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https://www.readbyqxmd.com/read/29236325/aml1-eto-trans-activates-c-kit-expression-through-the-long-range-interaction-between-promoter-and-intronic-enhancer
#1
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/29236299/apicomplexa-specific-%C3%AE-hairpin-of-plasmodium-and-toxoplasma-profilins-a-molecular-dynamics-simulation-study
#2
Priyadarsini Kadirvel, Sharmila Anishetty
Profilin is one of the actin-binding proteins that regulate dynamics of actin polymerization. It plays a key role in cell motility and invasion. It also interacts with several other proteins notably through its poly-L-proline (PLP) binding site. Profilin in apicomplexa is characterized by a unique mini-domain consisting of a large β-hairpin extension and an acidic loop which is relatively longer in Plasmodium species. Profilin is essential for the invasive blood stages of Plasmodium falciparum. In the current study, unbound profilins from Plasmodium falciparum (Pf), Toxoplasma gondii (Tg) and Homo sapiens (Hs) were subjected to molecular dynamics (MD) simulations for a timeframe of 100 ns each to understand the conformational dynamics of these proteins...
December 13, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/29236253/iclip-of-the-piwi-protein-aubergine-in-drosophila-embryos
#3
Bridlin Barckmann, Jérémy Dufourt, Martine Simonelig
Piwi-interacting RNAs (piRNAs) are a class of small noncoding RNAs bound to specific Argonaute proteins, the PIWI proteins. piRNAs target mRNAs by complementarity to silence them; they play an important role in the repression of transposable elements in the germ line of many species. piRNAs and PIWI proteins are also involved in diverse biological processes through their role in the regulation of cellular mRNAs. In the Drosophila embryo, they contribute to the maternal mRNA decay occurring during the maternal-to-zygotic transition...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29235978/rigid-amphipathic-fusion-inhibitors-demonstrate-antiviral-activity-against-african-swine-fever-virus
#4
Astghik Hakobyan, Inmaculada Galindo, Almudena Nañez, Erik Arabyan, Zaven Karalyan, Alexey A Chistov, Philipp P Streshnev, Vladimir A Korshun, Covadonga Alonso, Hovakim Zakaryan
Rigid amphipathic fusion inhibitors (RAFIs) are a family of nucleoside derivatives that inhibit the infectivity of several enveloped viruses by interacting with virion envelope lipids and inhibiting fusion between viral and cellular membranes. Here we tested the antiviral activity of two RAFIs, 5-(Perylen-3-ylethynyl)-arabino-uridine (aUY11) and 5-(Perylen-3-ylethynyl)uracil-1-acetic acid (cm1UY11) against African swine fever virus (ASFV), for which no effective vaccine is available. Both compounds displayed a potent, dose-dependent inhibitory effect on ASFV infection in Vero cells...
December 13, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/29235971/western-blot-analysis-of-cells-encapsulated-in-self-assembling-peptide-hydrogels
#5
Kyle A Burgess, Aline F Miller, Delvac Oceandy, Alberto Saiani
Continuous optimization of in vitro analytical techniques is ever more important, especially given the development of new materials for tissue engineering studies. In particular, isolation of cellular components for downstream applications is often hindered by the presence of biomaterials, presenting a major obstacle in understanding how cell-matrix interactions influence cell behavior. Here, we describe an approach for western blot analysis of cells that have been encapsulated in self-assembling peptide hydrogels (SAPHs), which highlights the need for complete solubilization of the hydrogel construct...
December 1, 2017: BioTechniques
https://www.readbyqxmd.com/read/29235861/kras-switch-mutants-d33e-and-a59g-crystallize-in-the-state-1-conformation
#6
Jia Lu, Asim Bera, Sudershan R Gondi, Kenneth Dale Westover
KRAS switch loop movements play a crucial role in regulating RAS signaling and alteration in these sensitive dynamics are a principal mechanism through which disease-associated RAS mutations lead to aberrant RAS activation. Prior studies suggest that despite high sequence similarity, the switches in KRAS are more dynamic than HRAS. We solved x-ray crystal structures of the rare tumorigenic KRAS mutants KRASD33E, in switch 1 (SW1), and KRASA59G, in switch 2 (SW2), bound to GDP and found these adopt nearly identical, open SW1 conformations as well as altered SW2 conformations...
December 13, 2017: Biochemistry
https://www.readbyqxmd.com/read/29235592/effect-of-immobilization-site-on-the-orientation-and-activity-of-surface-tethered-enzymes
#7
Yaoxin Li, Tadeusz L Ogorzalek, Shuai Wei, Xiaoxian Zhang, Pei Yang, Joshua Jasensky, Charles L Brooks, E Neil G Marsh, Zhan Chen
Tethering peptides and proteins to abiotic surfaces has the potential to create biomolecule-functionalized surfaces with useful properties. Commonly used methods of immobilization lack control over the orientation in which biological molecules are covalently or physically bound to the surface, leading to sub-optimal materials. Here we use an engineered beta-galactosidase that can be chemically immobilized on a surface with a well-defined orientation through unique surface-accessible cysteine residues. A combined study using sum frequency generation (SFG) vibrational spectroscopy and coarse grained molecular dynamics (MD) simulations was performed to determine the effects of enzyme immobilization site and abiotic surface chemistry on enzyme surface orientation, surface coverage, and catalytic activity...
December 13, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29235590/unravelling-the-hydrophobicity-of-urea-in-water-using-thermodiffusion-implications-for-protein-denaturation
#8
Doreen Niether, Silvia Di Lecce, Fernando Bresme, Simone Wiegand
Urea is widely used as a protein denaturant in aqueous solutions. Experimental and computer simulation studies have shown that it dissolves in water almost ideally at high concentrations, introducing little disruption in the water hydrogen bonded structure. However, at concentrations of the order of 5 M or higher, urea induces denaturation in a wide range of proteins. The origin of this behaviour is not completely understood, but it is believed to stem from a balance between urea-protein and urea-water interactions, with urea becoming possibly hydrophobic at a specific concentration range...
December 13, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29235532/investigation-of-the-effects-of-the-cftr-potentiator-ivacaftor-on-human-p-glycoprotein-abcb1
#9
Swathi Lingam, Nopnithi Thonghin, Robert C Ford
Ivacaftor is a potentiator of the CFTR chloride channel and is in worldwide clinical use for the chronic treatment of cystic fibrosis in patients. There is evidence that the bioavailability of ivacaftor in the body may be influenced by the multi-drug exporter P-glycoprotein. Here we have employed purified and reconstituted P-glycoprotein to study its interaction with ivacaftor as well as the ability of the drug to compete with a known transported substrate of the protein. We find that ivacaftor stimulates the ATPase activity of the purified protein and can compete with the transport of the fluorescent substrate Hoechst 33342...
December 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29235485/quantification-of-interacting-cognate-odorants-with-olfactory-receptors-in-nanovesicles
#10
Marta Sanmartí-Espinal, Patrizia Iavicoli, Annalisa Calò, Marta Taulés, Roger Galve, M Pilar Marco, Josep Samitier
This study aims to improve our understanding of the interaction between olfactory receptors and odorants to develop highly selective biosensing devices. Natural nanovesicles (NVs) from Saccharomyces cerevisiae, ~100 nm in diameter, carrying either the human OR17-40 or the chimpanzee OR7D4 olfactory receptor (OR) tagged with the c-myc epitope at their N-terminus, are presented as model systems to quantify the interaction between odorant and olfactory receptors. The level of expression of olfactory receptors was determined at individual NVs using a novel competitive ELISA immunoassay comparing the values obtained against those from techniques involving the solubilization of cell membrane proteins and the identification of c-myc-carrying receptors...
December 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29235404/understanding-the-interactions-of-different-substrates-with-wild-type-and-mutant-acylaminoacyl-peptidase-using-molecular-dynamics-simulations
#11
Jingxuan Zhu, Yan Wang, Xin Li, Weiwei Han, Li Zhao
Acylaminoacylpeptidase (AAP) belongs to peptidase protein family (POP), which can degrade amyloid β-peptide forms in the brains of patients and hence leads to Alzheimer's disease. And so, AAP is considered to be a novel target in the design of drugs against Alzheimer's disease. In this investigation, six molecular dynamics simulations were used to find that the interaction between the wild-type and R526V AAP with two different substrates (p-nitrophenylcaprylate and Ac-Leu-p-nitroanilide). Our results were as follows: firstly, Ac-Leu-p-nitroanilide bound to R526V AAP to form a more disordered loop (residues 552-562) in the α/β-hydrolase fold like of AAP, which caused an open and inactive AAP domain form, secondly, binding p-nitrophenylcaprylate and Ac-Leu-p-nitroanilide to AAP can decrease the flexibility of residues 225-250, 260-270 and 425-450, in which the ordered secondary structures may contain the suitable geometrical structure and so it is useful to serine attack...
December 13, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29235352/systems-approaches-to-understanding-and-designing-allosteric-proteins
#12
Srivatsan Raman
The study of allostery has a central place in biology due to the myriad roles of allosteric proteins in cellular function. As technologies to probe spatiotemporal resolution of biomolecules have become increasingly sophisticated, so has our understanding of the diverse structural and molecular mechanisms of allosteric proteins. Studies have shown that allosteric signal is transmitted a through a network of residue-residue interactions connecting distal sites on a protein. Linking structural and dynamical changes to the functional role of individual residues will give a more complete molecular view of allostery...
December 13, 2017: Biochemistry
https://www.readbyqxmd.com/read/29235273/-current-status-and-challenging-of-direct-target-study-of-traditional-chinese-medicine-complex-system-based-on-solid-coupling-beads
#13
Ke-Wu Zeng, Peng-Fei Tu
Traditional Chinese medicine(TCM) is a complex system with multiple chemical compositions. The most significant character of TCM is that the chemical compositions interact with each other by multi-target synergism to treat diseases. Previous reports mainly focused on the investigation of single signaling pathway detection or the phenotypic analysis of proteomics difference; however, no studies have been conducted on the identification of direct targets of TCM. Therefore, it is difficult to analyze the molecular mechanism of traditional Chinese medicine from the target source, and it is difficult to explain its traditional efficacy scientifically, thus seriously affecting its clinical application and internationalization...
October 2017: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/29235250/discovery-and-mechanistic-elucidation-of-a-class-of-pdi-inhibitors-for-the-treatment-of-glioblastoma
#14
Anahita Kyani, Shuzo Tamura, Suhui Yang, Andrea Shergalis, Soma Somanta, Yuting Kuang, Mats Ljungman, Nouri Neamati
Protein disulfide isomerase (PDI) is overexpressed in glioblastoma, the most aggressive form of brain cancer, and folds nascent proteins responsible for the progression and spread of the disease. Herein, we describe a novel, nanomolar PDI inhibitor, pyrimidotriazinedione 35G8, that is toxic in a panel of human glioblastoma cell lines. We performed a medium throughput 20,000-compound screen of a diverse subset of 1,000,000 compounds to identify cytotoxic small molecules. Cytotoxic compounds were screened for PDI inhibition, and, from the screen, 35G8 emerged as the most cytotoxic inhibitor of PDI...
December 12, 2017: ChemMedChem
https://www.readbyqxmd.com/read/29235198/substrate-interaction-defects-in-histidyl-trna-synthetase-linked-to-dominant-axonal-peripheral-neuropathy
#15
Jamie A Abbott, Rebecca Meyer-Schuman, Vincenzo Lupo, Shawna Feely, Inès Mademan, Stephanie N Oprescu, Laurie B Griffin, M Antonia Alberti, Carlos Casasnovas, Sharon Aharoni, Lina Basel-Vanagaite, Stephan Züchner, Peter De Jonghe, Jonathan Baets, Michael E Shy, Carmen Espinós, Borries Demeler, Anthony Antonellis, Christopher Francklyn
Histidyl-tRNA synthetase (HARS) ligates histidine to cognate tRNA molecules, which is required for protein translation. Mutations in HARS cause the dominant axonal peripheral neuropathy Charcot Marie-Tooth disease type 2W (CMT2W); however, the precise molecular mechanism remains undefined. Here, we investigated three HARS missense mutations associated with CMT2W (p.Tyr330Cys, p.Ser356Asn, and p.Val155Gly). The three mutations localize to the HARS catalytic domain and failed to complement deletion of the yeast ortholog (HTS1)...
December 12, 2017: Human Mutation
https://www.readbyqxmd.com/read/29235176/roles-of-elusive-translational-gtpases-come-to-light-and-inform-on-the-process-of-ribosome-biogenesis-in-bacteria
#16
REVIEW
Michelle R Gibbs, Kurt Fredrick
Protein synthesis relies on several translational GTPases (trGTPases), related proteins that couple the hydrolysis of GTP to specific molecular events on the ribosome. Most bacterial trGTPases, including IF2, EF-Tu, EF-G, and RF3, play well-known roles in translation. The cellular functions of LepA (also termed EF4) and BipA (also termed TypA), on the other hand, have remained enigmatic. Recent studies provide compelling in vivo evidence that LepA and BipA function in biogenesis of the 30S and 50S subunit, respectively...
December 13, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/29235146/development-of-metal-active-site-and-zinccluster-tool-to-predictactive-site-pockets
#17
M Ajitha, K Sundar, S Arul Mugilan, S Arumugam
The advent of whole genome sequencing leads to increasing number of proteins with known amino acid sequences. Despite many efforts, the number of proteins with resolved three dimensional structures is still low. One of the challenging tasks the structural biologists face is the prediction of the interaction of metal ion with any protein for which the structure is unknown. Based on the information available in PDB, a site (METALACTIVE INTERACTION) has been generated which displays information for significant high preferential and low-preferential combination of endogenous ligands for 49 metal ions...
December 13, 2017: Proteins
https://www.readbyqxmd.com/read/29235119/v-set-and-ig-domain-containing-4-vsig4-expressing-hepatic-f4-80-cells-regulate-oral-antigen-specific-responses-in-mouse
#18
Wonhwa Shin, Youkyoung Jeon, Inhak Choi, Yeon-Jeong Kim
Oral tolerance can prevent unnecessary immune responses against dietary antigens. Members of the B7 protein family play critical roles in the positive and/or negative regulation of T cell responses to interactions between APCs and T cells. V-set and Ig domain-containing 4 (VSIG4), a B7-related co-signaling molecule, has been known to act as a co-inhibitory ligand and may be critical in establishing immune tolerance. Therefore, we investigated the regulation of VSIG4 signaling in a food allergy and experimental oral tolerance murine models...
December 13, 2017: European Journal of Immunology
https://www.readbyqxmd.com/read/29235019/investigation-of-the-interaction-of-%C3%AE-methylamino-l-alanine-with-eukaryotic-and-prokaryotic-proteins
#19
Brendan J Main, Carly J Italiano, Kenneth J Rodgers
There is a strong body of evidence linking the non-protein amino acid (NPAA) β-methylamino-L-alanine (BMAA) to the development of a number of neurodegenerative diseases. BMAA has been found globally, is produced by a number of organisms including cyanobacteria, diatoms, and dinoflagellates; and has been shown to biomagnify through trophic levels. The role of BMAA in neurodegenerative disease is highlighted by its presence in the brains of a number of neurodegenerative disease patients, where it was found in a protein-bound form...
December 12, 2017: Amino Acids
https://www.readbyqxmd.com/read/29234892/how-accurate-is-the-description-of-ligand-protein-interactions-by-a-hybrid-qm-mm-approach
#20
Jakub Kollar, Vladimir Frecer
During the last decades, the application of hybrid quantum mechanical/molecular mechanical (QM/MM) methods has been extended to the field of drug design. In principle, the approximate QM/MM approach offers a more complete description of drug-receptor non-covalent interactions. This is especially true when charge or proton transfer, chelation of metal ions or strong polarization of ligand and protein or surface chemical groups are involved. The aim of this work was to assess the accuracy of calculated non-covalent ligand-protein interaction energies ([Formula: see text]) obtained by the hybrid QM/MM approach employed in QSite/Jaguar of Schrödinger's Small-Molecule Drug Discovery Suite on a set of small-molecule model systems when compared to rigorous QM calculations...
December 12, 2017: Journal of Molecular Modeling
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