Figure 1. Comparison of the Lac repressor DNA binding domain (DBD) dimer – nonoperator and operator DNA complexes. (a) When binding to a nonoperator (‘nonspecific’) DNA sequence (black), the helix-turn-helix motif of each DBD (purple) forms a network of electrostatic and hydrogen bond interactions primarily with the DNA phosphate backbone. Residues 50–58 (cyan) are disordered and the structure of the DNA site is unaltered. (b) In the complex formed between the repressor DBD and its highest affinity DNA operator sequence (O^sym), the helix-turn-helix motif docks in the major grooves, making extensive contacts to base functional groups and the DNA backbone. On binding, both the protein and DNA undergo significant conformational changes. Residues 50–58, which are disordered in the free protein, fold into an helix called the hinge helix. To accommodate two hinge helices, the minor groove widens, causing a ~40° bend in the DNA (PDB file 1CJG; see Kalodimos et al., 2004). Figure 1a drawn from Protein Databank file 1OSL; see Kalodimos CG, Boelens R and Kaptein R (2004) Toward an integrated model of protein–DNA recognition as inferred from NMR studies on the Lac repressor system. Chemical Reviews 140: 3567–3586. Figure 1b drawn from Protein Databank File 1CJG; see Spronk CA, Bonvin AM, Radha PK et al. (1999) The solution structure of Lac repressor headpiece 62 complexed to a symmetrical lac operator. Structure 7: 1483–1492.

Figure 2. Structure of the single-stranded DNA binding protein (SSB) from E. coli bound to two DNA (dC₃₅) oligomers. SSB forms a tetramer of identical subunits (coloured orange, green, yellow and blue). The structure reveals that on binding, the DNA backbone (shown as a black ribbon) wraps in the surface grooves of SSB monomers with many of the bases (shown as sticks) unstacked. Some the bases of the oligomer are not resolved in the structure; this disorder is consistent with the nature of a semi-loosely associated nonspecific complex. Figure drawn from Protein Databank file 1EYG; see Raghunathan S, Kozlov, AG, Lohman, TM and Waksman G (2000) Structure of the DNA binding domain of E. coli SSB bound to ssDNA. Nature Structural Biology 7: 648–652.

Figure 3. Histone–DNA Interactions. Arginine (red) – minor groove interactions are highlighted. While arginine side chains are observed to uniformly penetrate the minor groove, no hydrogen bonds are formed with base functional groups. Instead, favourable electrostatic interactions allow the minor groove to narrow, causing the DNA to bend and wrap on the surface of the histone octamer. Figure drawn from Protein Databank file 1KX5; see Davey CA, Sargent DF, Luger K, Maeder AW and Richmond TJ (2002) Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 Å resolution. Journal of Molecular Biology 319:1097–1113.