Induced fit for mRNA/TIS11d complex.

TIS11d tandem zinc finger (TZF) domain can bind the class II AU-rich element of target mRNA and regulate mRNA turnover by promoting or inhibiting degradation. NMR spectra show that TIS11d(TZF) undergoes a transition from disordered to well folded upon binding to Zn and mRNA. To gain an insight into the mechanism, we have performed explicit-solvent molecular dynamics simulations (MD) for both bound and apo-TIS11d(TZF) to study the interdependence of binding and folding in the mRNA-TIS11d(TZF) complex. These results are in qualitative agreement with NMR experiment. Furthermore, this method could be used to other study about protein folding upon ligand binding.