Equilibrium study of Protein/DNA Complexes from Crystal Structure Data

Abstract

From the crystal structure data and using the concept of equilbrium statistical mechanics we show how to calculate the thermodynamics of protein/DNA complexes. We apply the method to the TATA-box binding protein (TBP)/TATA sequence complex. We have estimated the change in free energy and entropy for each of the base pair (bp). The local rigidity of the DNA is estimated from the curvature of the free energy. We also estimate the free energy gain of the protein due to bond formation with a particular bp. We thus figure out the bps responsible for specific binding.