A method for in silico identification of SNAIL/SLUG DNA binding potentials to the E-box sequence using molecular dynamics and evolutionary conserved amino acids

摘要

Binding of transcription factors to DNA is a dynamic process allowing for spatial- and sequence-specificity. Many methods for determination of DNA-protein structures do not allow for identification of dynamics of the search process, but only a single snap shot of the most stable binding. In order to better understand dynamics of DNA binding, as a protein encounters its cognate site, we have created a computer based DNA scanning array macro which sequentially inserts high affinity DNA consensus binding site at all possible locations in a predicted protein-DNA interface. We show that using short molecular dynamic simulations at each location in the interface, energy minimized states and decreased movement of evolutionary conserved amino acids can be readily observed and used to predict the consensus binding site. This macro is applied to SNAIL class C2H2 zinc finger family proteins. The analysis suggests that 1) SNAIL binds to the E-box in multiple states during encounter with its cognate site; 2) several different amino acids contribute to the E-box binding in each state; 3) the linear array of zinc fingers contributes differentially to overall folding and base-pair recognition, and; 4) each finger may be specialized for stability and sequence specificity. Moreover, the macromolecular movement observed using this dynamic approach may allow the NH2-terminal finger to bind without sequence specificity yet result in higher binding energy. This macro and overall approach could be applicable to many evolutionary conserved transcription factor families and should help elucidate better the varied mechanisms used for DNA sequence specific binding.