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) co ntaining the three N-terminal zinc fingers of the Xenopus laevis transcript ion factor TFIIIA with its cognate DNA sequence, contained in a 15 bp DNA d uplex were studied using isothermal titration calorimetry (ITC), differenti al scanning calorimetry (DSC) and fluorescence titration, The use of both I TC and DSC is necessary to provide values for the thermodynamic parameters that have been corrected for thermal fluctuations of the interacting molecu les. In the temperature range from 13 degrees C to 45 degrees C (where all the binding reaction components are folded), formation of the complex is en thalpically driven with a negative heat capacity effect (Delta C-p), In thi s respect, the binding reaction of zf1-3 is similar to those of other prote ins that bind in the major groove of DNA, It is dissimilar to the associati on reactions of proteins, however, that bind in the minor groove of DNA and that are driven by a dominating entropy factor. Comparison of the experime ntal values of Delta H-ass and Delta C-p with expected values of these para meters, calculated from the burial of polar and nonpolar molecular surfaces , indicates that the polar groups at the protein/DNA interface are not comp letely dehydrated upon formation of the complex. It also seems that the exp ected large positive entropy of dehydration upon forming the zf1-3/DNA comp lex (similar to 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 da mping of torsional motions in the DNA duplex. (C) 2000 Wiley-Liss, Inc.