Browsing by Author "Orozco, Modesto"

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  • A DNA methylation map of human cancer at single base-pair resolution
    Vidal Ocabo, Enrique; Sayols, Sergi; Moran, Sebastian; Guillaumet-Adkins, Amy; Schroeder, Michael Philipp, 1986-; Royo, Romina; Orozco, Modesto; Gut, Marta; Gut, Ivo Glynne; López Bigas, Núria; Heyn, Holger; Esteller, Manel (Nature Publishing Group, 2017)
    Although single base-pair resolution DNA methylation landscapes for embryonic and different somatic cell types provided important insights into epigenetic dynamics and cell-type specificity, such comprehensive profiling ...
  • A glutamine-based single α-helix scaffold to target globular proteins
    Escobedo, Albert; Piccirillo, Jonathan; Aranda, Juan; Diercks, Tammo; Mateos, Borja; Garcia-Cabau, Carla; Sánchez-Navarro, Macarena; Topal, Busra; Biesaga, Mateusz; Staby, Lasse; Kragelund, Birthe B.; García, Jesús; Millet, Oscar; Orozco, Modesto; Coles, Murray; Crehuet, Ramon; Salvatella, Xavier (Nature Research, 2022)
    The binding of intrinsically disordered proteins to globular ones can require the folding of motifs into α-helices. These interactions offer opportunities for therapeutic intervention but their modulation with small molecules ...
  • Changes in the free-energy landscape of p38α MAP kinase through its canonical activation and binding events as studied by enhanced molecular dynamics simulations
    Kuzmanic, Antonija; Sutto, Ludovico; Saladino, Giorgio; Nebreda, Ángel R.; Gervasio, Francesco L.; Orozco, Modesto (eLife, 2017)
    p38α is a Ser/Thr protein kinase involved in a variety of cellular processes and pathological conditions, which makes it a promising pharmacological target. Although the activity of the enzyme is highly regulated, its ...
  • Compaction of duplex nucleic acids upon native electrospray mass spectrometry
    Porrini, Massimiliano; Rosu, Frédéric; Rabin, Clémence; Darré, Leonardo; Gómez, Hansel; Orozco, Modesto; Gabelica, Valérie (American Chemical Society (ACS), 2017)
    We report on the fate of nucleic acids conformation in the gas phase as sampled using native mass spectrometry coupled to ion mobility spectrometry. On the basis of several successful reports for proteins and their complexes, ...
  • Exploring the complete mutational space of the LDL receptor LA5 domain using molecular dynamics: linking SNPs with disease phenotypes in familial hypercholesterolemia
    Espinosa Angarica, Vladimir; Orozco, Modesto; Sancho, Javier (Oxford University Press, 2016)
    Familial hypercholesterolemia (FH), a genetic disorder with a prevalence of 0.2%, represents a high-risk factor to develop cardiovascular and cerebrovascular diseases. The majority and most severe FH cases are associated ...
  • Impact of DNA methylation on 3D genome structure
    Buitrago, Diana; Labrador, Mireia; Arcon, Juan Pablo; Lema, Rafael; Flores, Oscar; Esteve-Codina, Anna; Blanc, Julie; Villegas, Núria; Bellido, David; Gut, Marta; Dans, Pablo D.; Heath, Simon; Gut, Ivo Glynne; Brun-Heath, Isabelle; Orozco, Modesto (Nature Research, 2021)
    Determining the effect of DNA methylation on chromatin structure and function in higher organisms is challenging due to the extreme complexity of epigenetic regulation. We studied a simpler model system, budding yeast, ...
  • Nucleosome architecture throughout the cell cycle
    Deniz, Özgen; Flores, Oscar; Aldea, Martí; Soler López, Montserrat; Orozco, Modesto (Nature Publishing Group, 2016)
    Nucleosomes provide additional regulatory mechanisms to transcription and DNA replication by mediating the access of proteins to DNA. During the cell cycle chromatin undergoes several conformational changes, however the ...
  • Nucleosome Dynamics: a new tool for the dynamic analysis of nucleosome positioning
    Buitrago, Diana; Codó, Laia; Illa, Ricard; Jorge, Pau de; Battistini, Federica; Flores, Oscar; Bayarri, Genis; Royo, Romina; Pino, Marc del; Heath, Simon; Hospital, Adam; Gelpí, Josep Lluís; Brun-Heath, Isabelle; Orozco, Modesto (Oxford University Press, 2019)
    We present Nucleosome Dynamics, a suite of programs integrated into a virtual research environment and created to define nucleosome architecture and dynamics from noisy experimental data. The package allows both the ...
  • PMut: A web-based tool for the annotation of pathological variants on proteins, 2017 update
    López Ferrando, Víctor; Gazzo, Andrea M.; Cruz, Xavier de la; Orozco, Modesto; Gelpí, Josep Lluís (Oxford University Press, 2017)
    We present here a full update of the PMut predictor, active since 2005 and with a large acceptance in the field of predicting Mendelian pathological mutations. PMut internal engine has been renewed, and converted into a ...
  • Saturation of recognition elements blocks evolution of new tRNA identities
    Saint-Léger, Adélaïde; Bello, Carla, 1990-; Dans, Pablo D.; Gabriel Torres, Adrian; Novoa, Eva Maria; Camacho, Noelia; Orozco, Modesto; Kondrashov, Fyodor A., 1979-; Ribas de Pouplana, Lluís (American Association for the Advancement of Science (AAAS), 2016)
    Understanding the principles that led to the current complexity of the genetic code is a central question in evolution. Expansion of the genetic code required the selection of new transfer RNAs (tRNAs) with specific ...
  • Unravelling the hidden DNA structural/physical code provides novel insights on promoter location
    Durán, Elisa; Djebali, Sarah; González, Santi; Flores, Oscar; Mercader Bigas, Josep Maria; Guigó Serra, Roderic; Torrents, David; Soler López, Montserrat; Orozco, Modesto (Oxford University Press, 2013)
    Although protein recognition of DNA motifs in promoter regions has been traditionally considered as a critical regulatory element in transcription, the location of promoters, and in particular transcription start sites ...