In the 1970s, it was discovered that isotherms of antibiotic binding to DNA indicate interactions between adsorbed molecules that propagate over several turns along the DNA. These interactions were described using long-range distance-dependent potentials between ligands. The interactions between distant DNA ligands were immediately compared with the previously discovered allostery in proteins, the mutual influence of ligands bound to a protein. Both cooperative and anticooperative interactions between ligands have been observed. It was hypothesized that a ligand, upon binding to DNA, induces a perturbed state of several nearby nucleotide pairs, and this perturbation propagates along the DNA. The mechanism of this phenomenon was elucidated later. X-ray diffraction studies of DNA-protein complexes revealed that bound proteins stretch the grooves, thereby creating more or less favorable binding sites for subsequent proteins in accordance with the helical symmetry of the DNA. Models have been developed further to describe the role of this mechanism in regulating gene expression. We expect that signaling pathways in the cell will be described at the level of systems biology through allosteric interactions of entire cascades of proteins, including DNA-mediated, coupled with conformational changes in DNA. Expanding databases and algorithms developing nowadays for predicting allosteric effects in protein pairs will facilitate the construction of interaction networks in the cell and can take epigenetics and proteomics to a qualitatively new level, providing a deeper understanding of links in protein cascades and spatial changes in complexes of proteins and DNA.
Nechipurenko et al. (Sun,) studied this question.