Molecular dynamics simulations of the Trp repressor–DNA complex and the AV77 mutant

Molecular dynamics simulations were performed on E. coli wild type (WT) Trp repressor and the AV77 mutant in interaction with DNA. Alanine to valine mutation at position 77 results in a repressor with enhanced activity at low concentrations of the L-Trp co-repressor. However, WT and AV77 mutant show an identical crystallographic structure, preventing to devise a clear structure-function correlation and suggesting that the different activity could be ascribed to a varied dynamical behavior. Root mean square deviations, dynamical cross correlation and hydrogen bond analysis have been performed to detect specific differences between the two repressor forms, showing that both ligand and DNA binding is different in the two complexes.