may be partially conjugated and can contribute to stability by ‘stacking’ like plates, akin to the stacking
seen for the bases in the nucleic acid. Much less frequently, weaker hydrogen bonds can form between the
DNA bases and the aromatic rings of Phe, Tyr and Trp and these are called ‘-hydrogen bonds’(not
shown). Water molecules can extend the surface of the DNA and bridge to an amino acid, for example the
mediation of interaction between a Thr hydroxyl group and the major groove exocyclic amino groups at a
C/A base step (Figure 10.4b). In addition, the amide backbone of a protein may participate in hydrogen-
bond interactions with the nucleic acid, as either a donor (NH) or acceptor (CO) (not shown).
From the nucleic acid bases, the carbonyl oxygen atoms of G, C and T (U in RNA) are commonly accept-
ors, as are also the heterocyclic N-7 and N-3 atoms of purines. Potential donors are the exocyclic amino
groups of A, G and C and the amido NH functions of T (U in RNA), G and C. In the case of unpaired
bases, the N-1 of purines and the N-3 of pyrimidines often form hydrogen bonds with protein. It might seem
surprising that the most common site of hydrogen-bonding interaction in the recognition of a nucleic acid
is not with the bases, but with the non-bridging oxygen atoms of phosphates. An example of this frequently
occurring interaction is shown in Figure 10.4c. The bridging oxygen atoms of the phosphate backbone and
the oxygen atom within the ribose sugar ring may act as acceptors of hydrogen bonds, but these are com-
paratively weaker interactions.
10.2.2 Salt Bridges
Salt bridgesare electrostatic interactions between groups of opposite charge. In protein–nucleic acid
complexes, salt bridges may be formed between the ionized, non-bridging oxygen atoms of the phosphate
backbone and the protonated, positively charged guanidinium moiety of Arg, the imidazole ring of His, the
-amino group of Lys, or the terminal -amino group in a protein (e.g.Figure 10.4c). The importance of
salt bridges in protein stability has been inferred by their frequent occurrence in the heat-stable proteins
isolated from extreme thermophilic organisms, where the salt bridges are found in co-operative networks.
Isolated salt bridges are entropically disfavoured because they place constraints on the side-chain conform-
ations and cause desolvation of the interacting side chains. However, networks of mutually supporting salt
bridges are favourable, since the co-operativity of their interaction compensates for the unfavourable
entropy change. This principle may also be true for salt bridges formed between amino acid side chains
and nucleic acid phosphate groups, which are often organized as intricate networks of mutually support-
ing interactions. Another type of salt bridge that is also observed in protein–nucleic acid complexes is an
electrostatic interaction mediated by bound counter-ions, such as chloride ions.
Unlike hydrogen bonds, which require alignment of the interacting groups for optimal strength, salt
bridges and counter-ion interactions are not directional. Salt bridges vary in strength in inverse proportion
to the square of the distance between the individual charges and to the dielectric constant, so that they are
greatly weakened as ionic strength increases and strengthened as the dielectric constant decreases. If salt
bridges or bound counter-ions become buried and isolated from bulk solvent, their interaction energy is
enhanced, especially if they are sequestered into a hydrophobic environment. Thus, the strength of salt
bridges is highly context-dependent, but a typical value in proteins corresponds to about 40 kJ mol^1. Salt-
bridging interactions play an important role in making a general electrostatic match of the polyanionic surface
of the DNA or RNA with the polycationic surface of the recognizing protein. Thus, a charged surface of
the protein may be used as a rough gauge of the groove width or to discriminate single-stranded nucleic
acids from double-stranded. However, electrostatic complementarity is unlikely to provide specificity by
itself. Indeed, specificity must originate from other effects, such as the pattern of hydrogen bonds described
above and complementary surface shapes (Sections 10.2.3 and 10.2.4).
10.2.3 The Hydrophobic Effect
The greatest contribution to the Gibbs free energy of complex formation is that of the hydrophobic effect.
This short-range effect is sometimes referred to as a force. However, it is not a real force in the classical
Protein–Nucleic Acid Interactions 389