title: Minimization of a protein-DNA dimerizer.
abstract: A protein-DNA dimerizer constructed from a DNA-binding polyamide and the peptide FYPWMKG facilitates the binding of a natural transcription factor Exd to an adjacent DNA site. The Exd binding domain can be reduced to a dipeptide WM attached to the polyamide through an epsilon-aminohexanoic acid linker with retention of protein-DNA dimerizer activity. Screening a library of analogues indicated that the tryptophan indole moiety is more important than methionine's side chain or the N-terminal acetamide. Remarkably, switching the stereochemistry of the tryptophan residue (l to d) stabilizes the dimerizer*Exd*DNA ternary complex at 37 degrees C. These observations provide design principles for artificial transcription factors that may function in concert with the cellular regulatory circuitry.
authors.affiliation: Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
authors.forename: Ryan L
authors.initials: RL
authors.lastname: Stafford
authors.forename: Hans-Dieter
authors.initials: HD
authors.lastname: Arndt
authors.forename: Mary L
authors.initials: ML
authors.lastname: Brezinski
authors.forename: Aseem Z
authors.initials: AZ
authors.lastname: Ansari
authors.forename: Peter B
authors.initials: PB
authors.lastname: Dervan
mesh_terms: D000081:Acetamides / Q000737:chemistry; D000595:Amino Acid Sequence; D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism; D019281:Dimerization; D004151:Dipeptides / Q000737:chemistry; D004591:Electrophoresis, Polyacrylamide Gel; D007211:Indoles / Q000737:chemistry; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D009757:Nylons / Q000737:chemistry; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D013696:Temperature; D014157:Transcription Factors / Q000737:chemistry / Q000378:metabolism; D014364:Tryptophan / Q000737:chemistry
chemical_list: D000081:Acetamides; D004268:DNA-Binding Proteins; D004151:Dipeptides; D007211:Indoles; D009757:Nylons; D011506:Proteins; D014157:Transcription Factors; D014364:Tryptophan; C030686:acetamide; D004247:DNA