10.3.4 The Orientations of -Helices in the DNA Major Groove
In Sections 10.3.2 and 10.3.3, a handful of representative examples of protein–DNA complexes were
described in which an -helix is docked snugly into the major groove. While it might seem that a snug fit
implies restricted orientation, there is in fact a wide range of orientations observed for the -helix within
the major groove. Indeed, there may be great variation in the orientation of the recognition -helix in the DNA
even within a domain class whose members have the same fold and very similar amino acid sequences.
Pabo and Nekludova^13 found a way to explain this observed variation by grouping complexes into two
principal families according to how the residues along a ‘ridge’ of the -helix align with respect to the
spiralling trajectory of the DNA. In one family, every fourth residue is aligned (i.e.the ridge formed by
residues along the i,i4 line) to maintain register with the contacting bases, whilst a second family uses
the line connecting every third residue (i, i3). For instance, the zinc fingers tend to use the i,i3 geometry.
Because the helical repeat of the relaxed -helix is 3.6 residues in one complete turn, the i, i3 line will
form a left-handed spiral on the helix surface, while the i, i4 line will form a right-handed spiral. Thus, the
two families use different geometries to match the spiralling pattern of amino acids with the curving path of
the major groove. These matches are only local, and typically correspond to contact with three to five bases.
There are interesting outliers to this grouping, such as the trp repressor and the GAL4 protein, where the
-helices tend to enter the major groove at a steep angle because of additional contacts made to the DNA
by other structural elements of the protein. While these family groupings indicate the importance of
matching the geometry of the -helix with the surface curvature of the DNA, they do not provide detailed
rules for the interaction, since the precise helix orientation is context-dependent.
10.3.5 Minor Groove Recognition via-Helices
The docking of an -helix into the major groove of DNA causes the groove to become slightly compressed,
on account of the tendency of the phosphate backbones of the DNA to clamp down on the -helix. The
resulting compression of the major groove tends to bend the DNA towards the protein. By contrast, the accom-
modation of an -helix into the narrow minor groove of B-form DNA tends to expand the groove tremen-
dously, with the result that the DNA bends away from the body of the protein. Representative examples of
minor groove recognition are provided by the widely occurring and well-conserved high-mobility group
(HMG) proteins, which play structural roles in the dynamic organization of chromatin (Section 10.6.1).
10.3.6 -Motifs
The specific recognition of DNA by the Escherichia colimet repressor protein resembles closely
-helix-DNA recognition, except that the amino acids, which directly contact the base pairs are from a
-sheet(which may be made up from a number of -strands) that make a snug fit into the major groove
(Figure 10.6a). With this mode of interaction, the met repressor protein recognises a conserved eight-base-pair
sequence of DNA (5-AGACGTCT), although only four of the eight individual bases are contacted (indicated
in bold). The adjacent G and A bases form hydrogen bonds with lysine and threonine residues from
different strands of the -sheet, while the outer two bases A and C in AGAC are not contacted directly by
the protein. Several phosphates on the DNA interact with various amino acids from the protein.
The met repressor protein has twofold rotational symmetry and it recognizes a palindromic DNA sequence,
just as in the DNA complexes of the 434 repressor and bZIP proteins (Figure 10.2b). But in addition, the
met-repressor dimers can bind to adjacent sites on the DNA, and the neighbouring dimers interact favourably
through protein–protein interactions. This gives a beneficial co-operativity of binding (Section 10.4.6).
Another protein that uses a -ribbon to contact the DNA is the integration host factor (IHF), which is a
20-kDa heterodimeric protein from E. colithat binds DNA with sequence-specificity and induces a sharp
bend in the DNA, of greater than 160°.14,15IHF functions as an architectural protein that assists assembly of
replication complexes and affects long-distance transcriptional regulation. The subunits of the heterodimer
394 Chapter 10