Leonardo Darré

The pseudotorsional space of RNA

Leandro Grille, Diego Gallego, Leonardo Darré, Gabriela da Rosa et autres

The characterization of the conformational landscape of the RNA backbone is rather complex due to the ability of RNA to assume a large variety of conformations. These backbone conformations can be depicted by pseudotorsional angles linking RNA backbone atoms, from which Ramachandran-like …

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The Pseudo-Torsional Space of RNA

Leandro Grille, Diego Gallego, Leonardo Darré, Gabriela da Rosa et autres

ABSTRACT The characterization of the conformational landscape of the RNA backbone is rather complex due to the ability of RNA to assume a big variety of conformations. These backbone conformations can be depicted by pseudo-torsional angles linking RNA backbone atoms, from which …

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A Potential Route of Capsaicin to Its Binding Site in the TRPV1 Ion Channel

Cármen Domene, Leonardo Darré, Victoria Oakes, Saul González-Resines

Transient receptor potential (TRP) ion channels are important pharmacological targets because of their role in the perception of pain, and so, understanding their chemical regulation is essential for the development of analgesic drugs. Among the currently known TRP channel chemical agonists, capsaicin, …

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The ligand-bound state of a G protein-coupled receptor stabilizes the interaction of functional cholesterol molecules

Laura Lemel, Katarzyna Nieścierowicz, María Dolores García-Fernández, Leonardo Darré et autres

Cholesterol is a major component of mammalian plasma membranes that not only affects the physical properties of the lipid bilayer but also is the function of many membrane proteins including G protein-coupled receptors. The oxytocin receptor (OXTR) is involved in parturition and …

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The Bilayer Collective Properties Govern the Interaction of an HIV-1 Antibody with the Viral Membrane

Pablo Carravilla, Leonardo Darré, Itziar R. Oar-Arteta, Arturo G. Vesga et autres

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VeriNA3d: an R package for nucleic acids data mining

Diego Gallego, Leonardo Darré, Pablo Daniel Dans, Modesto Orozco

SUMMARY: veriNA3d is an R package for the analysis of nucleic acids structural data, with an emphasis in complex RNA structures. In addition to single-structure analyses, veriNA3d also implements functions to handle whole datasets of mmCIF/PDB structures that could be retrieved from …

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From quantum to subcellular scales: multi-scale simulation approaches and the SIRAH force field

Matías Rodrigo Machado, Ari Zeida, Leonardo Darré, Sergio Pantano

Modern molecular and cellular biology profits from astonishing resolution structural methods, currently even reaching the whole cell level. This is encompassed by the development of computational methods providing a deep view into the structure and dynamics of molecular processes happening at very …

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Anti-HIV antibody-lipid interactions enhance affinity for the native Env glycoprotein as revealed by single virion STED microscopy

Pablo Carravilla, Jakub Chojnacki, Edurne Rujas, Sara Insausti et autres

Modeling, Simulations, and Bioinformatics at the Service of RNA Structure

Pablo Daniel Dans, Diego Gallego, Alexandra Balaceanu, Leonardo Darré et autres

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Dimerization confers increased stability to nucleases in 5′ halves from glycine and glutamic acid tRNAs

Juan Pablo Tosar, Fabiana Gámbaro, Leonardo Darré, Sergio Pantano et autres

We have previously shown that 5' halves from tRNAGlyGCC and tRNAGluCUC are the most enriched small RNAs in the extracellular space of human cell lines, and especially in the non-vesicular fraction. Extracellular RNAs are believed to require protection by either encapsulation in …

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Molecular Modelling of Nucleic Acids

Hansel Gómez, Jürgen Walther, Leonardo Darré, Iván Ivani et autres

Nucleic acids (NAs) are biomolecules essential to all known forms of life that exhibit a remarkable structural and functional diversity. NAs are studied through several different techniques, including experimental and theoretical methods. The notorious improvements of the latter, together with the increased …

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Functional mapping of the N-terminal arginine cluster and C-terminal acidic residues of Kir6.2 channel fused to a G protein-coupled receptor

Maria Antonietta Principalli, Laura Lemel, Anaëlle Rongier, Anne-Claire Godet et autres

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