scholarly journals Mechanisms of active regulation of biomolecular condensates

2019 ◽  
Author(s):  
Johannes Söding ◽  
David Zwicker ◽  
Salma Sohrabi-Jahromi ◽  
Marc Boehning ◽  
Jan Kirschbaum
Keyword(s):  
Protein Interactions ◽  
Actin Polymerization ◽  
Reaction Rates ◽  
Microtubule Assembly ◽  
Active Regulation ◽  
Condensate Formation ◽  
Organizational Principle ◽  
Splicing Speckles ◽  
Specific Proteins ◽  
The Many

AbstractLiquid-liquid phase separation is a key organizational principle in eukaryotic cells, on par with intracellular membranes. It allows cells to concentrate specific proteins into condensates, increasing reaction rates and achieving switch-like regulation. However, it is unclear how cells trigger condensate formation or dissolution and regulate their sizes. We predict from first principles two mechanisms of active regulation by post-translational modifications such as phosphorylation: In enrichment-inhibition, the regulating modifying enzyme enriches in condensates and the modifications of proteins inhibit their interactions. Stress granules, Cajal bodies, P granules, splicing speckles, and synapsin condensates obey this model. In localization-induction, condensates form around an immobilized modifying enzyme, whose modifications strengthen protein interactions. Spatially targeted condensates formed during transmembrane signaling, microtubule assembly, and actin polymerization conform to this model. The two models make testable predictions that can guide studies into the many emerging roles of biomolecular condensates.

Presynaptic targets for acute ethanol sensitivity

2010 ◽  
Vol 38 (1) ◽  
pp. 172-176 ◽  
Author(s):  
Jeff W. Barclay ◽  
Margaret E. Graham ◽  
Mark R. Edwards ◽  
James R. Johnson ◽  
Alan Morgan ◽  
...  
Keyword(s):  
Nervous System ◽  
Caenorhabditis Elegans ◽  
Alcohol Abuse ◽  
Synaptic Vesicle ◽  
Protein Interactions ◽  
Model Organism ◽  
Acute Exposure ◽  
Ethanol Sensitivity ◽  
Acute Ethanol ◽  
Specific Proteins

Acute exposure to ethanol is known to modulate signalling within the nervous system. Physiologically these effects are both presynaptic and postsynaptic in origin; however, considerably more research has focused primarily on postsynaptic targets. Recent research using the model organism Caenorhabditis elegans has determined a role for specific proteins (Munc18-1 and Rab3) and processes (synaptic vesicle recruitment and fusion) in transducing the presynaptic effects of ethanol. In the present paper, we review these results, identifying the proteins and protein interactions involved in ethanol sensitivity and discuss their links with mammalian studies of alcohol abuse.

scholarly journals Tubulin-nucleotide interactions. Effects of removal of exchangeable guanine nucleotide on protein conformation and microtubule assembly

1987 ◽  
Vol 241 (1) ◽  
pp. 105-110 ◽  
Author(s):  
E J Manser ◽  
P M Bayley
Keyword(s):  
Alkaline Phosphatase ◽  
Binding Site ◽  
Protein Interactions ◽  
Tertiary Structure ◽  
Nucleotide Binding ◽  
Nucleotide Binding Site ◽  
Microtubule Assembly ◽  
Structural Requirement ◽  
Tubulin Dimer ◽  
Microtubule Protein

The removal of tightly bound GDP from the exchangeable nucleotide-binding site of tubulin has been performed with alkaline phosphatase under conditions which essentially retain the assembly properties of the protein. When microtubule protein is treated with alkaline phosphatase, nucleotide is selectively removed from tubulin dimer rather than from MAP (microtubule-associated protein)-containing oligomeric species. Tubulin devoid of E-site (the exchangeable nucleotide-binding site of the tubulin dimer) nucleotide shows enhanced proteolytic susceptibility of the beta-subunit to thermolysin and decreased protein stability, consistent with nucleotide removal causing changes in protein tertiary structure. Pyrophosphate ion (3 mM) is able to promote formation of normal microtubules in the complete absence of GTP by incubation at 37 degrees C either with nucleotide-depleted microtubule protein or with nucleotide-depleted tubulin dimer to which MAPs have been added. The resulting microtubules contain up to 80% of tubulin lacking E-site nucleotide. In addition to its effects on nucleation, pyrophosphate competes weakly with GDP bound at the E-site. It is deduced that binding of pyrophosphate at a vacant E-site can promote microtubule assembly. The minimum structural requirement for ligands to induce tubulin assembly apparently involves charge neutralization at the E-site by bidentate ligation, which stabilizes protein domains in a favourable orientation for promoting the supramolecular protein-protein interactions involved in microtubule formation.

scholarly journals "Platinum on the road": Interactions of antitumoral cisplatin with proteins

2008 ◽  
Vol 80 (12) ◽  
pp. 2715-2725 ◽  
Author(s):  
Fabio Arnesano ◽  
Giovanni Natile
Keyword(s):  
Biological Activity ◽  
Antitumor Activity ◽  
Cell Membrane ◽  
The Road ◽  
Specific Proteins ◽  
On The Road ◽  
The Many

When the antitumor activity of cisplatin was discovered, no one would have thought of the existence of specific proteins able to transport Pt across the cell membrane or to specifically recognize DNA modified by this drug. However, such proteins do exist and, furthermore, are specific for the Pt substrate considered. It follows that proteins are deeply involved in managing the biological activity of cisplatin. It is expected that, after the first 20 years in which most of the efforts were devoted to understanding its mode of interaction with DNA and consequent structural and functional alterations, the role of proteins will be more deeply scavenged. How cisplatin can survive the attack of the many platinophiles present in the extracellular and intracellular media is the issue addressed in this article. Significantly, differences are observed between cisplatin, carboplatin, and oxaliplatin.

scholarly journals Loop I of U1 small nuclear RNA is the only essential RNA sequence for binding of specific U1 small nuclear ribonucleoprotein particle proteins.

1988 ◽  
Vol 8 (11) ◽  
pp. 4787-4791 ◽  
Author(s):  
J Hamm ◽  
V L van Santen ◽  
R A Spritz ◽  
I W Mattaj
Keyword(s):  
Protein Interactions ◽  
Protein C ◽  
Small Nuclear Rna ◽  
Structural Element ◽  
Rna Sequence ◽  
Small Nuclear Ribonucleoprotein ◽  
Nuclear Rna ◽  
Egg Extracts ◽  
Specific Proteins ◽  
Nuclear Ribonucleoprotein

The binding of the U1 small nuclear ribonucleoprotein (snRNP)-specific proteins C, A, and 70K to U1 small nuclear RNA (snRNA) was analyzed. Assembly of U1 snRNAs from bean and soybean and a set of mutant Xenopus U1 snRNAs into U1 snRNPs in Xenopus egg extracts was studied. The ability to bind proteins was analyzed by immunoprecipitation with monospecific antibodies and by a protein-sequestering assay. The only sequence essential for binding of the U1-specific proteins was the conserved loop sequence in the 5' hairpin of U1. Further analysis suggested that protein C binds directly to the loop and that the assembly of proteins A and 70K into the RNP requires mainly protein-protein interactions. Protein C apparently recognizes a specific RNA sequence rather than a secondary structural element in the RNA.

scholarly journals Topical ripasudil stimulates neuroprotection and axon regeneration in adult mice following optic nerve injury

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Euido Nishijima ◽  
Kazuhiko Namekata ◽  
Atsuko Kimura ◽  
Xiaoli Guo ◽  
Chikako Harada ◽  
...  
Keyword(s):  
Optic Nerve ◽  
Nerve Regeneration ◽  
Nerve Injury ◽  
Actin Polymerization ◽  
Mitogen Activated Protein Kinase ◽  
Microtubule Assembly ◽  
Nerve Degeneration ◽  
Optic Nerve Injury ◽  
Optic Nerve Regeneration ◽  
Adult Mice

Abstract Optic nerve injury induces optic nerve degeneration and retinal ganglion cell (RGC) death that lead to visual disturbance. In this study, we examined if topical ripasudil has therapeutic potential in adult mice after optic nerve crush (ONC). Topical ripasudil suppressed ONC-induced phosphorylation of p38 mitogen-activated protein kinase and ameliorated RGC death. In addition, topical ripasudil significantly suppressed the phosphorylation of collapsin response mediator protein 2 and cofilin, and promoted optic nerve regeneration. These results suggest that topical ripasudil promotes RGC protection and optic nerve regeneration by modulating multiple signaling pathways associated with neural cell death, microtubule assembly and actin polymerization.

scholarly journals U1 small nuclear ribonucleoprotein particle-specific proteins interact with the first and second stem-loops of U1 RNA, with the A protein binding directly to the RNA independently of the 70K and Sm proteins.

1989 ◽  
Vol 9 (8) ◽  
pp. 3360-3368 ◽  
Author(s):  
J R Patton ◽  
W Habets ◽  
W J van Venrooij ◽  
T Pederson
Keyword(s):  
Protein Interactions ◽  
Protein Protein Interactions ◽  
Ribonucleoprotein Particle ◽  
Small Nuclear Ribonucleoprotein ◽  
Core Proteins ◽  
U1 Snrnp ◽  
Specific Proteins ◽  
C Proteins ◽  
Nuclear Ribonucleoprotein ◽  
Small Nuclear Ribonucleoprotein Particle

The U1 small nuclear ribonucleoprotein particle (U1 snRNP), a cofactor in pre-mRNA splicing, contains three proteins, termed 70K, A, and C, that are not present in the other spliceosome-associated snRNPs. We studied the binding of the A and C proteins to U1 RNA, using a U1 snRNP reconstitution system and an antibody-induced nuclease protection technique. Antibodies that reacted with the A and C proteins induced nuclease protection of the first two stem-loops of U1 RNA in reconstituted U1 snRNP. Detailed analysis of the antibody-induced nuclease protection patterns indicated the existence of relatively long-range protein-protein interactions in the U1 snRNP, with the 5' end of U1 RNA and its associated specific proteins interacting with proteins bound to the Sm domain near the 3' end. UV cross-linking experiments in conjunction with an A-protein-specific antibody demonstrated that the A protein bound directly to the U1 RNA rather than assembling in the U1 snRNP exclusively via protein-protein interactions. This conclusion was supported by additional experiments revealing that the A protein could bind to U1 RNA in the absence of bound 70K and Sm core proteins.

Compartmentalization and metabolic regulation of glycolysis

2021 ◽  
Vol 134 (20) ◽  
Author(s):  
Gregory G. Fuller ◽  
John K. Kim
Keyword(s):  
Protein Interactions ◽  
Mammalian Cells ◽  
Energy Production ◽  
Metabolic Regulation ◽  
Tca Cycle ◽  
Synaptic Function ◽  
Protein Protein Interactions ◽  
C Elegans ◽  
Physiological Importance ◽  
Condensate Formation

ABSTRACT Hypoxia inhibits the tricarboxylic acid (TCA) cycle and leaves glycolysis as the primary metabolic pathway responsible for converting glucose into usable energy. However, the mechanisms that compensate for this loss in energy production due to TCA cycle inactivation remain poorly understood. Glycolysis enzymes are typically diffuse and soluble in the cytoplasm under normoxic conditions. In contrast, recent studies have revealed dynamic compartmentalization of glycolysis enzymes in response to hypoxic stress in yeast, C. elegans and mammalian cells. These messenger ribonucleoprotein (mRNP) structures, termed glycolytic (G) bodies in yeast, lack membrane enclosure and display properties of phase-separated biomolecular condensates. Disruption of condensate formation correlates with defects such as impaired synaptic function in C. elegans neurons and decreased glucose flux in yeast. Concentrating glycolysis enzymes into condensates may lead to their functioning as ‘metabolons’ that enhance rates of glucose utilization for increased energy production. Besides condensates, glycolysis enzymes functionally associate in other organisms and specific tissues through protein–protein interactions and membrane association. However, as discussed in this Review, the functional consequences of coalescing glycolytic machinery are only just beginning to be revealed. Through ongoing studies, we anticipate the physiological importance of metabolic regulation mediated by the compartmentalization of glycolysis enzymes will continue to emerge.

Loop I of U1 small nuclear RNA is the only essential RNA sequence for binding of specific U1 small nuclear ribonucleoprotein particle proteins

1988 ◽  
Vol 8 (11) ◽  
pp. 4787-4791
Author(s):  
J Hamm ◽  
V L van Santen ◽  
R A Spritz ◽  
I W Mattaj
Keyword(s):  
Protein Interactions ◽  
Protein C ◽  
Small Nuclear Rna ◽  
Structural Element ◽  
Rna Sequence ◽  
Small Nuclear Ribonucleoprotein ◽  
Nuclear Rna ◽  
Egg Extracts ◽  
Specific Proteins ◽  
Nuclear Ribonucleoprotein

The binding of the U1 small nuclear ribonucleoprotein (snRNP)-specific proteins C, A, and 70K to U1 small nuclear RNA (snRNA) was analyzed. Assembly of U1 snRNAs from bean and soybean and a set of mutant Xenopus U1 snRNAs into U1 snRNPs in Xenopus egg extracts was studied. The ability to bind proteins was analyzed by immunoprecipitation with monospecific antibodies and by a protein-sequestering assay. The only sequence essential for binding of the U1-specific proteins was the conserved loop sequence in the 5' hairpin of U1. Further analysis suggested that protein C binds directly to the loop and that the assembly of proteins A and 70K into the RNP requires mainly protein-protein interactions. Protein C apparently recognizes a specific RNA sequence rather than a secondary structural element in the RNA.

scholarly journals A cell-based high-content screen identifies isocotoin as a small molecule inhibitor of the meiosis-specific MEIOB–SPATA22 complex†

2020 ◽  
Vol 103 (2) ◽  
pp. 333-342 ◽  
Author(s):  
Yang Xu ◽  
Rong Liu ◽  
N Adrian Leu ◽  
Lei Zhang ◽  
Ilsiya Ibragmova ◽  
...  
Keyword(s):  
Small Molecule ◽  
Protein Interactions ◽  
Cultured Cells ◽  
Bimolecular Fluorescence Complementation ◽  
Hek293 Cells ◽  
Dependent Manner ◽  
Bifc Assay ◽  
Small Molecule Libraries ◽  
A Cell ◽  
Specific Proteins

Abstract MEIOB and SPATA22 are meiosis-specific proteins, interact with each other, and are essential for meiotic recombination and fertility. Aspartic acid 383 (D383) in MEIOB is critical for its interaction with SPATA22 in biochemical studies. Here we report that genetic studies validate the requirement of D383 for the function of MEIOB in mice. The MeiobD383A/D383A mice display meiotic arrest due to depletion of both MEIOB and SPATA22 proteins in the testes. We developed a cell-based bimolecular fluorescence complementation (BiFC) assay, in which MEIOB and SPATA22 are fused to split YFP moieties and their co-expression in cultured cells leads to the MEIOB–SPATA22 dimerization and reconstitution of the fluorophore. As expected, the interaction-disrupting D383A substitution results in the absence of YFP fluorescence in the BiFC assay. A high-throughput screen of small molecule libraries identified candidate hit compounds at a rate of 0.7%. Isocotoin, a hit compound from the natural product library, inhibits the MEIOB–SPATA22 interaction and promotes their degradation in HEK293 cells in a dose-dependent manner. Therefore, the BiFC assay can be employed to screen for small molecule inhibitors that disrupt protein–protein interactions or promote degradation of meiosis-specific proteins.

Sign in / Sign up

Export Citation Format

Share Document