p38α Kinase Auto-Activation through Its Conformational Transition Induced by Tyr323 Phosphorylation

Abstract

p38α is a key serine/threonine kinase that can enable atypical auto-activation through Zap70 phosphorylation and initiate T cell receptor signaling. The auto-activation plays an important role in autoimmune diseases. Although the classical activation mechanism of p38α has been studied in-depth, the atypical activation mechanism of Y323 phosphorylation-induced p38α auto-activation remains largely unexplained, especially the regulatory effects of phosphorylation on different sites (Y323 vs T180). From the X-ray experimental data, we identified the inactive and active states of p38α using principal component analysis. To understand the auto-activation process and the internal driving mechanism, a computational paradigm that couples the targeted molecular dynamics simulations, the String Method, and the umbrella sampling strategy were employed to generate the conformational landscape of p38α, including p38α T180–Y323, p38α T180–pY323, and p38α pT180–pY323 systems (pT180/pY323: phosphorylated T180/Y323). We explored that pY323 could change the conformational distribution and promote the conformational transition of p38α from the inactive state to the active state. Auto-activation of p38α is regulated by pY323 through destabilization of the hydrophobic core structure and aided by R173. This study will further explain the conformational transition of p38α induced by Y323 phosphorylation and provide insights into the universal molecular auto-activation mechanism of the p38 subfamily at the atomic level.

Arginine Di-methylation of RIPK3 Safeguards Necroptosis for Intestinal Homeostasis

“…Details of the MD simulation was published previously (Li et al, 2019b; Yang et al, 2022; Zang et al, 2022). In brief, the transferable intermolecular potential with three points (TIP3P) water model (Berendsen et al, 1981) was employed to describe the solvent.…”

“…The three protein structures (RIP1 and RIP3) were geometrically optimized using the conjugate gradient (CG) method and further refined by 100-ns explicit solvent molecular dynamics (MD) simulations using GROMACS 2018.8 (Abraham et al, 2015) and the Charmm36m force field (Huang et al, 2017). Details of the MD simulation was published previously (Li et al, 2019b;Yang et al, 2022;Zang et al, 2022). In brief, the transferable intermolecular potential with three points (TIP3P) water model (Berendsen et al, 1981) was employed to describe the solvent.…”

Simultaneous Improvement in the Thermostability and Catalytic Activity of Epoxidase Lsd18 for the Synthesis of Lasalocid A

“…This was followed by constant-temperature equilibration at 310 K for 1.0 ns, with a positional restraint of 10.0 kcal/mol•Å 2 on protein atoms in a canonical ensemble (NVT). Subsequently, an equilibration simulation was performed for 1.0 ns at 1 atm and 310 K in the NPT ensemble with a positional restraint of 4.0 kcal/mol•Å 2 on backbone atoms of the protein [19]. The production MD simulations were carried out at 310 K and 1 atm with a time step of 2.0 fs.…”

Molecular Simulations of Conformational Transitions within the Insulin Receptor Kinase Reveal Consensus Features in a Multistep Activation Pathway

“…These conformational differences raise the question of whether their conformational changes to the active conformation occur through similar or different mechanisms. To this end, computational studies have played a significant role in advancing our understanding of this topic. − For example, the Roux group has conducted extensive investigations on the conformational change of cSrc, focusing on the transitions between the DFG-in inactive conformation and the active conformation. , Their findings revealed that the A-loop conformational change occur prior to the inward rotation of the αC helix, and both transitions occur with relatively small free-energy barriers. In a separate study, the same group examined DFG flipping in the inactive conformation and compared it with the Abl kinase .…”