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https://www.readbyqxmd.com/read/28110333/requirements-for-septal-localization-and-chromosome-segregation-activity-of-the-dna-translocase-sfta-from-bacillus-subtilis
#1
Nina El Najjar, Christine Kaimer, Thomas Rösch, Peter L Graumann
Bacillus subtilis possesses 2 DNA translocases that affect late stages of chromosome segregation: SftA separates nonsegregated DNA prior to septum closure, while SpoIIIE rescues septum-entrapped DNA. We provide evidence that SftA is associated with the division machinery via a stretch of 47 amino acids within its N-terminus, suggesting that SftA is recruited by protein-protein interactions with a component of the division machinery. SftA was also recruited to mid-cell in the absence of its first 20 amino acids, which are proposed to contain a membrane-binding motif...
January 21, 2017: Journal of Molecular Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28110185/computational-analysis-of-amsacrine-resistance-in-human-topoisomerase-ii-alpha-mutants-r487k-and-e571k-using-homology-modeling-docking-and-all-atom-molecular-dynamics-simulation-in-explicit-solvent
#2
Safaa Sader, Chun Wu
Amsacrine is an effective topoisomerase II enzyme inhibitor in acute lymphatic leukemia. Previous experimental studies have successfully identified two important mutations (R487K and E571K) conferring 100 and 25 fold resistance to Amsacrine respectively. Although the reduction of the cleavage ligand-DNA-protein ternary complex has been well thought as the major cause of drug resistance, the detailed energetic, structural and dynamic mechanisms remain to be elusive. In this study, we constructed human topoisomerase II alpha (hTop2α) homology model docked with Amsacrine based on crystal structure of human Top2β in complex with etoposide...
January 4, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28109299/in-utero-exposure-to-germinated-brown-rice-and-its-oryzanol-rich-extract-attenuated-high-fat-diet-induced-insulin-resistance-in-f1-generation-of-rats
#3
Hadiza Altine Adamu, Mustapha Umar Imam, Der-Jiun Ooi, Norhaizan Mohd Esa, Rozita Rosli, Maznah Ismail
BACKGROUND: The development of insulin resistance is multifactorial, with maternal pre- and postnatal nutrition having significant influences. In this regard, high fat diet (HFD) feeding in pregnancy has been shown to increase risks of metabolic diseases. Thus, we investigated the effects of supplementation of HFD with germinated brown rice (GBR) and GBR-derived gamma oryzanol-rich extract (OE) on insulin resistance and its epigenetic implications in pregnant rats and their offsprings...
January 21, 2017: BMC Complementary and Alternative Medicine
https://www.readbyqxmd.com/read/28108764/letr-is-a-tetr-family-transcription-factor-from-lysobacter-controlling-antifungal-antibiotic-biosynthesis
#4
Ping Wang, Hongfu Chen, Guoliang Qian, Fengquan Liu
Heat-stable antifungal factor (HSAF) is a newly identified and broad-spectrum antifungal antibiotic from Lysobacter enzymogenes, a ubiquitous environmental proteobacterium. Yet, the regulatory mechanism for HSAF biosynthesis in L. enzymogenes remains poorly understood. Here, we report the identification of a TetR-family protein Le1552 (LetR) from L. enzymogenes strain OH11 that is involved in transcriptional repression of HSAF production. Bacterial one-hybrid and gel mobility shift assays show that LetR directly binds to PHSAF (the promoter region of the HSAF biosynthesis operon)...
January 20, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28108532/tdp-43-prions
#5
Takashi Nonaka, Masato Hasegawa
The most common neurodegenerative diseases, such as Alzheimer's, Parkinson's, and amyotrophic lateral sclerosis, are all protein-misfolding diseases and are characterized by the presence of disease-specific protein aggregates in affected neuronal cells. Recent studies have shown that, like tau and α-synuclein, TAR-DNA binding protein of 43 kDa (TDP-43) can form aggregates in vitro in a seed-dependent, self-templating, prion-like manner. Insoluble TDP-43 prepared from the brains of patients has been classified into several strains, which can be transferred from cell to cell in vitro, suggesting the involvement of mechanisms reminiscent of those by which prions spread through the nervous system...
January 20, 2017: Cold Spring Harbor Perspectives in Medicine
https://www.readbyqxmd.com/read/28108011/interference-between-triplex-and-protein-binding-to-distal-sites-on-supercoiled-dna
#6
Agnes Noy, Anthony Maxwell, Sarah A Harris
We have explored the interdependence of the binding of a DNA triplex and a repressor protein to distal recognition sites on supercoiled DNA minicircles using MD simulations. We observe that the interaction between the two ligands through their influence on their DNA template is determined by a subtle interplay of DNA mechanics and electrostatics, that the changes in flexibility induced by ligand binding play an important role and that supercoiling can instigate additional ligand-DNA contacts that would not be possible in simple linear DNA sequences...
January 17, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28107987/generation-of-biostable-l-aptamers-against-achiral-targets-by-chiral-inversion-of-existing-d-aptamers
#7
Huapei Chen, Sitao Xie, Hao Liang, Cuichen Wu, Liang Cui, Shuang-Yan Huan, Xiaobing Zhang
In this paper, based on reciprocal chiral substrate specificity, taking achiral molecules, ethanolamine (EA) and malachite green (MG) as two model targets, biostable L- DNA aptamers and L-RNA aptamers were generated respectively by chiral inversion of existing D-aptamers. In the detection of EA with L-DNA aptamer-based sensors, the feasibility of our strategy was confirmed, while in the detection of MG with L-RNA aptamers, linear calibration curves were obtained in the range from 0.1 to 5µm with the detection limit of 0...
March 1, 2017: Talanta
https://www.readbyqxmd.com/read/28107917/binding-induced-strand-displacement-amplification-for-homogeneous-protein-assay
#8
Yubin Li, Sheng Liu, Zike Zhao, Yuner Zheng, Zirui Wang
An ultrasensitive and homogenous strategy for protein assay was established based upon binding-induced strand displacement amplification (BI-SDA). Binding-Induced DNA strand-displacement occurred between Apt-T•signal DNA and Apt-C, and release of signal DNA upon addition of platelet-derived growth factor (PDGF BB). The released signal DNA further hybridized with multifunctional hairpin DNA probe and induced the strand-displacement amplification in the presence of Klenow Fragment (exo(-)) and dNTPs. The BI-SDA product contain G-quaruplex DNA, which could be recognized and reported by the fluorescence of fluorochrome N-methyl porphyrin propionic acid IX (NMM)...
March 1, 2017: Talanta
https://www.readbyqxmd.com/read/28107820/evidence-against-a-role-for-jaagsiekte-sheep-retrovirus-in-human-lung-cancer
#9
A Dusty Miller, Marcelo De Las Heras, Jingyou Yu, Fushun Zhang, Shan-Lu Liu, Andrew E Vaughan, Thomas L Vaughan, Raul Rosadio, Stefano Rocca, Giuseppe Palmieri, James J Goedert, Junya Fujimoto, Ignacio I Wistuba
BACKGROUND: Jaagsiekte sheep retrovirus (JSRV) causes a contagious lung cancer in sheep and goats that can be transmitted by aerosols produced by infected animals. Virus entry into cells is initiated by binding of the viral envelope (Env) protein to a specific cell-surface receptor, Hyal2. Unlike almost all other retroviruses, the JSRV Env protein is also a potent oncoprotein and is responsible for lung cancer in animals. Of concern, Hyal2 is a functional receptor for JSRV in humans. RESULTS: We show here that JSRV is fully capable of infecting human cells, as measured by its reverse transcription and persistence in the DNA of cultured human cells...
January 20, 2017: Retrovirology
https://www.readbyqxmd.com/read/28107649/rpa-interacts-with-hira-and-regulates-h3-3-deposition-at-gene-regulatory-elements-in-mammalian-cells
#10
Honglian Zhang, Haiyun Gan, Zhiquan Wang, Jeong-Heon Lee, Hui Zhou, Tamas Ordog, Marc S Wold, Mats Ljungman, Zhiguo Zhang
The histone chaperone HIRA is involved in depositing histone variant H3.3 into distinct genic regions, including promoters, enhancers, and gene bodies. However, how HIRA deposits H3.3 to these regions remains elusive. Through a short hairpin RNA (shRNA) screening, we identified single-stranded DNA binding protein replication protein A (RPA) as a regulator of the deposition of newly synthesized H3.3 into chromatin. We show that RPA physically interacts with HIRA to form RPA-HIRA-H3.3 complexes, and it co-localizes with HIRA and H3...
January 19, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28107648/parp-1-controls-the-adipogenic-transcriptional-program-by-parylating-c-ebp%C3%AE-and-modulating-its-transcriptional-activity
#11
Xin Luo, Keun Woo Ryu, Dae-Seok Kim, Tulip Nandu, Carlos J Medina, Rebecca Gupte, Bryan A Gibson, Raymond E Soccio, Yonghao Yu, Rana K Gupta, W Lee Kraus
Poly(ADP-ribosyl)ation (PARylation) is a post-translational modification of proteins mediated by PARP family members, such as PARP-1. Although PARylation has been studied extensively, few examples of definitive biological roles for site-specific PARylation have been reported. Here we show that C/EBPβ, a key pro-adipogenic transcription factor, is PARylated by PARP-1 on three amino acids in a conserved regulatory domain. PARylation at these sites inhibits C/EBPβ's DNA binding and transcriptional activities and attenuates adipogenesis in various genetic and cell-based models...
January 19, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28107481/bet-inhibitors-disrupt-rad21-dependent-conformational-control-of-kshv-latency
#12
Horng-Shen Chen, Alessandra De Leo, Zhuo Wang, Andrew Kerekovic, Robert Hills, Paul M Lieberman
Kaposi's Sarcoma-associated Herpesvirus (KSHV) establishes stable latent infection in B-lymphocytes and pleural effusion lymphomas (PELs). During latency, the viral genome persists as an epigenetically constrained episome with restricted gene expression programs. To identify epigenetic regulators of KSHV latency, we screened a focused small molecule library containing known inhibitors of epigenetic factors. We identified JQ1, a Bromodomain and Extended Terminal (BET) protein inhibitor, as a potent activator of KSHV lytic reactivation from B-cells carrying episomal KSHV...
January 20, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28107006/facilitated-diffusion-of-transcription-factor-proteins-with-anomalous-bulk-diffusion
#13
Lin Liu, Andrey G Cherstvy, Ralf Metzler
What are the physical laws of the diffusive search of proteins for their specific binding sites on DNA in the presence of the macromolecular crowding in cells? We performed extensive computer simulations to elucidate the protein target search on DNA. The novel feature is the viscoelastic non-Brownian protein bulk diffusion recently observed experimentally. We examine the influence of the protein-DNA binding affinity and the anomalous diffusion exponent on the target search time. In all cases an optimal search time is found...
January 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28106189/microsolvation-of-the-pyrrole-cation-py-with-nonpolar-and-polar-ligands-infrared-spectra-of-py-ln-with-l-ar-n2-and-h2o-n-%C3%A2-3
#14
Markus Schütz, Yoshiteru Matsumoto, Aude Bouchet, Murat Öztürk, Otto Dopfer
The solvation of aromatic (bio-)molecular building blocks has a strong impact on the intermolecular interactions and function of supramolecular assemblies, proteins, and DNA. Herein we characterize the initial microsolvation process of the heterocyclic aromatic pyrrole cation (Py(+)) in its (2)A2 ground electronic state with nonpolar, quadrupolar, and dipolar ligands (L = Ar, N2, and H2O) by infrared photodissociation (IRPD) spectroscopy of cold mass-selected Py(+)-Ln (n ≤ 3) clusters in a molecular beam and dispersion-corrected density functional theory calculations at the B3LYP-D3/aug-cc-pVTZ level...
January 20, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28106119/early-secreted-antigenic-target-of-6-kda-of-mycobacterium-tuberculosis-stimulates-il-6-production-by-macrophages-through-activation-of-stat3
#15
Bock-Gie Jung, Xisheng Wang, Na Yi, Justin Ma, Joanne Turner, Buka Samten
As early secreted antigenic target of 6 kDa (ESAT-6) of Mycobacterium tuberculosis (Mtb) is an essential virulence factor and macrophages are critical for tuberculosis infection and immunity, we studied ESAT-6 stimulated IL-6 production by macrophages. ESAT-6 stimulated significantly higher IL-6 secretion by murine bone marrow derived macrophages (BMDM) compared to culture filtrate protein 10 kDa (CFP10) and antigen 85A. Polymyxin B, an LPS blocker, did not affect ESAT-6 stimulated macrophage IL-6 production...
January 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28105927/candidate-snp-markers-of-aggressiveness-related-complications-and-comorbidities-of-genetic-diseases-are-predicted-by-a-significant-change-in-the-affinity-of-tata-binding-protein-for-human-gene-promoters
#16
Irina V Chadaeva, Mikhail P Ponomarenko, Dmitry A Rasskazov, Ekaterina B Sharypova, Elena V Kashina, Marina Yu Matveeva, Tatjana V Arshinova, Petr M Ponomarenko, Olga V Arkova, Natalia P Bondar, Ludmila K Savinkova, Nikolay A Kolchanov
BACKGROUND: Aggressiveness in humans is a hereditary behavioral trait that mobilizes all systems of the body-first of all, the nervous and endocrine systems, and then the respiratory, vascular, muscular, and others-e.g., for the defense of oneself, children, family, shelter, territory, and other possessions as well as personal interests. The level of aggressiveness of a person determines many other characteristics of quality of life and lifespan, acting as a stress factor. Aggressive behavior depends on many parameters such as age, gender, diseases and treatment, diet, and environmental conditions...
December 28, 2016: BMC Genomics
https://www.readbyqxmd.com/read/28105698/characterization-and-in-vivo-regulon-determination-of-an-ecf-sigma-factor-and-its-cognate-anti-sigma-factor-in-nostoc-punctiforme
#17
Nicole Bell, Jamie J Lee, Michael L Summers
Based on primary sequence comparisons and genomic context, Npun_F4153 (SigG)/Npun_F4154 (SapG) of the cyanobacterium Nostoc punctiforme were hypothesized to encode an ECF sigma factor/anti-sigma factor pair. Transcription of sigG increased in heterocysts and akinetes, and after EDTA treatment. Interaction between SigG and the predicted cytoplasmic domain of SapG was observed in vitro. A SigG-GFP translational fusion protein localized to the periphery of vegetative cells in vivo, but lost this association following heat stress...
January 20, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28105234/interaction-of-cyclophilin-a-with-a-novel-binding-protein-sr-25-and-characterization-of-their-expression-pattern-in-chinese-hepatocellular-carcinoma-patients
#18
Jian Chen, Ning Li, Peiwen Lian, Jiahui Wang, Peng Li, Zhaohua Gong, Lixin Jiang
Cyclophilin (Cyp) A has been reported to be overexpressed in the majority of cancer cells, including hepatocellular carcinoma (HCC). However, the biological functions of CypA in HCC are far from being understood. To determine the biological functions of CypA in HCC, the present study screened human fetal liver complementary DNA for proteins interacting with CypA using the yeast two-hybrid system. A nuclear protein, serine/arginine-rich (SR)-25, was isolated as a novel CypA-binding protein that is distinct from those previously described in the literature...
December 2016: Oncology Letters
https://www.readbyqxmd.com/read/28104810/the-foxp2-forkhead-domain-binds-to-a-variety-of-dna-sequences-with-different-rates-and-affinities
#19
Helen Webb, Olga Steeb, Ashleigh Blane, Lia Rotherham, Shaun Aron, Phillip Machanick, Heini Dirr, Sylvia Fanucchi
FOXP2 is a member of the P subfamily of FOX transcription factors, the DNA binding domain of which is the winged helix forkhead domain. In this work we show that the FOXP2 forkhead domain is able to bind to various DNA sequences, including a novel sequence identified in this work, with different affinities and rates as detected using surface plasmon resonance. Combining the experimental work with molecular docking, we show that high affinity sequences remain bound to the protein for longer, form a greater number of interactions with the protein and induce a greater structural change in the protein than low affinity sequences...
January 18, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/28104429/using-lysine-adducts-of-human-serum-albumin-to-investigate-the-disposition-of-exogenous-formaldehyde-in-human-blood
#20
Luca G Regazzoni, Hasmik Grigoryan, Zhiying Ji, Xi Chen, Sarah I Daniels, Deyin Huang, Sylvia Sanchez, Naijun Tang, Fenna C M Sillé, Anthony T Iavarone, Evan R Williams, Luoping Zhang, Stephen M Rappaport
Formaldehyde is a human carcinogen that readily binds to nucleophiles, including proteins and DNA. To investigate whether exogenous formaldehyde produces adducts in extracellular fluids, we characterized modifications to human serum albumin (HSA) following incubation of whole blood, plasma, and saliva with formaldehyde at concentrations of 1, 10 and 100μM. The only HSA locus that showed the presence of formaldehyde modifications was Lys199. A N(6)-Lys adduct with added mass of 12Da, representing a putative intramolecular crosslink, was detected in biological fluids that had been incubated with formaldehyde but not in control fluids...
January 16, 2017: Toxicology Letters
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