Simulation Study of the Plasticity of k-Turn Motif in Different Environments

Abstract

The k-turn is a widespread and important motif in RNA. According to the internal hydrogen bond network, it has two stable states, called N1 and N3. The relative stability between the states changes with the environment. It is able to accept different conformations in different environments. This is called the ''plasticity'' of a molecule. In this work, we study the plasticity of k-turn by the mixing REMD method in explicit solvent. The results are concluded as follows. First, N1 and N3 are almost equally stable when k-turn is in the solvent alone. The molecule is quite flexible as a hinge. However, after binding to different proteins, such as the proteins L7Ae and L24e, k-turn falls into one global minimum. The preferred state could be either N1 or N3. On the contrary, the other nonpreferred state becomes unstable with a weaker binding affinity to the protein. It reveals that RNAbinding protein is able to modulate the representative state of k-turn at equilibrium. This is in agreement with the findings in experiments. Moreover, free energy calculations show that the free energy barrier between the N1 and N3 states of k-turn increases in the complexes. The state-to-state transition is greatly impeded. We also give a deep discussion on the mechanism of the high plasticity of k-turn in different environments.