Physics-driven coarse-grained model for biomolecular phase separation with near-quantitative accuracy

2021 ◽  
Author(s):  
Jerelle A. Joseph ◽  
Aleks Reinhardt ◽  
Anne Aguirre ◽  
Pin Yu Chew ◽  
Kieran O. Russell ◽  
...  
Keyword(s):  
Phase Separation ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Quantitative Accuracy

scholarly journals A predictive coarse-grained model for position-specific effects of post-translational modifications on disordered protein phase separation

2020 ◽  
Author(s):  
T. M. Perdikari ◽  
N. Jovic ◽  
G. L. Dignon ◽  
Y. C. Kim ◽  
N. L. Fawzi ◽  
...  
Keyword(s):  
Amino Acids ◽  
Phase Separation ◽  
Phase Behavior ◽  
Intrinsically Disordered Proteins ◽  
Coarse Grained ◽  
Disordered Proteins ◽  
Post Translational Modifications ◽  
Coarse Grained Model ◽  
Intrinsically Disordered ◽  
Liquid Liquid Phase Separation

AbstractBiomolecules undergo liquid-liquid phase separation (LLPS) resulting in the formation of multicomponent protein-RNA membraneless organelles in cells. However, the physiological and pathological role of post translational modifications (PTMs) on the biophysics of phase behavior is only beginning to be probed. To study the effect of PTMs on LLPS in silico, we extend our transferable coarse-grained model of intrinsically disordered proteins to include phosphorylated and acetylated amino acids. Using the parameters for modified amino acids available for fixed charge atomistic forcefields, we parameterize the size and atomistic hydropathy of the coarse-grained modified amino acid beads, and hence the interactions between the modified and natural amino acids. We then elucidate how the number and position of phosphorylated and acetylated residues alter the protein’s single chain compactness and its propensity to phase separate. We show that both the number and the position of phosphorylated threonines/serines or acetylated lysines can serve as a molecular on/off switch for phase separation in the well-studied disordered regions of FUS and DDX3X, respectively. We also compare modified residues to their commonly used PTM mimics for their impact on chain properties. Importantly, we show that the model can predict and capture experimentally measured differences in the phase behavior for position-specific modifications, showing that the position of modifications can dictate phase separation. In sum, this model will be useful for studying LLPS of post-translationally modified intrinsically disordered proteins and predicting how modifications control phase behavior with position-specific resolution.Statement of SignificancePost-translational modifications are important regulators of liquid-liquid phase separation (LLPS) which drives the formation of biomolecular condensates. Theoretical methods can be used to characterize the biophysical properties of intrinsically disordered proteins (IDPs). Our recent framework for molecular simulations using a Cα-centered coarse-grained model can predict the effect of various perturbations such as mutations (Dignon et al. PloS Comput. Biol, 2018) and temperature (Dignon et al, ACS Cent. Sci., 2019) on LLPS. Here, we expand this framework to incorporate modified residues like phosphothreonine, phosphoserine and acetylysine. This model will prove useful for simulating the phase separation of post-translationally modified IDPs and predicting how position-specific modifications can control phase behavior across the large family of proteins known to be phosphorylated and acetylated.

scholarly journals Condensates in RNA Repeat Sequences are Heterogeneously Organized and Exhibit Reptation-like Dynamics

2021 ◽  
Author(s):  
Hung Nguyen ◽  
Naoto Hori ◽  
Dave Thirumalai
Keyword(s):  
Phase Separation ◽  
Trinucleotide Repeat ◽  
Driving Forces ◽  
High Viscosity ◽  
Coarse Grained ◽  
Liquid Droplets ◽  
Coarse Grained Model ◽  
Extended States ◽  
Experimental Findings ◽  
Lateral Sclerosis

Abstract Although it is known that RNA undergoes liquid–liquid phase separation (LLPS), the interplay between the molecular driving forces and the emergent features of the condensates, such as their morphologies and dynamical properties, is not well understood. We introduce a coarse-grained model to simulate phase separation of trinucleotide repeat RNAs, which are implicated in neurological disorders such as Huntington disease and amyotrophic lateral sclerosis. After establishing that the simulations reproduce key experimental findings (length and concentration dependence of the phase transition in (CAG)n repeats), we show that once recruited inside the liquid droplets, the monomers transition from hairpin-like structures to extended states. Interactions between the monomers in the condensates result in the formation of an intricate and dense intermolecular network, which severely restrains the fluctuations and mobilities of the RNAs inside large droplets. In the largest densely packed high viscosity droplets, the mobility of RNA chains is best characterized by reptation, reminiscent of the dynamics in polymer melts.

scholarly journals Condensates in RNA Repeat Sequences are Heterogeneously Organized and Exhibit Reptation-like Dynamics

2021 ◽  
Author(s):  
Hung T. Nguyen ◽  
Naoto Hori ◽  
D. Thirumalai
Keyword(s):  
Phase Separation ◽  
Trinucleotide Repeat ◽  
Driving Forces ◽  
High Viscosity ◽  
Coarse Grained ◽  
Liquid Droplets ◽  
Coarse Grained Model ◽  
Extended States ◽  
Experimental Findings ◽  
Lateral Sclerosis

ABSTRACTAlthough it is known that RNA undergoes liquid–liquid phase separation (LLPS), the interplay between the molecular driving forces and the emergent features of the condensates, such as their morphologies and dynamical properties, are not well understood. We develop a coarse-grained model to investigate the phase separation of trinucleotide repeat RNAs, which are implicated in neurological disorders such as Huntington disease and amyotrophic lateral sclerosis. After establishing that the simulations reproduce key experimental findings (length and concentration dependence of the phase transition in (CAG)n repeats), we show that once recruited inside the liquid droplets, the monomers transition from hairpin-like structures to extended states. Interactions between the monomers in the condensates result in the formation of an intricate and dense intermolecular network, which severely restrains the fluctuation and mobility of the RNAs inside large droplets. In the largest densely packed high viscosity droplets, the mobility of RNA chains is best characterized by reptation, reminiscent of the dynamics in polymer melts.

scholarly journals Deciphering how naturally occurring sequence features impact the phase behaviors of disordered prion-like domains

2021 ◽  
Author(s):  
Anne Bremer ◽  
Mina Farag ◽  
Wade M. Borcherds ◽  
Ivan Peran ◽  
Erik W. Martin ◽  
...  
Keyword(s):  
Phase Separation ◽  
Rna Binding ◽  
Driving Forces ◽  
Rna Binding Proteins ◽  
Low Complexity ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Intrinsically Disordered ◽  
Lysine Residues ◽  
Arginine Residues

AbstractPhase separation of intrinsically disordered prion-like low-complexity domains (PLCDs) derived from RNA-binding proteins enable the formation of biomolecular condensates in cells. PLCDs have distinct amino acid compositions, and here we decipher the physicochemical impact of conserved compositional biases on the driving forces for phase separation. We find that tyrosine residues make for stronger drivers of phase separation than phenylalanine. Depending on their sequence contexts, arginine residues enhance or weaken phase separation, whereas lysine residues weaken cohesive interactions within PLCDs. Increased net charge per residue (NCPR) weakens the driving forces for phase separation of PLCDs and this effect can be modeled quantitatively. The effects of NCPR also weaken known correlations between the dimensions of single chains in dilute solution and the driving forces for phase separation. We build on experimental data to develop a coarse-grained model for accurate simulations of phase separation that yield novel insights regarding PLCD phase behavior.

scholarly journals Valency and Binding Affinity Variations Can Regulate the Multilayered Organization of Protein Condensates with Many Components

Biomolecules ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 278
Author(s):  
Ignacio Sanchez-Burgos ◽  
Jorge R. Espinosa ◽  
Jerelle A. Joseph ◽  
Rosana Collepardo-Guevara
Keyword(s):  
Surface Tension ◽  
Phase Separation ◽  
Liquid Phase ◽  
Binding Affinity ◽  
Multilayered Structure ◽  
Scaffold Proteins ◽  
Coarse Grained ◽  
Binding Affinities ◽  
Coarse Grained Model ◽  
Liquid Liquid Phase Separation

Biomolecular condensates, which assemble via the process of liquid–liquid phase separation (LLPS), are multicomponent compartments found ubiquitously inside cells. Experiments and simulations have shown that biomolecular condensates with many components can exhibit multilayered organizations. Using a minimal coarse-grained model for interacting multivalent proteins, we investigate the thermodynamic parameters governing the formation of multilayered condensates through changes in protein valency and binding affinity. We focus on multicomponent condensates formed by scaffold proteins (high-valency proteins that can phase separate on their own via homotypic interactions) and clients (proteins recruited to condensates via heterotypic scaffold–client interactions). We demonstrate that higher valency species are sequestered to the center of the multicomponent condensates, while lower valency proteins cluster towards the condensate interface. Such multilayered condensate architecture maximizes the density of LLPS-stabilizing molecular interactions, while simultaneously reducing the surface tension of the condensates. In addition, multilayered condensates exhibit rapid exchanges of low valency proteins in and out, while keeping higher valency proteins—the key biomolecules involved in condensate nucleation—mostly within. We also demonstrate how modulating the binding affinities among the different proteins in a multicomponent condensate can significantly transform its multilayered structure, and even trigger fission of a condensate into multiple droplets with different compositions.

scholarly journals Oligonucleotides can act as superscaffolds that enhance liquid-liquid phase separation of intracellular mixtures

2020 ◽  
Author(s):  
Jerelle A. Joseph ◽  
Jorge R. Espinosa ◽  
Ignacio Sanchez-Burgos ◽  
Adiran Garaizar ◽  
Daan Frenkel ◽  
...  
Keyword(s):  
Phase Separation ◽  
Liquid Phase ◽  
Liquid Phase Separation ◽  
Scaffold Proteins ◽  
Coarse Grained ◽  
Granule Formation ◽  
Coarse Grained Model ◽  
Liquid Liquid Phase Separation ◽  
Kinetic Barriers ◽  
Oligonucleotide Binding

AbstractIntracellular liquid-liquid phase separation (LLPS) enables the formation of biomolecular condensates, which play a crucial role in the spatiotemporal organisation of biomolecules (proteins, oligonucleotides). While LLPS of biopolymers has been demonstrated in both experiments and computer simulations, the physical determinants governing phase separation of protein-oligonucleotide systems are not fully understood. Here, we introduce a minimal coarse-grained model to investigate concentration-dependent features of protein-oligonucleotide mixtures. We demonstrate that adding oligonucleotides to biomolecular condensates composed of oligonucleotide-binding scaffold proteins enhances LLPS; since oligonucleotides act as ultra-high-valency molecules (termed ‘superscaffolds’) that increase the molecular connectivity among scaffold proteins. Importantly, we find that oligonucleotides promote protein LLPS via a seeding-type mechanism; recruiting numerous protein molecules and reducing the thermodynamic and kinetic barriers for nucleation and phase separation. By probing the conformational properties of oligonucleotides within droplets, we show that these biopolymers can undergo phase separation-driven compaction, which may be entropic in nature. Finally, we provide a quantitative comparison between mixture composition, protein valency, and protein-oligonucleotide interaction strengths. We find that superscaffolds preferentially recruit higher valency proteins to condensates, and that multiphase immiscibility within condensates can be achieved by modulating the relative protein-oligonucleotide binding strengths. These results shed light on the roles of oligonucleotides in ribonu-cleoprotein granule formation, heterochromatin compaction, and internal structuring of the nucleolus and stress granules.

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