Our
understanding of sequence specific protein-DNA interactions evolved over the
last thirty years with the development of the methods available to study these
interactions. It was first believed that the protein recognizes its target site
by direct contact with the side chains of the protein and the hydrogen donor
and the acceptor groups on the DNA bases in the major groove of the double
helix. This mode of interaction was termed direct readout. The analysis of the
crystal structure of the trp repressor/operator complex revealed only a
few direct hydrogen bonds in the direct mode of interaction. However, there
were specific interactions of the protein side chains to the donor and acceptor
groups of the DNA bases mediated through water molecules. This mode of
interaction was termed indirect readout.
Our current view of specific protein-DNA interactions is a combination of
direct readout, indirect readout and structural readout. Structural readout is
the recognition of the structural parameters of the double helix as well as its
deformations from standard B-DNA structure. The relative contribution of each
mode of recognition to the formation and stability of the complex varies
largely from one complex to another. It is currently believed that protein-DNA
interactions are based primarily on direct and indirect readout, whereas
structural recognition has only a supportive role in this interaction.
In this study we asked the question of whether a specific interaction can
be based primarily on structural recognition. The trp repressor/operator
complex as revealed from the crystallographic structure has only a few direct
and indirect hydrogen bonds. On the other hand it contains many hydrogen bonds
to the sugar-phosphate backbone of the DNA, which is thought to reflect the
three-dimensional structure of the DNA sequence. Another aspect of this
interaction is the significant distortions of the operator from standard B-DNA
structure. Therefore, the trp repressor/operator complex is a good
candidate for a model system for specific interactions based primarily on the
structural parameters of the operator sequence. To test this hypothesis we
selected the DNA sequences that bind the trp repressor from a pool of
random sequences, by separating the different complexes with the trp
repressor from one another, and from the free DNA, by gel electrophoresis.
From the analysis of the motifs characterizing the selected sequences we
can conclude that the basis for specific interaction between the trp
repressor with its target site, is direct and indirect readouts, whereas
structural recognition has mainly an assisting role.
