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

Behzadi, H ; Sharif University of Technology | 2008

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  1. Type of Document: Article
  2. DOI: 10.1016/j.bpc.2008.07.006
  3. Publisher: 2008
  4. Abstract:
  5. 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. © 2008 Elsevier B.V. All rights reserved
  6. Keywords:
  7. Histidine rich protein ii ; Oxygen 17 ; Protozoal protein ; Unclassified drug ; Alpha helix ; Amino acid sequence ; Electrostimulation ; Hydrogen bond ; Molecular dynamics ; Priority journal ; Protein conformation ; Protein structure ; Theoretical study ; Animals ; Antigens, Protozoan ; Computer Simulation ; Hydrogen Bonding ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Structure ; Oxygen Isotopes ; Peptide Fragments ; Protein Conformation ; Protein Structure, Secondary ; Protozoan Proteins ; Quantum Theory
  8. Source: Biophysical Chemistry ; Volume 137, Issue 2-3 , 2008 , Pages 76-80 ; 03014622 (ISSN)
  9. URL: https://www.sciencedirect.com/science/article/abs/pii/S0301462208001464