Binding Free Energy and the structural changes determination in hGH protein with different concentrations of copper ions (A molecular dynamics simulation study)

作者：Tazikeh Lemeski Elham^*

来源：Journal of Theoretical and Computational Chemistry, 2016, 15(5): 1650045.

DOI：10.1142/S0219633616500450

• Human growth hormone
• molecular dynamics simulation
• molecular mechanics Poisson-Boltzmann surface area
• dictionary of the secondary structure of protein
• solvent accessible surface area

In this study, we estimated the optimum concentration of copper ions that are effective in the stability and the structural changes of human growth hormone (hGH) protein in the combination of different concentrations of these ions at the molecular level using molecular dynamics simulation by Gromacs 4.6.5 software. Moreover, to estimate the binding affnity of copper ions to hGH protein, binding free energies is calculated by the molecular mechanics Poisson-Boltzmann Surface Area (MM-PBSA). The analysis of molecular dynamics (MD) trajectories as dictionary of the secondary structure of protein (DSSP), solvent accessible surface area (SASA) and binding free energy calculations show that hGH protein structure is more stabilized by increasing a limited concentration of copper ions. These findings align with our previous experimental studies.

• 出版日期2016-8