The nucleosomal histones contact the DNA through -helices and loops. Some of the long -helices are
oriented so that their helix dipoles form favourable interactions with the electronegative phosphate back-
bone. Water molecules and counter-ions are also involved in fitting together the protein and DNA surfaces.
The DNA follows a highly curved trajectory on the surface of the protein (Figure 10.15b). This requires
in-plane bending and a small accommodating change in twist. The bending is achieved by compression of
the minor groove where it contacts the surface of the protein, and by widening of the minor groove on the
outer surface of the curved DNA. The DNA on the nucleosome is overwound at about 10.2 base pairs/turn
(in comparison with 10.6 base pairs/turn for relaxed DNA in solution). This overwinding aligns the minor
grooves of the DNA, so that there are little gaps through which the terminal tails of the histone proteins
protrude. Although the nucleosome has no sequence preference per se, there are notable preferences for peri-
odic composition patterns to occupy the regions where the grooves compress or expand. There is a periodic
variation in twist and roll at base steps, and these angles on average are larger in magnitude than for free DNA.
A string of nucleosomes can assemble into a helical structure known as the solenoid, in which there are
six nucleosomes in a superhelical turn. The termini of the histones, which protrude from the surface as
mentioned above, are thought to be important for mediating the contacts within the solenoid, and hence
modifications such as methylation or acetylation of lysine amino groups on the histones can affect the
assembly or the recruitment of other regulatory proteins. The solenoid assembly is consolidated by a fifth
class of histone protein, known as the H1 (or H5) histones, which are not structurally related to the octamer
core histones H2A, H2B, H3 and H4. These H1 and H5 histones have a DNA-binding motif that is remark-
ably similar to that found in the bacterial CAP gene activator protein and the SAP-1 protein. The H1/H5
proteins are probably located near the dyad of the nucleosome.
Binding sites within nucleosomes are occasionally exposed, but at sufficiently rapid rates to allow site
access under physiological conditions.41,42The sequential binding of a number of factors independently to
DNA sites exerts co-operativity through their mutual effects on the chromatin. The binding of one protein
at its recognition site on the DNA may help to alter the nucleosome position and thus expose the binding
site of a second protein, favouring its binding.
10.6.2 Packaging and Architectural Proteins in Archaebacteria and Eubacteria
Archaea in the euryarchaeotasub-branch also have histone-core-like proteins. There is a remarkable
structural similarity of the archaeal histone dimer made by the HMfB and HMfb proteins with the eukary-
otic H3–H4 dimer (Figure 10.16a). This similarity suggests that the H3–H4 tetramer may represent an
earlier organization of chromatin during the early stages of the evolution of the eukaryotic cell.^10
The crenarchaeota sub-branch appears not to have histones, but instead a variety of abundant non-
sequence-specific DNA-binding proteins. For instance, the Sul7d protein binds non-specifically in the DNA
minor groove by means of a three-stranded -sheet, with intercalation of hydrophobic side chains between
the bases (Figure 10.16b). Another protein used in packaging the DNA is the homodimeric Alba, which pro-
motes negative supercoiling in DNA. The protein has two highly conserved loops that may contact the DNA.
The genomes of eubacterial species are also compacted by proteins. These organisms use small, basic
proteins such as HU and FIS. The HU protein can supercoil DNA to form beaded structures.
10.7 Polymerases
10.7.1 DNA-Directed DNA Polymerases
DNA-directed DNA polymerases(E.C. 2.7.7.7) catalyse the sequential, DNA template-directed extension
of the 3-end of a DNA strand by addition of single nucleotides. The enzymes replicate genomic DNA with
high fidelity and processivity. Crystal structures of DNA polymerases reveal the role of two metal ions in the
active site. A mechanism has been proposed to be common for polynucleotide polymerases.^43 This involves
a metal ion that activates the deprotonation of the 3-hydroxyl group at the terminus of the growing chain,
Protein–Nucleic Acid Interactions 409