Transcriptional cooperativity in molecular dynamics based on normal mode analysis

Transcriptional regulation is an important component in genetics, with transcriptional factors (TFs) and regulatory DNA regions involved in. In this paper, we observe cooperativity between two significant TFs Oct-1 and Sox-2 at their enhancer DNA binding sites in collective motions. Normal mode analysis (NMA) is carried out to simulate the motions of two POU/HMG/DNA complexes, with molecular dynamics (MD) results used as a comparison. We have discovered several types of cooperative interactions between the two TFs in these obtained motions.