TAB1 binding induced p38α conformation change: an accelerated molecular dynamics simulation study

Abstract

p38α Mitogen-activated protein kinase (MAPK) undergoes the autophosphorylation induced by the binding of TGFβ-activated kinase 1 binding protein 1 (TAB1) in myocardial ischemia. Investigation of the conformational transformations in p38α...

SARS-CoV-2 spike protein-ACE2 interaction increases carbohydrate sulfotransferases and reduces N-acetylgalactosamine-4-sulfatase by p38 MAPK

“…Phospho p38-MAPK has been implicated in critical interactions among exogenous exposures, intracellular signaling, and transcriptional events in a wide range of experiments. 57 – 60 TAB1 has been reported to participate in the activation of phospho-p38α following exogenous stimulation, 61 – 63 but silencing TAB1 did not affect phospho-p38 activation in the experiments in this report (Figs. 2g, h , 3b ).…”

Simulations of a PKA RIα homodimer reveal cAMP-coupled conformational dynamics of each protomer and the dimer interface with functional implications

“…The principal component analysis (PCA) was often used to characterize the motions of proteins during structural transition. 36 Here, it was carried out with gmx anaeig in GROMACS. A contact between two heavy atoms was defined if they were within 0.5 nm.…”

Recognition between CD147 and cyclophilin A deciphered by accelerated molecular dynamics simulations

“…The ‘dual-boost’ version of aMD simulation was employed in each system, as previously described. 48 It modifies the energy, V *( r ), landscape by adding a boost potential, Δ V ( r ), to the original potential energy surface when V ( r ) is below the reference energy E : 29,42,49,50 The boost potential, Δ V ( r ) is given bywhere α modulates the depth and local roughness of the energy basins in the modified potential. A boost potential was applied to both dihedral angles and the total energy across all individual atoms with E dihed , α dihed , E total , α total : V dihed_avg and V total_avg are the average dihedral and total potential energies calculated from cMD simulations.…”

“…32,[42][43][44][45][46][47] The 'dual-boost' version of aMD simulation was employed in each system, as previously described. 48 It modifies the energy, V*(r), landscape by adding a boost potential, DV(r), to the original potential energy surface when V(r) is below the reference energy E: 29,42,49,50…”