scholarly journals Interplay Between Short-range Attraction and Long-range Repulsion Controls Reentrant Liquid Condensation of Ribonucleoprotein-RNA Complexes

2019 ◽  
Author(s):  
Ibraheem Alshareedah ◽  
Taranpreet Kaur ◽  
Jason Ngo ◽  
Hannah Seppala ◽  
Liz-Audrey Djomnang Kounatse ◽  
...  
Keyword(s):  
Phase Separation ◽  
Long Range ◽  
Short Range ◽  
Rna Binding ◽  
Driving Forces ◽  
Low Complexity ◽  
Model Systems ◽  
Supramolecular Organization ◽  
Cluster Phase ◽  
Rna Complexes

AbstractIn eukaryotic cells, ribonucleoproteins (RNPs) form mesoscale condensates by liquid-liquid phase separation that play essential roles in subcellular dynamic compartmentalization. The formation and dissolution of many RNP condensates are finely dependent on the RNA-to-RNP ratio, giving rise to a window-like phase separation behavior. This is commonly referred to as reentrant liquid condensation (RLC). Here, using RNP-inspired polypeptides with low-complexity RNA-binding sequences as well as the C-terminal disordered domain of the ribonucleoprotein FUS as model systems, we investigate the molecular driving forces underlying this non-monotonous phase transition. We show that an interplay between short-range cation-π attractions and long-range electrostatic forces governs the heterotypic RLC of RNP-RNA complexes. Short-range attractions, which can be encoded by both polypeptide chain primary sequence and nucleic acid base sequence, are activated by RNP-RNA condensate formation. After activation, the short-range forces regulate material properties of polypeptide-RNA condensates and subsequently oppose their reentrant dissolution. In the presence of excess RNA, a competition between short-range attraction and long-range electrostatic repulsion drives the formation of a colloid-like cluster phase. With increasing short-range attraction, the fluid dynamics of the cluster phase is arrested, leading to the formation of a colloidal gel. Our results reveal that phase behavior, supramolecular organization, and material states of RNP-RNA assemblies are controlled by a dynamic interplay between molecular interactions at different length scales.

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 A computational study of surface-directed phase separation in polymer blends under temperature gradient

2021 ◽  
Author(s):  
Mohammad Tabatabaieyazdi
Keyword(s):  
Growth Rate ◽  
Phase Separation ◽  
Temperature Gradient ◽  
Long Range ◽  
Spinodal Decomposition ◽  
Surface Potential ◽  
Short Range ◽  
Computational Study ◽  
Polymeric Materials ◽  
Partial Wetting

To apprehend the real industrial behavior of polymeric materials phase separation phenomenon, the nonlinear Cahn-Hilliard theory incorporating the Flory-Huggins-de Gennes free energy theory was used to study the non-uniform thermal-induced phase separation phenomenon in a symmetric binary polymer blend in which surface(s) with short- and long-range attraction to one polymer component compete with temperature gradient effects. The numerical results indicate that an increase of diffusion coefficient value will increase the rate of phase separation in the bulk but will decrease the growth rate of the wetting layer on the surface regardless of the surface potential strength. Also, the morphology transition from complete to partial wetting of the surface with short range surface attraction is successfully demonstrated. However, no partial wetting is observed for the surface with long-range potential. For shallow quenches, first, a growth rate of t 0.5 is observed in the early stage of spinodal decomposition phase separation at the surface and then a decline in the growth rate to t 0.13 in the intermediate stage occurred. For short- and long-range surface potential, the growth rate value of t 0.33 obtained in the bulk. The morphology results of temperature gradient effect on surface directed spinodal decomposition in short-range, long- range and multiple-surface attraction cases have been presented for the first time. It is realized that regardless of surface potential magnitude, surface enrichment is increased by higher temperature gradient (deep quenches on the side with no surface attraction). The studied models would provide more in depth understanding of polymer blendiprocesses.

scholarly journals Heat shock chaperone HSPB1 regulates cytoplasmic TDP-43 phase separation and liquid-to-gel transition

2021 ◽  
Author(s):  
Shan Lu ◽  
Jiaojiao Hu ◽  
Bankhole Aladesuyi ◽  
Alexander Goginashvili ◽  
Sonia Vazquez-Sanchez ◽  
...  
Keyword(s):  
Phase Separation ◽  
Heat Shock ◽  
Motor Neurons ◽  
Rna Binding ◽  
Isotope Labeling ◽  
Small Heat Shock Protein ◽  
Proteasome Inhibition ◽  
Low Complexity ◽  
Spinal Motor Neurons ◽  
Hsp70 Family

Abstract While the RNA binding protein TDP-43 reversibly phase separates within nuclei into complex droplets (anisosomes) with TDP-43-containing liquid outer shells and liquid centers of HSP70 family chaperones, cytoplasmic aggregates of TDP-43 are hallmarks of multiple neurodegenerative diseases, including ALS. Here we show that transient oxidative stress, proteasome inhibition, or inhibition of HSP70’s ATP-dependent chaperone activity provokes reversible cytoplasmic TDP-43 de-mixing and transition from liquid to gel/solid, independent of RNA binding or stress granules. Isotope labeling mass spectrometry is used to identify that phase separated cytoplasmic TDP-43 is primarily bound by the small heat shock protein HSPB1. Binding is direct, mediated through TDP-43’s RNA binding and low complexity domains. HSPB1 partitions into TDP-43 droplets, inhibits TDP-43 assembly into fibrils, and is essential for disassembly of stress-induced, TDP-43 droplets. Decrease of HSPB1 promotes cytoplasmic TDP-43 de-mixing and mislocalization. HSPB1 depletion is identified within ALS-patient spinal motor neurons containing aggregated TDP-43. These findings identify HSPB1 to be a regulator of cytoplasmic TDP-43 phase separation and aggregation.

scholarly journals The low-complexity domain of the FUS RNA binding protein self-assembles via the mutually exclusive use of two distinct cross-β cores

2021 ◽  
Vol 118 (42) ◽  
pp. e2114412118
Author(s):  
Masato Kato ◽  
Steven L. McKnight
Keyword(s):  
Phase Separation ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Low Complexity ◽  
Terminal Region ◽  
Aqueous Environment ◽  
Fused In Sarcoma ◽  
Biochemical Assays ◽  
Biologic Function

The low-complexity (LC) domain of the fused in sarcoma (FUS) RNA binding protein self-associates in a manner causing phase separation from an aqueous environment. Incubation of the FUS LC domain under physiologically normal conditions of salt and pH leads to rapid formation of liquid-like droplets that mature into a gel-like state. Both examples of phase separation have enabled reductionist biochemical assays allowing discovery of an N-terminal region of 57 residues that assembles into a labile, cross-β structure. Here we provide evidence of a nonoverlapping, C-terminal region of the FUS LC domain that also forms specific cross-β interactions. We propose that biologic function of the FUS LC domain may operate via the mutually exclusive use of these N- and C-terminal cross-β cores. Neurodegenerative disease–causing mutations in the FUS LC domain are shown to imbalance the two cross-β cores, offering an unanticipated concept of LC domain function and dysfunction.

scholarly journals Heat shock chaperone HSPB1 regulates cytoplasmic TDP-43 phase separation and liquid-to-gel transition

2021 ◽  
Author(s):  
Shan Lu ◽  
Jiaojiao Hu ◽  
Olubankole Aladesuyi Arogundade ◽  
Alexander Goginashvili ◽  
Sonia Vazquez-Sanchez ◽  
...  
Keyword(s):  
Phase Separation ◽  
Heat Shock ◽  
Motor Neurons ◽  
Rna Binding ◽  
Isotope Labeling ◽  
Small Heat Shock Protein ◽  
Proteasome Inhibition ◽  
Low Complexity ◽  
Spinal Motor Neurons ◽  
Hsp70 Family

While the RNA binding protein TDP-43 reversibly phase separates within nuclei into complex droplets (anisosomes) with TDP-43-containing liquid outer shells and liquid centers of HSP70 family chaperones, cytoplasmic aggregates of TDP-43 are hallmarks of multiple neurodegenerative diseases, including ALS. Here we show that transient oxidative stress, proteasome inhibition, or inhibition of HSP70's ATP-dependent chaperone activity provokes reversible cytoplasmic TDP-43 de-mixing and transition from liquid to gel/solid, independent of RNA binding or stress granules. Isotope labeling mass spectrometry is used to identify that phase separated cytoplasmic TDP-43 is primarily bound by the small heat shock protein HSPB1. Binding is direct, mediated through TDP-43's RNA binding and low complexity domains. HSPB1 partitions into TDP-43 droplets, inhibits TDP-43 assembly into fibrils, and is essential for disassembly of stress-induced, TDP-43 droplets. Decrease of HSPB1 promotes cytoplasmic TDP-43 de-mixing and mislocalization. HSPB1 depletion is identified within ALS-patient spinal motor neurons containing aggregated TDP-43. These findings identify HSPB1 to be a regulator of cytoplasmic TDP-43 phase separation and aggregation.

scholarly journals Distinct roles of hnRNPH1 low-complexity domains in splicing and transcription

2021 ◽  
Vol 118 (50) ◽  
pp. e2109668118
Author(s):  
Ga Hye Kim ◽  
Ilmin Kwon
Keyword(s):  
Phase Separation ◽  
Transcriptional Activation ◽  
Rna Splicing ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Lymphoblastic Leukemia ◽  
Large Family ◽  
Low Complexity ◽  
Reversible Polymers

Heterogeneous nuclear ribonucleoproteins (hnRNPs) represent a large family of RNA-binding proteins that control key events in RNA biogenesis under both normal and diseased cellular conditions. The low-complexity (LC) domain of hnRNPs can become liquid-like droplets or reversible amyloid-like polymers by phase separation. Yet, whether phase separation of the LC domains contributes to physiological functions of hnRNPs remains unclear. hnRNPH1 contains two LC domains, LC1 and LC2. Here, we show that reversible phase separation of the LC1 domain is critical for both interaction with different kinds of RNA-binding proteins and control of the alternative-splicing activity of hnRNPH1. Interestingly, although not required for phase separation, the LC2 domain contributes to the robust transcriptional activation of hnRNPH1 when fused to the DNA-binding domain, as found recently in acute lymphoblastic leukemia. Our data suggest that the ability of the LC1 domain to phase-separate into reversible polymers or liquid-like droplets is essential for function of hnRNPH1 as an alternative RNA-splicing regulator, whereas the LC2 domain may contribute to the aberrant transcriptional activity responsible for cancer transformation.

scholarly journals Interplay between Short-Range Attraction and Long-Range Repulsion Controls Reentrant Liquid Condensation of Ribonucleoprotein–RNA Complexes

2019 ◽  
Vol 141 (37) ◽  
pp. 14593-14602 ◽  
Author(s):  
Ibraheem Alshareedah ◽  
Taranpreet Kaur ◽  
Jason Ngo ◽  
Hannah Seppala ◽  
Liz-Audrey Djomnang Kounatse ◽  
...  
Keyword(s):  
Long Range ◽  
Short Range ◽  
Rna Complexes

scholarly journals A computational study of surface-directed phase separation in polymer blends under temperature gradient

2021 ◽  
Author(s):  
Mohammad Tabatabaieyazdi
Keyword(s):  
Growth Rate ◽  
Phase Separation ◽  
Temperature Gradient ◽  
Long Range ◽  
Spinodal Decomposition ◽  
Surface Potential ◽  
Short Range ◽  
Computational Study ◽  
Polymeric Materials ◽  
Partial Wetting

To apprehend the real industrial behavior of polymeric materials phase separation phenomenon, the nonlinear Cahn-Hilliard theory incorporating the Flory-Huggins-de Gennes free energy theory was used to study the non-uniform thermal-induced phase separation phenomenon in a symmetric binary polymer blend in which surface(s) with short- and long-range attraction to one polymer component compete with temperature gradient effects. The numerical results indicate that an increase of diffusion coefficient value will increase the rate of phase separation in the bulk but will decrease the growth rate of the wetting layer on the surface regardless of the surface potential strength. Also, the morphology transition from complete to partial wetting of the surface with short range surface attraction is successfully demonstrated. However, no partial wetting is observed for the surface with long-range potential. For shallow quenches, first, a growth rate of t 0.5 is observed in the early stage of spinodal decomposition phase separation at the surface and then a decline in the growth rate to t 0.13 in the intermediate stage occurred. For short- and long-range surface potential, the growth rate value of t 0.33 obtained in the bulk. The morphology results of temperature gradient effect on surface directed spinodal decomposition in short-range, long- range and multiple-surface attraction cases have been presented for the first time. It is realized that regardless of surface potential magnitude, surface enrichment is increased by higher temperature gradient (deep quenches on the side with no surface attraction). The studied models would provide more in depth understanding of polymer blendiprocesses.

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