Backbone-mediated weakening of pairwise interactions enables percolation in peptide-based mimics of protein condensates DOI Creative Commons
Xiangze Zeng, Rohit V. Pappu

Communications Chemistry, Journal Year: 2025, Volume and Issue: 8(1)

Published: April 6, 2025

Biomolecular condensates formed by intrinsically disordered proteins (IDPs) are semidilute solutions. These can be approximated as solutions of blob-sized segments, which peptide-sized motifs. We leveraged the blob picture and molecular dynamics simulations to quantify differences between inter-residue interactions in model compound peptide-based mimics dense versus dilute phases. The all-atom use a polarizable forcefield. In solutions, aromatic residues stronger than cationic residues. This holds Cooperativity within phases enhances pairwise leading finite-sized nanoscale clusters. results for paint different picture. Backbone amides add valence associating molecules. While this phases, it weakens pair doing so concentration-dependent manner. Weakening enables fluidization characterized short-range order long-range disorder. higher afforded peptide backbone generates system-spanning networks. As result, peptides best described percolated network fluids. Overall, our show how backbones enhance while weakening these enable percolation

Language: Английский

Nuclear speckle proteins form intrinsic and MALAT1-dependent microphases DOI Open Access
Min Kyung Shinn, Dylan T. Tomares,

Vicky Liu

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 27, 2025

Nuclear speckles are enriched in serine / arginine rich splicing factors (SRSFs), such as SRSF1. Splicing and proteins TDP-43 concentrate into distinct speckle territories to enable pre-mRNA processing. We have discovered that SRSFs block copolymers the protein-specific interplay of inter-block repulsions attractions drives spontaneous microphase separation. This gives rise size-limited, ordered assemblies, 30 - 45 nm diameter. Depending on protein, each comprises several tens hundreds molecules. The sub-micron scale observed cells shown be clusters microphases. regulatory lncRNA MALAT1 binds preferentially SRSF1 microphases enhance separation alter structures. Microphase enables concentration finite numbers assemblies with nanoscale structures can modulated by . Our findings provide a structural framework for functional organization factors.

Language: Английский

Citations

0
Backbone-mediated weakening of pairwise interactions enables percolation in peptide-based mimics of protein condensates DOI Creative Commons
Xiangze Zeng, Rohit V. Pappu

Communications Chemistry, Journal Year: 2025, Volume and Issue: 8(1)

Published: April 6, 2025

Biomolecular condensates formed by intrinsically disordered proteins (IDPs) are semidilute solutions. These can be approximated as solutions of blob-sized segments, which peptide-sized motifs. We leveraged the blob picture and molecular dynamics simulations to quantify differences between inter-residue interactions in model compound peptide-based mimics dense versus dilute phases. The all-atom use a polarizable forcefield. In solutions, aromatic residues stronger than cationic residues. This holds Cooperativity within phases enhances pairwise leading finite-sized nanoscale clusters. results for paint different picture. Backbone amides add valence associating molecules. While this phases, it weakens pair doing so concentration-dependent manner. Weakening enables fluidization characterized short-range order long-range disorder. higher afforded peptide backbone generates system-spanning networks. As result, peptides best described percolated network fluids. Overall, our show how backbones enhance while weakening these enable percolation

Language: Английский

Citations

0