atoms, the substituents of the bases, and the non-bridging oxygen atoms of the phosphate backbone. Such
buried water molecules may be isolated from the bulk solvent and become in effect non-covalent exten-
sions of the protein or DNA. In general, protein–DNA interfaces are significantly more hydrated than pro-
tein interiors.^8 In some cases, water-mediated hydrogen-bonding patterns account for base recognition
(e.g.the trp repressor–operator complex).^19
Protein–Nucleic Acid Interactions 399
Figure 10.9 The energy decomposition of a representative specific protein–DNA complex. (a) The black arrows on the
left are estimated contributions of hydrogen bonding and the release of bulk solvent and counter-ions. The
energy penalty for deforming the DNA is shown by the downward arrow. On the right side the energetic
decomposition of the non-specific binding event. (Adapted from L. Jen-Jacobson Biopolymers, 1997, 44 ,
153–180. © (1997), with permission from John Wiley and Sons, Inc.) (b) An example of the thermodynamic
correlations of protein–DNA complex formation with DNA distortion. (Adapted from L. Jen-Jacobson,
L.E. Engle and L.A. Jacobson, Struct. Fold Design, 2000, 8 , 1015–1023. © (2000), with permission
from Elsevier)