Published online 9 July 2004
Nucleic Acids Research, Vol. 32 No. 12 © Oxford University Press 2004; all rights reserved
A phage display selection of engrailed homeodomain mutants and the importance of residue Q50
1 Department of Chemistry, University of California, Berkeley, CA 94720, USA, 2 Department of Chemistry, University of California, Irvine, CA 92697, USA and 3 Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143, USA
* To whom correspondence should be addressed. Tel: +1 415 514 0472; Fax: +1 415 514 0822; Email: shokat{at}cmp.ucsf.edu
Received May 7, 2004; Revised and Accepted June 18, 2004
Mutants of engrailed homeodomain (HD) that retain DNA-binding activity were isolated using a phage display selection. This selection was used to enrich for active DNA-binding clones from a complex library consisting of over a billion members. A more focused library of mutant homeodomains consisting of all possible amino acid combinations at two DNA-contacting residues (I47 and Q50) was constructed and screened for members capable of binding tightly and specifically to the engrailed consensus sequence, TAATTA. The isolated mutants largely recapitulated the distribution of amino acids found at these positions in natural homeodomains thus validating the in vitro selection conditions. In particular, the unequivocal advantage enjoyed by glutamine at residue 50 is surprising in light of reports that minimize the importance of this residue. Here, the subtle contributions of residue Q50 are demonstrated to play a functionally important role in specific recognition of DNA. These results highlight the complex subtlety of protein–DNA interactions, underscoring the value of the first reported in vitro selection of a homeodomain.
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