Abstract
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 MD and scaled MD (sMD). Materials & methods: Three different structures of calmodulin are compared, obtaining a total of 2.5 μs 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.
Calmodulin, a very flexible protein, has been studied taking advantage of the new available methodologies such as scaled and accelerated molecular dynamics. The results will be important to determine how this protein behaves when binding to its partners, as many new roles have been recently found for this protein.
Papers of special note have been highlighted as: •• of considerable interest
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