Molecular dynamics of the immune checkpoint programmed cell death protein I PD-1: conformational changes of the BC-loop upon binding of the ligand PD-L1 and the monoclonal antibody nivolumab

摘要

Binding partners influence flexibility of loops. The RMSF of Cαs of PD-1 unbound (black) and bound to either PD-L1 (red) or nivolumab (blue), when fitted to its respective first frame are shown. Whereas the impact of the binding partners on structured domains is negligible, the RMSF of the loops can change drastically. PD-1Apo has the greatest flexibility except for the BC-loop. The fact that PD-L1 seems to induce more flexibility in the BC-loop led to detailed examination of the BC-loop