Study of the Structure of the Peptides Stabilized by the Hydrogen-Bond Surrogate Approach Using Molecular Dynamics Simulation

To study the path of biological reactions peptides are used from the secondary and tertiary structures of peptides that have an important role in the equilibrium of protein-protein interaction (PPI) inhibitors. Different methods are used to stabilize peptides the method of hydrogen bond surrogate is a unique way to stabilize the peptides, because this method (HBS) while stabilization the peptides keep side chains stable, which can be modified to control attachment and peptide interactions. HBS method create the peptides by forming large 16 - membered rings, and we used three groups disulfide, thioether, olefin for the stability of the α-helix and β-sheet statures. [8]. In this paper, we examine the structure of peptide β-hairpin stabilized peptide structures, using GROMACS and analysis of RMSD, Gyration, Hydrogen bond interactions with the environment and in terms of stability and structural properties.