Y. Mandelgutfreund et H. Margalit, QUANTITATIVE PARAMETERS FOR AMINO ACID-BASE INTERACTION - IMPLICATIONS FOR PREDICTION OF PROTEIN-DNA BINDING-SITES, Nucleic acids research, 26(10), 1998, pp. 2306-2312
Inspection of the amino acid-base interactions in protein-DNA complexe
s is essential to the understanding of specific recognition of DNA tar
get sites by regulatory proteins. The accumulation of information on p
rotein-DNA co-crystals challenges the derivation of quantitative param
eters for amino acid-base interaction based on these data. Here we use
the coordinates of 53 solved protein-DNA complexes to extract all non
homologous pairs of amino acid-base that are in close contact, includi
ng hydrogen bonds and hydrophobic interactions. By comparing the frequ
ency distribution of the different pairs to a theoretical distribution
and calculating the log odds, a quantitative measure that expresses t
he likelihood of interaction for each pair of amino acid-base could be
extracted. A score that reflects the compatibility between a protein
and its DNA target can be calculated by summing up the individual meas
ures of the pairs of amino acid-base involved in the complex, assuming
additivity in their contributions to binding. This score enables rank
ing of different DNA binding sites given a protein binding site and vi
ce verse and can be used in molecular design protocols. We demonstrate
its validity by comparing the predictions using this score with exper
imental binding results of sequence variants of zif268 zinc fingers an
d their DNA binding sites.