Fig. 3: Kinetic model for the endosteric hierarchical closing of the LID and NMP domain.
From: Allostery can convert binding free energies into concerted domain motions in enzymes
The model includes the four observed states for the LID and NMP domain, and the hidden ligand-bound states. The ATP-induced endosteric effect was implemented by removing the M* → M** transition. The AMP-induced endosteric effect was implemented by allowing the M* \(\leftrightarrow\) M2* and M** \(\leftrightarrow\) M2** states to have different rates. The rates were retrieved by fitting the kinetic data to a Hidden Markov Model (HMM) based on the four observable states and using different ligand concentration. Confidence intervals for the estimated rates are given in Supplementary Table 7. The asterisks indicate whether one (*) or two (**) ligands are bound.
