A theoretical study of repeating sequence in HRP II: a combination of molecular dynamics simulations and (17)O quadrupole coupling tensors.
Histidine rich protein II derived peptide (HRP II 169-182) was investigated by molecular dynamics, MD, simulation and (17)O electric field gradient, EFG, tensor calculations. MD simulation was performed in water at 300 K with alpha-helix initial structure. It was found that peptide loses its initial alpha-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 (17)O EFG tensors of backbone carbonyl oxygens. Calculations were performed using B3LYP method and 6-31+G basis set. Calculated (17)O EFG tensors were used to evaluate quadrupole coupling constants, QCC, and asymmetry parameters, eta(Q). Difference between the calculated QCC and eta(Q) values revealed how hydrogen-bonding interactions affect EFG tensors at the sites of each oxygen nucleus.
Behzadi
Hadi
H
Department of Chemistry, Tarbiat Modares University, Tehran, Iran.
Esrafili
Mehdi D
MD
van der Spoel
David
D
Hadipour
Nasser L
NL
Parsafar
Gholamabbas
G
D000818:Animals; D000953:Antigens, Protozoan / Q000737:chemistry*; D003198:Computer Simulation; D006860:Hydrogen Bonding; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D015394:Molecular Structure; D010103:Oxygen Isotopes / Q000737:chemistry; D010446:Peptide Fragments / Q000737:chemistry*; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D015800:Protozoan Proteins / Q000737:chemistry*; D011789:Quantum Theory
D000953:Antigens, Protozoan; C514457:HRP-2 antigen, Plasmodium falciparum; D010103:Oxygen Isotopes; D010446:Peptide Fragments; D015800:Protozoan Proteins