DNA-Protein recognition

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Conformational changes play an even more important role in protein-DNA recognition. As in protein-protein interactions, extensive changes accompany the formation of large interfaces disordered segments of the polypeptide chain become ordered, and whole subunits and domains move and loops rearrange on the protein surface (Nadassy et al., 1999). In protein-DNA interactions, the abundance of disorder-to-order transitions is probably underestimated, because many proteins that undergo such transitions do not yield useful crystals or NMR spectra in the free state. 

The energetics of protein-DNA recognition and protein-nucleic acid recognition in general are less well understood than those of protein-protein complexes. The association process in these systems generally involves large conformational changes and/or order-disorder transitions that affect both the protein and nucleic acid moieties. It furthermore often involves protein-protein association in addition to protein-DNA interactions. A number of theoretical studies have been devoted to the analysis... 

A further hurdle that must be overcome is the incorporation of a better representation of the solvent contributions, including those of specific interactions with water molecules and counterions. As shown in this chapter, these latter types of interactions play a crucial role in specific protein-DNA recognition, and as the repertoire of known 3D structures of protein complexes grows, we may well And them commonly mediating protein-protein association as well. 

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