Energetics of the specific binding interaction of the first three zinc fingers of the transcription factor TFIIIA with its cognate DNA sequence

The energetics of the specific interaction of a protein fragment (zf1-3) containing the three N-terminal zinc fingers of the Xenopus laevis transcription factor TFIIIA with its cognate DNA sequence, contained in a 15 bp DNA duplex were studied using isothermal titration calorimetry (ITC), differential scanning calorimetry (DSC) and fluorescence titration. The use of both ITC and DSC is necessary to provide values for the thermodynamic parameters that have been corrected for thermal fluctuations of the interacting molecules. In the temperature range from 13°C to 45°C (where all the binding reaction components are folded), formation of the complex is enthalpically driven with a negative heat capacity effect (ΔC(p)). In this respect, the binding reaction of zf1-3 is similar to those of other proteins that bind in the major groove of DNA. It is dissimilar to the association reactions of proteins, however, that bind in the minor groove of DNA and that are driven by a dominating entropy factor. Comparison of the experimental values of ΔH(ass) and ΔC(p) with expected values of these parameters, calculated from the burial of polar and nonpolar molecular surfaces, indicates that the polar groups at the protein/DNA interface are not completely dehydrated upon formation of the complex. It also seems that the expected large positive entropy of dehydration upon forming the zf1-3/DNA complex (~1900 J · K^-1 · mol^-1) cannot be balanced by the reduction in translational/rotational and configurational freedom of the protein to the level of the observed entropy of binding (38 J · K^-1 · mol^-1). It is suggested that the additional negative entropy contribution comes from a damping of torsional motions in the DNA duplex. (C) 2000 Wiley-Liss, Inc.