Kinetic and thermodynamic insights into sodium ion translocation through the μ-opioid receptor from molecular dynamics and machine learning analysis
Fig 3
Transition networks formed by the metastable states obtained from the Markov state models constructed for the inactive MOR (panel a) and active MOR with charged or protonated D1142.50 (panels b and c, respectively).
States are labeled according to the Na+ position relative to the receptor as extracellular or cytoplasmic states, while bound states are highlighted with a black contour. The size of the circles depicting the metastable states is proportional to the probability of individual states and the thickness of the arrows connecting them is proportional to the transition flux between the states. Three-dimensional structures are shown in insets for each metastable state and represent the center of the corresponding PCCA cluster. Residues highlighted as sticks are the highly coupled residues from tICA with the most significant sidechain conformational change among different PCCA cluster center structures based on visual inspection.