Figure 5.

Peptide P27 binds the modified hASL^Lys3_UUU with high affinity and specificity. (A) The computed equilibrium binding structure of the modified hASL^Lys3_UUU bound by P27. The peptide backbone is in gold, and the ribose-phosphodiester backbone of the hASL^Lys3_UUU is colored in green. (B) Enlargement of the interaction demonstrating the specificity achieved in the binding of the two modifications by the amino acids R₁ (red), F₇ (light green), W₁₁ (light purple), and R₁₂ (dark green). The peptide backbone is in gold and the side chains in color. The modifications ms²t⁶A₃₇ (purple) and mcm⁵s²U₃₄ (blue) are bound by amino acids at the beginning, middle, and end of the peptide. The ribose-phosphodiester backbone of the hASL^Lys3_UUU is not shown. The table characterizes the contributions of different binding modes: ΔG_Binding, Gibbs free energy of binding; BE_w/o GBSUR, binding energy without GBSUR; VDW, van der Waals energy; ELE, electrostatic energy; EGB, polar solvation energy based on the generalized Born (implicit solvent) model; and GBSUR, nonpolar solvation energy, which is the product of the solvent-accessible surface area of the solute molecules and the interfacial tension between the solute and solvent. (C) Individual contributions of each amino acid to the VDW, ELE + EGB, and GBSUR. The amino acids are colored as in B. (D) Individual contributions of each nucleoside to the VDW, ELE + EGB, and GBSUR. The nucleosides engaged in the interaction with P27 are those of the anticodon loop, particularly the modified nucleosides at U₃₄ and A₃₇. The modified nucleosides are colored as in B.