scholarly journals Phase separation in plants: new insights into cellular compartmentalization

2021 ◽  
Author(s):  
Xiumei Xu ◽  
Canhui Zheng ◽  
Dandan Lu ◽  
Chun‐Peng Song ◽  
Lixin Zhang
Keyword(s):  
Phase Separation ◽  
Cellular Compartmentalization

scholarly journals Learning the molecular grammar of protein condensates from sequence determinants and embeddings

2021 ◽  
Vol 118 (15) ◽  
pp. e2019053118
Author(s):  
Kadi L. Saar ◽  
Alexey S. Morgunov ◽  
Runzhang Qi ◽  
William E. Arter ◽  
Georg Krainer ◽  
...  
Keyword(s):  
Phase Separation ◽  
Phase Behavior ◽  
Language Model ◽  
Data Bank ◽  
Hydrophobic Residues ◽  
Knowledge Based ◽  
Comparable Accuracy ◽  
Unstructured Proteins ◽  
Separation Of Proteins ◽  
Cellular Compartmentalization

Intracellular phase separation of proteins into biomolecular condensates is increasingly recognized as a process with a key role in cellular compartmentalization and regulation. Different hypotheses about the parameters that determine the tendency of proteins to form condensates have been proposed, with some of them probed experimentally through the use of constructs generated by sequence alterations. To broaden the scope of these observations, we established an in silico strategy for understanding on a global level the associations between protein sequence and phase behavior and further constructed machine-learning models for predicting protein liquid–liquid phase separation (LLPS). Our analysis highlighted that LLPS-prone proteins are more disordered, less hydrophobic, and of lower Shannon entropy than sequences in the Protein Data Bank or the Swiss-Prot database and that they show a fine balance in their relative content of polar and hydrophobic residues. To further learn in a hypothesis-free manner the sequence features underpinning LLPS, we trained a neural network-based language model and found that a classifier constructed on such embeddings learned the underlying principles of phase behavior at a comparable accuracy to a classifier that used knowledge-based features. By combining knowledge-based features with unsupervised embeddings, we generated an integrated model that distinguished LLPS-prone sequences both from structured proteins and from unstructured proteins with a lower LLPS propensity and further identified such sequences from the human proteome at a high accuracy. These results provide a platform rooted in molecular principles for understanding protein phase behavior. The predictor, termed DeePhase, is accessible from https://deephase.ch.cam.ac.uk/.

scholarly journals Phase separation-mediated formation of condensed GIT/PIX enzyme complex module for compartmentalized signaling

2019 ◽  
Author(s):  
Jinwei Zhu ◽  
Qingqing Zhou ◽  
Yitian Xia ◽  
Lin Lin ◽  
Jianchao Li ◽  
...  
Keyword(s):  
Phase Separation ◽  
Focal Adhesions ◽  
Enzyme Complex ◽  
Cellular Processes ◽  
Regulatory Enzymes ◽  
Neuronal Synapses ◽  
Metabolic Reactions ◽  
Cellular Compartments ◽  
Cellular Compartmentalization ◽  
Enzyme Complexes

AbstractCells compartmentalize enzymes for broad physiological functions such as efficient metabolic reactions and spatiotemporally controlled signaling. A given enzyme or enzyme complex can participate in multiple cellular processes in response to different signal inputs by forming different cellular compartments. Here, we demonstrate that association of GIT1 and β-Pix, a pair of GTPase regulatory enzymes involved in diverse cellular processes, leads to autonomous condensation of the complex via phase separation without additional scaffolding molecules. The atomic structure of the GIT/PIX complex reveals the molecular basis governing the phase separation-mediated condensation of the GIT1/β-Pix complex. Importantly, the GIT1/β-Pix condensates can function as a versatile modular membrane-less organelle- like structure for distinct cellular compartmentalization by binding to upstream proteins such as Paxillin in focal adhesions, Shank3 in neuronal synapses, and Scribble in cellular junctions. Thus, phase separation-mediated formation of condensed enzyme complexes provides a powerful way of dynamically concentrating limited amounts of cooperating enzymes to specific cellular compartments for optimal signaling.

Phase Separation: Linking Cellular Compartmentalization to Disease

2016 ◽  
Vol 26 (7) ◽  
pp. 547-558 ◽  
Author(s):  
Adriano Aguzzi ◽  
Matthias Altmeyer
Keyword(s):  
Phase Separation ◽  
Cellular Compartmentalization

Bulk standards for low-temperature biological x-ray microanalysis

1984 ◽  
Vol 42 ◽  
pp. 282-283
Author(s):  
P. Echlin ◽  
M. McKoon ◽  
E.S. Taylor ◽  
C.E. Thomas ◽  
K.L. Maloney ◽  
...  
Keyword(s):  
Phase Separation ◽  
Low Temperature ◽  
Analytical Method ◽  
Salt Solutions ◽  
Absolute Concentration ◽  
Cooling Process ◽  
X Ray ◽  
The Absolute ◽  
Analytical Procedures ◽  
Electrical Conductors

Although sections of frozen salt solutions have been used as standards for x-ray microanalysis, such solutions are less useful when analysed in the bulk form. They are poor thermal and electrical conductors and severe phase separation occurs during the cooling process. Following a suggestion by Whitecross et al we have made up a series of salt solutions containing a small amount of graphite to improve the sample conductivity. In addition, we have incorporated a polymer to ensure the formation of microcrystalline ice and a consequent homogenity of salt dispersion within the frozen matrix. The mixtures have been used to standardize the analytical procedures applied to frozen hydrated bulk specimens based on the peak/background analytical method and to measure the absolute concentration of elements in developing roots.

Phase separation in sol gel-derived ceramic films of silica-zirconia, alumina-zirconia, and titania-zirconia system

1994 ◽  
Vol 52 ◽  
pp. 646-647
Author(s):  
J. Tong ◽  
L. Eyring
Keyword(s):  
Fracture Toughness ◽  
Phase Separation ◽  
Sol Gel ◽  
Great Influence ◽  
High Strength ◽  
Chemical Durability ◽  
Separation Method ◽  
Toughening Mechanism ◽  
Ceramic Films ◽  
Zirconia Toughened Alumina

There is increasing interest in composites containing zirconia because of their high strength, fracture toughness, and its great influence on the chemical durability in glass. For the zirconia-silica system, monolithic glasses, fibers and coatings have been obtained. There is currently a great interest in designing zirconia-toughened alumina including exploration of the processing methods and the toughening mechanism.The possibility of forming nanocrystal composites by a phase separation method has been investigated in three systems: zirconia-alumina, zirconia-silica and zirconia-titania using HREM. The morphological observations initially suggest that the formation of nanocrystal composites by a phase separation method is possible in the zirconia-alumina and zirconia-silica systems, but impossible in the zirconia-titania system. The separation-produced grain size in silica-zirconia system is around 5 nm and is more uniform than that in the alumina-zirconia system in which the sizes of the small polyhedron grains are around 10 nm. In the titania-zirconia system, there is no obvious separation as was observed in die alumina-zirconia and silica-zirconia system.

Phase separation in fluid additive hard sphere mixtures?

1998 ◽  
Vol 95 (2) ◽  
pp. 131-135 ◽  
Author(s):  
DOUGLAS HENDERSON DEZSO BODA KWONG-YU CHAN
Keyword(s):  
Phase Separation ◽  
Hard Sphere

The plant response to heat requires phase separation

Nature ◽  
2020 ◽  
Vol 585 (7824) ◽  
pp. 191-192 ◽  
Author(s):  
Simon Alberti
Keyword(s):  
Phase Separation ◽  
Plant Response

Smectic a1 ↔ a2 transition of n_c-60.8 : a two-dimensional phase separation of the molecular endgroups

1989 ◽  
Vol 50 (3) ◽  
pp. 375-385 ◽  
Author(s):  
H. Fadel ◽  
D. Guillon ◽  
A. Skoulios ◽  
F. Barbarin ◽  
M. Dugay
Keyword(s):  
Phase Separation ◽  
Two Dimensional

Influence of Polymer Charge, Temperature, and Surfactants on Surface Sizing of Liner and Greaseproof Paper With Hydrophobically Modified Starch

TAPPI Journal ◽  
2009 ◽  
Vol 8 (2) ◽  
pp. 33-38 ◽  
Author(s):  
ANNA JONHED ◽  
LARS JÄRNSTRÖM
Keyword(s):  
Phase Separation ◽  
Contact Angles ◽  
Low Ph ◽  
Hydrophobically Modified ◽  
Paper Sizing ◽  
Surface Sizing ◽  
Separation Temperature ◽  
Hydrophobic Nature ◽  
Sizing Agents ◽  
Charge Temperature

The aim of this study was to investigate the properties of hydrophobically modified (HM) quaterna-ry ammonium starch ethers for paper sizing. These starches possess temperature-responsive properties; that is, gelation or phase separation occurs at a certain temperature upon cooling. This insolubility of the HM starches in water at room temperature improved their performance as sizing agents. The contact angles for water on sized liner were substantially larger than on unsized liner. When the application temperature was well above the critical phase-separation temperature, larger contact angles were obtained for liner independently of pH compared with those at the lower application temperature. Cobb60 values for liner decreased upon surface sizing, with a low pH and high application temperature giving lower water penetration. Contact angles on greaseproof paper decreased upon sur-face sizing as compared to unsized greaseproof paper, independently of pH and temperature. Greaseproof paper showed no great difference between unsized substrates and substrates sized with HM starch at different pH. This is probably due to the already hydrophobic nature of greaseproof paper. However, the Cobb60 values increased at low pH and low application temperature. Surfactants were added to investigate how they affect the sized surface. Addition of surfactant reduces the contact angles, in spite of indications of complex formation.

Ordering, phase separation, and phase transformations in Fe'M alloys

2006 ◽  
Vol 176 (6) ◽  
pp. 611 ◽  
Author(s):  
Yu.I. Ustinovshchikov ◽  
B.E. Pushkarev
Keyword(s):  
Phase Separation ◽  
Phase Transformations
Sign in / Sign up

Export Citation Format

Share Document