Abstract
A simulation procedure based on molecular dynamics has been developed for modeling the interaction of peptides with n-alkylsilica reversed phase chromatographic sorbents. A four-step docking procedure was used which included the following stages: (1) interactive rigid-body docking of the peptide with an n-butylsilica sorbent using amino acid hydrophobicity coefficients to direct the orientation; (2) automated rigid-body docking by a Monte Carlo simulated annealing procedure in the space of six orientational parameters; (3) solvation of the peptide−sorbent complex with water, and (4) automated docking by molecular dynamics simulated annealing in the full Cartesian coordinate space. The procedure has been validated with the simulation of the binding of the peptide bombesin to an n-butylsilica C4 sorbent. The results were analyzed in terms of the change in conformation of both the n-butyl ligand chains and the peptide solute following peptide docking. These studies demonstrate that the partial helical chara...
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