Intermolecular and Intramolecular Readout Mechanisms in Protein–DNA Recognition

Protein–DNA recognition plays an essential role in the regulation of gene expression. Regulatory proteins are known to recognize specific DNA sequences directly through atomic contacts (intermolecular readout) and/or indirectly through the conformational properties of the DNA (intramolecular readout). However, little is known about the respective contributions made by these so-called direct and indirect readout mechanisms. We addressed this question by making use of information extracted from a structural database containing many protein–DNA complexes. We quantified the specificity of intermolecular (direct) readout by statistical analysis of base–amino acid interactions within protein–DNA complexes. The specificity of the intramolecular (indirect) readout due to DNA was quantified by statistical analysis of the sequence-dependent DNA conformation. Systematic comparison of these specificities in a large number of protein–DNA complexes revealed that both intermolecular and intramolecular readouts contribute to the specificity of protein–DNA recognition, and that their relative contributions vary depending upon the protein–DNA complexes. We demonstrated that combination of the intermolecular and intramolecular energies derived from the statistical analyses lead to enhanced specificity, and that the combined energy could explain experimental data on binding affinity changes caused by base mutations. These results provided new insight into the relationship between specificity and structure in the process of protein–DNA recognition, which would lead to prediction of specific protein–DNA binding sites.