A theoretical study of repeating sequence in HRP II: A combination of molecular dynamics simulations and 17O quadrupole coupling tensors

Histidine rich protein II derived peptide (HRP II 169-182) was investigated by molecular dynamics, MD, simulation and 17O electric field gradient, EFG, tensor calculations. MD simulation was performed in water at 300 K with α-helix initial structure. It was found that peptide loses its initial α-helix structure rapidly and is converted to random coil and bent secondary structures. To understand how peptide structure affects EFG tensors, initial structure and final conformations resulting from MD simulations were used to calculate 17O EFG tensors of backbone carbonyl oxygens. Calculations were performed using B3LYP method and 6-31 + G⁎ basis set. Calculated 17O EFG tensors were used to evaluate quadrupole coupling constants, QCC, and asymmetry parameters, ηQ. Difference between the calculated QCC and ηQ values revealed how hydrogen-bonding interactions affect EFG tensors at the sites of each oxygen nucleus.