SIDE CHAIN AND BACKBONE CONFORMATIONAL PREFERENCES OF -CXC- CONTAINING PEPTIDES: EVIDENCED BY COMPUTATIONAL STUDIES

摘要

In this study, we expand our previous searchl of the influence of the (S,S)-CXC-motif on peptide's backbone conformation and side chain side chain interaction. We apply this investigation to a series of linear and cyclic (through disulfide bond) RGD peptide analogues (Table 1). Molecular Dynamics simulations were used to sample the conformational space of the peptides and trajectories received were analyzed. To characterize the backbone conformation we used the Φ/Ψ dihedral angles in order to assign a conformational state to each residue according to Zimmerman. In the sequences -XCYC- or -CXCY-(linear or cyclic), we used the the Pdoβ (pseudo dihedral angle of orientation) defined by the C~β(X)-C~α(X)-C~α(Y)-C~β(Y) atoms, as a measure of the orientation of the side chains. This is similar to our previous work1 and to Stote.