Evaluation of Sox2 binding affinities for distinct DNA patterns using steered molecular dynamics simulation.

ABSTRACT: Transcription factors (TFs) are gene expression regulators that bind to DNA in a sequence-specific manner and determine the functional characteristics of the gene. It is worthwhile to study the unique characteristics of such specific TF-binding pattern in DNA. Sox2 recognizes a 6- to 7-base pair consensus DNA sequence; the central four bases of the binding site are highly conserved, whereas the two to three flanking bases are variable. Here, we attempted to analyze the binding affinity and specificity of the Sox2 protein for distinct DNA sequence patterns via steered molecular dynamics, in which a pulling force is employed to dissociate Sox2 from Sox2-DNA during simulation to study the behavior of a complex under nonequilibrium conditions. The simulation results revealed that the first two

SUBMITTER: Yesudhas D 

PROVIDER: S-EPMC5666385 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature