Peptides binding sites

The peptide-binding site is a hydrophobic groove flanked by the RT loop between pi and p2 and the n-Src loop between p3 and P4 (see Figure 13.28a). The latter is so named because neuronal Src has an insertion of six residues in this loop. The groove is lined with conserved aromatic residues. 

Zhang, J., and Walker, G.C. (1996) Identification of elements of the peptide binding site of dnaK by peptide cross-linking./. Biol. Chem. 271, 19668. 

The design of this successful system started with an enzyme with a ready-made peptide binding site, with well established specificity. The cyclophilins catalyze the cis-trans isomerization of peptide bonds to proline ... 

Fig. 7.4. Structural features of the c-Cbl RING E3 for substrate and E2 binding. (A) A conserved surface channel is found at one side of c-Cbl running from the peptide-binding site to the vicinity of the E2 active site. (B) The...

Similarly, photolabels such as 4-azidobenzoylglycine can be attached to peptides and used to detect the peptide binding sites in proteins.127 128... 

Fig. 7.2. Structure and substrate binding sites of Ser/Thr-spedfic protein kinases, a) Peptide binding site structure of the catalytic subunit of the cAMP-dependent protein kinase A from mouse, with bound inhibitor peptide PKI (5-22), shown in dark in the figure. PKI (5-22) is a fragment (amino adds 5-22) of the naturally occurring heat-stable protein kinase inhibitor PKI. The inhibitor peptide binds in the region of the substrate binding site between the two lobes of protein kinase A (Knighton et al., 1991). The P-loop is involved in binding the phosphate residue of ATP. b) ATP binding site structure of casein kinase I with bound Mg-ATP. The Mg is shown as a sphere. MOLSKRIPT representation according to Kraulis, (1991).

The deviation of the data from the dashed curve is greater than can be explained by experimental error and arises from the fact that the peptides do not bind to a planar interface that varies smoothly in its dielectric, rigidity, and solvent accessibility. This property might also explain the deviation of the observed repeat of 3.3 residues from the ideal value of 3.6 residues for an a helix. Thus, the deviations of the experimental points from the smooth curve provide information concerning the fine structure of the peptide-binding site. For instance, data points on the upper portion of the curve in Fig. 11 correspond to residues on the apolar side of the... 

Rothman RB, Mahboubi A, Bykov V, Kim C-H, de Costa BR, Jacobson AE, Rice KC. Probing the opioid receptor complex with (+ )-trans-superfit. II Evidence that p ligands are noncompetitive inhibitors of the 6CX opioid peptide binding site. Peptides 1992 13 1137-1143. 

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