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Structure and Dynamics of the Copper-binding Octapeptide Region in the Human Prion Protein
KTH, School of Chemical Science and Engineering (CHE), Chemistry.
2005 (English)Licentiate thesis, comprehensive summary (Other scientific)
Abstract [en]

The copper-binding ability of the prion protein may be closely connected to its function. Identifying the exact function of the prion protein can clarify the underlying mechanism in prion diseases. In this work, the copper-binding octapeptide region in the human prion protein has been studied. The structural characteristics of the binding site are examined by quantum chemical structural optimization. The calculations aim at identifying a substitute for copper(II) to be used in NMR-spectroscopic studies of the copper-binding region. The dynamical and structural features of the peptide region are investigated in molecular dynamics simulations. Aspects of importance in the development of model systems in molecular dynamics simulation are addressed.

Place, publisher, year, edition, pages
Stockholm: KTH , 2005. , 40 p.
Series
Trita-OOK, ISSN 0348-825X ; 1080
Keyword [en]
Inorganic chemistry, prion protein, copper, molecular dynamics simulation, solvation model, metal ions, coordination
Keyword [sv]
Oorganisk kemi
National Category
Inorganic Chemistry
Identifiers
URN: urn:nbn:se:kth:diva-250OAI: oai:DiVA.org:kth-250DiVA: diva2:8101
Presentation
2005-05-27, E3, Huvudbyggnaden, Osquarsbacke 14, Stockholm, 10:00
Supervisors
Note
QC 20101220Available from: 2005-05-31 Created: 2005-05-31 Last updated: 2010-12-20Bibliographically approved
List of papers
1. An evaluation of non-periodic boundary condition models in molecular dynamics simulations using prion octapeptides as probes
Open this publication in new window or tab >>An evaluation of non-periodic boundary condition models in molecular dynamics simulations using prion octapeptides as probes
2006 (English)In: Journal of Molecular Structure: THEOCHEM, ISSN 0166-1280, Vol. 760, no 1-3, 91-98 p.Article in journal (Refereed) Published
Abstract [en]

Molecular dynamics simulations have been performed under periodic boundary conditions and using four non-periodic solvation models. The biomolecular probe in these simulations was a single repeat of the copper-binding octapeptide in the human prion protein, PHGGGWGQ. Although the alternative non-periodic solvation models enable a reduction in computational time, the dynamical disadvantages are considerable when using any of these four non-periodic models. For simulations of systems similar to the test system, periodic boundary conditions are a better alternative than any of the four local models.

Keyword
Molecular dynamics; Non-periodic boundary conditions; Prion protein; Solvation model
National Category
Inorganic Chemistry
Identifiers
urn:nbn:se:kth:diva-7295 (URN)10.1016/j.theochem.2005.11.027 (DOI)000236566300011 ()2-s2.0-33644817645 (Scopus ID)
Note
QC 20100816Available from: 2007-06-04 Created: 2007-06-04 Last updated: 2010-08-16Bibliographically approved
2. Molecular Dynamics Simulations of the Copper-binding Octapeptide Region in the Human Prion Protein
Open this publication in new window or tab >>Molecular Dynamics Simulations of the Copper-binding Octapeptide Region in the Human Prion Protein
(English)Article in journal (Refereed) Submitted
National Category
Inorganic Chemistry
Identifiers
urn:nbn:se:kth:diva-5236 (URN)
Note
QC 20101220Available from: 2005-05-31 Created: 2005-05-31 Last updated: 2010-12-20Bibliographically approved
3. Computational Comparison of Cation Coordination to Human Prion Peptide Models
Open this publication in new window or tab >>Computational Comparison of Cation Coordination to Human Prion Peptide Models
2006 (English)In: Inorganic Chemistry, ISSN 0020-1669, E-ISSN 1520-510X, Vol. 45, no 21, 8509-8516 p.Article in journal (Refereed) Published
Abstract [en]

The coordination of the cations Cu(II), Co(II), Rh(III), Ir(III), Ni(II), Pd(II), Pt(II), and Zn(II) to the copper-binding octapeptide region in the human prion protein has been compared through structural optimization. The initial coordination mode used in the calculations is a five-coordinated mode obtained from previously published crystallographic data for Cu(II). The computational results show that, among these cations, the coordinations of Co(II) and Rh(III) are the most similar to that of Cu(II). The cations Ni(II), Pd(II), and Pt(II) prefer a four-coordinate square-planar coordination by the peptide ligand. The paramagnetic Co(II) ion with its large quadrupole moment is not a good substitute for Cu(II) to be used in NMR spectroscopic studies of the coordinated peptide region. Rh(III) has more attractive NMR spectroscopic characteristics than Cu(II) and Co(II) and may represent a suitable substitute for Cu(II) in these types of studies. Some preliminary experimental studies using NMR spectroscopic methods indicate that Rh(III) coordinates the copper-binding octapeptide region of the human prion protein, although further studies are required to determine the mode of interaction in detail.

Keyword
copper; divalent cation; iron; nickel; peptide fragment; platinum; rhodium; zinc; article; chemical structure; chemistry; human; metabolism; nuclear magnetic resonance spectroscopy; prion; protein conformation; Cations, Divalent; Copper; Humans; Iron; Magnetic Resonance Spectroscopy; Models, Molecular; Nickel; Peptide Fragments; Platinum; Prions; Protein Conformation; Rhodium; Zinc
National Category
Inorganic Chemistry
Identifiers
urn:nbn:se:kth:diva-7296 (URN)10.1021/ic052079k (DOI)000241106700013 ()2-s2.0-33750345360 (Scopus ID)
Note
QC 20100816Available from: 2007-06-04 Created: 2007-06-04 Last updated: 2010-08-16Bibliographically approved

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