Figure 1 - full size

 

Figure 1.
(a) Chemical structures of DANA, 4-DAPA and 6-DMNA. (b) In the crystal structure of the DR1–HA peptide complex, a tyrosine residue is buried deep into the hydrophobic P1 pocket^5. DANA, 4-DAPA and 6-DMNA were modeled in silico into this pocket in place of tyrosine. Residues shown lining the pocket are (clockwise from upper right) Phe 54, Phe 32, Trp 43 (behind), Ile 7, Trp 153, Phe 48, Thr 90, Val 91, Tyr 83, Gly 86 and Val 85. The side chains of Asn 82 and His 81 (upper left) form hydrogen bonds with the peptide main chain at the mouth of the P1 pocket. Other residues lining the pocket but not shown are Phe 24, Phe 26 and Phe 48. (c) Binding of fluorogenic peptides to DR1 assessed using a competitive binding assay. DR1 was incubated with biotin–HA peptide and various concentrations of unlabeled inhibitor peptides, and biotin-HA binding was quantified by a sandwich ELISA assay using streptavidin alkaline phosphatase. Binding of Fmoc-(4-DAPA) was assessed to evaluate nonspecific binding of the fluorophore. IC[50] values for these and other peptides (Supplementary Table 1) were determined as described (Supplementary Methods).

The above figure is reprinted by permission from Macmillan Publishers Ltd: Nat Chem Biol (2007, 3, 222-228) copyright 2007.