Common Principles in DNA Target Recognition by Proteins:
Implication for Prediction of Protein-DNA Binding Sites
Hanah Margalit
The Hebrew University of Jerusalem
Specific recognition is achieved by structural complementarity between
the protein and the DNA, and by specific interactions between the
protein amino acids and the DNA bases. The question we address is what
determines amino acid-base recognition and can a general recognition
code be delineated. The database for the analysis consists of 53
crystallographically solved protein-DNA complexes. By analyzing all
pairs of amino acid-base that are involved in recognition, it is
demonstrated that while a general recognition code is not evident,
common principles that are consistent with electrostatic considerations
can be derived. The data set of amino acid-base interactions has been
used to derive knowledge-based parameters, that express the likelihood
of interaction for each pair of amino acid-base. The usefulness of
these parameters in the prediction of favorable protein-DNA binding
sites is demonstrated