scholarly journals Evidence for widespread cytoplasmic structuring into mesoscopic condensates

2021 ◽  
Author(s):  
Felix C Keber ◽  
Thao Nguyen ◽  
Clifford P Brangwynne ◽  
Martin W&uumlhr
Keyword(s):  
Quantitative Proteomics ◽  
Differential Pressure ◽  
Size Exclusion ◽  
Small Length ◽  
Length Scales ◽  
Pressure Filtration ◽  
Global Organization ◽  
Dilution Experiments ◽  
Membrane Bound

Eukaryotic cytoplasm organizes itself via both membrane-bound organelles and membrane-less biomolecular condensates (BMCs). Known BMCs exhibit liquid-like properties and are typically visualized on the scale of ~1 um. They have been studied mostly by microscopy, examining select individual proteins. Here, we investigate the global organization of native cytoplasm with quantitative proteomics, using differential pressure filtration, size exclusion, and dilution experiments. These assays reveal that BMCs form throughout the cytosplasm, predominantly at the mesoscale of ~100 nm. Our data indicate that at least 18% of the proteome is organized via such mesoscale BMCs, suggesting that cells widely employ dynamic liquid-like clustering to organize their cytoplasm, at surprisingly small length scales.

scholarly journals Spin-charge separation at small length scales in the 2D t-J Model

1995 ◽  
Vol 99 (3-4) ◽  
pp. 509-511
Author(s):  
Roser Valent� ◽  
Claudius Gros
Keyword(s):  
Charge Separation ◽  
Small Length ◽  
Length Scales

scholarly journals Transmission x-ray microscopy at low temperatures: Irregular supercurrent flow at small length scales

2018 ◽  
Vol 97 (13) ◽  
Author(s):  
J. Simmendinger ◽  
S. Ruoss ◽  
C. Stahl ◽  
M. Weigand ◽  
J. Gräfe ◽  
...  
Keyword(s):  
Low Temperatures ◽  
Small Length ◽  
Length Scales ◽  
X Ray

scholarly journals VirB8 homolog TraE from plasmid pKM101 forms a hexameric ring structure and interacts with the VirB6 homolog TraD

2018 ◽  
Vol 115 (23) ◽  
pp. 5950-5955 ◽  
Author(s):  
Bastien Casu ◽  
Charline Mary ◽  
Aleksandr Sverzhinsky ◽  
Aurélien Fouillen ◽  
Antonio Nanci ◽  
...  
Keyword(s):  
Molecular Mass ◽  
Secretion System ◽  
High Molecular Mass ◽  
Full Length ◽  
Size Exclusion ◽  
Cross Linking ◽  
X Ray ◽  
Exclusion Chromatography ◽  
Plasmid Pkm101 ◽  
Membrane Bound

Type IV secretion systems (T4SSs) are multiprotein assemblies that translocate macromolecules across the cell envelope of bacteria. X-ray crystallographic and electron microscopy (EM) analyses have increasingly provided structural information on individual T4SS components and on the entire complex. As of now, relatively little information has been available on the exact localization of the inner membrane-bound T4SS components, notably the mostly periplasmic VirB8 protein and the very hydrophobic VirB6 protein. We show here that the membrane-bound, full-length version of the VirB8 homolog TraE from the plasmid pKM101 secretion system forms a high-molecular-mass complex that is distinct from the previously characterized periplasmic portion of the protein that forms dimers. Full-length TraE was extracted from the membranes with detergents, and analysis by size-exclusion chromatography, cross-linking, and size exclusion chromatography (SEC) multiangle light scattering (MALS) shows that it forms a high-molecular-mass complex. EM and small-angle X-ray scattering (SAXS) analysis demonstrate that full-length TraE forms a hexameric complex with a central pore. We also overproduced and purified the VirB6 homolog TraD and show by cross-linking, SEC, and EM that it binds to TraE. Our results suggest that TraE and TraD interact at the substrate translocation pore of the secretion system.

Molecular Aspects of Herbicide Action on Protoporphyrinogen Oxidase

1993 ◽  
Vol 48 (3-4) ◽  
pp. 326-333 ◽  
Author(s):  
Beate Nicolaus ◽  
Gerhard Sandmann ◽  
Peter Böger
Keyword(s):  
Diphenyl Ether ◽  
Protoporphyrin Ix ◽  
Protoporphyrinogen Oxidase ◽  
Relative Specificity ◽  
Oxidase Inhibition ◽  
Dilution Experiments ◽  
Membrane Bound ◽  
The Common ◽  
Molecular Aspects ◽  
Derivatives Of

Abstract Protoporphyrinogen oxidase, the last enzyme of the common tetrapyrrole biosynthetic pathway, is inhibited by several peroxidizing compounds resulting in accumulation of photodynamic tetrapyrroles, mainly protoporphyrin IX. The inhibition characteristics of two chemi­cally unrelated compounds were studied using membrane bound protoporphyrinogen oxidase from corn etioplasts. As shown by Lineweaver-Burk-analysis, the inhibition of enzyme activity by the diphenyl ether oxyfluorfen and the cyclic imide MCI 15 are competitive with respect to the substrate. The competitive interaction of protoporphyrinogen and the two chemically un­related inhibitors indicate a relative specificity of the binding site. The reversibility of oxyfluorfen inhibition was evaluated by dilution experiments and was shown to be independent of the presence of DTT. The analysis of structure-activity-relationship on protoporphyrinogen oxidase inhibition was investigated with para-substituted derivatives of phenyl-3,4,5,6-tetrahydro-phthalimides. The results obtained by QSAR -calculation yielded a good correlation of the inhibitory activity determined by the lipophilicity of the para-substituent. These data point to one binding region of the inhibitors within a lipophilic environment associated with the active center of the enzyme.

scholarly journals Ribosome binding to the endoplasmic reticulum: a 180-kD protein identified by crosslinking to membrane-bound ribosomes is not required for ribosome binding activity.

1991 ◽  
Vol 114 (4) ◽  
pp. 639-649 ◽  
Author(s):  
P G Collins ◽  
R Gilmore
Keyword(s):  
Signal Sequence ◽  
Signal Recognition Particle ◽  
Membrane Vesicles ◽  
Immunoblot Analysis ◽  
Binding Activity ◽  
Size Exclusion ◽  
Ribosome Binding ◽  
Specific Subset ◽  
Microsomal Membranes ◽  
Membrane Bound

We have used the membrane-impermeable, thiol-cleavable, crosslinker 3,3'-dithio bis (sulfosuccinimidylpropionate) to identify proteins that are in the vicinity of membrane-bound ribosomes of the RER. A specific subset of RER proteins was reproducibly crosslinked to the ribosome. Immunoblot analysis of the crosslinked products with antibodies raised against signal recognition particle receptor, ribophorin I, and the 35-kD subunit of the signal sequence receptor demonstrated that these translocation components had been crosslinked to the ribosome, but each to a different extent. The most prominent polypeptide among the crosslinked products was a 180-kD protein that has recently been proposed to be a ribosome receptor (Savitz, A.J., and D.I. Meyer, 1990. Nature (Lond.). 346: 540-544). RER membrane proteins were reconstituted into liposomes and assayed with radiolabeled ribosomes to determine whether ribosome binding activity could be ascribed to the 180-kD protein. Differential detergent extraction was used to prepare soluble extracts of microsomal membrane vesicles that either contained or lacked the 180-kD protein. Liposomes reconstituted from both extracts bound ribosomes with essentially identical affinity. Additional fractionation experiments demonstrated that the bulk of the ribosome binding activity present in detergent extracts of microsomal membranes could be readily resolved from the 180-kD protein by size exclusion chromatography. Taken together, we conclude that the 180-kD protein is in the vicinity of membrane bound ribosomes, yet does not correspond to the ribosome receptor.

Vibration Characteristics of Multiwalled Carbon Nanotubes Embedded in Elastic Media by a Nonlocal Elastic Shell Model

2007 ◽  
Vol 74 (6) ◽  
pp. 1087-1094 ◽  
Author(s):  
Renfu Li ◽  
George A. Kardomateas
Keyword(s):  
Carbon Nanotubes ◽  
Shell Model ◽  
Multiwalled Carbon Nanotubes ◽  
Van Der Waals ◽  
Van Der Waals Forces ◽  
Elastic Media ◽  
Small Length ◽  
Multiwalled Carbon ◽  
Resonant Frequencies ◽  
Length Scales

In this paper, the vibrational behavior of the multiwalled carbon nanotubes (MWCNTs) embedded in elastic media is investigated by a nonlocal shell model. The nonlocal shell model is formulated by considering the small length scales effects, the interaction of van der Waals forces between two adjacent tubes and the reaction from the surrounding media, and a set of governing equations of motion for the MWCNTs are accordingly derived. In contrast to the beam models in the literature, which would only predict the resonant frequencies of bending vibrational modes by taking the MWCNT as a whole beam, the current shell model can find the resonant frequencies of three modes being classified as radial, axial, and circumferential for each nanotube of a MWCNT. Big influences from the small length scales and the van der Waals’ forces are observed. Among these, noteworthy is the reduction in the radial frequencies due to the van der Waals’ force interaction between two adjacent nanotubes. The numerical results also show that when the spring constant k0 of the surrounding elastic medium reaches a certain value, the lowest resonant frequency of the double walled carbon nanotube drops dramatically.

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