Toward understanding calmodulin plasticity by molecular dynamics

Aim: Calmodulin interacts in many different ways with its ligands. We aim to shed light on its plasticity analyzing the changes followed by the linker region and the relative position of the lobes using conventional molecular dynamics, accelerated MDand scaled MD (sMD). Materials & methods: Three different structures of calmodulin are compared, obtaining a total of 2.5 mu s of molecular dynamics, which have been analyzed using the principal component analysis and clustering methodologies. Results: sMD simulations reach conformations that conventional molecular dynamics is not able to, without compromising the stability of the protein. On the other hand, accelerated MD requires optimization of the setup parameters to be useful. Conclusion: sMD is useful to study flexible proteins, highlighting those factors that justify its promiscuity. [GRAPHICS]