scholarly journals Biophysical and biochemical properties of Deup1 self-assemblies: a potential driver for deuterosome formation during multiciliogenesis

Biology Open ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. bio056432 ◽  
Author(s):  
Shohei Yamamoto ◽  
Ryoichi Yabuki ◽  
Daiju Kitagawa
Keyword(s):  
Self Assembly ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Coiled Coil ◽  
Biochemical Properties ◽  
The Self ◽  
Centrosomal Protein ◽  
Biochemical Analyses ◽  
Stable Structures

ABSTRACTThe deuterosome is a non-membranous organelle involved in large-scale centriole amplification during multiciliogenesis. Deuterosomes are specifically assembled during the process of multiciliogenesis. However, the molecular mechanisms underlying deuterosome formation are poorly understood. In this study, we investigated the molecular properties of deuterosome protein 1 (Deup1), an essential protein involved in deuterosome assembly. We found that Deup1 has the ability to self-assemble into macromolecular condensates both in vitro and in cells. The Deup1-containing structures formed in multiciliogenesis and the Deup1 condensates self-assembled in vitro showed low turnover of Deup1, suggesting that Deup1 forms highly stable structures. Our biochemical analyses revealed that an increase of the concentration of Deup1 and a crowded molecular environment both facilitate Deup1 self-assembly. The self-assembly of Deup1 relies on its N-terminal region, which contains multiple coiled coil domains. Using an optogenetic approach, we demonstrated that self-assembly and the C-terminal half of Deup1 were sufficient to spatially compartmentalize centrosomal protein 152 (Cep152) and polo like kinase 4 (Plk4), master components for centriole biogenesis, in the cytoplasm. Collectively, the present data suggest that Deup1 forms the structural core of the deuterosome through self-assembly into stable macromolecular condensates.This article has an associated First Person interview with the first author of the paper.

scholarly journals Engineering Tissues without the Use of a Synthetic Scaffold: A Twenty-Year History of the Self-Assembly Method

2018 ◽  
Vol 2018 ◽  
pp. 1-13 ◽  
Author(s):  
Ingrid Saba ◽  
Weronika Jakubowska ◽  
Stéphane Bolduc ◽  
Stéphane Chabaud
Keyword(s):  
Extracellular Matrix ◽  
Self Assembly ◽  
Large Scale ◽  
Dermal Fibroblasts ◽  
The Self ◽  
Production Costs ◽  
Scale Production ◽  
Assembly Method ◽  
Assembly Technique

Twenty years ago, Dr. François A. Auger, the founder of the Laboratory of Experimental Organogenesis (LOEX), introduced the self-assembly technique. This innovative technique relies on the ability of dermal fibroblasts to produce and assemble their own extracellular matrix, differing from all other tissue-engineering techniques that use preformed synthetic scaffolds. Nevertheless, the use of the self-assembly technique was limited for a long time due to its main drawbacks: time and cost. Recent scientific breakthroughs have addressed these limitations. New protocol modifications that aim at increasing the rate of extracellular matrix formation have been proposed to reduce the production costs and laboratory handling time of engineered tissues. Moreover, the introduction of vascularization strategies in vitro permits the formation of capillary-like networks within reconstructed tissues. These optimization strategies enable the large-scale production of inexpensive native-like substitutes using the self-assembly technique. These substitutes can be used to reconstruct three-dimensional models free of exogenous materials for clinical and fundamental applications.

scholarly journals EGCG binds intrinsically disordered N-terminal domain of p53 and disrupts p53-MDM2 interaction

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jing Zhao ◽  
Alan Blayney ◽  
Xiaorong Liu ◽  
Lauren Gandy ◽  
Weihua Jin ◽  
...  
Keyword(s):  
Large Scale ◽  
Molecular Mechanisms ◽  
Epigallocatechin Gallate ◽  
Cancer Drug ◽  
Dynamic Interactions ◽  
Cancer Drug Discovery ◽  
Intrinsically Disordered ◽  
Terminal Domain ◽  
Cancerous Cells

AbstractEpigallocatechin gallate (EGCG) from green tea can induce apoptosis in cancerous cells, but the underlying molecular mechanisms remain poorly understood. Using SPR and NMR, here we report a direct, μM interaction between EGCG and the tumor suppressor p53 (KD = 1.6 ± 1.4 μM), with the disordered N-terminal domain (NTD) identified as the major binding site (KD = 4 ± 2 μM). Large scale atomistic simulations (>100 μs), SAXS and AUC demonstrate that EGCG-NTD interaction is dynamic and EGCG causes the emergence of a subpopulation of compact bound conformations. The EGCG-p53 interaction disrupts p53 interaction with its regulatory E3 ligase MDM2 and inhibits ubiquitination of p53 by MDM2 in an in vitro ubiquitination assay, likely stabilizing p53 for anti-tumor activity. Our work provides insights into the mechanisms for EGCG’s anticancer activity and identifies p53 NTD as a target for cancer drug discovery through dynamic interactions with small molecules.

scholarly journals Biochemical reconstitutions reveal principles of human γ-TuRC assembly and function

2021 ◽  
Vol 220 (3) ◽  
Author(s):  
Michal Wieczorek ◽  
Shih-Chieh Ti ◽  
Linas Urnavicius ◽  
Kelly R. Molloy ◽  
Amol Aher ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Self Assembly ◽  
The Self ◽  
Dependent Manner ◽  
Guanine Nucleotide ◽  
Partial Cone ◽  
Ring Complex ◽  
Microtubule Networks ◽  
And Function

The formation of cellular microtubule networks is regulated by the γ-tubulin ring complex (γ-TuRC). This ∼2.3 MD assembly of >31 proteins includes γ-tubulin and GCP2-6, as well as MZT1 and an actin-like protein in a “lumenal bridge” (LB). The challenge of reconstituting the γ-TuRC has limited dissections of its assembly and function. Here, we report a biochemical reconstitution of the human γ-TuRC (γ-TuRC-GFP) as a ∼35 S complex that nucleates microtubules in vitro. In addition, we generate a subcomplex, γ-TuRCΔLB-GFP, which lacks MZT1 and actin. We show that γ-TuRCΔLB-GFP nucleates microtubules in a guanine nucleotide–dependent manner and with similar efficiency as the holocomplex. Electron microscopy reveals that γ-TuRC-GFP resembles the native γ-TuRC architecture, while γ-TuRCΔLB-GFP adopts a partial cone shape presenting only 8–10 γ-tubulin subunits and lacks a well-ordered lumenal bridge. Our results show that the γ-TuRC can be reconstituted using a limited set of proteins and suggest that the LB facilitates the self-assembly of regulatory interfaces around a microtubule-nucleating “core” in the holocomplex.

scholarly journals The C-terminal region of the plasmid partitioning protein TubY is a tetramer that can bind membranes and DNA

2020 ◽  
Vol 295 (51) ◽  
pp. 17770-17780
Author(s):  
Ikuko Hayashi
Keyword(s):  
Lipid Membranes ◽  
Binding Protein ◽  
Coiled Coil ◽  
Type Iii ◽  
Daughter Cells ◽  
Lysine Residues ◽  
Stable Maintenance ◽  
Biochemical Analyses

Bacterial low-copy-number plasmids require partition (par) systems to ensure their stable inheritance by daughter cells. In general, these systems consist of three components: a centromeric DNA sequence, a centromere-binding protein and a nucleotide hydrolase that polymerizes and functions as a motor. Type III systems, however, segregate plasmids using three proteins: the FtsZ/tubulin-like GTPase TubZ, the centromere-binding protein TubR and the MerR-like transcriptional regulator TubY. Although the TubZ filament is sufficient to transport the TubR-centromere complex in vitro, TubY is still necessary for the stable maintenance of the plasmid. TubY contains an N-terminal DNA-binding helix-turn-helix motif and a C-terminal coiled-coil followed by a cluster of lysine residues. This study determined the crystal structure of the C-terminal domain of TubY from the Bacillus cereus pXO1-like plasmid and showed that it forms a tetrameric parallel four-helix bundle that differs from the typical MerR family proteins with a dimeric anti-parallel coiled-coil. Biochemical analyses revealed that the C-terminal tail with the conserved lysine cluster helps TubY to stably associate with the TubR-centromere complex as well as to nonspecifically bind DNA. Furthermore, this C-terminal tail forms an amphipathic helix in the presence of lipids but must oligomerize to localize the protein to the membrane in vivo. Taken together, these data suggest that TubY is a component of the nucleoprotein complex within the partitioning machinery, and that lipid membranes act as mediators of type III systems.

A self-assembly based on a hydrogel interface: facile, rapid, and large-scale preparation of colloidal photonic crystals

2020 ◽  
Vol 4 (8) ◽  
pp. 2409-2417
Author(s):  
Mengfan Wu ◽  
Chuyan Zhang ◽  
Fujing Wei ◽  
Huifang An ◽  
Xiaqing Wang ◽  
...  
Keyword(s):  
Photonic Crystals ◽  
Self Assembly ◽  
Large Scale ◽  
The Self ◽  
Colloidal Photonic Crystals ◽  
Large Scale Preparation ◽  
Scale Preparation ◽  
First Time

This is the first time that a hydrogel interface has been used as an assembly interface for the self-assembly of photonic crystals with excellent performances.

Self-assembly of linear diblock copolymers in selective solvents: from single micelles to particles with tri-continuous inner structures

Soft Matter ◽  
2020 ◽  
Vol 16 (26) ◽  
pp. 6056-6062 ◽  
Author(s):  
Xianggui Ye ◽  
Bamin Khomami
Keyword(s):  
Diblock Copolymer ◽  
Self Assembly ◽  
Large Scale ◽  
Diblock Copolymers ◽  
Dissipative Particle Dynamics ◽  
Particle Dynamics ◽  
The Self ◽  
Selective Solvent ◽  
Selective Solvents

Large-scale dissipative particle dynamics (DPD) simulations have been performed to investigate the self-assembly of over 20 000 linear diblock copolymer chains in a selective solvent.

scholarly journals Cotranslational folding allows misfolding-prone proteins to circumvent deep kinetic traps

2020 ◽  
Vol 117 (3) ◽  
pp. 1485-1495 ◽  
Author(s):  
Amir Bitran ◽  
William M. Jacobs ◽  
Xiadi Zhai ◽  
Eugene Shakhnovich
Keyword(s):  
Self Assembly ◽  
Molecular Mechanisms ◽  
Folding Kinetics ◽  
Rare Codons ◽  
Cotranslational Folding ◽  
Nascent Chain ◽  
Kinetic Traps ◽  
Optimal Window

Many large proteins suffer from slow or inefficient folding in vitro. It has long been known that this problem can be alleviated in vivo if proteins start folding cotranslationally. However, the molecular mechanisms underlying this improvement have not been well established. To address this question, we use an all-atom simulation-based algorithm to compute the folding properties of various large protein domains as a function of nascent chain length. We find that for certain proteins, there exists a narrow window of lengths that confers both thermodynamic stability and fast folding kinetics. Beyond these lengths, folding is drastically slowed by nonnative interactions involving C-terminal residues. Thus, cotranslational folding is predicted to be beneficial because it allows proteins to take advantage of this optimal window of lengths and thus avoid kinetic traps. Interestingly, many of these proteins’ sequences contain conserved rare codons that may slow down synthesis at this optimal window, suggesting that synthesis rates may be evolutionarily tuned to optimize folding. Using kinetic modeling, we show that under certain conditions, such a slowdown indeed improves cotranslational folding efficiency by giving these nascent chains more time to fold. In contrast, other proteins are predicted not to benefit from cotranslational folding due to a lack of significant nonnative interactions, and indeed these proteins’ sequences lack conserved C-terminal rare codons. Together, these results shed light on the factors that promote proper protein folding in the cell and how biomolecular self-assembly may be optimized evolutionarily.

Self-Assembly of Graphene Nanoribbons with Unsaturated Edges

2012 ◽  
Vol 1407 ◽  
Author(s):  
Andrew L. J. Pang ◽  
Viacheslav Sorkin ◽  
Yong-Wei Zhang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Self Assembly ◽  
Bond Order ◽  
Graphene Nanoribbons ◽  
The Self ◽  
Graphene Nanoscrolls ◽  
Simulation Results ◽  
Dynamics Simulations ◽  
Stable Structures

ABSTRACTWe studied the self-assembly mechanisms of Graphene Nanoribbon (GNR) with unsaturated edges and demonstrated the ability of GNR to self-assemble into novel stable structures. We proposed three mechanisms which dictate the self-assembly evolution of GNR with unsaturated edges. Using the Adaptive Intermolecular Reactive Empirical Bond-Order (AIREBO) potential, we performed molecular dynamics simulations on initially-planar GNRs with unsaturated edges. The simulation results showed that the self-assembly mechanisms and final conformations of the GNRs correlate well with the proposed GNR self-assembly mechanisms. Furthermore, the simulations also showed the ability of a narrow GNR to self-assemble into various nanostructures, such as tapered graphene nano-rings and graphene nanoscrolls with an embedded nanotube.

scholarly journals Self-Assembly of Ternary Particles for Tough Colloidal Crystals with Vivid Structure Colors

2013 ◽  
Vol 2013 ◽  
pp. 1-14 ◽  
Author(s):  
Binfu Bao ◽  
Duo Liu ◽  
Youyou Yang ◽  
Zhehong Shen ◽  
Bo You
Keyword(s):  
Carbon Black ◽  
Self Assembly ◽  
Large Scale ◽  
Colloidal Crystals ◽  
The Self ◽  
Natural Conditions ◽  
Practical Applications ◽  
Structural Colors ◽  
Crystal Films ◽  
Nanosilica Particles

Self-assembly of colloidal spheres is the most frequently used method for structural colors, but the chroma of the structural colors is usually so low that people cannot observe it under natural conditions. This paper presents a facile method for fabrications of vivid structural colors by doping carbon black into the self-assembly of colloidal polymer spheres and nanosilica particles. This approach can generate very gorgeous structural colors which can be very easily seen under natural conditions. The fabrication conditions for the self-assembly of composite dispersions of polymer/silica/carbon black were optimized to obtain colloidal crystals with vivid colors. Thus, robust mechanical properties, large-scale, and brilliant structural colors can guarantee the obtained crystal films to find practical applications, which are demonstrated by the fact that the successful applications of structural colors beautify the original simple and tedious surface of bamboo strand board (BSB).

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