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Protein dna interaction

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https://www.readbyqxmd.com/read/29244742/fibrinogen-gamma-chain-mutations-provoke-fibrinogen-and-apolipoprotein-b-plasma-deficiency-and-liver-storage
#1
Francesco Callea, Isabella Giovannoni, Sinan Sari, Esendagli Guldal, Buket Dalgic, Gulen Akyol, Tsuyoshi Sogo, Abdulrahman Al-Hussaini, Giuseppe Maggiore, Andrea Bartuli, Renata Boldrini, Paola Francalanci, Emanuele Bellacchio
p.R375W (Fibrinogen Aguadilla) is one out of seven identified mutations (Brescia, Aguadilla, Angers, Al du Pont, Pisa, Beograd, and Ankara) causing hepatic storage of the mutant fibrinogen γ. The Aguadilla mutation has been reported in children from the Caribbean, Europe, Japan, Saudi Arabia, Turkey, and China. All reported children presented with a variable degree of histologically proven chronic liver disease and low plasma fibrinogen levels. In addition, one Japanese and one Turkish child had concomitant hypo-APOB-lipoproteinemia of unknown origin...
December 15, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29244486/going-vertical-to-improve-the-accuracy-of-atomic-force-microscopy-based-single-molecule-force-spectroscopy
#2
Robert Walder, William J Van Patten, Ayush Adhikari, Thomas T Perkins
Single-molecule force spectroscopy (SMFS) is a powerful technique to characterize the energy landscape of individual proteins, the mechanical properties of nucleic acids, and the strength of receptor-ligand interactions. Atomic-force-microscopy (AFM)-based SMFS benefits from ongoing progress in improving the precision and stability of cantilevers and the AFM itself. Underappreciated is that the accuracy of such AFM studies remains hindered by inadvertently stretching molecules at an angle while measuring only the vertical component of the force and extension, degrading both measurements...
December 15, 2017: ACS Nano
https://www.readbyqxmd.com/read/29244169/circular-dichroism-spectroscopic-study-on-structural-alterations-of-histones-induced-by-post-translational-modifications-in-dna-damage-responses-lysine-9-methylation-of-h3
#3
Yudai Izumi, Koichi Matsuo, Kentaro Fujii, Akinari Yokoya, Masaki Taniguchi, Hirofumi Namatame
We report the global structural alterations in histone H3 proteins induced by lysine-9 mono-, di- and trimethylation, which are part of the critical post-translational modifications for DNA damage responses, identified using synchrotron radiation circular dichroism (CD) spectroscopy. Compared with unmodified H3, mono- and dimethylation increases the number of α-helices and decreases the numbers of β-strands, while trimethylation decreases the α-helix content and increases the β-strand content. Comparison of the secondary-structure contents of these histone H3 proteins suggests that the methylation-induced structural alterations occur at residues not only close to but also distant from the methylated sites...
December 13, 2017: Journal of Radiation Research
https://www.readbyqxmd.com/read/29244163/regulation-of-chromosome-segregation-in-oocytes-and-the-cellular-basis-for-female-meiotic-errors
#4
Jessica Greaney, Zhe Wei, Hayden Homer
BACKGROUND: Meiotic chromosome segregation in human oocytes is notoriously error-prone, especially with ageing. Such errors markedly reduce the reproductive chances of increasing numbers of women embarking on pregnancy later in life. However, understanding the basis for these errors is hampered by limited access to human oocytes. OBJECTIVE AND RATIONALE: Important new discoveries have arisen from molecular analyses of human female recombination and aneuploidy along with high-resolution analyses of human oocyte maturation and mouse models...
December 13, 2017: Human Reproduction Update
https://www.readbyqxmd.com/read/29244158/znf830-mediates-cancer-chemoresistance-through-promoting-homologous-recombination-repair
#5
Guo Chen, Jianxiang Chen, Yiting Qiao, Yaru Shi, Wei Liu, Qi Zeng, Hui Xie, Xiaorui Shi, Youwei Sun, Xu Liu, Tongyu Li, Liqian Zhou, Jianqin Wan, Tian Xie, Hangxiang Wang, Fu Wang
Homologous recombination (HR), which mediates the repair of DNA double-strand breaks (DSB), is crucial for maintaining genomic integrity and enhancing survival in response to chemotherapy and radiotherapy in human cancers. However, the mechanisms of HR repair in treatment resistance for the improvement of cancer therapy remains unclear. Here, we report that the zinc finger protein 830 (ZNF830) promotes HR repair and the survival of cancer cells in response to DNA damage. Mechanistically, ZNF830 directly participates in DNA end resection via interacting with CtIP and regulating CtIP recruitment to DNA damage sites...
December 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29244022/the-structural-basis-for-dynamic-dna-binding-and-bridging-interactions-which-condense-the-bacterial-centromere
#6
Gemma Lm Fisher, César L Pastrana, Victoria A Higman, Alan Koh, James A Taylor, Annika Butterer, Timothy Craggs, Frank Sobott, Heath Murray, Matthew P Crump, Fernando Moreno-Herrero, Mark S Dillingham
The ParB protein forms DNA bridging interactions around parS to condense DNA and earmark the bacterial chromosome for segregation. The molecular mechanism underlying the formation of these ParB networks is unclear. We show here that while the central DNA binding domain is essential for anchoring at parS, this interaction is not required for DNA condensation. Structural analysis of the C-terminal domain reveals a dimer with a lysine-rich surface that binds DNA non-specifically and is essential for DNA condensation in vitro...
December 15, 2017: ELife
https://www.readbyqxmd.com/read/29243212/controlling-centriole-numbers-geminin-family-members-as-master-regulators-of-centriole-amplification-and-multiciliogenesis
#7
REVIEW
Marina Arbi, Dafni-Eleftheria Pefani, Stavros Taraviras, Zoi Lygerou
To ensure that the genetic material is accurately passed down to daughter cells during mitosis, dividing cells must duplicate their chromosomes and centrosomes once and only once per cell cycle. The same key steps-licensing, duplication, and segregation-control both the chromosome and the centrosome cycle, which must occur in concert to safeguard genome integrity. Aberrations in genome content or centrosome numbers lead to genomic instability and are linked to tumorigenesis. Such aberrations, however, can also be part of the normal life cycle of specific cell types...
December 14, 2017: Chromosoma
https://www.readbyqxmd.com/read/29242641/ubiquitin-ligases-in-oncogenic-transformation-and-cancer-therapy
#8
REVIEW
Daniela Senft, Jianfei Qi, Ze'ev A Ronai
The cellular response to external stress signals and DNA damage depends on the activity of ubiquitin ligases (E3s), which regulate numerous cellular processes, including homeostasis, metabolism and cell cycle progression. E3s recognize, interact with and ubiquitylate protein substrates in a temporally and spatially regulated manner. The topology of the ubiquitin chains dictates the fate of the substrates, marking them for recognition and degradation by the proteasome or altering their subcellular localization or assembly into functional complexes...
December 15, 2017: Nature Reviews. Cancer
https://www.readbyqxmd.com/read/29242605/ddias-suppresses-trail-mediated-apoptosis-by-inhibiting-disc-formation-and-destabilizing-caspase-8-in-cancer-cells
#9
Joo-Young Im, Bo-Kyung Kim, Ji-Young Lee, Seung-Ho Park, Hyun Seung Ban, Kyeong Eun Jung, Misun Won
DNA damage-induced apoptosis suppressor (DDIAS) has an anti-apoptotic function during DNA damage in lung cancer. However, the anti-apoptotic mechanism of DDIAS in cancer cells under other conditions has not been reported. We report here that DDIAS protects cancer cells from tumor necrosis factor-related apoptosis-inducing ligand (TRAIL)-induced apoptosis by two distinct mechanisms in non-small cell lung cancer (NSCLC) and hepatocellular carcinoma (HCC) cells. DDIAS depletion sensitized NSCLC and HCC cells to TRAIL-mediated apoptosis, an effect that was abrogated by pharmacological or genetic inhibition of caspase-8 and was independent of caspase-9, p53, or mitogen-activated protein kinase signaling...
December 15, 2017: Oncogene
https://www.readbyqxmd.com/read/29242386/dosage-dependent-expression-variation-suppressed-on-the-drosophila-male-x-chromosome
#10
Hangnoh Lee, Dong-Yeon Cho, Damian Wojtowicz, Susan T Harbison, Steven Russell, Brian Oliver, Teresa Przytycka
DNA copy number variation is associated with many high phenotypic heterogeneity disorders. We systematically examined the impact of Drosophila melanogaster deletions on gene expression profiles to ask if increased expression variability due to reduced gene dose might underlie this phenotypic heterogeneity. Indeed, we find that one dose genes have higher gene expression variability relative to two dose genes. We then asked if this increase in variability could be explained by intrinsic noise within cells, due to stochastic biochemical events, or if expression variability is due to extrinsic noise arising from more complex interactions...
December 13, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29241329/epitope-binning-assay-using-an-electron-transfer-modulated-aptamer-sensor
#11
Min Li, Xudong Guo, Hui Li, Xiaolei Zuo, Rongzhang Hao, Hongbin Song, Ali Aldalbahi, Zhilei Ge, Jiang Li, Qian Li, Shiping Song, Shaohua Li, Ningsheng Shao, Chunhai Fan, Lihua Wang
Surface plasmon resonance (SPR) and quartz crystal microbalance (QCM) are workhorses of protein-DNA interaction research for over 20 years, providing ways to quantitatively determine the protein-DNA binding. However, the cost, necessary technical expertise and severe non-specific adsorption poses barriers to their use. Convenient and effective techniques for the measurement of protein-DNA binding affinity and the epitope binning between DNA and proteins for developing highly sensitive detection platform remain challenging...
December 15, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29240809/interaction-mode-of-cide-family-proteins-in-fly-drep1-and-drep3-acidic-surfaces-interact-with-drep2-and-drep4-basic-surfaces
#12
Chang Min Kim, Sun Hee Jeon, Jun-Hyuk Choi, Jun Hyuck Lee, Hyun Ho Park
Cell death-inducing DNA fragmentation factor 45 (DFF45)-like effector (CIDE) domains were initially identified as protein interaction modules in apoptotic nucleases and are now known to form a highly conserved family with diverse functions that range from cell death to lipid homeostasis. In the fly, four CIDE domain-containing proteins (DFF-related protein [DREP]-1-4) and their functions, including interaction relationships, have been identified. In this study, we introduced and investigated acidic side-disrupted mutants of DREP1, DREP2, and DREP3...
2017: PloS One
https://www.readbyqxmd.com/read/29240261/mitochondrial-dysfunction-rad51-and-ku80-proteolysis-promote-apoptotic-effects-of-dinaciclib-in-bcl-xl-silenced-cells
#13
Daniel R Premkumar, Esther P Jane, Swetha Thambireddy, Philip A Sutera, Jonathon M Cavaleri, Ian F Pollack
In the present study, we investigated the effect of CDK inhibitors (ribociclib, palbociclib, seliciclib, AZD5438 and dinaciclib) on malignant human glioma cells for cell viability, apoptosis, oxidative stress and mitochondrial function using various assays. None of the CDK inhibitors induced cell death at a clinically relevant concentration. However, low nanomolar concentrations of dinaciclib showed higher cytotoxic activity against Bcl-xL silenced cells in a time- and concentration-dependent manner. This effect was not seen with other CDK inhibitors...
December 14, 2017: Molecular Carcinogenesis
https://www.readbyqxmd.com/read/29239233/in-vitro-metabolism-study-of-a-novel-p38-kinase-inhibitor-in-silico-predictions-structure-elucidation-using-ms-ms-i
#14
Hanaa Ma Hashem, Marianne A Mahrouse
AIM: Metabolism study of PH-797804, a promising newly developed drug for treatment of chronic inflammation which inhibits P38 mitogen-activated protein kinase. MATERIALS & METHODS: Susceptibility of PH-797804 to metabolism was first investigated using SMARTCyp and Xenosite web servers. Molecular docking of the drug into CYP3A4 crystal structures evaluated binding interactions with active site. The predicted results were confirmed by in vitro incubation with rat S9 fraction...
December 14, 2017: Future Medicinal Chemistry
https://www.readbyqxmd.com/read/29236673/zbp1-innate-sensor-regulating-cell-death-and-inflammation
#15
REVIEW
Teneema Kuriakose, Thirumala-Devi Kanneganti
Z-DNA-binding protein 1 (ZBP1), initially reported as an interferon (IFN)-inducible tumor-associated protein, harbors nucleic acid-binding domains for left-handed helix (Z-form) and receptor-interacting protein homotypic interaction motif (RHIM) domains for protein homotypic interactions. Recent studies have identified ZBP1 as an innate sensor of viral infections and a target of viral evasion strategies, regulating cell death, inflammasome activation, and proinflammatory responses. ZBP1 also functions during development and can trigger perinatal lethality when its RHIM-dependent interactions are not restricted...
November 24, 2017: Trends in Immunology
https://www.readbyqxmd.com/read/29236325/aml1-eto-trans-activates-c-kit-expression-through-the-long-range-interaction-between-promoter-and-intronic-enhancer
#16
Ying Tian, Genjie Wang, Qingzhu Hu, Xichun Xiao, Shuxia Chen
The AML1/ETO onco-fusion protein is crucial for the genesis of t(8;21) acute myeloid leukemia (AML) and is well documented as a transcriptional repressor through dominant-negative effect. However, little is known about the transactivation mechanism of AML1/ETO. Through large cohort of patient's expression level data analysis and a series of experimental validation, we report here that AML1/ETO transactivates c-KIT expression through directly binding to and mediating the long-range interaction between the promoter and intronic enhancer regions of c-KIT...
December 13, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/29234590/an-integrative-analysis-of-dna-methylation-in-osteosarcoma
#17
Jie Xu, Deng Li, Zhiqing Cai, Yingbin Zhang, Yulin Huang, Baohua Su, Ruofan Ma
Background: The study aimed to analyze aberrantly methylated genes, relevant pathways and transcription factors (TFs) in osteosarcoma (OS) development. Methods: Based on the DNA methylation microarray data GSE36002 that were downloaded from GEO database, the differentially methylated genes in promoter regions were identified between OS and normal samples. Pathway and function enrichment analyses of differentially methylated genes was performed. Subsequently, protein-protein interaction (PPI) network was constructed, followed by identification of cancer-associated differentially methylated genes and significant differentially methylated TFs...
November 2017: Journal of Bone Oncology
https://www.readbyqxmd.com/read/29234047/inhibition-of-nhej-repair-by-type-ii-a-crispr-cas-systems-in-bacteria
#18
Aude Bernheim, Alicia Calvo-Villamañán, Clovis Basier, Lun Cui, Eduardo P C Rocha, Marie Touchon, David Bikard
Type II CRISPR-Cas systems introduce double-strand breaks into DNA of invading genetic material and use DNA fragments to acquire novel spacers during adaptation. These breaks can be the substrate of several DNA repair pathways, paving the way for interactions. We report that non-homologous end-joining (NHEJ) and type II-A CRISPR-Cas systems only co-occur once among 5563 fully sequenced prokaryotic genomes. We investigated experimentally the possible molecular interactions using the NHEJ pathway from Bacillus subtilis and the type II-A CRISPR-Cas systems from Streptococcus thermophilus and Streptococcus pyogenes...
December 12, 2017: Nature Communications
https://www.readbyqxmd.com/read/29233925/a20-regulates-the-dna-damage-response-and-mediates-tumor-cell-resistance-to-dna-damaging-therapy
#19
Chuanzhen Yang, Weicheng Zang, Zefang Tang, Yapeng Ji, Ruidan Xu, Yongfeng Yang, Aiping Luo, Bin Hu, Zemin Zhang, Zhihua Liu, Xiaofeng Zheng
A competent DNA damage response (DDR) helps prevent cancer, but once cancer has arisen DDR can blunt the efficacy of chemotherapy and radiotherapy which cause lethal DNA breakage in cancer cells. Thus, blocking DDR may improve the efficacy of these modalities. Here we report a new DDR mechanism that interfaces with inflammatory signaling and might be blocked to improve anticancer outcomes. Specifically, we report that the ubiquitin-editing enzyme A20 binds and inhibits the E3 ubiquitin ligase RNF168, which is responsible for regulating histone H2A turnover critical for proper DNA repair...
December 12, 2017: Cancer Research
https://www.readbyqxmd.com/read/29232693/host-factors-that-promote-retrotransposon-integration-are-similar-in-distantly-related-eukaryotes
#20
Sudhir Kumar Rai, Maya Sangesland, Michael Lee, Caroline Esnault, Yujin Cui, Atreyi Ghatak Chatterjee, Henry L Levin
Retroviruses and Long Terminal Repeat (LTR)-retrotransposons have distinct patterns of integration sites. The oncogenic potential of retrovirus-based vectors used in gene therapy is dependent on the selection of integration sites associated with promoters. The LTR-retrotransposon Tf1 of Schizosaccharomyces pombe is studied as a model for oncogenic retroviruses because it integrates into the promoters of stress response genes. Although integrases (INs) encoded by retroviruses and LTR-retrotransposons are responsible for catalyzing the insertion of cDNA into the host genome, it is thought that distinct host factors are required for the efficiency and specificity of integration...
December 12, 2017: PLoS Genetics
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