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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).
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