Structural and modelling insights into the dynamic association between the transcription factor and DNA

Abstract

The DNA recognition mechanisms by transcription factor (TF) was a significant scientific issue in the gene transcription and regulation. Multiple research technology including the experimental and modelling method has been introduced into the study of this aspect. In this article bioinformatic, protein modelling and dynamic simulation method was employed to display the overview of the dynamic binding between TF and DNA. Physical properties of positional change and freedom of atoms in addition with the volume exchange and the interaction analysis revealed the flexible binding sites of this element. The association of TF increased its stability with dynamic conformational change. The different levels of resistance to the thermal fluctuations of the residues and the nucleotides in the binding site stabilize the overall structure of the complex and initiated the open of the double helix that indicated the molecular mechanisms of the recognition and regulation of the elements.