Minimization of a protein-DNA dimerizer.
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.
Stafford
Ryan L
RL
Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
Arndt
Hans-Dieter
HD
Brezinski
Mary L
ML
Ansari
Aseem Z
AZ
Dervan
Peter B
PB
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
D000081:Acetamides; D004268:DNA-Binding Proteins; D004151:Dipeptides; D007211:Indoles; D009757:Nylons; D011506:Proteins; D014157:Transcription Factors; D014364:Tryptophan; C030686:acetamide; D004247:DNA