1,721,050 research outputs found
Structural and hydration properties of the partially unfolded states of the prion protein
No full textMisfolding and aggregation of the prion protein (PrP) is responsible for the development of transmissible spongiform encephalopathies (TSE). To gain insights into possible aggregation-prone intermediate states, we construct the free energy surface of the C-terminal globular domain of the PrP from enhanced sampling of replica exchange molecular dynamics. This cellular domain is characterized by three helices H1-H3 and a small beta-sheet. In agreement with experimental studies, the partially unfolded states display a stable core built from the central portions of helices H2 and H3 and a high mobility of helix H1 from the core. Among all identified conformational basins, a marginally populated state appears to be a very good candidate for aggregation. This intermediate is stabilized by four TSE-sensitive key interactions, displays a longer helix H1 with both a dry and solvated surface, and is featured by a significant detachment of helix H1 from the PrP-core
Backbone NMR assignments of the C-terminal domain of the human prion protein and its disease-associated T183A variant
No full textTransmissible spongiform encephalopathies (TSEs) are fatal neurodegenerative disorders associated with the misfolding and aggregation of the human prion protein (huPrP). Despite efforts into investigating the process of huPrP aggregation, the mechanisms triggering its misfolding remain elusive. A number of TSE-associated mutations of huPrP have been identified, but their role at the onset and progression of prion diseases is unclear. Here we report the NMR assignments of the C-terminal globular domain of the wild type huPrP and the pathological mutant T183A. The differences in chemical shifts between the two variants reveal conformational alterations in some structural elements of the mutant, whereas the analyses of secondary shifts and random coil index provide indications on the putative mechanisms of misfolding of T183A huPrP
Metal interactions of α-synuclein probed by NMR amide-proton exchange
No full text: The aberrant aggregation of α-synuclein (αS), a disordered protein primarily expressed in neuronal cells, is strongly associated with the underlying mechanisms of Parkinson's disease. It is now established that αS has a weak affinity for metal ions and that these interactions alter its conformational properties by generally promoting self-assembly into amyloids. Here, we characterised the nature of the conformational changes associated with metal binding by αS using nuclear magnetic resonance (NMR) to measure the exchange of the backbone amide protons at a residue specific resolution. We complemented these experiments with 15N relaxation and chemical shift perturbations to obtain a comprehensive map of the interaction between αS and divalent (Ca2+, Cu2+, Mn2+, and Zn2+) and monovalent (Cu+) metal ions. The data identified specific effects that the individual cations exert on the conformational properties of αS. In particular, binding to calcium and zinc generated a reduction of the protection factors in the C-terminal region of the protein, whereas both Cu(II) and Cu(I) did not alter the amide proton exchange along the αS sequence. Changes in the R2/R1 ratios from 15N relaxation experiments were, however, detected as a result of the interaction between αS and Cu+ or Zn2+, indicating that binding to these metals induces conformational perturbations in distinctive regions of the protein. Collectively our data suggest that multiple mechanisms of enhanced αS aggregation are associated with the binding of the analysed metals
Replica-averaged orientational-restrained ensembles of DWORF and P15A-DWORF in lipid bilayers
No full textReplica-averaged orientational-restrained molecular dynamics (RAOR-MD) ensembles of DWORF and the DWORF-P15A mutant in lipid bilayers. Restrained to 15N chemical shift anisotropy and 1H-15N dipolar coupling data obtained from oriented sample solid-state NMR spectroscopy.National Institutes of Health (R01HL143816, R01HL092321)American Heart Association (19POST34420009)Uddigiri, Venkateswara Reddy; Weber, Daniel K; Wang, Songlin; Larsen, Erik K; Gopinath, Tata; De Simone, Alfonso; Robia, Seth; Veglia, Gianluigi. (2021). Replica-averaged orientational-restrained ensembles of DWORF and P15A-DWORF in lipid bilayers. Retrieved from the University Digital Conservancy, https://doi.org/10.13020/2vf6-y268
α-Synuclein and biological membranes: the danger of loving too much
No full text: The aberrant aggregation of α-Synuclein (αS), a disordered protein primarily localised at the neuronal synapses, is associated with a number of neurodegenerative disorders including Parkinson's disease (PD). The biological properties of αS are strictly connected with its ability to bind synaptic membranes under both physiological and pathological conditions. Here we overview the recent studies on the structural and biological properties of the membrane interaction by αS. The characterisation of this state is particularly challenging as the membrane binding of αS is weak, transient and features a considerable degree of conformational disorder. Advancements in this area have been achieved through combinations of nuclear magnetic resonance (NMR), super-resolution microscopy, cryo-EM and cellular biophysics. Current data clarified the central role of the equilibrium between ordered and disordered states of αS at the membrane surface, which regulates the membrane affinity, the aggregation into amyloid fibrils and the promotion of vesicle clustering. Recent results on toxic oligomeric species of αS also revealed common features in the membrane interaction of functional and aberrant forms of this protein. These findings therefore evidence the challenging nature of identifying suitable therapeutics to target the aberrant aggregation of αS in PD while leaving its normal physiological form unperturbed
Computational studies of the structure, dynamics and native content of amyloid-like fibrils of ribonuclease A
No full textThe characterization at atomic resolution of amyloid-like protein
aggregates is one of the fundamental problems of modern biology. In
particular, the question whether native-like domains are retained or
completely refolded in the amyloid state and the identification of
possible mechanisms for macromolecular ordered aggregation represent
major unresolved puzzles. To address these issues, in this article we
examine the stability, dynamics, and conservation of native-like
properties of several models of a previously designed amyloid-like
fibril of RNase A (Sambashivan et al., Nature 2005, 437:266-269).
Through the use of molecular dynamics (MD) simulations, we have provided
molecular-level insights into the role of different parts of the
sequence on the stability of fibrils, the collective properties of
supramolecular complexes, and the presence of native-like conformations
and dynamics in supramolecular aggregates. We have been able to show
that within the fibrils the three-dimensional globular domain-swapped
units preserve the conformational, dynamical, and hydration properties
typical of the monomeric state, providing a rationalization for the
experimentally observed catalytic activity of fibrils. The nativeness of
the globular domains is not affected by the amyloidogenic stretches,
which determine the molecular recognition process underlying aggregation
through the formation of a stable steric zipper motif. Moreover, through
the study of the hydration features of a single sheet model, we have
been able to show that polyglutamine stretches of the domain-swapped
ribonuclease tend to minimize the interaction with water in favor of
sidechain-sidechain interactions, shedding light on the factors leading
to the supramolecular assembly of beta-sheet layers into dry steric
zippers
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
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