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Binding Mechanism and Magnetic Properties of a Multifunctional Spin Label for Targeted EPR Imaging of Amyloid Proteins: Insight from Atomistic Simulations and First-Principles Calculations
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.ORCID iD: 0000-0001-6508-8355
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. (Swedish E-Science Research Center (SeRC))ORCID iD: 0000-0003-2729-0290
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.ORCID iD: 0000-0003-0185-5724
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2012 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 8, no 11, 4766-4774 p.Article in journal (Refereed) Published
Abstract [en]

Electron paramagnetic resonance (EPR) imaging techniques provide a promising approach to detect amyloid structures which are of paramount importance in early-stage diagnosis of conformational diseases. Here, we report a combined molecular dynamics and density functional theory/molecular mechanics computational scheme for evaluation of the binding mechanism between a multifunctional spin label and the target amyloid protein. In addition, we consider evaluation of EPR spin Hamiltonian parameters with the aim of providing a better microscopic understanding and interpretation of EPR spectroscopy. The results from molecular dynamics simulations suggest that the oligothiophene conjugate part of the spin label interacts with hydrophobic residues of the amyloid protein through hydrophobic attraction and that both the N-O bond length and the N-O out-of-plane tilt angle in the nitroxide group are slightly diminished after, complexation with the protein. The translational and rotational motions of the protein bound spin label are considerably slowed compared to those of the free spin label in aqueous solution, but interestingly, hydrogen bonds formed between the nitroxide oxygen group and the surrounding water molecules are hardly affected by the presence Of the amyloid protein. First principles calculation's suggest that EPR spin Hamiltonian parameters including the nitroxide nitrogen hyperfine coupling tensor A(N) and electronic g tensor suffer noticeable changes upon complexation with the protein. The magnitude of the A(N) tensor is found,to:be. closely related to the nitroxide N-O out tilt angle, while the g tensor is affected by both the nitroxide N-O bond length as well as the interaction between the spin label and the amyloid protein With this work we show that state-of-the-art simulation techniques represent a promising way of providing a detailed understanding of the microscopic mechanisms responsible for the formation and stability of a spin label complexed with amyloid structures as well as the magnetic properties of the free and protein-bound spin label.

Place, publisher, year, edition, pages
2012. Vol. 8, no 11, 4766-4774 p.
Keyword [en]
Hyperfine Coupling-Constants, Electronic G-Tensors, Amber Force-Field, Molecular-Dynamics, Alzheimers-Disease, Free-Radicals, Charges, Probes, Solvation, Continuum
National Category
Chemical Sciences
Identifiers
URN: urn:nbn:se:kth:diva-109201DOI: 10.1021/ct300606qISI: 000311191900075Scopus ID: 2-s2.0-84962446566OAI: oai:DiVA.org:kth-109201DiVA: diva2:582766
Funder
Swedish e‐Science Research Center
Note

QC 20130107

Available from: 2013-01-07 Created: 2012-12-21 Last updated: 2017-12-06Bibliographically approved

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Li, XinNatarajan Arul, MuruganÅgren, Hans

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