Recognition of different DNA sequences by a DNA-binding protein alters protein dynamics differentially

λ-Repressor–operator sites interaction, particularly OR1 and OR2, is a key component of the λ-genetic switch. FRET from the dansyl bound to the C-terminal domain of the protein, to the intercalated EtBr in the operator DNA indicates that the structure of the protein is more compact in the OR2 complex than in the OR1 complex. Fluorescence anisotropy reveals enhanced flexibility of the C-terminal domain of the repressor at fast timescales after complex formation with OR1. In contrast, OR2 bound repressor shows no significant enhancement of protein dynamics at these timescales. These differences are shown to be important for correct protein–protein interactions. Altered protein dynamics upon specific DNA sequence recognition may play important roles in assembly of regulatory proteins at the correct positions.

► Transcription factor CI changes its structure upon DNA-binding.
► Differential protein dynamics upon binding with different DNA sequences.
► Exploration of dynamical time scale associated with the protein–DNA interaction.
► Structural aspects of DNA-bound CI–CI co-operative interactions are investigated.