AIMC Topic: Biomolecular Condensates

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Proteome-wide computational analyses reveal links between protein condensate formation and RNA biology.

Science advances
Biomolecular condensates mediate dynamic compartmentalization of cellular processes. The multivalent interactions that underlie biomolecular condensation are often promoted by intrinsically disordered regions (IDRs) within proteins. Although the role...

Predicting Saturation Concentrations of Phase-Separating Proteins via Thermodynamic Integration.

Journal of chemical theory and computation
Phase separation of proteins and nucleic acids into biomolecular condensates contributes to the regulation of cellular compartmentalization in membrane-less environments. A key parameter controlling the onset of biomolecular condensate formation is t...

Comprehensive protein datasets and benchmarking for liquid-liquid phase separation studies.

Genome biology
BACKGROUND: Proteins self-organize in dynamic cellular environments by assembling into reversible biomolecular condensates through liquid-liquid phase separation (LLPS). These condensates can comprise single or multiple proteins, with different roles...

PICNIC accurately predicts condensate-forming proteins regardless of their structural disorder across organisms.

Nature communications
Biomolecular condensates are membraneless organelles that can concentrate hundreds of different proteins in cells to operate essential biological functions. However, accurate identification of their components remains challenging and biased towards p...

Protein Condensate Atlas from predictive models of heteromolecular condensate composition.

Nature communications
Biomolecular condensates help cells organise their content in space and time. Cells harbour a variety of condensate types with diverse composition and many are likely yet to be discovered. Here, we develop a methodology to predict the composition of ...

Molecular Graph-Based Deep Learning Algorithm Facilitates an Imaging-Based Strategy for Rapid Discovery of Small Molecules Modulating Biomolecular Condensates.

Journal of medicinal chemistry
Biomolecular condensates are proposed to cause diseases, such as cancer and neurodegeneration, by concentrating proteins at abnormal subcellular loci. Imaging-based compound screens have been used to identify small molecules that reverse or promote b...

Distinct chemical environments in biomolecular condensates.

Nature chemical biology
Diverse mechanisms have been described for selective enrichment of biomolecules in membrane-bound organelles, but less is known about mechanisms by which molecules are selectively incorporated into biomolecular assemblies such as condensates that lac...

Screening membraneless organelle participants with machine-learning models that integrate multimodal features.

Proceedings of the National Academy of Sciences of the United States of America
Protein self-assembly is one of the formation mechanisms of biomolecular condensates. However, most phase-separating systems (PS) demand multiple partners in biological conditions. In this study, we divided PS proteins into two groups according to th...

Unambiguous assignment of kinked-β sheets leads to insights into molecular grammar of reversibility in biomolecular condensates.

Protein science : a publication of the Protein Society
Kinked- sheets are short peptide motifs that appear as distortions in strands and often mediate formation of reversible amyloid fibrils in prion-like proteins. Standard methods for assigning secondary structures cannot distinguish these esoteric mo...

Quantitative spatial analysis of chromatin biomolecular condensates using cryoelectron tomography.

Proceedings of the National Academy of Sciences of the United States of America
Phase separation is an important mechanism to generate certain biomolecular condensates and organize the cell interior. Condensate formation and function remain incompletely understood due to difficulties in visualizing the condensate interior at hig...