Figure 4.

Mechanism of truncated TR toward cyclic and acyclic peptide substrates. The peptide substrate is positioned in the active site such that nucleophilic Cys_IC thiolate can attack the Cys₁ position, and cause the release of X (magenta). A) In the case of the cyclic peptide, when X = S, the ring is critical for positioning X near the conserved His, to receive a proton to stabilize the leaving group. When X = Se, the position of the ring near the His matters less due to the much lower pK_a of a selenolate in comparison to that of a thiolate. B) In the case of the flexible, acyclic peptide, which has more degrees of motion in comparison the cyclic peptide, protonation of X is much less likely to occur due to the “floppy” nature of the peptide. However, when X = Se, protonation does not need to occur for transition-state stabilization due to its lower pK_a. Experimentally we observe that when X = S, the acyclic peptides are extremely poor substrates.