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Conformational landscape of an amyloid intra-cellular domain and Landau-Ginzburg-Wilson paradigm in protein dynamics
Beijing Inst Technol, Sch Phys, Beijing 100081, Peoples R China..
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics. Beijing Inst Technol, Sch Phys, Beijing 100081, Peoples R China.; Univ Tours, CNRS, Lab Math & Phys Theor, Federat Denis Poisson,UMR 6083, Parc Grandmont, F-37200 Tours, France..
Beijing Inst Technol, Sch Phys, Beijing 100081, Peoples R China..
2016 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 145, no 4, 045103Article in journal (Refereed) Published
Abstract [en]

The Landau-Ginzburg-Wilson paradigm is proposed as a framework, to investigate the conformational landscape of intrinsically unstructured proteins. A universal Ca-trace Landau free energy is deduced from general symmetry considerations, with the ensuing all-atom structure modeled using publicly available reconstruction programs Pulchra and Scwrl. As an example, the conformational stability of an amyloid precursor protein intra-cellular domain (AICD) is inspected; the reference conformation is the crystallographic structure with code 3DXC in Protein Data Bank (PDB) that describes a heterodimer of AICD and a nuclear multi-domain adaptor protein Fe65. Those conformations of AICD that correspond to local or near-local minima of the Landau free energy are identified. For this, the response of the original 3DXC conformation to variations in the ambient temperature is investigated, using the Glauber algorithm. The conclusion is that in isolation the AICD conformation in 3DXC must be unstable. A family of degenerate conformations that minimise the Landau free energy is identified, and it is proposed that the native state of an isolated AICD is a superposition of these conformations. The results are fully in line with the presumed intrinsically unstructured character of isolated AICD and should provide a basis for a systematic analysis of AICD structure in future NMR experiments.

Place, publisher, year, edition, pages
2016. Vol. 145, no 4, 045103
National Category
Physical Chemistry
Identifiers
URN: urn:nbn:se:uu:diva-303118DOI: 10.1063/1.4959582ISI: 000381679800059OAI: oai:DiVA.org:uu-303118DiVA: diva2:971256
Funder
Swedish Research CouncilCarl Tryggers foundation
Available from: 2016-09-15 Created: 2016-09-15 Last updated: 2016-09-15Bibliographically approved

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Niemi, Antti J.
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