Molecular dynamics simulations on the heterocyclic cyclodecapeptide and its linear analogous in water and octanol solvents

Abstract

Abstract In this study, the behavior of the heterocyclic cyclodecapeptide (HCD), composed of nine glycine amino acids and one threonine, was studied by the molecular dynamics simulations. For this purpose, the linear analogous of HCD was designed in silico and the molecular simulation study for the linear and cyclic peptides was performed in the solvents of water and octanol. The diffusion constant, radial distribution function and hydrophobic accessible surface, root-mean-square deviation (RMSD) and root mean square fluctuation (RMSF) were evaluated in order to compare the behavior of linear and cyclic peptides. The values of the diffusion coefficients for the linear and cyclic forms were found to be 0.616 and 0.215 cm 2 /S in water; 0.175 and 0.148 cm 2 /S in octanol, respectively. The results show that the diffusion coefficients in water solvent for both the linear and cyclic forms of peptides are higher than those in octanol solvent. Also, the diffusion coefficients for the linear form, in both solvents, are higher than those in the cyclic form. Based on the analysis of the solvent accessible surface, the hydrophobic accessible surface areas for the linear and cyclic forms of peptides are 4.38 and 4.17 in water; 3.93 and 4.03 in octanol, respectively. The RDF results showed that the strength of O H hydrogen bonds for both linear and cyclic peptides in water is greater than N H hydrogen bonds. However, the strength of each kind of hydrogen bonds in the cyclic peptide is stronger than that of the linear peptide in water solvent. The interactions between the peptide and octanol solvent were found to be weak.