Ignacio Sanchez‐Burgos

RNA synthesis and degradation regulate biomolecular condensates through non-equilibrium feedback

Ignacio Sanchez‐Burgos, Andrés R. Tejedor, Alberto Ocana, Jorge R. Espinosa et autres

Transcriptional condensates operate far from equilibrium, where continuous RNA synthesis and degradation dynamically reshape condensate composition. To investigate how RNA synthesis regulates condensate properties at sub-molecular resolution, we introduce REACT-RNA, a chemically specific coarse-grained molecular dynamics framework that explicitly couples RNA polymerisation, …

gb, es (code pays fourni par la source)

Supporting code for Coarse Grained RNA polymerization MD simulations

Ignacio Sanchez‐Burgos

This upload contains all the necessary LAMMPS scripts and input files of the simulations shown in the associated manuscript. The forcefield used is Mpipi-recharged, run using custom compiled LAMMPS (2 Apr 2025).

gb (code pays fourni par la source)

Supporting code for Coarse Grained RNA polymerization MD simulations

Ignacio Sanchez‐Burgos

This upload contains all the necessary LAMMPS scripts and input files of the simulations shown in the associated manuscript. The forcefield used is Mpipi-recharged, run using custom compiled LAMMPS (2 Apr 2025).

gb (code pays fourni par la source)

The physical origin of ageing at biomolecular condensate interfaces

Alejandro Castro, Juan Luengo-Márquez, Andrés R. Tejedor, Marcell Papp et autres

The interface separating a biomolecular condensate from its surroundings is increasingly recognised as a unique physical and chemical environment that actively regulates condensate behaviour. It controls surface tension, molecular organisation and chemical reactivity, and is also where pathological ageing often begins, with …

es, gb, ch (code pays fourni par la source)

Understanding How Synthetic Impurities Affect Glyphosate Solubility and Crystal Growth Using Free Energy Calculations and Molecular Dynamics Simulations

Alejandro Castro, Ignacio Sanchez‐Burgos, Nuria H. Espejo, Adiran Garaizar et autres

Glyphosate, the most widely used herbicide worldwide, crystallizes through complex intermolecular interactions that are strongly influenced by synthesis-derived impurities. Understanding this process at the molecular scale is critical for optimizing production, ensuring product quality, and assessing the environmental impact. Here, we employ …

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Determination of Nucleotide–Nucleotide and Nucleotide–Amino Acid Binding Interactions from All-Atom Potential-of-Mean-Force Calculations

Alejandro Feito, Eduardo Pedraza, Estefania Cuesta, Alejandro Castro et autres

Biomolecular condensates emerge from multivalent interactions between proteins and nucleic acids and are frequently modeled by using coarse-grained molecular dynamics simulations. The parametrization of these models critically depends on atomistic data describing the underlying molecular interactions. In this work, we employ all-atom …

es, gb (code pays fourni par la source)

Determination of Nucleotide–Nucleotide and Nucleotide–Amino Acid Binding Interactions from All-Atom Potential-of-Mean-Force Calculations

Alejandro Feito, Eduardo Pedraza, Estefania Cuesta, Alejandro Castro et autres

Biomolecular condensates emerge from multivalent interactions between proteins and nucleic acids and are frequently modeled using coarse-grained molecular dynamics simulations. The parametrization of these models critically depends on atomistic data describing the underlying molecular interactions. In this work, we employ all-atom molecular …

Molecular insights on the mechanism of α1-antitrypsin condensate formation and maturation

Ignacio Sanchez‐Burgos, Andrés R. Tejedor, Jorge Bernardino de la Serna, Jorge R. Espinosa

The deficiency of [Formula: see text]-antitrypsin protein is a genetic disorder characterized by the accumulation of misfolded protein aggregates within hepatocytes, leading to liver dysfunction. In the lung, it is found in macrophages, bronchial and epithelial alveolar cells type 2, leading to …

gb, es (code pays fourni par la source)

Determination of nucleotide-nucleotide and nucleotide-amino acid binding interactions from all-atom potential-of-mean-force calculations

Alejandro Feito, Eduardo Pedraza, Estefania Cuesta, Alejandro Castro et autres

Biomolecular condensates emerge from multivalent interactions between proteins and nucleic acids and are frequently modeled using coarse-grained molecular dynamics simulations. The parametrization of these models critically depends on atomistic data describing the underlying molecular interactions. In this work, we employ all-atom molecular …

es, gb (code pays fourni par la source)

Compositional Control of Aging Kinetics in TDP-43 Condensates

Nuria H. Espejo, Alejandro Feito, Ignacio Sanchez‐Burgos, Adiran Garaizar et autres

The spontaneous self-assembly of proteins and nucleic acids into biomolecular condensates has been shown to ubiquitously contribute to the functional compartmentalization of the cell. However, their liquid-to-solid transformation (i.e., aging) driven by interprotein β -sheet transitions represents a hallmark of multiple neurodegenerative …

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Charged mutations in the FUS low-complexity domain modulate condensate aging kinetics

Eduardo Pedraza, Daniel Merino Hoyos, Alejandro Feito, Francisco Javier Martínez Gámez et autres

The assembly of biomolecular condensates is tightly regulated by the intracellular environment. Disruptions in the balance between condensate formation and dissolution—such as irreversible aggregation of low-complexity aromatic-rich kinked segments (LARKSs)—have been implicated in multiple neuropathologies. Here, we employ non-equilibrium, residue-resolution coarse-grained simulations …

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Charged peptides enriched in aromatic residues decelerate condensate ageing driven by cross-β-sheet formation

Ignacio Sanchez‐Burgos, Andrés R. Tejedor, Alejandro Castro, Alejandro Feito et autres

Biomolecular condensates play wide-ranging roles in cellular compartmentalization and biological processes. However, their transition from a functional liquid-like phase into a solid-like state-usually termed as condensate ageing-represents a hallmark associated with the onset of multiple neurodegenerative diseases. In this study, we design …

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