Structural and Thermodynamic Strategies for Site-Specific DNA Binding Proteins

Abstract

Isothermal enthalpy-entropy compensation implies that a structurally optimal, unstrained fit is achieved only at the cost of entropically unfavorable immobilization, whereas an enthalpically weaker, strained interface entails smaller entropic penalties.

The contribution of the methyl groups on thymine bases to binding specificity and affinity by alanine-rich mutants of the bZIP motif

“…Yet freeenergy prediction is complicated by the ability of enthalpy and entropy, which usually move in opposite directions, to compensate for changes in order to maintain fairly stable overall free energies of binding. 23,33 Compensation occurs frequently in biological systems, for enthalpy and entropy values can vary widely in dependent fashion, even though ÁG values cluster in a relatively narrow range. 23 A potential source of unfavorable enthalpy change is from strain, often arising from energetically costly DNA distortions; crystal structures show that GCN4 binds to AP-1 DNA with no distortion, 5 but the GCN4-ATF/CREB structure shows that the central base pairs exhibit A-form character and a 20 bend.…”

“…23,33 Compensation occurs frequently in biological systems, for enthalpy and entropy values can vary widely in dependent fashion, even though ÁG values cluster in a relatively narrow range. 23 A potential source of unfavorable enthalpy change is from strain, often arising from energetically costly DNA distortions; crystal structures show that GCN4 binds to AP-1 DNA with no distortion, 5 but the GCN4-ATF/CREB structure shows that the central base pairs exhibit A-form character and a 20 bend. 4 Berger et al used microcalorimetry to show that although ÁG is the same for GCN4 binding to either AP-1 or ATF/CREB sites, and GCN4-DNA complexation was accompanied by a favorable ÁH and an unfavorable ÁS at all temperatures studied, ÁH was more favorable for the undistorted AP-1 site.…”

“…Changes in binding affinity are not dramatic, and this study may underscore the multivalent nature of protein-DNA interactions, as our protein mutations that severely decrease ability for Coulombic interactions, yet increase ability for van der Waals contacts, still yield functioning proteins exhibiting native-like behavior. Additionally, proteins can compensate for mutations that can affect enthalpic and/ or entropic contributions toward DNA-binding in order to maintain binding free energies similar to that of the native protein-DNA complex, 23 and therefore, compensatory changes in our proteins may alleviate the losses of van der Waals interactions with thymine C5 methyl groups. Table 1 shows the dissociation constants for all four bZIP mutants binding to the u-AP-1 target site.…”

Free Energy Contributions to Direct Readout of a DNA Sequence

“…Additive-For the analysis of the DNA binding interface, we interpreted the effects of mutation on a strictly local basis, and as such, the observed energetic differences are likely to be additive (8,32). This is also an assumption of most of the theoretical models of protein-DNA interaction developed to date (35,36).…”

“…Precisely how these two mechanisms contribute to the overall binding energetics is not known, and statistically based potentials predict that their relative contributions are not the same for all protein-DNA pairs (3). Experimental determination of the energetic contributions of direct and indirect readout requires modification of amino acid side chains and/or DNA bases, perturbations that would normally affect the structural and energetic properties of distant, non-targeted contacts (7,8). These mutually dependent effects preclude a straightforward assignment of the energetic contributions to DNA binding in most protein-DNA systems.…”