Dynamics and recognition within a protein-DNA complex: A molecular dynamics study of the SKN-1/DNA interaction

Abstract

Molecular dynamics simulations of the Caenorhabditis elegans transcription factor SKN-1 bound to its cognate DNA site show that the protein-DNA interface undergoes significant dynamics on the microsecond timescale. A detailed analysis of the simulation shows that movements of two key arginine side chains between the major groove and the backbone of DNA generate distinct conformational substates that each recognize only part of the consensus binding sequence of SKN-1, while the experimentally observed binding specificity results froma timeaveraged view of the dynamic recognition occurring within this complex.