Energy landscapes for clusters of hexapeptides

The Journal of Chemical Physics, Год журнала: 2024, Номер 161(5)

Опубликована: Авг. 2, 2024

We present the results for energy landscapes of hexapeptides obtained using interfaces to Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) program. have used basin-hopping global optimization and discrete path sampling explore hexapeptide monomers, dimers, oligomers containing 10, 100, 200 monomers modeled a residue-level coarse-grained potential, Mpipi, implemented in LAMMPS. find that dimers peptides amino acid residues are better at promoting phase separation, such as tyrosine arginine, melting peaks higher temperature their heat capacity compared phenylalanine lysine, respectively. This observation correlates with previous work on same uncapped atomistic potential. For oligomers, we compare variation monomer conformations radial distance observe trends selected angles calculated each monomer. The LAMMPS GMIN OPTIM programs landscape exploration offer new opportunities investigate larger systems provide access potentials within

Язык: Английский

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Nucleoprotein phase-separation affinities revealed via atomistic simulations of short peptide and RNA fragments

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Сен. 26, 2024

Liquid-liquid phase separation of proteins and nucleic acids into condensate phases is a versatile mechanism for ensuring compartmentalization cellular biochemistry. RNA molecules play critical roles in these condensates, particularly transcriptional regulation stress responses, exhibiting wide range thermodynamic dynamic behaviors. However, deciphering the molecular grammar that governs stability dynamics protein-RNA condensates remains challenging due to multicomponent heterogeneous nature biomolecular mixtures. In this study, we employ atomistic simulations twenty distinct mixtures containing minimal peptide fragments dissect phase-separating affinities all amino presence RNA. Our findings elucidate chemically specific interactions, hydration profiles, ionic effects synergistically promote or suppress separation. We map ternary diagram identifying four groups residues promote, maintain, suppress, disrupt clusters.

Язык: Английский

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Nucleoprotein Phase-Separation Affinities Revealed via Atomistic Simulations of Short Peptide and RNA Fragments

The Journal of Physical Chemistry Letters, Год журнала: 2024, Номер 15(43), С. 10811 - 10817

Опубликована: Окт. 21, 2024

Liquid–liquid phase separation of proteins and nucleic acids into condensate phases is a versatile mechanism for ensuring the compartmentalization cellular biochemistry. RNA molecules play critical roles in these condensates, particularly transcriptional regulation stress responses, exhibiting wide range thermodynamic dynamic behaviors. However, deciphering molecular grammar that governs stability dynamics protein–RNA condensates remains challenging due to multicomponent heterogeneous nature condensates. In this study, we employ atomistic simulations 20 distinct mixtures containing minimal peptide fragments which allows us dissect phase-separating affinities all amino presence RNA. Our findings elucidate chemically specific interactions, hydration profiles, ionic effects synergistically promote or suppress separation. We map ternary diagram identifying four groups residues promote, maintain, suppress, disrupt clusters.

Язык: Английский

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