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Structural Variation of Alpha-synuclein with Temperature by a Coarse-grained Approach with Knowledge-based Interactions (Postprint)

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Journal Article

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Materials and Manufacturing Directorate, Air Force Research Laboratory Wright Patterson Air Force Base

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Despite enormous efforts, our understanding the structure and dynamics of alpha-synuclein ASN, a disordered protein that plays a key role in neurodegenerative disease is far from complete. In order to better understand sequence-structure-property relationships in -SYNUCLEIN we have developed a coarse-grained model using knowledge-based residue-residue interactions and used it to study the structure of free ASN as a function of temperature T with a large-scale Monte Carlo simulation. Snapshots of the simulation and contour contact maps show changes in structure formation due to self-assembly as a function of temperature. Variations in the residue mobility profiles reveal clear distinction among three segments along the protein sequence. The N-terminal 1-60 and C-terminal 96-140 regions contain the least mobile residues, which are separated by the higher mobility non-amyloid component NAC 61-95. Our analysis of the intra-protein contact profile shows a higher frequency of residue aggregation clumping in the N-terminal region relative to that in the C-terminal region, with little or no aggregation in the NAC region. The radius of gyration Rg of ASN decays monotonically with decreasing the temperature, consistent with the finding of Allison et al. JACS, 2009.

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