nemo8130 / salt-bridge-dynamics-in-idp-s Goto Github PK

The frames totalling 40 ns in length, (taken at an interval of 50 ps) from the closing half of the trajectory (60-100 ns) have been displayed and played in slow motion (half of the original speed). Salt-bridges with an overall persistence of 10% or more (pers ≥ 0.10) with respect to the full 100 ns trajectory, have been displayed as dashed lines along with the length between the corresponding ionic groups in each frame. The residues (3-GLU, 5-ARG, 11-GLU, 13-HIP) involved in 'persistent' salt-bridges (pers ≥ 0.25) have been coloured by element while the rest of the charged residues coloured by the colouring method ResName in VMD [1]. For visual clarity, residue legends have been skipped which would otherwise have made it clumsy. The video portrays how an IDP can potentially accommodate a pull of oppositely charged residues by allowing the formation of an optimal set of salt-bridges without having to compromise for their desired dynamic flexibility. As could be seen in the video, the key to achieve this is to continuously interchanging between salt-bridges alongside having a variety of persistence in the salt-bridges, through different distant conformations in the dynamic ensemble.