Institut de Recerca Biomèdica (IRB Barcelona): Enviaments recents
Ara mostrant els elements 41-60 de 418
Molecular dynamics modelling of the interaction of a synthetic zinc-finger miniprotein with DNA
We report the modelling of the DNA complex of an artificial miniprotein composed of two zinc finger modules and an AT-hook linking peptide. The computational study provides for the first time a structural view of these ...
Sensitive high-throughput single-cell RNA-seq reveals within-clonal transcript correlations in yeast populations
Single-cell RNA sequencing has revealed extensive cellular heterogeneity within many organisms, but few methods have been developed for microbial clonal populations. The yeast genome displays unusually dense transcript ...
Rhodium-Catalyzed Pauson−Khand Reaction Using a Small-Bite-Angle P‑Stereogenic C1‑Diphosphine Ligand
The asymmetric Pauson−Khand reaction catalyzed by [Rh(COD)(MaxPHOS)]BF4 is described. Several 1,6-enynes have been chosen as model substrates affording moderate yields and selectivities of up to 86% ee. Besides binap-type ...
Alterations in the abundance of protamine proteoforms related to sperm chromatin packaging, obesity, and age in normozoospermic men
Protamines are considered among the most relevant sperm proteins because of their functional implications on paternal genome packaging and protection. Although the proteomic evaluation of protamines is technically challenging, ...
CGeNArateWeb: a web server for the atomistic study of the structure and dynamics of chromatin fibers
We present CGeNArateWeb, a new web tool for the three-dimensional simulation of naked DNA and protein-bound chromatin fibers. The server allows the user to obtain a dynamic representation of long segments of linear, circular, ...
Origins of Second Malignancies in Children and Mutational Footprint of Chemotherapy in Normal Tissues
Pediatric cancers are rare diseases, and children without known germline predisposing conditions who develop a second malignancy during developmental ages are extremely rare. We present four such clinical cases and, through ...
Exploring the early stages of chemical unfolding of proteins at the proteome scale
After decades of using urea as denaturant, the kinetic role of this molecule in the unfolding process is still undefined: does urea actively induce protein unfolding or passively stabilize the unfolded state? By analyzing ...
Proteomic tools for the quantitative analysis of artificial peptide libraries: detection and characterization of target-amplified PD-1 inhibitors
We report a quantitative proteomics data analysis pipeline which, coupled to protein-directed dynamic combinatorial chemistry (DDC) experiments, enables the rapid discovery and direct characterization of protein-protein ...
Modulation of the helical properties of DNA: next-to-nearest neighbour effects and beyond
We used extensive molecular dynamics simulations to study the structural and dynamic properties of the central d(TpA) step in the highly polymorphic d(CpTpApG) tetranucleotide. Contrary to the assumption of the dinucleotide-model ...
The epidermal circadian clock integrates and subverts brain signals to guarantee skin homeostasis
In mammals, the circadian clock network drives daily rhythms of tissue-specific homeostasis. To dissect daily inter-tissue communication, we constructed a mouse minimal clock network comprising only two nodes: the peripheral ...
Hog1 activation delays mitotic exit via phosphorylation of Net1
Adaptation to environmental changes is crucial for cell fitness. In Saccharomyces cerevisiae, variations in external osmolarity trigger the activation of the stress-activated protein kinase Hog1 (high-osmolarity glycerol ...
BioSuper: A web tool for the superimposition of biomolecules and assemblies with rotational symmetry
Background Most of the proteins in the Protein Data Bank (PDB) are oligomeric complexes consisting of two or more subunits that associate by rotational or helical symmetries. Despite the myriad of superimposition tools in ...
Variable efficiency of nonsense-mediated mRNA decay across human tissues, tumors and individuals
BackgroundNonsense-mediated mRNA decay (NMD) is a quality-control pathway that degrades mRNA bearing premature termination codons (PTCs) resulting from mutation or mis-splicing, and that additionally participates in gene ...
The efficacy of chemotherapy is limited by intratumoral senescent cells expressing PD-L2
Chemotherapy often generates intratumoral senescent cancer cells that strongly modify the tumor microenvironment, favoring immunosuppression and tumor growth. We discovered, through an unbiased proteomics screen, that the ...
RINGO/Speedy proteins, a family of non-canonical activators of CDK1 and CDK2
Cyclin-dependent kinases (CDKs) require the binding to a regulatory subunit to acquire enzymatic activity, and cyclins are the canonical CDK activators. However, there are specific situations in which CDKs can be activated ...
OpenVariant: a toolkit to parse and operate multiple input file formats
Advances in high-throughput DNA sequencing technologies and decreasing costs have fueled the identification of small genetic variants (such as single nucleotide variants and indels) across tumors. Despite efforts to ...
Nucleotide depletion reveals the impaired ribosomebiogenesis checkpoint as a barrier against DNA damage
Many oncogenes enhance nucleotide usage to increase ribosome content, DNA replication, and cell proliferation, but in parallel trigger p53 activation. Both the impaired ribosome biogenesis checkpoint (IRBC) and the DNA ...
Mutational signature dynamics shaping the evolution of oesophageal adenocarcinoma
A variety of mutational processes drive cancer development, but their dynamics across the entire disease spectrum from pre-cancerous to advanced neoplasia are poorly understood. We explore the mutagenic processes shaping ...
Detecting similar binding pockets to enable systems polypharmacology
In the era of systems biology, multi-target pharmacological strategies hold promise for tackling disease-related networks. In this regard, drug promiscuity may be leveraged to interfere with multiple receptors: the so-called ...
Tumour stroma-derived lipocalin-2 promotes breast cancer metastasis
Tumour cell-secreted factors skew infiltrating immune cells towards a tumour-supporting phenotype, expressing pro-tumourigenic mediators. However, the influence of lipocalin-2 (Lcn2) on the metastatic cascade in the tumour ...
