1,721,021 research outputs found
An atomistic view of Hsp70 allosteric crosstalk: from the nucleotide to the substrate binding domain and back
No full textThe Hsp70 is an allosterically regulated family of molecular chaperones.
They consist of two structural domains, NBD and SBD, connected by a
flexible linker. ATP hydrolysis at the NBD modulates substrate
recognition at the SBD, while peptide binding at the SBD enhances ATP
hydrolysis. In this study we apply Molecular Dynamics (MD) to elucidate
the molecular determinants underlying the allosteric communication from
the NBD to the SBD and back. We observe that local structural and
dynamical modulation can be coupled to large-scale rearrangements, and
that different combinations of ligands at NBD and SBD differently affect
the SBD domain mobility. Substituting ADP with ATP in the NBD induces
specific structural changes involving the linker and the two NBD lobes.
Also, a SBD-bound peptide drives the linker docking by increasing the
local dynamical coordination of its C-terminal end: a partially docked
DnaK structure is achieved by combining ATP in the NBD and peptide in
the SBD. We propose that the MD-based analysis of the inter domain
dynamics and structure modulation could be used as a tool to
computationally predict the allosteric behaviour and functional response
of Hsp70 upon introducing mutations or binding small molecules, with
potential applications for drug discovery
Durable and efficient gene silencing in vivo by hit-and-run epigenome editing
Full text linkPermanent epigenetic silencing using programmable editors equipped with transcriptional repressors holds great promise for the treatment of human diseases1-3. However, to unlock its full therapeutic potential, an experimental confirmation of durable epigenetic silencing after the delivery of transient delivery of editors in vivo is needed. To this end, here we targeted Pcsk9, a gene expressed in hepatocytes that is involved in cholesterol homeostasis. In vitro screening of different editor designs indicated that zinc-finger proteins were the best-performing DNA-binding platform for efficient silencing of mouse Pcsk9. A single administration of lipid nanoparticles loaded with the editors' mRNAs almost halved the circulating levels of PCSK9 for nearly one year in mice. Notably, Pcsk9 silencing and accompanying epigenetic repressive marks also persisted after forced liver regeneration, further corroborating the heritability of the newly installed epigenetic state. Improvements in construct design resulted in the development of an all-in-one configuration that we term evolved engineered transcriptional repressor (EvoETR). This design, which is characterized by a high specificity profile, further reduced the circulating levels of PCSK9 in mice with an efficiency comparable with that obtained through conventional gene editing, but without causing DNA breaks. Our study lays the foundation for the development of in vivo therapeutics that are based on epigenetic silencing.Experiments in mice show that designed epigenome editors that contain domains of transcriptional repressors can enable stable epigenetic silencing of Pcsk9, a gene with a role in cholesterol homeostasis, without inducing DNA breaks
NuChart-II: The road to a fast and scalable tool for Hi-C data analysis
Full text linkRecent advances in molecular biology and bioinformatic techniques have brought about an explosion of information about the spatial organisation of the DNA in the nucleus of a cell. High-throughput molecular biology techniques provide a genome-wide capture of the spatial organisation of chromosomes at unprecedented scales, which permit one to identify physical interactions between genetic elements located throughout a genome. This important information is, however, hampered by the lack of biologist-friendly analysis and visualisation software: these disciplines are literally caught in a flood of data and are now facing many of the scale-out issues that high-performance computing has been addressing for years. Data must be managed, analysed and integrated, with substantial requirements of speed (in terms of execution time), application scalability and data representation. In this work, we present NuChart-II, an efficient and highly optimised tool for genomic data analysis that provides a gene-centric, graph-based representation of genomic information and which proposes an ex-post normalisation technique for Hi-C data. While designing NuChart-II, we addressed several common issues in the parallelisation of memory-bound algorithms for shared-memory systems
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
Molecular Mechanism of Allosteric Communication in Hsp70 Revealed by Molecular Dynamics Simulations
No full textInvestigating ligand-regulated allosteric coupling between protein domains is fundamental to understand cell-life regulation. The Hsp70 family of chaperones represents an example of proteins in which ATP binding and hydrolysis at the Nucleotide Binding Domain (NBD) modulate substrate recognition at the Substrate Binding Domain (SBD). Herein, a comparative analysis of an allosteric (Hsp70-DnaK) and a non-allosteric structural homolog (Hsp110-Sse1) of the Hsp70 family is carried out through molecular dynamics simulations, starting from different conformations and ligand-states. Analysis of ligand-dependent modulation of internal fluctuations and local deformation patterns highlights the structural and dynamical changes occurring at residue level upon ATP-ADP exchange, which are connected to the conformational transition between closed and open structures. By identifying the dynamically responsive protein regions and specific cross-domain hydrogen-bonding patterns that differentiate Hsp70 from Hsp110 as a function of the nucleotide, we propose a molecular mechanism for the allosteric signal propagation of the ATP-encoded conformational signal
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
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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