scholarly journals Poly(ADP-ribose): An organizer of cellular architecture

2014 ◽  
Vol 205 (5) ◽  
pp. 613-619 ◽  
Author(s):  
Anthony K.L. Leung
Keyword(s):  
Dna Repair ◽  
Self Assembly ◽  
Structural Diversity ◽  
Low Complexity ◽  
Cellular Organization ◽  
Rna Granules ◽  
Cellular Architecture ◽  
Spindle Poles ◽  
Granule Proteins

Distinct properties of poly(ADP-ribose)—including its structural diversity, nucleation potential, and low complexity, polyvalent, highly charged nature—could contribute to organizing cellular architectures. Emergent data indicate that poly(ADP-ribose) aids in the formation of nonmembranous structures, such as DNA repair foci, spindle poles, and RNA granules. Informatics analyses reported here show that RNA granule proteins enriched for low complexity regions, which aid self-assembly, are preferentially modified by poly(ADP-ribose), indicating how poly(ADP-ribose) could direct cellular organization.

scholarly journals Exploring the Self-Assembled Tacticity in Aurophilic Polymeric Arrangements of Diphosphanegold(I) Fluorothiolates

Molecules ◽  
2019 ◽  
Vol 24 (23) ◽  
pp. 4422 ◽  
Author(s):  
Moreno-Alcántar ◽  
Salazar ◽  
Romo-Islas ◽  
Flores-Álamo ◽  
Torrens
Keyword(s):  
Solid State ◽  
Self Assembly ◽  
Structural Diversity ◽  
Supramolecular Structures ◽  
X Ray Diffraction ◽  
Ligand Effects ◽  
Rational Control ◽  
Solid State Structures ◽  
Further Development ◽  
Aurophilic Interactions

Despite the recurrence of aurophilic interactions in the solid-state structures of gold(I) compounds, its rational control, modulation, and application in the generation of functional supramolecular structures is an area that requires further development. The ligand effects over the aurophilic-based supramolecular structures need to be better understood. This paper presents the supramolecular structural diversity of a series of new 1,3-bis(diphenylphosphane)propane (dppp) gold(I) fluorinated thiolates with the general formula [Au2(SRF)2(μ-dppp)] (SRF = SC6F5 (1); SC6HF4-4 (2); SC6H3(CF3)2-3,5 (3); SC6H4CF3-2 (4); SC6H4CF3-4 (5); SC6H3F2-3,4 (6); SC6H3F2-3,5 (7); SC6H4F-2 (8); SC6H4F-3 (9); SC6H4F-4 (10)). These compounds were synthesized and characterized, and six of their solid-state crystalline structures were determined using single-crystal X-ray diffraction. In the crystalline arrangement, they form aurophilic-bridged polymers. In these systems, the changes in the fluorination patterns of the thiolate ligands tune the aurophilic-induced self-assembly of the compounds causing tacticity and chiral differentiation of the monomers. This is an example of the use of ligand effects on the tune of the supramolecular association of gold complexes.

scholarly journals Spinophilin and the immune synapse

2008 ◽  
Vol 181 (2) ◽  
pp. 181-183 ◽  
Author(s):  
Brian Seed ◽  
Ramnik Xavier
Keyword(s):  
T Cells ◽  
Dendritic Cells ◽  
Fusion Protein ◽  
Target Cells ◽  
Cellular Organization ◽  
Immune Synapse ◽  
Cellular Architecture ◽  
Gfp Fusion Protein ◽  
Cell Biol ◽  
In Cells

Extensive alterations in cellular organization are known to accompany the responses of sensitized T cells to target cells presenting an antigen of interest. Now, equally if not more dramatic changes are found to take place in cells presenting an antigen. With the help of a spinophilin-GFP fusion protein, Bloom et al. (Bloom, O., J.J. Unternaehrer, A. Jiang, J.-S. Shin, L. Delamarre, P. Allen, and I. Mellman. 2008. J. Cell Biol. 181:203–211) have captured a remarkable polarization of the cellular architecture of dendritic cells presenting an antigen to T cells.

Amalgamating 4′-substituted 4,2′:6′,4′′-terpyridine ligands with double-helical chains or ladder-like networks

RSC Advances ◽  
2016 ◽  
Vol 6 (11) ◽  
pp. 9270-9277 ◽  
Author(s):  
Guoqi Zhang ◽  
Jiawen Tan ◽  
Tonya Phoenix ◽  
David R. Manke ◽  
James A. Golen ◽  
...  
Keyword(s):  
Coordination Polymers ◽  
Self Assembly ◽  
Structural Diversity ◽  
Metal Organic ◽  
Terpyridine Ligands ◽  
First Time

HgII-mediated self-assembly of metal–organic coordination polymers based on 4,2′:6′,4′′-terpyridine derivatives is for the first time presented and the structural diversity dependent upon the use of 4′-substituents of ligand is revealed.

scholarly journals RGG-motif protein Sbp1 is required for Processing body (P-body) disassembly

2021 ◽  
Author(s):  
Raju Roy ◽  
Ishwarya Achappa Kuttanda ◽  
Nupur Bhatter ◽  
Purusharth I Rajyaguru
Keyword(s):  
Mrna Decay ◽  
Glucose Deprivation ◽  
Low Complexity ◽  
Wild Type ◽  
Processing Bodies ◽  
P Bodies ◽  
Rna Granules ◽  
Processing Body ◽  
Mrna Fate

AbstractRNA granules are conserved mRNP complexes that play an important role in determining mRNA fate by affecting translation repression and mRNA decay. Processing bodies (P-bodies) harbor enzymes responsible for mRNA decay and proteins involved in modulating translation. Although many proteins have been identified to play a role in P-body assembly, a bonafide disassembly factor remains unknown. In this report, we identify RGG-motif translation repressor protein Sbp1 as a disassembly factor of P-bodies. Disassembly of Edc3 granules but not the Pab1 granules (a conserved stress granule marker) that arise upon sodium azide and glucose deprivation stress are defective in Δsbp1. Disassembly of other P-body proteins such as Dhh1 and Scd6 is also defective in Δsbp1. Complementation experiments suggest that the wild type Sbp1 but not an RGG-motif deletion mutant rescues the Edc3 granule disassembly defect in Δsbp1. We observe that purified Edc3 forms assemblies, which is promoted by the presence of RNA and NADH. Strikingly, addition of purified Sbp1 leads to significantly decreased Edc3 assemblies. Although low complexity sequences have been in general implicated in assembly, our results reveal the role of RGG-motif (a low-complexity sequence) in the disassembly of P-bodies.

At the Interface of Three Nucleic Acids: The Role of RNA-Binding Proteins and Poly(ADP-ribose) in DNA Repair

Acta Naturae ◽  
2017 ◽  
Vol 9 (2) ◽  
pp. 4-16 ◽  
Author(s):  
E. E. Alemasova ◽  
O. I. Lavrik
Keyword(s):  
Dna Damage ◽  
Dna Repair ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Binding Protein ◽  
Regulation Of Gene Expression ◽  
Rna Granules ◽  
Dna And Rna ◽  
Cytoplasmic Rna

RNA-binding proteins (RBPs) regulate RNA metabolism, from synthesis to decay. When bound to RNA, RBPs act as guardians of the genome integrity at different levels, from DNA damage prevention to the post-transcriptional regulation of gene expression. Recently, RBPs have been shown to participate in DNA repair. This fact is of special interest as DNA repair pathways do not generally involve RNA. DNA damage in higher organisms triggers the formation of the RNA-like polymer - poly(ADP-ribose) (PAR). Nucleic acid-like properties allow PAR to recruit DNA- and RNA-binding proteins to the site of DNA damage. It is suggested that poly(ADP-ribose) and RBPs not only modulate the activities of DNA repair factors, but that they also play an important role in the formation of transient repairosome complexes in the nucleus. Cytoplasmic biomolecules are subjected to similar sorting during the formation of RNA assemblages by functionally related mRNAs and promiscuous RBPs. The Y-box-binding protein 1 (YB-1) is the major component of cytoplasmic RNA granules. Although YB-1 is a classic RNA-binding protein, it is now regarded as a non-canonical factor of DNA repair.

scholarly journals Molecular structure and interactions within amyloid-like fibrils formed by a low-complexity protein sequence from FUS

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Myungwoon Lee ◽  
Ujjayini Ghosh ◽  
Kent R. Thurber ◽  
Masato Kato ◽  
Robert Tycko
Keyword(s):  
Self Assembly ◽  
Structural Model ◽  
Rna Binding ◽  
Low Complexity ◽  
Growth Direction ◽  
Structural Basis ◽  
Amyloid Formation ◽  
Hydrophobic Residues ◽  
Dynamics Simulations ◽  
Lateral Sclerosis

AbstractProtein domains without the usual distribution of amino acids, called low complexity (LC) domains, can be prone to self-assembly into amyloid-like fibrils. Self-assembly of LC domains that are nearly devoid of hydrophobic residues, such as the 214-residue LC domain of the RNA-binding protein FUS, is particularly intriguing from the biophysical perspective and is biomedically relevant due to its occurrence within neurons in amyotrophic lateral sclerosis, frontotemporal dementia, and other neurodegenerative diseases. We report a high-resolution molecular structural model for fibrils formed by the C-terminal half of the FUS LC domain (FUS-LC-C, residues 111-214), based on a density map with 2.62 Å resolution from cryo-electron microscopy (cryo-EM). In the FUS-LC-C fibril core, residues 112-150 adopt U-shaped conformations and form two subunits with in-register, parallel cross-β structures, arranged with quasi-21 symmetry. All-atom molecular dynamics simulations indicate that the FUS-LC-C fibril core is stabilized by a plethora of hydrogen bonds involving sidechains of Gln, Asn, Ser, and Tyr residues, both along and transverse to the fibril growth direction, including diverse sidechain-to-backbone, sidechain-to-sidechain, and sidechain-to-water interactions. Nuclear magnetic resonance measurements additionally show that portions of disordered residues 151-214 remain highly dynamic in FUS-LC-C fibrils and that fibrils formed by the N-terminal half of the FUS LC domain (FUS-LC-N, residues 2-108) have the same core structure as fibrils formed by the full-length LC domain. These results contribute to our understanding of the molecular structural basis for amyloid formation by FUS and by LC domains in general.

scholarly journals Sequence-Dependent Nanofiber Structures of Phenylalanine and Isoleucine Tripeptides

2020 ◽  
Vol 21 (22) ◽  
pp. 8431
Author(s):  
Qinsi Xiong ◽  
Ziye Liu ◽  
Wei Han
Keyword(s):  
Self Assembly ◽  
Molecular Design ◽  
Hydrophobic Interactions ◽  
Structural Diversity ◽  
Building Blocks ◽  
Peptide Sequence ◽  
Sequence Dependence ◽  
Resolution Model ◽  
Structure Relationship ◽  
Relationship Of

The molecular design of short peptides to achieve a tailor-made functional architecture has attracted attention during the past decade but remains challenging as a result of insufficient understanding of the relationship between peptide sequence and assembled supramolecular structures. We report a hybrid-resolution model to computationally explore the sequence–structure relationship of self-assembly for tripeptides containing only phenylalanine and isoleucine. We found that all these tripeptides have a tendency to assemble into nanofibers composed of laterally associated filaments. Molecular arrangements within the assemblies are diverse and vary depending on the sequences. This structural diversity originates from (1) distinct conformations of peptide building blocks that lead to different surface geometries of the filaments and (2) unique sidechain arrangements at the filament interfaces for each sequence. Many conformations are available for tripeptides in solution, but only an extended β-strand and another resembling a right-handed turn are observed in assemblies. It was found that the sequence dependence of these conformations and the packing of resulting filaments are determined by multiple competing noncovalent forces, with hydrophobic interactions involving Phe being particularly important. The sequence pattern for each type of assembly conformation and packing has been identified. These results highlight the importance of the interplay between conformation, molecular packing, and sequences for determining detailed nanostructures of peptides and provide a detailed insight to support a more precise design of peptide-based nanomaterials.

Structural diversity in the self-assembly of Ag(I) complexes containing dicyano and quinolinyl ligands

Polyhedron ◽  
2014 ◽  
Vol 81 ◽  
pp. 273-281 ◽  
Author(s):  
Chun-Wei Yeh ◽  
Chi-Hui Tsou ◽  
Fu-Chang Huang ◽  
Ay Jong ◽  
Maw-Cherng Suen
Keyword(s):  
Self Assembly ◽  
Structural Diversity ◽  
The Self
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