All-atom molecular dynamics(MD) simulations and chemical shifts were used to study interactions and structures in the glycine-water system.Radial distribution functions and the hydrogen-bond network were applied in MD simulations.Aggregates in the aqueous glycine solution could be classified into different regions by analysis of the hydrogen-bonding network.Temperature-dependent NMR spectra and the viscosity of glycine in aqueous solutions were measured to compare with the results of MD simulations.The variation tendencies of the hydrogen atom chemical shifts and viscosity with concentration of glycine agree with the statistical results of hydrogen bonds in the MD simulations.
Molecular dynamic simulations and molecular docking are performed to study the conformations and hydrogen bonding interactions of ACE inhibitory tripeptide VEF. Intramolecular distance, radius of gyration, solvent-accessible surface, and root-mean-square deviations are used to characterize the properties of VEF in aqueous solution. The VEF molecule is highly flexible in water and conformations can shift between the extended and folded states. The VEF molecule exists in extended state mostly in aqueous solution and the conformations bonded with ACE are also the extended ones. The findings indicate that MD simulations have a good agreement with the molecular docking analysis.
All-atom molecular dynamic simulations and 2D-NOESY spectra were used to study the conformations and hydrogen bonds of ACE inhibitory tripeptide Ile-Ile-Pro(IIP) in aqueous and DMSO solutions. RMSD, Dis, Rg and SASA were adopted to characterize the properties of tripeptide Ile-Ile-Pro in the MD simulations. Interestingly, the tripeptide molecule IIP exhibited different behaviors in aqueous and DMSO solutions. In aqueous solution, IIP was very flexible. The conformation could shift between extended and folded states very quickly. However,in DMSO solution, more folded conformations were observed. The interesting phenomena were proved by 2D-NOESY spectra.
A database of 38 tripeptides with C-terminal proline was constructed to study QSAR of ACE inhibitory peptides. The model was established using PLS based on the three z-scores of 20 coded amino acids. The prediction ability of tripeptides model was improved with proline as terminal. The coefficient of determination(R2) and the cross validated coefficient(Q2LOO) of the model are 0.856 and 0.782 respectively. According to the model, two potential ACE inhibitory tripeptides IIP and IVP were synthesized. Their IC50(inhibitor concentration that reduced enzyme activity by 50%) were proved to be 1.58 and 1.39 μM respectively by direct spectrophotometric measurement, and they are very close to the predicted value by the model.
