The effect of conformation on the solution stability of linear vs. cyclic RGD peptides

The objective of this study was to evaluate the relationship between confor mational flexibility and solution stability of a linear RGD peptide (Arg-Gl y-Asp-Phe-OH; 1) and a cyclic RGD peptide (cyclo-(1, 6)-Ac-Cys-Arg-Gly-Asp- Phe-Pen-NH2; 2); as a function of pH. Previously, it was found that cyclic peptide 2 was 30-fold more stable than linear peptide 1. Therefore, this st udy was performed to explain the increase in chemical stability based on th e preferred conformation of the peptides. Molecular dynamics simulations an d energy minimizations were conducted to evaluate the backbone flexibility of both peptides under simulated pH conditions of 3, 7 and 10 in the presen ce of water. The reactive sites for degradation for both molecules were als o followed during the simulations. The backbone of linear peptide 1 exhibit ed more flexibility than that of cyclic peptide 2, which was reflected in t he rotation about the phi and psi dihedral angles. This was further support ed by the low r.m.s, deviations of the backbone atoms for peptide 2 compare d with those of peptide 1 that were observed among structures sampled durin g the molecular dynamics simulations. The presence of a salt bridge between the side chain groups of the Arg and Asp residues was also indicated for t he cyclic peptide under simulated conditions of neutral pH. The increase in stability of the cyclic peptide 2 compared with the linear peptide 1, espe cially at neutral pH, is due to decreased structural flexibility imposed by the ring, as well as salt bridge formation between the side chains of the Arg and Asp residues in cyclic peptide 2. This rigidity would prevent the A sp side chain carboxylic acid from orienting itself in the appropriate posi tion for attach on the peptide backbone.