Structural basis of neurophysin hormone specificity: Geometry, polarity, and polarizability in aromatic ring interactions

The structural origins of the specificity of the neurophysin hormone-bindin g site for an aromatic residue in peptide position 2 were explored by analy zing the binding of a series of peptides in the context of the crystal stru cture of Liganded neurophysin. A new modeling method for describing the van der Waals surface of binding sites assisted in the analysis. Particular at tention was paid to the unusually large (5 kcal/mol) difference in binding free energy between Phe and Leu in position 2, a value representing more th an three times the maximum expected based on hydrophobicity alone, and addi tionally remarkable since modeling indicated that the Leu side chain was re adily accommodated by the binding pocket. Although evidence was obtained of a weak thermodynamic linkage between the binding interactions of the resid ue 2 side chain and of the peptide alpha-amino group, two factors are consi dered central. (1) The bound Leu side chain can establish only one-third of the van der Waals contacts available to a Phe side chain. (2) The bound Ph e side chain appears to be additionally stabilized relative to Leu by more favorable dipole and induced dipole interactions with nonaromatic polar and sulfur ligands in the binding pocket, as evidenced by examination of its i nteractions in the pocket, analysis of the detailed energetics of transfer of Phe and Leu side chains from water to other phases, and comparison with thermodynamic and structural data for the binding of residue I side chains in this system. While such polar interactions of aromatic rings have been p reviously observed, the present results suggest their potential for signifi cant thermodynamic contributions to protein structure and ligand recognitio n.