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DNA-binding proteins

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https://www.readbyqxmd.com/read/29775751/expression-pattern-and-functional-analysis-of-the-two-ring-box-protein-rbx-in-spermatogenesis-of-chinese-mitten-crab-eriocheir-sinensis
#1
Jia-Shun Zhang, Xue-Jie Li, Lei Yang, Wei-Wei Li, Qun Wang
Studies in E. sinensis have shown that ubiquitination mediated by Cullin-RING E3 ligases (CRLs) plays important roles in spermatogenesis. In other species, CRLs are also essential in cell cycle progression, DNA replication, signal transduction, gene transcription, and development. The catalytic RING component, the RING box protein, is an important part of CRLs. However, there have been few studies on CRLs in crustaceans. In this study, we cloned two RING box protein genes from the Chinese mitten crab, Eriocheir sinensis, termed Es-RBX1 and Es-RBX2 The full length Es-RBX1 cDNA comprises 741 nucleotides, and encodes a protein of 124 amino acid residues, whereas the Es-RBX2 cDNA comprises 1325 nucleotides, and encodes a protein of 110 amino acid residues...
May 15, 2018: Gene
https://www.readbyqxmd.com/read/29775245/subunits-of-the-dna-polymerase-alpha-primase-complex-promote-notch-mediated-proliferation-with-discrete-and-shared-functions-in-c-elegans-germline
#2
Dong Suk Yoon, Dong Seok Cha, Mohammad A Alfhili, Brett D Keiper, Myon-Hee Lee
Notch receptor signaling is a highly conserved cell communication system in most multicellular organisms and plays a critical role at several junctures in animal development. In C. elegans, GLP-1/Notch signaling is essential for both germline stem cell maintenance and germ cell proliferation during gonad development. Here, we show that subunits (POLA-1, DIV-1, PRI-1, and PRI-2) of the DNA polymerase alpha-primase complex are required for germ cell proliferation in response to GLP-1/Notch signaling in different tissues at different developmental stages...
May 18, 2018: FEBS Journal
https://www.readbyqxmd.com/read/29774437/lexa-binds-to-transcription-regulatory-site-of-cell-division-gene-ftsz-in-toxic-cyanobacterium-microcystis-aeruginosa
#3
Takashi Honda, Daichi Morimoto, Yoshihiko Sako, Takashi Yoshida
Previously, we showed that DNA replication and cell division in toxic cyanobacterium Microcystis aeruginosa are coordinated by transcriptional regulation of cell division gene ftsZ and that an unknown protein specifically bound upstream of ftsZ (BpFz; DNA-binding protein to an upstream site of ftsZ) during successful DNA replication and cell division. Here, we purified BpFz from M. aeruginosa strain NIES-298 using DNA-affinity chromatography and gel-slicing combined with gel electrophoresis mobility shift assay (EMSA)...
May 17, 2018: Marine Biotechnology
https://www.readbyqxmd.com/read/29773845/aicar-inhibits-nf%C3%AE%C2%BAb-dna-binding-independently-of-ampk-to-attenuate-lps-triggered-inflammatory-responses-in-human-macrophages
#4
Johannes Kirchner, Bernhard Brüne, Dmitry Namgaladze
5-aminoimidazole-4-carboxamide-1-β-D-ribofuranoside (AICAR) is an established pharmacological activator of AMP-activated protein kinase (AMPK). Both, AICAR and AMPK were reported to attenuate inflammation. However, AICAR is known for many AMPK-independent effects, although the mechanisms remain incompletely understood. Here we report a potent suppression of lipopolysaccharide (LPS)-induced inflammatory gene expression by AICAR in primary human macrophages, which occurred independently of its conversion to AMPK-activating 5-aminoimidazole-4-carboxamide-1-β-D-ribofuranosyl monophosphate...
May 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29772714/modulating-chemosensitivity-of-tumors-to-platinum-based-antitumor-drugs-by-transcriptional-regulation-of-copper-homeostasis
#5
REVIEW
Yu-Hsuan Lai, Chin Kuo, Macus Tien Kuo, Helen H W Chen
Platinum (Pt)-based antitumor agents have been effective in treating many human malignancies. Drug importing, intracellular shuffling, and exporting-carried out by the high-affinity copper (Cu) transporter ( hCtr1 ), Cu chaperone (Ato x1), and Cu exporters (ATP7A and ATP7B), respectively-cumulatively contribute to the chemosensitivity of Pt drugs including cisplatin and carboplatin, but not oxaliplatin. This entire system can also handle Pt drugs via interactions between Pt and the thiol-containing amino acid residues in these proteins; the interactions are strongly influenced by cellular redox regulators such as glutathione...
May 16, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29772469/synthesis-of-steroidal-imidazolidinthiones-as-potential-apoptotic-agents-investigation-by-theoretical-and-experimental-studies
#6
Ayaz Mahmood Dar, Rizwan Nabi, Shafia Mir, Manzoor Ahmad Gatoo, Shamsuzzaman, Shabir H Lone
New steroidal imidazolidinthione derivatives (4-6) were synthesized from steroidal thiosemicarbazones and dichloroethane. The synthesized compounds were characterized using spectral data analysis. Theoretical DFT involving B3LYP/6-31G∗∗ level of theory was employed to gain insights into the molecular structure of the target compounds. MEPS and FMO analysis were carried out. HOMO-LUMO energy gap was determined which helped to evaluate various global descriptors like hardness, chemical potential, electronegativity, nucleophilicity and electrophilicity index, etc...
May 2, 2018: Bioorganic Chemistry
https://www.readbyqxmd.com/read/29772428/lncrna-h19-interacts-with-s-adenosylhomocysteine-hydrolase-to-regulate-line-1-methylation-in-human-lung-derived-cells-exposed-to-benzo-a-pyrene
#7
Ye Fu, Wubin Wang, Xuejing Li, Yanli Liu, Yingying Niu, Bin Zhang, Jisheng Nie, Baolong Pan, Ruisheng Wang, Jin Yang
Benzo [a]pyrene (BaP) have been demonstrated to induce lung cancer risk in humans and many different animal models, with aberrant gene methylation as one of the epigenetic errors; however, the molecular mechanisms remain unclear. Here, we used three types of human lung-derived cells with BaP exposure as a model and attempted to investigate the long non-coding RNA (lncRNA) H19/S-adenosylhomocysteine hydrolase (SAHH) pathway that regulates gene methylation in vitro exposure to BaP. Results showed that compared to the controls, BaP-treated cells H19 expressions were increased in a dose- and time-dependent manner, whereas SAHH protein expressions were decreased...
May 9, 2018: Chemosphere
https://www.readbyqxmd.com/read/29772230/replacing-c189-in-the-bzip-domain-of-zta-with-s-t-v-or-a-changes-dna-binding-specificity-to-four-types-of-double-stranded-dna
#8
Sreejana Ray, Desiree Tillo, Nima Assad, Aniekanabasi Ufot, Christopher Deppmann, Stewart R Durell, Aleksey Porollo, Charles Vinson
Zta is a bZIP transcription factor (TF) in the Epstein-Barr virus that binds unmethylated and methylated DNA sequences. Substitution of cysteine 189 of Zta to serine (Zta(C189S)) results in a virus that is unable to execute the lytic cycle which was attributed to a change in binding to methylated DNA sequences. To learn more about the role of this position in defining sequence-specific DNA binding, we mutated cysteine 189 to four other amino acids producing Zta(C189S), Zta(C189T), Zta(C189A), and Zta(C189V) mutants...
May 14, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29772028/randomized-phase-i-trial-hiv-core-003-depletion-of-serum-amyloid-p-component-and-immunogenicity-of-dna-vaccination-against-hiv-1
#9
Nicola J Borthwick, Thirusha Lane, Nathifa Moyo, Alison Crook, Jung Min Shim, Ian Baines, Edmund G Wee, Philip N Hawkins, Julian D Gillmore, Tomáš Hanke, Mark B Pepys
BACKGROUND: The failure of DNA vaccination in humans, in contrast to its efficacy in some species, is unexplained. Observational and interventional experimental evidence suggests that DNA immunogenicity may be prevented by binding of human serum amyloid P component (SAP). SAP is the single normal DNA binding protein in human plasma. The drug (R)-1-[6-[(R)-2-carboxypyrrolidin-1-yl]-6-oxo-hexanoyl]pyrrolidine-2-carboxylic acid (CPHPC, miridesap), developed for treatment of systemic amyloidosis and Alzheimer's disease, depletes circulating SAP by 95-99%...
2018: PloS One
https://www.readbyqxmd.com/read/29771928/chip-exo-interrogation-of-crp-dna-and-rnap-holoenzyme-interactions
#10
Haythem Latif, Stephen Federowicz, Ali Ebrahim, Janna Tarasova, Richard Szubin, Jose Utrilla, Karsten Zengler, Bernhard O Palsson
Numerous in vitro studies have yielded a refined picture of the structural and molecular associations between Cyclic-AMP receptor protein (Crp), the DNA motif, and RNA polymerase (RNAP) holoenzyme. In this study, high-resolution ChIP-exonuclease (ChIP-exo) was applied to study Crp binding in vivo and at genome-scale. Surprisingly, Crp was found to provide little to no protection of the DNA motif under activating conditions. Instead, Crp demonstrated binding patterns that closely resembled those generated by σ70...
2018: PloS One
https://www.readbyqxmd.com/read/29771376/rna-dna-and-dna-dna-base-pairing-at-the-upstream-edge-of-the-transcription-bubble-regulate-translocation-of-rna-polymerase-and-transcription-rate
#11
Maria KIreeva, Cyndi Trang, Gayane Matevosyan, Joshua Turek-Herman, Vitaly Chasov, Lucyna Lubkowska, Mikhail Kashlev
Translocation of RNA polymerase (RNAP) along DNA may be rate-limiting for transcription elongation. The Brownian ratchet model posits that RNAP rapidly translocates back and forth until the post-translocated state is stabilized by NTP binding. An alternative model suggests that RNAP translocation is slow and poorly reversible. To distinguish between these two models, we take advantage of an observation that pyrophosphorolysis rates directly correlate with the abundance of the pre-translocated fraction. Pyrophosphorolysis by RNAP stabilized in the pre-translocated state by bacteriophage HK022 protein Nun was used as a reference point to determine the pre-translocated fraction in the absence of Nun...
May 16, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29770276/the-evaluation-of-anoxia-responsive-e2f-dna-binding-activity-in-the-red-eared-slider-turtle-trachemys-scripta-elegans
#12
Kyle K Biggar, Kenneth B Storey
In many cases, the DNA-binding activity of a transcription factor does not change, while its transcriptional activity is greatly influenced by the make-up of bound proteins. In this study, we assessed the protein composition and DNA-binding ability of the E2F transcription factor complex to provide insight into cell cycle control in an anoxia tolerant turtle through the use of a modified ELISA protocol. This modification also permits the use of custom DNA probes that are tailored to a specific DNA binding region, introducing the ability to design capture probes for non-model organisms...
2018: PeerJ
https://www.readbyqxmd.com/read/29769404/dna-activates-the-nse2-mms21-sumo-e3-ligase-in-the-smc5-6-complex
#13
Nathalia Varejão, Eva Ibars, Jara Lascorz, Neus Colomina, Jordi Torres-Rosell, David Reverter
Modification of chromosomal proteins by conjugation to SUMO is a key step to cope with DNA damage and to maintain the integrity of the genome. The recruitment of SUMO E3 ligases to chromatin may represent one layer of control on protein sumoylation. However, we currently do not understand how cells upregulate the activity of E3 ligases on chromatin. Here we show that the Nse2 SUMO E3 in the Smc5/6 complex, a critical player during recombinational DNA repair, is directly stimulated by binding to DNA Activation of sumoylation requires the electrostatic interaction between DNA and a positively charged patch in the ARM domain of Smc5, which acts as a DNA sensor that subsequently promotes a stimulatory activation of the E3 activity in Nse2...
May 16, 2018: EMBO Journal
https://www.readbyqxmd.com/read/29769265/reciprocal-negative-regulation-between-lmx1a-and-lmo4-is-required-for-inner-ear-formation
#14
Yanhan Huang, Jennifer Hill, Andrew Yatteau, Loksum Wong, Tao Jiang, Jelena Petrovic, Lin Gan, Lijin Dong, Doris K Wu
LIM-domain containing transcription factors (LIM-TFs) are conserved factors important for embryogenesis. The specificity of these factors in transcriptional regulation is conferred by the complexes they form with other proteins such as LIM-domain-binding (Ldb) proteins and LIM-domain only (LMO) proteins. Unlike LIM-TF, these proteins do not bind DNA directly. LMO are negative regulators of LIM-TF and they function by competing with LIM-TFs for binding to Ldbs. Although the LIM-TF Lmx1a is expressed in the developing mouse hindbrain, which provides many of the extrinsic signals for inner ear formation, conditional knockout embryos of both sexes show that the inner ear source of Lmx1a is the major contributor of ear patterning...
May 16, 2018: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/29769246/small-molecule-positive-allosteric-modulators-of-the-%C3%AE-2-adrenoceptor-isolated-from-dna-encoded-libraries
#15
Seungkirl Ahn, Biswaranjan Pani, Alem W Kahsai, Eva K Olsen, Gitte Husemoen, Mikkel Vestrgaard, Lei Jin, Shuai Zhao, Laura M Wingler, Paula K Rambarat, Rishabh K Simhal, Thomas T Xu, Lillian D Sun, Paul J Shim, Dean P Staus, Li-Yin Huang, Thomas Franch, Xin Chen, Robert J Lefkowitz
Conventional drug discovery efforts at the β2 -adrenoceptor (β2 AR) have led to the development of ligands that bind almost exclusively to the receptor's hormone-binding orthosteric site. However, targeting the largely unexplored and evolutionarily unique allosteric sites has potential for developing more specific drugs with fewer side effects than orthosteric ligands. Using our recently developed approach for screening G protein-coupled receptors (GPCRs) with DNA-encoded small molecule libraries, we have discovered and characterized the first β2 AR small molecule positive allosteric modulators (PAMs) - compound-6 [(R)-N-(4-amino-1-(4-(tert-butyl)phenyl)-4-oxobutan-2-yl)-5-(N-isopropyl-N-methylsulfamoyl)-2-((4-methoxyphenyl) thio)benzamide] and its analogs...
May 16, 2018: Molecular Pharmacology
https://www.readbyqxmd.com/read/29769162/increased-pregnancy-losses-following-serial-somatic-cell-nuclear-transfer-in-goats
#16
Min Yang, Iuri Perisse, Zhiqiang Fan, Misha Regouski, Mirella Meyer-Ficca, Irina A Polejaeva
Serial cloning by somatic cell nuclear transfer (SCNT) is a critical tool for the expansion of precious transgenic lines or resetting the lifespan of primary transgenic cells for multiple genetic modifications. We successfully produced second-generation cloned goats using donor neonatal fibroblasts from first-generation clones. However, our attempts to produce any third-generation clones failed. SCNT efficiency decreased progressively with the clonal generations. The rate of pregnancy loss was significantly greater in recloning groups (P<0...
May 17, 2018: Reproduction, Fertility, and Development
https://www.readbyqxmd.com/read/29768267/type-2-diabetes-promotes-cell-centrosome-amplification-via-akt-ros-dependent-signalling-of-rock1-and-14-3-3%C3%AF
#17
Pu Wang, Yu Cheng Lu, Jie Wang, Lan Wang, Hanry Yu, Yuan Fei Li, Alice Kong, Juliana Chan, Shaochin Lee
BACKGROUND/AIMS: Type 2 diabetes is associated with oxidative stress and DNA damage which can cause centrosome amplification. Thus, the study investigated centrosome amplification in type 2 diabetes and the underlying mechanisms. METHODS: Centrosome numbers in human peripheral blood mononuclear blood cells (PBMC) from healthy subjects and patients with type 2 diabetes were compared to access the association between type 2 diabetes and centrosome amplification. Colon cancer cells were used to investigate the molecular mechanisms underlying the centrosome amplification triggered by high glucose, insulin and palmitic acid...
May 11, 2018: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29767969/single-molecule-imaging-reveals-conformational-manipulation-of-holliday-junction-dna-by-the-junction-processing-protein-ruva
#18
Dalton Gibbs, Soma Dhakal
Interactions between DNA and motor proteins regulate nearly all biological functions of DNA such as gene expression, DNA replication and repair, and transcription. During the late stages of homologous recombination (HR), the Escherichia coli recombination machinery, RuvABC, resolves the four-way DNA motifs called Holliday junctions (HJs) that are formed during exchange of nucleotide sequences between two homologous duplex DNA. Although the formation of RuvA-HJ complex is known to be the first critical step in the RuvABC pathway, the mechanism for the binding interaction between RuvA and HJ has remained elusive...
May 16, 2018: Biochemistry
https://www.readbyqxmd.com/read/29767241/transcriptome-sequencing-analysis-reveals-the-effect-of-combinative-treatment-with-low%C3%A2-intensity-pulsed-ultrasound-and-magnesium-ions-on-hfob1-19-human-osteoblast-cells
#19
Haiyue Zu, Xueting Yi, Dewei Zhao
Biodegradable magnesium (Mg) materials are considered ideal as osteosynthesis implants. However, clinical application has proven complex. This is primarily associated with the issue of reducing the extent of implant degradation to a range acceptable for the human body, while simultaneously enhancing osteogenesis or osteoinduction. In the present study, a combination of Mg ions and low‑intensity pulsed ultrasound (LIPUS) treatment was applied in hFOB 1.19 human osteoblast cells as a potential strategy to resolve this issue...
May 11, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29766280/novel-insights-into-nucleoamino-acids-biomolecular-recognition-and-aggregation-studies-of-a-thymine-conjugated-l-phenyl-alanine
#20
Giovanni N Roviello
This article deals with the synthesis in solid phase and characterization of a nucleoamino amide, based on a phenylalaninamide moiety which was N-conjugated to a thymine nucleobase. In analogy to the natural nucleobase-amino acid conjugates, endowed with a wide range of biological properties, the nucleoamino amide interacts with single-stranded nucleic acids as verified in DNA- and RNA-binding assays conducted by CD and UV spectroscopies. These technologies were used to show also that this conjugate binds serum proteins altering significantly their secondary structure, as evidenced by CD and UV using BSA as a model...
May 15, 2018: Amino Acids
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