Conformational dynamics of Peb4 exhibit “mother’s arms” chain model: a molecular dynamics study

Peb4 gene deletion alters the outer membrane protein profile and impairs cellular adhesion and biofilm formation for C. jejuni . Earlier crystallographic study has proposed that the PPIase domains are flexible and might form a cradle for holding the substrate and these aspects of Peb4 were explored using sub-microsecond molecular dynamics simulations in solution environment.

Our simulations have revealed that PPIase domains are highly flexible and undergo a large structural change where they move apart from each other by 8 nm starting at .5 nm. Further, this large conformational change renders Peb4 as a compact protein with crossed-over conformation, forms a central cavity, which can “cradle” the target substrate. As reported for other chaperone proteins, flexibility of linker region connecting the chaperone and PPIase domains is key to forming the “crossed-over” conformation.