A5071122911- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- Ubiquitin and proteasome pathways
- Protein Degradation and Inhibitors
- Advanced Proteomics Techniques and Applications
- Protein Structure and Dynamics
- Retinal Development and Disorders
- Galectins and Cancer Biology
- Mass Spectrometry Techniques and Applications
- Animal Virus Infections Studies
- Cancer Research and Treatments
- Genetic and Kidney Cyst Diseases
- Glycosylation and Glycoproteins Research
- SARS-CoV-2 and COVID-19 Research
- DNA and Nucleic Acid Chemistry
- Microbial Metabolic Engineering and Bioproduction
- RNA Research and Splicing
- Marine Invertebrate Physiology and Ecology
- Monoclonal and Polyclonal Antibodies Research
- Photoreceptor and optogenetics research
- Biofuel production and bioconversion
- Planarian Biology and Electrostimulation
- Zebrafish Biomedical Research Applications
- Machine Learning in Materials Science
- Developmental Biology and Gene Regulation
Barcelona Institute for Science and Technology
2019-2025
Centre for Genomic Regulation
2019-2025
Universitat Pompeu Fabra
2023
A new version of FoldX, whose main features allows running classic FoldX commands on structures containing RNA molecules and includes a module that parametrization ligands or small (ParamX) were not previously recognized in old versions, has been released. An extended graphical user interface also being developed (available as python plugin for the YASARA molecular viewer) allowing user-friendly custom encoded using JSON format.http://foldxsuite.crg.eu/.
The assembly of the neuronal and other major cell type programs occurred early in animal evolution. We can reconstruct this process by studying non-bilaterians like placozoans. These small disc-shaped animals not only have nine morphologically described types no neurons but also show coordinated behaviors triggered peptide-secreting cells. investigated possible affinities these peptidergic cells using phylogenetics, chromatin profiling, comparative single-cell genomics four found conserved...
The FoldX force field was originally validated with a database of 1000 mutants at time when there were few high-resolution structures. Here we have manually curated 5556 affecting protein stability, resulting in 2484 highly confident mutations denominated Stability Dataset (FSD), represented non-redundant X-ray structures less than 2.5 Å resolution, not involving duplicates, metals or prosthetic groups. Using this database, created new version the by introducing Pi stacking, pH dependency...
Retinal photoreceptors have a distinct transcriptomic profile compared to other neuronal subtypes, likely reflecting their unique cellular morphology and function in the detection of light stimuli by way ciliary outer segment. We discovered layer this molecular specialization revealing that vertebrate retina expresses largest number tissue-enriched microexons all tissue types. A subset these is included exclusively photoreceptor transcripts, particularly genes involved cilia biogenesis...
The coronavirus disease COVID-19 constitutes the most severe pandemic of last decades having caused more than 1 million deaths worldwide. SARS-CoV-2 virus recognizes angiotensin converting enzyme 2 (ACE2) on surface human cells through its spike protein. It has been reported that can mildly infect cats, and ferrets, perhaps dogs while not pigs, mice, chicken ducks. Differences in viral infectivity among different species or individuals could be due to amino acid differences at key positions...
Abstract Developing antibodies is complex and resource-intensive, methods for designing targeting specific epitopes are lacking. We introduce a de novo antibody design approach leveraging the empirical force field FoldX to complementarity determining regions (CDRs). Starting from scaffold VHH, we tackled three challenges of increasing difficulty: 1) CDRs optimize VHH stability affinity its original target; 2) high human ortholog; 3) low nanomolar pre-defined epitope on unrelated...
Since AlphaFold2's rise, many deep learning methods for protein design have emerged. Here, we validate widely used and recognized tools, compare them with first-principle methods, explore their combinations, focusing on effectiveness in redesign potential therapeutic repurposing. We address two challenges: evaluating tools combinations ability to detect the effects of multiple concurrent mutations variants, leveraging large-scale datasets modeling-free namely force fields, which handle point...
Abstract Triple‐negative breast cancer (TNBC) often develops resistance to single‐agent treatment, which can be circumvented using targeted combinatorial approaches. Here, we demonstrate that the simultaneous inhibition of LOXL2 and BRD4 synergistically limits TNBC proliferation in vitro vivo . Mechanistically, interacts nucleus with short isoform (BRD4S), MED1, cell cycle transcriptional regulator B‐MyB. These interactions sustain formation MED1 nuclear foci control progression at gene...
Significance Protein–RNA interactions, key in biological processes, remained refractory to prediction algorithms. Here we present a new extension of the ModelX tool suite designed for this purpose. RNA–protein complexes Protein Data Bank were decomposed into small peptide–oligonucleotide interacting fragment pairs and used as building blocks assemble big scaffolds representing complex interactions. This method has already been successful designing DNA–protein protein–protein interfaces....
Accurate 3D modelling of protein-protein interactions (PPI) is essential to compensate for the absence experimentally determined complex structures. Here, we present a new set commands within ModelX toolsuite capable generating atomic-level protein complexes suitable interface design. Among these commands, tool ProteinFishing proposes known and/or putative alternative PPI given complex. The algorithm exploits backbone compatibility fragments generate mutually exclusive interfaces that are...
Abstract Proteins are often referred to as the workhorses of cells, and their interactions necessary facilitate specific cellular functions. Despite recognition that protein-protein interactions, thus protein functions, determined by proteoform states, such mutations post-translational modifications (PTMs), methods for determining differential abundance proteoforms across conditions very limited. Classically, immunoprecipitation coupled with mass spectrometry (IP-MS) has been used understand...
While it is recognised that protein functions are determined by their proteoform state, such as mutations and post-translational modifications, methods to determine differential abundance between conditions limited. Here, we present a novel workflow for classical immunoprecipitation coupled mass spectrometry (IP-MS) data focuses on identifying peptidoforms of the bait conditions, providing additional information about function.
ABSTRACT Retinal photoreceptors differ in their transcriptomic profiles from other neuronal subtypes, likely as a reflection of unique cellular morphology and function the detection light thorough ciliary outer segment. We discovered new layer this molecular specialization by revealing that vertebrate retina expresses largest number tissue-enriched microexons all tissue types. A subset these is included exclusively photoreceptor transcripts, particularly genes involved cilia biogenesis...
Abstract Triple-negative breast cancer often develops resistance to single-agent treatments, which can be circumvented with targeted combinatorial approaches. Here, we demonstrate that the simultaneous inhibition of LOXL2 and BRD4 cooperate reduce triple-negative proliferation in vitro vivo . Mechanistically, reveal interacts nucleus short isoform MED1 control cell cycle progression at gene expression level via sustaining formation BRD4-MED1 nuclear transcriptional foci. Indeed,...