A5006399866- DNA and Nucleic Acid Chemistry
- Protein Structure and Dynamics
- RNA and protein synthesis mechanisms
- Spectroscopy and Quantum Chemical Studies
- Advanced biosensing and bioanalysis techniques
- Enzyme Structure and Function
- Computational Drug Discovery Methods
- Advanced Chemical Physics Studies
- Genomics and Chromatin Dynamics
- Bacteriophages and microbial interactions
- Mass Spectrometry Techniques and Applications
- Crystallography and molecular interactions
- Photochemistry and Electron Transfer Studies
- Free Radicals and Antioxidants
- RNA modifications and cancer
- RNA Research and Splicing
- Epigenetics and DNA Methylation
- Chemical Reaction Mechanisms
- RNA Interference and Gene Delivery
- Analytical Chemistry and Chromatography
- Bacterial Genetics and Biotechnology
- Genomics and Phylogenetic Studies
- Bioinformatics and Genomic Networks
- Molecular spectroscopy and chirality
- Biochemical and Molecular Research
Institute for Research in Biomedicine
2016-2025
Universitat de Barcelona
2016-2025
Institute of Science and Technology
2015-2025
Universitat Politècnica de Catalunya
2012-2024
Barcelona Supercomputing Center
2010-2024
Hospital Universitario Río Hortega
2023
Rutgers, The State University of New Jersey
2009-2023
Institute for Research in Biomedicine
2018-2022
Centro de Investigación Biomédica en Red
2022
Centre for Biomedical Network Research on Rare Diseases
2022
Chronic lymphocytic leukaemia (CLL), the most frequent in adults Western countries, is a heterogeneous disease with variable clinical presentation and evolution. Two major molecular subtypes can be distinguished, characterized respectively by high or low number of somatic hypermutations region immunoglobulin genes. The changes leading to pathogenesis are still poorly understood. Here we performed whole-genome sequencing four cases CLL identified 46 mutations that potentially affect gene...
Summary: PMUT allows the fast and accurate prediction (~80% success rate in humans) of pathological character single point amino acidic mutations based on use neural networks. The program also scanning mutational hot spots, which are obtained by three procedures: (1) alanine scanning, (2) massive mutation (3) genetically accessible mutations. A graphical interface for Protein Data Bank (PDB) structures, when available, a database containing spot profiles all non-redundant PDB structures from server.
The RNA hairpin loops represent important topologies with indispensable biological functions in folding and tertiary interactions. 5′-UNCG-3′ 5′-GNRA-3′ tetraloops are the most classes of loops. Both highly structured characteristic signature three-dimensional features recurrently seen functional RNAs ribonucleoprotein particles. Explicit solvent molecular dynamics (MD) simulation is a computational technique which can efficiently complement experimental data provide unique structural...
ADVERTISEMENT RETURN TO ISSUEPerspectiveNEXTTarget Flexibility: An Emerging Consideration in Drug Discovery and Design†Pietro Cozzini*‡§, Glen E. Kellogg*#, Francesca Spyrakis‡§, Donald J. Abraham‡, Gabriele Costantino∥, Andrew Emerson⊥, Fanelli∞, Holger Gohlke×, Leslie A. Kuhn¶, Garrett M. Morris●, Modesto Orozco◇, Thelma Pertinhez◆, Menico Rizzi∇, Christoph Sotriffer⊗View Author Information Department of General Inorganic Chemistry, University Parma, Via G.P. Usberti 17/A 43100, Italy,...
It is well recognized that base sequence exerts a significant influence on the properties of DNA and plays role in protein–DNA interactions vital for cellular processes. Understanding predicting effects requires an extensive structural dynamic dataset which currently unavailable from experiment. A consortium laboratories was consequently formed to obtain this information using molecular simulations. This article describes results providing not only all 10 unique pair steps, but also possible...
The classic organization of a gene structure has followed the Jacob and Monod bacterial model proposed more than 50 years ago. Since then, empirical determinations complexity transcriptomes found in yeast to human blurred definition physical boundaries genes. Using multiple analysis approaches we have characterized individual mapping on chromosomes 21 22. Analyses locations 5′ 3′ transcriptional termini 492 protein coding genes revealed that for 85% these extend beyond current annotated...
We present here a full update of the PMut predictor, active since 2005 and with large acceptance in field predicting Mendelian pathological mutations. internal engine has been renewed, converted into fully featured standalone training prediction that not only powers web portal, but can generate custom predictors alternative sets or validation schemas. Web portal allows user to perform pathology predictions, access complete repository pre-calculated validate new predictors. The default...
One of the hallmarks cancer is disruption gene expression patterns. Many molecular lesions contribute to this phenotype, and importance aberrant DNA methylation profiles increasingly recognized. Much research effort in area has examined proximal promoter regions epigenetic alterations at other loci are not well characterized. Using whole genome bisulfite sequencing examine uncharted epigenome, we identify a type far-reaching alteration cells distal regulatory sequences described as...
We present the results of microsecond molecular dynamics simulations carried out by ABC group laboratories on a set B-DNA oligomers containing 136 distinct tetranucleotide base sequences. demonstrate that resulting trajectories have extensively sampled conformational space accessible to at room temperature. confirm sequence effects depend strongly not only specific pair step, but also pairs flank each step. Beyond average helical parameters and fluctuations, we identify sequences oscillate...
To understand the role of extensive senescence-associated 3D genome reorganization, we generated genome-wide chromatin interaction maps, epigenome, replication-timing, whole-genome bisulfite sequencing, and gene expression profiles from cells entering replicative senescence (RS) or upon oncogene-induced (OIS). We identify heterochromatin domains (SAHDs). Differential intra- versus inter-SAHD interactions lead to formation foci (SAHFs) in OIS but not RS. This OIS-specific configuration brings...
In eukaryotic cells, different organelles interact at membrane contact sites stabilized by tethers. Mitochondrial mitofusin 2 (MFN2) acts as a tether that interacts with an unknown partner on the endoplasmic reticulum (ER). this work, we identified MFN2 splice variant ERMIT2 ER tethering of MFN2. Splicing produced and ERMIN2, two ER-specific variants. ERMIN2 regulated morphology, whereas localized ER-mitochondria interface interacted mitochondrial mitofusins to mitochondria. This allowed...
Tautomerism and protonation of guanine cytosine in the gas phase aqueous solution have been examined by theoretical methods. High level ab initio calculations with inclusion correlation effects at Møller−Plesset used to study these processes phase. The influence solvent has using self-consistent reaction field Monte Carlo free energy perturbation simulations. results provide a complete accurate picture tautomerism nucleic acid bases. Comparison available experimental data gives confidence...
We have developed a web tool, PupasView, for the selection of single nucleotide polymorphisms (SNPs) with potential phenotypic effect. PupasView constitutes an interactive environment in which functional information and population frequency data can be used as sequential filters over linkage disequilibrium parameters to obtain final list SNPs optimal genotyping purposes. is first resource that integrates effects caused by at both translational transcriptional level. retrieves could affect...
The importance of cation->aromatic polarization effects on cation-π interactions has been explored. Theoretical calculations demonstrate that is a large contribution to cation-aromatic interactions, and particularly interactions. For series compounds with similar aromatic core, constant makes small influence in the relative cation-binding energies. However, when core changes contributions might be very different. We found generalized molecular interaction potential fast powerful tool for...
We present the first microsecond MD simulation of B-DNA. Trajectory shows good agreement with available data and clarifies μs dynamics DNA. The duplex is sampling B-conformation, but many relevant local transitions are found, including S → N repuckers (up to 7 N-sugars found simultaneously), BII (15% dinucleotides in BII-form; some these forms stable for up ns), sequence-dependent α/γ (happening 7−50 ns time scale, being 80 ns). Partial total openings often detected, no base flipping found....