Fig. 6: The PH domain alters Arf switch 1 conformation.
From: An active allosteric mechanism in ASAP1-mediated Arf1 GTP hydrolysis redefines PH domain function
A (left) Cartoon representation of the conformation of switch 1 for Arf (blue) or Arf+ wt PH (red). The average structure calculated over the entire length of the simulation is represented. The thickness of the worm is proportional to the RMSD. (right) Histogram of the distance distribution between COM of residue 40–45 (top) or residue 47–50 (bottom) of switch 1 and GTP-Pγ for Arf (blue) and Arf + wt PH (red) calculated over the entire length of the simulations. B (left) Histogram of the distance distribution between γ-OH atom of Thr48 and Mg2+ for Arf (blue) and Arf + wt PH (red) calculated over the entire length of the simulations. (middle) Histogram of the distance distribution between ζ-N of Lys30 and GTP-Pγ for Arf (blue) and Arf + wt PH (red) calculated over the entire length of the simulations. (right) Cartoon representation of the position of Thr48 and Lys30 of Arf near GTP-Pγ as observed in MD simulations. C (left) 31P NMR spectra of Arf bound to GTPγS in the presence (bottom) and absence of ASAP1 PH (top). Phosphates observed are labeled by phosphate types (P-α,β,γ: GTP; PPIP2, PC: Lipid headgroup). The inset shows deshielding of GTP-Pγ chemical shift in the presence of ASAP1 PH. *, trace γ-Pi. (right) Cartoon representation of the electrostatic charge variation in GTP as observed by 31P NMR. GTP-Pγ is less negatively charged when Arf is bound to ASAP1 PH, facilitating the nucleophilic attack of water. All images created using Chimera56. Source data are provided as a Source data file.
