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

Abstract

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 (ΔCp). 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 ΔHass and ΔCp 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 zfl‐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. Proteins 2000;41:50–62. © 2000 Wiley‐Liss, Inc.

Approaches to the Description and Prediction of the Binding Affinity of Small-Molecule Ligands to Macromolecular Receptors

“…Thus, it appears likely that they involve water which is ubiquitously present in all binding processes. Liggins and Privalov608 assume that the enthalpic contributions to binding resulting from hydrogen bonds formed in the complex are exaggerated. The enthalpy of dehydration necessary for complex formation is also included in this contribution.…”

What Drives Proteins into the Major or Minor Grooves of DNA?

“…[2][3][4][5][6][15][16][17][18][19][20][21][22][23][24][25][26][27][28][29][30] For the present analysis, we have selected data obtained under similar conditions (20°C, near neutral pH, 100 mM NaCl) and analyzed by the same approach, namely correcting for refolding effects and resolving the electrostatic and non-electrostatic components of the binding characteristics, as outlined in Figures 1 and 2. All these data are illustrated in Figure 3 and summarized in Table 1 in Supplementary Materials.…”

Prevalence of Temperature-Dependent Heat Capacity Changes in Protein-DNA Interactions

“…To investigate this issue further, however, we similarly analyzed 47 additional protein-DNA interaction data sets from the scientific literature, from 21 different publications (5,6,(15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28)(29)(30)(31)(32)(33). Data sets where the protein clearly and identifiably begins unfolding at higher binding temperatures were not included (e.g., (34)(35)(36)(37)).…”