Exploring RNA destabilization mechanisms in biomolecular condensates through atomistic simulations DOI Creative Commons
Matteo Boccalini, Yelyzaveta Berezovska, Giovanni Bussi

и другие.

Proceedings of the National Academy of Sciences, Год журнала: 2025, Номер 122(15)

Опубликована: Апрель 9, 2025

Biomolecular condensates are currently recognized to play a key role in organizing cellular space and orchestrating biochemical processes. Despite an increasing interest characterizing their internal organization at the molecular scale, not much is known about how densely crowded environment within these affects structural properties of recruited macromolecules. Here, we adopted explicit-solvent all-atom simulations based on combination enhanced sampling approaches investigate conformational ensemble RNA hairpin reshaped highly concentrated peptide solution that mimics interior biomolecular condensate. Our indicate structure greatly perturbed by this distinctive physico-chemical environment, which weakens secondary promotes extended nonnative conformations. The resulting high-resolution picture reveals unfolding driven effective solvation nucleobases through hydrogen bonding stacking interactions with surrounding peptides. This solvent effect can be modulated amino acid composition model condensate as proven differential behavior observed case arginine-rich lysine-rich

Язык: Английский

Exploring RNA destabilization mechanisms in biomolecular condensates through atomistic simulations DOI Creative Commons
Matteo Boccalini, Yelyzaveta Berezovska, Giovanni Bussi

и другие.

Proceedings of the National Academy of Sciences, Год журнала: 2025, Номер 122(15)

Опубликована: Апрель 9, 2025

Biomolecular condensates are currently recognized to play a key role in organizing cellular space and orchestrating biochemical processes. Despite an increasing interest characterizing their internal organization at the molecular scale, not much is known about how densely crowded environment within these affects structural properties of recruited macromolecules. Here, we adopted explicit-solvent all-atom simulations based on combination enhanced sampling approaches investigate conformational ensemble RNA hairpin reshaped highly concentrated peptide solution that mimics interior biomolecular condensate. Our indicate structure greatly perturbed by this distinctive physico-chemical environment, which weakens secondary promotes extended nonnative conformations. The resulting high-resolution picture reveals unfolding driven effective solvation nucleobases through hydrogen bonding stacking interactions with surrounding peptides. This solvent effect can be modulated amino acid composition model condensate as proven differential behavior observed case arginine-rich lysine-rich

Язык: Английский

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