMSD, RMSF, energy, dynamic cross-correlation matrix (DCCM) results
MD simulation of three phosphorylated form of IKK2 available withim simulation_apo_200ns folder
MD simulation of ADP/ATP complex with three phosphorylated form of IKK2 available withim simulation_complex_10ns folder
MM-PBSA of all phosphorylated form of IKK2 complexed with ADP/ATP available within mmpbsa folder

Scripts and Analysis Code:

Python scripts used for data analysis and plot visualizations available within script folder. 

Below is the abstract of the corresponding manuscript:

"Rapid and high-fidelity phosphorylation of serine residues at positions 32 and 36 of IkBa by IKK2, a prototypical Ser/Thr kinase, is critical for canonical NF-kB activation. Here, we report that IKK2 not only phosphorylates substrate serine residues and autophosphorylates its own activation loop, but also autophosphorylates at a tyrosine residue proximal to the active site  and is, therefore, a dual-specificity kinase. We observed that mutation of Y169, an autophosphorylatable tyrosine located at the DFG+1 (DLG in IKK1) position, to phenylalanine renders IKK2 incapable of catalyzing phosphorylation at S32 within its IkBa substrate. We also observed that mutation of the phylogenetically conserved ATP-contacting residue K44 in IKK2 to methionine converts IKK2 to an enzyme that no longer catalyzes specific phosphorylation of IkBa at S32 or S36, but rather directs phosphorylation of IkBa at other residues. Lastly, we report evidence of a phospho-relay from autophosphorylated IKK2 to IkBa in the presence of ADP. These observations suggest an unusual evolution of IKK2, in which autophosphorylation of tyrosine(s) in the activation loop, and the conserved ATP-contacting K44 residue provide its signal-responsive substrate specificity and ensure fidelity during NF-kB activation."