Fig. 5: Molecular dynamics simulation of the (MET:InlB321)2 dimer. | Nature Communications

Fig. 5: Molecular dynamics simulation of the (MET:InlB321)2 dimer.

From: Single-molecule imaging and molecular dynamics simulations reveal early activation of the MET receptor in cells

Fig. 5

A Renders of the initial form II (MET:InlB321)2 complex model (Sema and PSI domain of MET in silver cartoon and IPT1 domain in red cartoon; InlB in blue cartoon. Water, ions, and glycans not shown for clarity). B RMSD time series of the form II (MET:InlB321)2 complex model replicas calculated with respect to the first frame. C Representative assemblies of the two different dimer interfaces explored during the simulations (InlB321 in cyan cartoon, MET in silver cartoon, positive side chains in blue, negative side chains in red). Replica 1 explored a broader dimer interface (black frame), while Replica 3 explored a more compact one (blue frame; water, ions, and glycans not shown for clarity). D Render of the proposed antisymmetric dimer structure (explored by R3, compact dimer interface) showing top view (top panel) and side view (bottom panel) (water, ions, and glycans not shown for clarity). Source data are provided as a Source Data file.

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