Fig. 5. Molecular dynamics (MD) reveals force induced PD-1–PD-L2 conformational change and formation of distinct atomic-level contacts.

A Snapshots of PD-1–PD-L2 complex undergoing conformational changes in response to force at indicated simulation times. B Changes in relative angle (black curve, left y-axis) and root mean square displacement (RMSD, red curve, right y-axis) between PD-1 and PD-L2 in response to force. Comparison of total number of hydrogen bond (H-bond, C), salt bridge (D), and hydrophobic contacts (E) between PD-1 and PD-L2 during free MD (FMD, blue) and force steered MD (SMD, red). F–H Comparison of dynamics of putative interactions between indicated residues of PD-1 and PD-L2 during FMD (blue) and SMD (red). Atomic-level contacts were defined by an interatomic distance of <3.5 Å, which were more frequently observed in SMD than in FMD. Source data are provided in Source Data file.