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A theoretical study of repeating sequence in HRP II: a combination of molecular dynamics simulations and (17)O quadrupole coupling tensors
Teheran.
Teheran.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
Teheran.
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2008 (English)In: Biophysical Chemistry, ISSN 0301-4622, E-ISSN 1873-4200, Vol. 137, no 2-3, 76-80 p.Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2008. Vol. 137, no 2-3, 76-80 p.
Keyword [en]
Nuclear quadrupole resonance, Density functional theory, Histidine rich protein II, MD simulations, Hydrogen bond
National Category
Chemical Sciences
Identifiers
URN: urn:nbn:se:uu:diva-104080DOI: 10.1016/j.bpc.2008.07.006ISI: 000260158600002PubMedID: 18708277OAI: oai:DiVA.org:uu-104080DiVA: diva2:219351
Available from: 2009-05-27 Created: 2009-05-27 Last updated: 2017-12-13Bibliographically approved

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