6.5 Conformational changes upon protein–DNA interactions
During binding, both the protein and the DNA can alter their conformation. In the case of proteins, this conformational change can involve small changes in side-chain location, but can also involve local refolding. These changes upon binding of specific DNA sequences serve to facilitate the interaction and also to enhance the binding of other proteins, such as when dimerization of two proteins occurs at a single recognition site. Changes such as these can be the basis of cooperative binding effects between proteins, where binding of one protein can enhance the binding of another.
Changes in DNA conformation also occur upon protein binding. Common conformational changes are bending of the DNA backbone or local untwisting of the helix. An example of this alteration to a short stretch of DNA helix is given in Figure 24, which shows the binding of a protein called TATA binding protein (TBP) to its recognition site (a sequence of eight base pairs containing the sequence TATA) in a eukaryotic gene promoter. Note how this short DNA duplex is almost bent back on itself. TBP is an evolutionarily highly conserved protein and binding of its specific recognition sequence occurs through interactions with DNA in the minor groove.
Why does the binding of TBP to the minor groove appear to present a paradox?
As a sequence-specific binding protein, TBP needs to be able to detect the bases that are ‘shielded’ within the minor groove of B-DNA. As discussed extensively above, most DNA recognition interactions occur in the major groove where bases are exposed (see Figure 9b).
To achieve interactions with the bases, upon binding to DNA, TBP inserts the side-chains of two hydrophobic phenylalanine residues between the bases in the minor groove, thereby disrupting base stacking – in a similar way to an intercalating agent – and causing the helix to untwist at the site of interaction.
What effect would this untwisting have upon the space between adjacent base pairs and the turn per base pair? (You may want to refresh your memory of normal B-DNA structure, covered in Section 3.1.)
It reduces the turn for each base pair and widens the spacing between bases.
Binding of TBP to its target DNA sequence actually decreases the turn in the DNA helix from 36° to 21° and bases are stretched apart to 5.5 Å separation, compared to 3.4 Å in B-DNA. The width of the minor groove effectively doubles, whilst at the same time it becomes shallower, bringing TBP into contact with the bases. Binding specificity is achieved through numerous hydrophobic interactions between TBP amino acid side-chains and atoms in the eight base-pairs that constitute the recognition site. Thus, by inducing an alteration in DNA conformation, specificity of interaction is achieved.
The effect of TBP binding is a bending and kinking of the helix backbone, shown in Figure 24. As a result, areas of the DNA chain are brought into closer proximity to each other.