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Open AccessJournal ArticleDOI

Burial of the polymorphic residue 129 in amyloid fibrils of prion stop mutants.

TLDR
It is demonstrated that stop mutants of the human prion protein have a conserved amyloid core and the 129 residue is deeply buried in the amyloids core structure, and its mutation strongly impacts aggregation.
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This article is published in Journal of Biological Chemistry.The article was published on 2013-02-01 and is currently open access. It has received 16 citations till now.

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Applications of hydrogen/deuterium exchange MS from 2012 to 2014.

TL;DR: This Review catalogs applications of HDX MS that have appeared in the literature during the 30 months from January 2012 to June 2014 as penetration of the method into nonacademic sectors where confidentiality is necessary is also at an all-time high.
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Analysis of protein aggregation in neurodegenerative disease.

TL;DR: Analytical methods for studying protein aggregation in neurodegenerative diseases are important for mapping pathophysiological events and ultimately for the development of new therapies and better diagnostic tools.
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N-terminal Prion Protein Peptides (PrP(120–144)) Form Parallel In-register β-Sheets via Multiple Nucleation-dependent Pathways

TL;DR: Light is shed on the amyloid core structures underlying prion strains and how I138M, I139M, and S143N affect prion protein aggregation kinetics.
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Protein-solvent interfaces in human Y145Stop prion protein amyloid fibrils probed by paramagnetic solid-state NMR spectroscopy.

TL;DR: The protein-solvent interfaces in human PrP23-144 amyloid fibrils generated from recombinant 13C,15N-enriched protein and incubated in aqueous solution containing paramagnetic Cu(II)-EDTA are determined by measuring residue-specific 15N longitudinal paramagnetic relaxation enhancements using two-dimensional magic-angle spinning solid-state NMR spectroscopy.
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Cryo-EM structures of prion protein filaments from Gerstmann–Sträussler–Scheinker disease

TL;DR: In this paper , the structure of PrP amyloid filaments was determined using cryogenic electron microscopy (cryo-EM) from the brain of two symptomatic prion protein F198S mutation carriers, where the filaments are composed of dimeric, trimeric and tetrameric left-handed protofilaments with their protomers sharing a common protein fold.
References
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NMRPipe: a multidimensional spectral processing system based on UNIX pipes

TL;DR: The asynchronous pipeline scheme provides other substantial advantages, including high flexibility, favorable processing speeds, choice of both all-in-memory and disk-bound processing, easy adaptation to different data formats, simpler software development and maintenance, and the ability to distribute processing tasks on multi-CPU computers and computer networks.
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MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification.

TL;DR: MaxQuant, an integrated suite of algorithms specifically developed for high-resolution, quantitative MS data, detects peaks, isotope clusters and stable amino acid isotope–labeled (SILAC) peptide pairs as three-dimensional objects in m/z, elution time and signal intensity space and achieves mass accuracy in the p.p.b. range.
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Spin diffusion measurements : spin echoes in the presence of a time-dependent field gradient

TL;DR: In this article, a derivation of the effect of a time-dependent magnetic field gradient on the spin-echo experiment, particularly in the presence of spin diffusion, is given.
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Andromeda: a peptide search engine integrated into the MaxQuant environment

TL;DR: A novel peptide search engine using a probabilistic scoring model that can handle data with arbitrarily high fragment mass accuracy, is able to assign and score complex patterns of post-translational modifications, and accommodates extremely large databases.
Journal ArticleDOI

Stop and Go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and lc/ms sample pretreatment in proteomics

TL;DR: A novel procedure in which a very small disk of beads embedded in a Teflon meshwork is placed as a microcolumn into pipet tips, finding that the Stage system is well-suited as a universal sample preparation system for proteomics.
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