Characterization of Conformation and Dynamics of CD4 Fragment (81-92) TYICEVEDQKEE and Its Benzylated Derivative by 1H NMR Spectroscopy and Molecular Modeling: Relevance of Conformation to Biological Function

Abstract

Two-dimensional 1H nuclear magnetic resonance (NMR) spectroscopy experiments were carried out to determine the conformation of a CD4 fragment (81-92) TYICEVEDQKEE and its di-benzylated analogue in aqueous solution. The refined structures obtained by use of distance geometry and simulated annealing for both peptides revealed a marked departure from that of the corresponding sequence within the D1D2 fragment of CD4 determined by x-ray crystal studies. Near the amino terminus of both peptides, a distinct loop exists that is stabilized by the hydrophobic interaction between the side chains of the amino acids in the region. For the parent peptide and Cys84 and Glu85 dibenzylated analogues, the orientation of the loop is different with respect to the reverse turn formed by Val86 through Gln89. In particular, the side chains of Val86 point in different directions for these two peptide analogues. The C- terminus of both peptide analogues exhibits a faster motional characteristic. The deuterium-proton exchange experiment showed a very slowly exchanged Gln89 backbone NH for the di-benzylated peptide, suggesting its participation in the hydrogen bond to Val86 C=O. The negatively charged side chains of Glu87 and Asp88 are found to jut out, similar to the crystal structure. The difference between the two peptides in inhibiting the syncytium formation is postulated to arise from the more defined Val86-Gln89 turn and the orientation of the apolar side chains of the residues in the stretch thought to participate in the cell-fusion process.