Coarse-Grained Model of Disordered RNA for Simulations of Biomolecular Condensates DOI
Ikki Yasuda, Sören von Bülow, Giulio Tesei

et al.

Journal of Chemical Theory and Computation, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 26, 2025

Protein–RNA condensates are involved in a range of cellular activities. Coarse-grained molecular models intrinsically disordered proteins have been developed to shed light on and predict single-chain properties phase separation. An RNA model compatible with such for would enable the study complex biomolecular mixtures involving RNA. Here, we present sequence-independent coarse-grained, two-beads-per-nucleotide disordered, flexible based hydropathy scale. We parametrize model, which term CALVADOS-RNA, using combination bottom-up top-down approaches reproduce local geometry intramolecular interactions atomistic simulations vitro experiments. The semiquantitatively captures several aspects RNA–RNA RNA–protein interactions. examined by comparing calculated experimental virial coefficients nonspecific interaction studying reentrant behavior protein–RNA mixtures. demonstrate utility simulating formation mixed consisting region MED1 chains selective partitioning regions from transcription factors into these compare results Despite simplicity our show that it key may therefore be used as baseline biophysics biology condensates.

Language: Английский

Coarse-Grained Model of Disordered RNA for Simulations of Biomolecular Condensates DOI
Ikki Yasuda, Sören von Bülow, Giulio Tesei

et al.

Journal of Chemical Theory and Computation, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 26, 2025

Protein–RNA condensates are involved in a range of cellular activities. Coarse-grained molecular models intrinsically disordered proteins have been developed to shed light on and predict single-chain properties phase separation. An RNA model compatible with such for would enable the study complex biomolecular mixtures involving RNA. Here, we present sequence-independent coarse-grained, two-beads-per-nucleotide disordered, flexible based hydropathy scale. We parametrize model, which term CALVADOS-RNA, using combination bottom-up top-down approaches reproduce local geometry intramolecular interactions atomistic simulations vitro experiments. The semiquantitatively captures several aspects RNA–RNA RNA–protein interactions. examined by comparing calculated experimental virial coefficients nonspecific interaction studying reentrant behavior protein–RNA mixtures. demonstrate utility simulating formation mixed consisting region MED1 chains selective partitioning regions from transcription factors into these compare results Despite simplicity our show that it key may therefore be used as baseline biophysics biology condensates.

Language: Английский

Citations

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