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Isolation and characterization of a minimal building block of polyubiquitin fibrils.

ABSTRACT: As a posttranslational modifier, polyubiquitin is involved in the regulation of diverse intracellular processes; however, it is also found in pathological protein aggregates associated with Alzheimer's disease and other neurodegenerative disorders. We previously observed that various types of polyubiquitin can form amyloid-like fibrils; however, the structural properties of these polyubiquitin fibrils have not been examined at an atomic level. Here we demonstrate that a soluble intermediate species can be extracted from disulfide-conjugated diubiquitin fibrils after cleaving the disulfide bonds in the fibrils. This newly discovered molecule is structurally and physicochemically distinguishable from native ubiquitin. In addition, it is thermodynamically metastable, as demonstrated by real-time NMR measurements. Collectively, our results suggest that the fibril-derived molecule is a minimal building block of polyubiquitin fibrils that reflects their structural and physicochemical properties.

SUBMITTER: Morimoto D

PROVIDER: S-EPMC5807323 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature

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Isolation and characterization of a minimal building block of polyubiquitin fibrils.

Morimoto Daichi D Walinda Erik E Shinke Mayo M Sugase Kenji K Shirakawa Masahiro M

Scientific reports 20180209 1

As a posttranslational modifier, polyubiquitin is involved in the regulation of diverse intracellular processes; however, it is also found in pathological protein aggregates associated with Alzheimer's disease and other neurodegenerative disorders. We previously observed that various types of polyubiquitin can form amyloid-like fibrils; however, the structural properties of these polyubiquitin fibrils have not been examined at an atomic level. Here we demonstrate that a soluble intermediate spec ...[more]

PMID: 29426858

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Project description:We describe why the cyclic heteropolyanion [P8W48O184]40- (abbreviated as {P8W48}) is an ideal building block for the construction of intrinsically porous framework materials by classifying and analyzing >30 coordination polymers incorporating this polyoxometalate (POM) ligand. This analysis shows that the exocyclic coordination of first-row transition metals (TMs) to {P8W48} typically yields frameworks which extend through {W-O-TM-O-W} bridges in one, two, or three dimensions. However, despite the rich structural diversity of such compounds, the coordination of TMs to the {P8W48} ring is poorly understood, and therefore largely unpredictable, and had not until now been present with any structural classification that could allow rational design. Herein, not only do we present a new approach to understand and classify this new class of materials, we also present three {P8W48}-based frameworks which complement those frameworks which have previously been described. These new compounds help us postulate a new taxonomy of these materials. This is possible because the TM coordination sites of the {P8W48} ring are found, once fully mapped, to lead to well-defined classes of connectivity. Together, analysis provides insight into the nature of the building block connectivity within each framework, to facilitate comparisons between related structures, and to fundamentally unite this family of compounds. Hence we have tentatively named these compounds as "POMzites" to reflect the POM-based composition and zeolitic nature of each family member, although crucially, POMzites differ from zeolites in the modular manner of their preparation. As the synthesis of further POMzites is anticipated, the classification system and terminology introduced here will allow new compounds to be categorized and understood in the context of the established materials. A better understanding of TM coordination to the {P8W48} ring may allow the targeted synthesis of new frameworks rather than the reliance on serendipity apparent in current methods.

Dataset Information

Isolation and characterization of a minimal building block of polyubiquitin fibrils.

Publications

Isolation and characterization of a minimal building block of polyubiquitin fibrils.

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