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Oligomerization

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https://www.readbyqxmd.com/read/28820334/evolutionary-analysis-of-a-novel-zinc-ribbon-in-the-n-terminal-region-of-threonine-synthase
#1
Gurmeet Kaur, Srikrishna Subramanian
Threonine synthase (TS) catalyzes the terminal reaction in the biosynthetic pathway of threonine and requires pyridoxal phosphate as a cofactor. TSs share a common catalytic domain with other fold type II PALP dependent enzymes. TSs are broadly grouped into two classes based on their sequence, quaternary structure, and enzyme regulation. We report the presence of a novel zinc ribbon domain in the N-terminal region preceding the catalytic core in TS. The zinc ribbon domain is present in TSs belonging to both classes...
August 18, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28820063/loss-in-toxic-function-of-aggregates-of-%C3%AE-synuclein-mutants-by-a-%C3%AE-synuclein-derived-peptide
#2
Soheila Mohammadi, Maryam Nikkhah, Saman Hosseinkhani
Parkinson's disease (PD) primarily results from a severe and selective damage of dopaminergic neurons. The neuropathological hallmark of the disease is the presence of inclusions known as Lewy bodies, that are enriched in α-Synuclein (αS) nanofibrils, within the surviving neurons. The inhibition of αS aggregation is considered as an efficient approach for preventing or treating PD. To date, several researchers have been focused on screening for the inhibitors that are able to block, slow down, or reverse αS aggregation, particularly at its early stages...
August 18, 2017: Protein and Peptide Letters
https://www.readbyqxmd.com/read/28819267/decoding-disease-causing-mechanisms-of-missense-mutations-from-supramolecular-structures
#3
Atsushi Hijikata, Toshiyuki Tsuji, Masafumi Shionyu, Tsuyoshi Shirai
The inheritance modes of pathogenic missense mutations are known to be highly associated with protein structures; recessive mutations are mainly observed in the buried region of protein structures, whereas dominant mutations are significantly enriched in the interfaces of molecular interactions. However, the differences in phenotypic impacts among various dominant mutations observed in individuals are not fully understood. In the present study, the functional effects of pathogenic missense mutations on three-dimensional macromolecular complex structures were explored in terms of dominant mutation types, namely, haploinsufficiency, dominant-negative, or toxic gain-of-function...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28818525/whole-transcriptome-microarray-analysis-reveals-regulation-of-rab4-by-rbm5-in-neurons
#4
Travis C Jackson, Shawn E Kotermanski, Patrick M Kochanek
RNA binding motif 5 (RBM5) is a nuclear protein that modulates gene transcription and mRNA splicing in cancer cells. The brain is among the highest RBM5 expressing organ in the body but its mRNA target(s) or functions in the CNS have not been elucidated. Here we knocked down (KO) RBM5 in primary rat cortical neurons and analyzed total RNA extracts by gene microarray vs. neurons transduced with lentivirus to deliver control (non-targeting) shRNA. The mRNA levels of Sec23A (involved in ER-Golgi transport) and the small GTPase Rab4a (involved in endocytosis/protein trafficking) were increased in RBM5 KO neurons relative to controls...
August 14, 2017: Neuroscience
https://www.readbyqxmd.com/read/28817282/tnf-induced-switching-of-columnar-rectangular-to-hexagonal-assemblies-in-a-new-class-of-triphenylene-based-room-temperature-discotic-liquid-crystals
#5
Monika Gupta, Santosh Prasad Gupta, Santanu Kumar Pal
A straightforward synthesis of triphenylene-based oligomeric systems that self-organize into room temperature columnar structures is presented. The compounds with longer spacer length (m = 10 and 12) exhibit columnar rectangular (Colr) mesophase whereas the compound with m = 8 exists in glassy Colr state. Interestingly, the Colr self-assembly of these compounds switches to columnar hexagonal (Colh) on doping the compounds with 2, 4, 7-trinitrofluorenone (TNF). For the dopant concentration of 1:1 with respect to native compound, an intermediate transition state between Colr and Colh phase was observed which completely transformed into the hexagonal phase on increasing the concentration to 1:2 (compound: TNF) and afterwards...
August 17, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28817259/sub-20-nm-stable-micelles-based-on-a-mixture-of-coiled-coils-a-platform-for-controlled-ligand-presentation
#6
JooChuan Ang, Dan Ma, Benson Thomas Jung, Sinan Keten, Ting Xu
Ligand-functionalized, multivalent nanoparticles have been extensively studied for biomedical applications from imaging agents to drug delivery vehicles. However, the ligand cluster size is usually heterogeneous and the local valency is ill-defined. Here, we present a mixed micelle platform hierarchically self-assembled from a mixture of two amphiphilic 3-helix and 4-helix peptide-PEG-lipid hybrid conjugates. We demonstrate that the local multivalent ligand cluster size on the micelle surface can be controlled based on the coiled-coil oligomeric state...
August 17, 2017: Biomacromolecules
https://www.readbyqxmd.com/read/28815215/structural-characterization-of-acidic-m17-leucine-aminopeptidases-from-the-tritryps-and-evaluation-of-their-role-in-nutrient-starvation-in-trypanosoma-brucei
#7
Jennifer Timm, Maria Valente, Daniel García-Caballero, Keith S Wilson, Dolores González-Pacanowska
Leucine aminopeptidase (LAP) is found in all kingdoms of life and catalyzes the metal-dependent hydrolysis of the N-terminal amino acid residue of peptide or amino acyl substrates. LAPs have been shown to participate in the N-terminal processing of certain proteins in mammalian cells and in homologous recombination and transcription regulation in bacteria, while in parasites, they are involved in host cell invasion and provision of essential amino acids for growth. The enzyme is essential for survival in Plasmodium falciparum, where its drug target potential has been suggested...
July 2017: MSphere
https://www.readbyqxmd.com/read/28814508/dynamic-functional-assembly-of-the-torsin-aaa-atpase-and-its-modulation-by-lap1
#8
Anna R Chase, Ethan Laudermilch, Jimin Wang, Hideki Shigematsu, Takeshi Yokoyama, Christian Schlieker
TorsinA is an essential AAA+ ATPase requiring LAP1 or LULL1 as cofactors. The dynamics of the Torsin/cofactor system remain poorly understood, with previous models invoking Torsin/cofactor assemblies with fixed stoichiometries. Here, we demonstrate that TorsinA assembles into homotypic oligomers in the presence of ATP. Torsin variants mutated at the 'back' interface disrupt homo-oligomerization but still show robust ATPase activity in the presence of its cofactors. These Torsin mutants are severely compromised in their ability to rescue nuclear envelope defects in Torsin-deficient cells, suggesting that TorsinA homo-oligomers play a key role in vivo Engagement of the oligomer by LAP1 triggers ATP hydrolysis and rapid complex disassembly...
August 16, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/28814160/elucidation-of-molecular-mechanism-of-stability-of-the-heme-regulated-eif2%C3%AE-kinase-upon-binding-of-its-ligand-hemin-in-its-catalytic-kinase-domain
#9
Varsha Bhavnani, Kaviraj Swarnendu, Priyabrata Panigrahi, C G Suresh, SuneelShekar Yapara, Jayanta Pal
The eIF2α kinase activity of the heme-regulated inhibitor (HRI) is regulated by heme which makes it a unique member of the family of eIF2α kinases. Since heme concentrations create an equilibrium for the kinase to be active/inactive, it becomes important to study the heme binding effects upon the kinase and understanding its mechanism of functionality. In the present study, we report the thermostability achieved by the catalytic kinase domain of HRI (HRI.CKD) upon ligand (heme) binding. Our CD data demonstrates that the HRI...
August 17, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28814068/the-activation-of-nlrp3-inflammsome-by-stimulation-of-diesel-exhaust-particles-in-lung-tissues-from-emphysema-model-and-raw-264-7-cell-line
#10
Soo-Taek Uh, So My Koo, Yangki Kim, Kiup Kim, Sungwoo Park, An Soo Jang, Dojin Kim, Yong Hoon Kim, Choon-Sik Park
Background/Aims: Diesel exhaust particles (DEPs) lead to elevation of reactive oxygen species, which can activate the nucleotide-binding oligomerization domain-like receptor (NLR) family members containing the pyrin domain 3 (NLRP3)-inf lammasome. In this study, we elucidated whether NLRP3 -inf lammasome is activated by DEPs and whether antioxidants (N-acetylcysteine [NAC]) could inhibit such activation. Methods: RAW 264.7 cells and ex vivo lung tissues explants obtained from elastase-induced emphysema animal models were stimulated with cigarette smoking extract (CSE), DEPs, and lipopolysaccharide, and levels of interleukin-1β (IL-1β), caspase-1 and nucleotide-binding oligomerization domain-like receptor (NLR) family members containing the pyrin domain (NLRP3)-inflammasome were assessed by Western blotting and immunohistochemistry...
August 18, 2017: Korean Journal of Internal Medicine
https://www.readbyqxmd.com/read/28813591/on-surface-oligomerization-of-self-terminating-molecular-chains-for-the-design-of-spintronic-devices
#11
Emil Sierda, Mikel Abadia, Jens Brede, Micha Elsebach, Bernhard Bugenhagen, Marc Heinrich Prosenc, Maciej Bazarnik, Roland Wiesendanger
Molecular spintronics is currently attracting a lot of attention due to its great advantages over traditional electronics. A variety of self-assembled molecule-based devices are under development, but studies regarding the reliability of the growth-process remain rare. Here, we present a method to control the length of molecular spintronic chains and to make their terminations chemically inert, thereby suppressing uncontrolled coupling to surface defects. The temperature evolution of chain formation was followed by X-ray photoelectron spectroscopy, to determine optimal growth conditions...
August 16, 2017: ACS Nano
https://www.readbyqxmd.com/read/28813514/the-helicobacter-pylori-type-iv-secretion-system-promotes-il-8-synthesis-in-a-model-of-pediatric-airway-epithelium-via-p38-map-kinase
#12
Myra G Dela Pena-Ponce, Monica T Jimenez, Lori M Hansen, Jay V Solnick, Lisa A Miller
Epidemiologic studies have reported an inverse relationship between childhood Helicobacter pylori infection and development of allergic asthma. Because lung epithelium plays an important role in allergic asthma pathogenesis, we hypothesized that H. pylori may directly influence airway epithelial cell innate immune function, particularly in early childhood. To test our hypothesis, we established an in vitro H. pylori infection model using primary tracheobronchial epithelial cell cultures derived from infant, juvenile and adult rhesus monkeys...
2017: PloS One
https://www.readbyqxmd.com/read/28813181/pathway-choice-between-proteasomal-and-autophagic-degradation
#13
Kefeng Lu, Fabian den Brave, Stefan Jentsch
Efficient degradation of abnormal or aggregated proteins is crucial to protect the cell against proteotoxic stress. Selective targeting and disposal of such proteins usually occurs in a ubiquitin-dependent manner by proteasomes and macroautophagy/autophagy. Whereas proteasomes are efficient in degrading abnormal soluble proteins, protein aggregates are typically targeted for degradation by autophagic vesicles. Both processes require ubiquitin-binding receptors, which are targeted to proteasomes via ubiquitin-like domains or to phagophores (the precursors to autophagosomes) via Atg8/LC3 binding motifs, respectively...
August 16, 2017: Autophagy
https://www.readbyqxmd.com/read/28812261/backbone-and-side-chain-1-h-15-n-and-13-c-resonance-assignments-of-two-sac10b-family-members-mvo10b-and-mth10btqqa-from-archaea
#14
Jinsong Xuan, Hongwei Yao, Yingang Feng, Jinfeng Wang
The Sac10b family proteins, also named as Alba, are small, basic, nucleic acid-binding proteins widely distributed in archaea. They possess divergent physiological functions such as binding to both DNA and RNA with a high affinity and involving in genomic DNA compaction, RNA transactions and transcriptional regulations. The structures of many Sac10b family proteins from hyperthermophilic archaea have been reported, while those from thermophilic and mesophilic archaea are largely unknown. As was pointed out, the homologous members from thermophilic and mesophilic archaea may have functions different from the hyperthermophilic members...
August 16, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28811697/role-of-iron-and-copper-in-the-pathogenesis-of-parkinson-s-disease
#15
Mohit Kumar Gangania, Jyoti Batra, Suman Kushwaha, Rachna Agarwal
Parkinson's disease (PD) is an old age disorder of basal ganglia which involves oligomerization of α-synuclein protein and formation of intercellular inclusions known as "Lewy bodies" in substantia nigra and caudate nuclei in brain which is progressive in nature. It is second most prevalent neurodegenerative disorder characterized by tremor at rest, muscle rigidity, slowness of movement (bradykinesia, akinesia), and changes in posture (instability). Both excess and deficiency in levels of transition metals (especially iron, copper) can be detrimental to the central nervous system...
July 2017: Indian Journal of Clinical Biochemistry: IJCB
https://www.readbyqxmd.com/read/28811267/app-a%C3%AE-structural-diversity-and-alzheimer-s-disease-pathogenesis
#16
REVIEW
Alex E Roher, Tyler A Kokjohn, Steven G Clarke, Michael R Sierks, Chera L Maarouf, Geidy E Serrano, Marwan S Sabbagh, Thomas G Beach
The amyloid cascade hypothesis of Alzheimer's disease (AD) proposes amyloid- β (Aβ) is a chief pathological element of dementia. AD therapies have targeted monomeric and oligomeric Aβ 1-40 and 1-42 peptides. However, alternative APP proteolytic processing produces a complex roster of Aβ species. In addition, Aβ peptides are subject to extensive posttranslational modification (PTM). We propose that amplified production of some APP/Aβ species, perhaps exacerbated by differential gene expression and reduced peptide degradation, creates a diverse spectrum of modified species which disrupt brain homeostasis and accelerate AD neurodegeneration...
August 12, 2017: Neurochemistry International
https://www.readbyqxmd.com/read/28810880/nlrp7-contributes-to-in-vitro-decidualization-of-endometrial-stromal-cells
#17
Jyun-Yuan Huang, Pei-Hsiu Yu, Yueh-Chun Li, Pao-Lin Kuo
BACKGROUND: Nucleotide-binding oligomerization domain (NACHT), leucine rich repeat (LRR) and pyrin domain (PYD) 7 containing protein, NLRP7, is a member of the NLR family which serves as innate immune sensors. Mutations and genetic variants of NLRP7 have been found in women with infertility associated conditions, such as recurrent hydatidiform mole, recurrent miscarriage, and preeclampsia. Decidualization of endometrial stromal cells is a hallmark of tissue remodeling to support embryo implantation and proper placental development...
August 15, 2017: Reproductive Biology and Endocrinology: RB&E
https://www.readbyqxmd.com/read/28810516/lectin-from-inflorescences-of-ornamental-crop-alpinia-purpurata-acts-on-immune-cells-to-promote-th1-and-th17-responses-nitric-oxide-release-and-lymphocyte-activation
#18
Jéssica de Santana Brito, Gustavo Ramos Salles Ferreira, Emeline Klimczak, Liliya Gryshuk, Nataly Diniz de Lima Santos, Leydianne Leite de Siqueira Patriota, Leyllane Rafael Moreira, Ana Karine Araújo Soares, Bruno Rafael Barboza, Patrícia Maria Guedes Paiva, Daniela Maria do Amaral Ferraz Navarro, Virgínia Maria Barros de Lorena, Cristiane Moutinho Lagos de Melo, Marília Cavalcanti Coriolano, Thiago Henrique Napoleão
Alpinia purpurata is an ornamental crop known as a source of bioactive molecules. This is the first study to report isolation of a lectin (carbohydrate-binding protein) from A. purpurata inflorescences (ApuL). The immunomodulatory potential of ApuL was evaluated by investigating its effects on the production of cytokines and release of nitric oxide by human peripheral blood mononuclear cells (PBMCs). In addition, the differentiation and activation of lymphocytes treated with ApuL was evaluated by immunophenotyping assays...
August 10, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28809479/natural-seminal-amyloids-as-targets-for-development-of-synthetic-inhibitors-of-hiv-transmission
#19
Daniel A Sheik, Stephen Dewhurst, Jerry Yang
Amyloids refer to a class of protein or peptide aggregates that are heterogeneous in size, morphology, and composition, and are implicated to play a central role in many neurodegenerative and systemic diseases. The strong correlation between biological activity and extent of aggregation of amyloidogenic proteins and peptides has led to an explosion of research efforts to target these materials with synthetic molecules or engineered antibodies to try to attenuate their function in disease pathology. Although many of these efforts to attenuate amyloid function have shown great promise in laboratory settings, the vast majority of work has been focused on targeting amyloids associated with neurologic diseases, which has been met with significant additional challenges that preclude clinical evaluation...
August 15, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28808107/structure-of-psb29-thf1-and-its-association-with-the-ftsh-protease-complex-involved-in-photosystem-ii-repair-in-cyanobacteria
#20
Martina Bec Ková, Jianfeng Yu, Vendula Krynická, Amanda Kozlo, Shengxi Shao, Peter Koník, Josef Komenda, James W Murray, Peter J Nixon
One strategy for enhancing photosynthesis in crop plants is to improve their ability to repair photosystem II (PSII) in response to irreversible damage by light. Despite the pivotal role of thylakoid-embedded FtsH protease complexes in the selective degradation of PSII subunits during repair, little is known about the factors involved in regulating FtsH expression. Here we show using the cyanobacterium Synechocystis sp. PCC 6803 that the Psb29 subunit, originally identified as a minor component of His-tagged PSII preparations, physically interacts with FtsH complexes in vivo and is required for normal accumulation of the FtsH2/FtsH3 hetero-oligomeric complex involved in PSII repair...
September 26, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
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