Assembly of model postsynaptic densities involves interactions auxiliary to stoichiometric binding

Lin, Yi‐Hsuan; Wu, Haowei; Jia, Bowen; Zhang, Mingjie; Chan, Hue Sun

doi:10.1016/j.bpj.2021.10.008

Cited by 27 publications

(25 citation statements)

References 97 publications

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“…We found that the tie lines diverge from dilute phases to condensed phases. This is consistent with the observation in a recent work of Chan’s group (42). In their work, they clarified that the two-component system containing stochiometric complex and promiscuous interaction exhibits the divergent pattern of tie lines.…”

Section: Resultssupporting

confidence: 94%

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The stoichiometric interaction model for mesoscopic molecular dynamics simulations of liquid-liquid phase separation

Murata

Niina

Takada

2022

Preprint

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Liquid-liquid phase separation (LLPS) has received considerable attention in recent years for explaining the formation of cellular biomolecular condensates. The fluidity and the complexity of their components make molecular simulation approaches indispensable for gaining structural insights. Domain-resolution mesoscopic model simulations have been explored for case in which condensates are formed by multivalent proteins with tandem domains. One problem with this approach is that interdomain pairwise interactions cannot regulate the valency of the binding domains. To overcome this problem, we propose a new potential, the stoichiometric interaction (SI) potential. First, we verified that the SI potential maintained the valency of the interacting domains for the test systems. We then examined a well-studied LLPS model system containing tandem repeats of SH3 domains and proline-rich motifs. We found that the SI potential alone cannot reproduce the phase diagram of LLPS quantitatively. We had to combine the SI and a pairwise interaction; the former and the latter represent the specific and non-specific interactions, respectively. Biomolecular condensates with the mixed SI and pairwise interaction exhibited fluidity, whereas those with the pairwise interaction alone showed no detectable diffusion. We also compared the phase diagrams of the systems containing different numbers of tandem domains with those obtained from the experiments, and found quantitative agreement in all but one case.SIGNIFICANCECells organize their interior structures as not only membrane-bound organelles but also as membrane-less organelles. Membrane-less organelles, such as stress granules, Cajal bodies, and postsynaptic density, are biomolecular condensates in which many biomolecules are gathered owing to their interactions. In some cases, biomolecular condensates are formed by tandemly connected multidomain proteins. In such cases, a mesoscopic simulation model representing each domain as a particle is effective; however, the problem with this approach is that a domain-domain pairwise interaction cannot regulate the well-defined valency. To overcome this problem, in this study, we have developed a new potential, viz. the stoichiometric interaction potential, and confirmed that this potential can reproduce the liquid-liquid phase separation of multidomain proteins, a hallmark of the membrane-less organelles.

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Section: Resultssupporting

confidence: 94%

“…We also found that the system with only the stoichiometric attractive interaction leads to the divergent tie line pattern (Fig. S2), which is distinct from the previous study (42).…”

Section: The Phase Diagram Of Phase Separationcontrasting

confidence: 87%

The stoichiometric interaction model for mesoscopic molecular dynamics simulations of liquid-liquid phase separation

Murata

Niina

Takada

2022

Preprint

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“…1 and Fig. 2 for illustration can be useful for modeling LLPS of folded proteins as well [57,58]. A step-by-step practical guide to the calculations in these simple FH models are discussed in Sect.…”

Section: Systems With Three or More Componentsmentioning

confidence: 99%

Numerical Techniques for Applications of Analytical Theories to Sequence-Dependent Phase Separations of Intrinsically Disordered Proteins

Lin¹,

Wessén²,

Pal³

et al. 2022

Preprint

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Biomolecular condensates, physically underpinned to a significant extent by liquid-liquid phase separation (LLPS), are now widely recognized by numerous experimental studies to be of fundamental biological, biomedical, and biophysical importance. In the face of experimental discoveries, analytical formulations emerged as a powerful yet tractable tool in recent theoretical investigations of the role of LLPS in the assembly and dissociation of these condensates. The pertinent LLPS often involves, though not exclusively, intrinsically disordered proteins engaging in multivalent interactions that are governed by their amino acid sequences. For researchers interested in applying these theoretical methods, here we provide a practical guide to a set of computational techniques devised for extracting sequence-dependent LLPS properties from analytical formulations. The numerical procedures covered include those for the determinination of spinodal and binodal phase boundaries from a general free energy function with examples based on the random phase approximation in polymer theory, construction of tie lines for multiple-component LLPS, and field-theoretic simulation of multiple-chain heteropolymeric systems using complex Langevin dynamics. Since a more accurate physical picture often requires comparing analytical theory against explicit-chain model predictions, a commonly utilized methodology for coarse-grained molecular dynamics simulations of sequence-specific LLPS is also briefly outlined.

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“…Both stochastic and specific interactions between IDPs contribute to PS and MLO assembly 37,40,41 . We hypothesised that cell cycle kinase-mediated phosphorylation might modulate such interactions.…”

Section: Cdks Regulate Idr Phase Separationmentioning

confidence: 99%

A CDK-mediated phosphorylation switch of disordered protein condensation

Altelaar

Valverde

Dubra

et al. 2022

Preprint

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Cell cycle transitions arise from collective changes in protein phosphorylation states triggered by cyclin-dependent kinases (CDKs), but conceptual and mechanistic explanations for the abrupt cellular reorganisation that occurs upon mitotic entry are lacking. Specific interactions between distinct CDK-cyclin complexes and sequence motifs encoded in substrates might result in highly ordered phosphorylation1, while bistability in the mitotic CDK1 control network can trigger switch-like phosphorylation2. Yet the dynamics of mitotic phosphorylation has not been demonstrated in vivo, and the roles of most cell cycle-regulated phosphorylations are unclear. Here, we show evidence that switch-like phosphorylation of intrinsically disordered proteins (IDPs) by CDKs contributes to mitotic cellular reorganisation by controlling protein-protein interactions and phase separation. We studied protein phosphorylation in single Xenopus embryos throughout synchronous cell cycles, performed parallel assignment of cell cycle phases using egg extracts, and analysed dynamics of mitotic phosphorylation using quantitative targeted phosphoproteomics. This provided a high-resolution map of dynamic phosphosites from the egg to the 16-cell embryo and showed that mitotic phosphorylation occurs on entire protein complexes involved in diverse subcellular processes and is switch-like in vivo. Most cell cycle-regulated phosphosites occurred in CDK consensus motifs and located to intrinsically disordered regions. We found that substrates of CDKs and other cell cycle kinases are significantly more disordered than phosphoproteins in general, a principle conserved from yeast to humans, while around half are components of membraneless organelles (MLOs), whose assembly is thought to involve phase separation. Analytical modelling predicts modulation of homotypic IDP interactions by CDK-mediated phosphorylation, which was confirmed by biophysical and biochemical analysis of a model IDP, Ki-67. These results highlight the dynamic control of intrinsic disorder as a conserved hallmark of the cell cycle and suggest a mechanism for CDK-mediated mitotic cellular reorganisation.

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Assembly of model postsynaptic densities involves interactions auxiliary to stoichiometric binding

Cited by 27 publications

References 97 publications

The stoichiometric interaction model for mesoscopic molecular dynamics simulations of liquid-liquid phase separation

The stoichiometric interaction model for mesoscopic molecular dynamics simulations of liquid-liquid phase separation

Numerical Techniques for Applications of Analytical Theories to Sequence-Dependent Phase Separations of Intrinsically Disordered Proteins

A CDK-mediated phosphorylation switch of disordered protein condensation

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