scholarly journals A large intermediate domain of vertebrate REV3 protein is dispensable for ultraviolet-induced translesion replication

DNA Repair ◽  
2021 ◽  
Vol 98 ◽  
pp. 103031
Author(s):  
Jun Takezawa ◽  
Anna Shimazaki ◽  
Hidemi Takimoto ◽  
Kagemasa Kajiwara ◽  
Kouichi Yamada
Keyword(s):  
Intermediate Domain

Microfabrication research at the National Submicron Facility

1983 ◽  
Vol 41 ◽  
pp. 86-89
Author(s):  
E.D. Wolf
Keyword(s):  
Integrated Circuits ◽  
Particle Physics ◽  
High Speed ◽  
New Technology ◽  
High Energy ◽  
High Energy Particle ◽  
New Science ◽  
Wide Range ◽  
Intermediate Domain ◽  
Circuit Function

Most microelectronics devices and circuits operate faster, consume less power, execute more functions and cost less per circuit function when the feature-sizes internal to the devices and circuits are made smaller. This is part of the stimulus for the Very High-Speed Integrated Circuits (VHSIC) program. There is also a need for smaller, more sensitive sensors in a wide range of disciplines that includes electrochemistry, neurophysiology and ultra-high pressure solid state research. There is often fundamental new science (and sometimes new technology) to be revealed (and used) when a basic parameter such as size is extended to new dimensions, as is evident at the two extremes of smallness and largeness, high energy particle physics and cosmology, respectively. However, there is also a very important intermediate domain of size that spans from the diameter of a small cluster of atoms up to near one micrometer which may also have just as profound effects on society as “big” physics.

scholarly journals Structure of putative tumor suppressor ALDH1L1

2022 ◽  
Vol 5 (1) ◽  
Author(s):  
Yaroslav Tsybovsky ◽  
Valentin Sereda ◽  
Marcin Golczak ◽  
Natalia I. Krupenko ◽  
Sergey A. Krupenko
Keyword(s):  
Tumor Suppressor ◽  
Aldehyde Dehydrogenase ◽  
Functional Domain ◽  
Formyl Group ◽  
Carrier Proteins ◽  
Catalytic Domains ◽  
Putative Tumor Suppressor ◽  
Enzymatic Systems ◽  
Domain Interactions ◽  
Intermediate Domain

AbstractPutative tumor suppressor ALDH1L1, the product of natural fusion of three unrelated genes, regulates folate metabolism by catalyzing NADP+-dependent conversion of 10-formyltetrahydrofolate to tetrahydrofolate and CO2. Cryo-EM structures of tetrameric rat ALDH1L1 revealed the architecture and functional domain interactions of this complex enzyme. Highly mobile N-terminal domains, which remove formyl from 10-formyltetrahydrofolate, undergo multiple transient inter-domain interactions. The C-terminal aldehyde dehydrogenase domains, which convert formyl to CO2, form unusually large interfaces with the intermediate domains, homologs of acyl/peptidyl carrier proteins (A/PCPs), which transfer the formyl group between the catalytic domains. The 4′-phosphopantetheine arm of the intermediate domain is fully extended and reaches deep into the catalytic pocket of the C-terminal domain. Remarkably, the tetrameric state of ALDH1L1 is indispensable for catalysis because the intermediate domain transfers formyl between the catalytic domains of different protomers. These findings emphasize the versatility of A/PCPs in complex, highly dynamic enzymatic systems.

scholarly journals Quantum Computer: Quantum Model and Reality

2020 ◽  
Author(s):  
Vasil Dinev Penchev
Keyword(s):  
Quantum Mechanics ◽  
Turing Machine ◽  
Quantum Computer ◽  
Classical Model ◽  
Hidden Variables ◽  
Quantum Model ◽  
Computational Process ◽  
Intermediate Domain ◽  
And Mathematics ◽  
The Axiom Of Choice

Any computer can create a model of reality. The hypothesis that quantum computer can generate such a model designated as quantum, which coincides with the modeled reality, is discussed. Its reasons are the theorems about the absence of “hidden variables” in quantum mechanics. The quantum modeling requires the axiom of choice. The following conclusions are deduced from the hypothesis. A quantum model unlike a classical model can coincide with reality. Reality can be interpreted as a quantum computer. The physical processes represent computations of the quantum computer. Quantum information is the real fundament of the world. The conception of quantum computer unifies physics and mathematics and thus the material and the ideal world. Quantum computer is a non-Turing machine in principle. Any quantum computing can be interpreted as an infinite classical computational process of a Turing machine. Quantum computer introduces the notion of “actually infinite computational process”. The discussed hypothesis is consistent with all quantum mechanics. The conclusions address a form of neo-Pythagoreanism: Unifying the mathematical and physical, quantum computer is situated in an intermediate domain of their mutual transformations.

scholarly journals Death-domain dimerization-mediated activation of RIPK1 controls necroptosis and RIPK1-dependent apoptosis

2018 ◽  
Vol 115 (9) ◽  
pp. E2001-E2009 ◽  
Author(s):  
Huyan Meng ◽  
Zhen Liu ◽  
Xingyan Li ◽  
Huibing Wang ◽  
Taijie Jin ◽  
...  
Keyword(s):  
Cell Death ◽  
Proinflammatory Cytokine ◽  
Kinase Activity ◽  
Kinase Domain ◽  
Death Domain ◽  
Degenerative Diseases ◽  
Intermediate Domain ◽  
A Charge ◽  
Mutant Cells

RIPK1 is a critical mediator of cell death and inflammation downstream of TNFR1 upon stimulation by TNFα, a potent proinflammatory cytokine involved in a multitude of human inflammatory and degenerative diseases. RIPK1 contains an N-terminal kinase domain, an intermediate domain, and a C-terminal death domain (DD). The kinase activity of RIPK1 promotes cell death and inflammation. Here, we investigated the involvement of RIPK1-DD in the regulation of RIPK1 kinase activity. We show that a charge-conserved mutation of a lysine located on the surface of DD (K599R in human RIPK1 or K584R in murine RIPK1) blocks RIPK1 activation in necroptosis and RIPK1-dependent apoptosis and the formation of complex II. Ripk1K584R/K584R knockin mutant cells are resistant to RIPK1 kinase-dependent apoptosis and necroptosis. The resistance of K584R cells, however, can be overcome by forced dimerization of RIPK1. Finally, we show that the K584R RIPK1 knockin mutation protects mice against TNFα-induced systematic inflammatory response syndrome. Our study demonstrates the role of RIPK1-DD in mediating RIPK1 dimerization and activation of its kinase activity during necroptosis and RIPK1-dependent apoptosis.

scholarly journals Dynamics of a Polymer Network Modeled by a Fractal Cactus

Polymers ◽  
2018 ◽  
Vol 10 (7) ◽  
pp. 787 ◽  
Author(s):  
Aurel Jurjiu ◽  
Mircea Galiceanu
Keyword(s):  
Power Law ◽  
Hydrodynamic Interaction ◽  
Strong Dependence ◽  
Polymer Network ◽  
Real Space ◽  
Hydrodynamic Interactions ◽  
Connectivity Matrix ◽  
Relaxation Dynamics ◽  
Intermediate Domain ◽  
Fractal Network

In this paper, we focus on the relaxation dynamics of a polymer network modeled by a fractal cactus. We perform our study in the framework of the generalized Gaussian structure model using both Rouse and Zimm approaches. By performing real-space renormalization transformations, we determine analytically the whole eigenvalue spectrum of the connectivity matrix, thereby rendering possible the analysis of the Rouse-dynamics at very large generations of the structure. The evaluation of the structural and dynamical properties of the fractal network in the Rouse type-approach reveals that they obey scaling and the dynamics is governed by the value of spectral dimension. In the Zimm-type approach, the relaxation quantities show a strong dependence on the strength of the hydrodynamic interaction. For low and medium hydrodynamic interactions, the relaxation quantities do not obey power law behavior, while for slightly larger interactions they do. Under strong hydrodynamic interactions, the storage modulus does not follow power law behavior and the average displacement of the monomer is very low. Remarkably, the theoretical findings with respect to scaling in the intermediate domain of the relaxation quantities are well supported by experimental results from the literature.

scholarly journals Unicellular-Multicellular Evolutionary Branching Driven by Resource Limitations

2021 ◽  
Author(s):  
Adriano Bonforti ◽  
Ricard Sole
Keyword(s):  
Life Forms ◽  
Limited Resources ◽  
Evolutionary Branching ◽  
Resource Limitations ◽  
Evolutionary Innovation ◽  
Multicellular Aggregates ◽  
Dividing Cells ◽  
Intermediate Domain ◽  
Critical Resource ◽  
Two Phases

Multicellular life forms have evolved many times in our planet, suggesting that this is a common evolutionary innovation. Multiple advantages have been proposed for multicellularity (MC) to emerge. In this paper we address the problem of how the first precondition for multicellularity, namely "stay together" might have occurred under spatially limited resources exploited by a population of unicellular agents. Using a minimal model of evolved cell-cell adhesion among growing and dividing cells that exploit a localised resource with a given size, we show that a transition occurs at a critical resource size separating a phase of evolved multicellular aggregates from a phase where unicellularity (UC) is favoured. The two phases are separated by an intermediate domain where where both UC and MC can be selected by evolution. This model provides a minimal approach to the early stages that were required to transition from Darwinian individuality to cohesive groups of cells associated with a physical cooperative effect: when resources are present only in a localised portion of the habitat, MC is a desirable property as it helps cells to keep close to the available local nutrients.

Conformational Changes In GROEL Induced by a Protein Substrate

2000 ◽  
Vol 6 (S2) ◽  
pp. 258-259
Author(s):  
S. Falke ◽  
M. Fisher ◽  
E. Gogol
Keyword(s):  
Conformational Changes ◽  
Three Dimensional ◽  
Central Cavity ◽  
En Bloc ◽  
Protein Substrate ◽  
E Coli ◽  
X Ray Crystallography ◽  
Denatured Protein ◽  
Intermediate Domain ◽  
Substrate Binding Sites

The GroEL/GroES chaperonin system of E. coli facilitates nucleotide dependent folding of select proteins. The structure of GroEL has been described by three-dimensional electron microscopy and at higher resolution by X-ray crystallography. The GroEL oligomer is a cylindrical tetradecamer composed of two heptameric rings of 57 kDa protein subunits, stacked back to back. Each subunit is comprised of two large domains, equatorial and apical, connected by a smaller intermediate domain. The intermediate “hinge” domain links the apical and equatorial domain and provides flexibility for en bloc rearrangement associated with nucleotide and GroES binding. Equatorial domains are responsible for interactions between the two heptamers and contain the ATPase activity of GroEL. Each ring of GroEL has a central cavity that is the binding site for denatured protein substrate. GroES and denatured substrate binding sites are located on the apical domains facing the central cavity.

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