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https://www.readbyqxmd.com/read/29679799/refolding-kinetics-of-cytochrome-c-studied-with-microsecond-timescale-continuous-flow-uv-vis-spectroscopy-and-rapid-freeze-quench-epr
#1
Batoul Srour, Marc J F Strampraad, Wilfred R Hagen, Peter-Leon Hagedoorn
The study of the structure, function, folding and conformational transitions of cytochrome c is of great interest because this protein plays an important role in biological electron transport and apoptosis. The different native and non-native conformations have been studied extensively under equilibrium conditions at different pH values, however, kinetic studies are rare because they require technically challenging rapid mixing and spectroscopic monitoring techniques. Here we present the refolding kinetics of acid denatured cytochrome c using the pH jump technique from pH 2 to pH 4...
April 11, 2018: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/29679766/aminoacyl-trna-synthetase-complex-interacting-multifunctional-protein-1-simultaneously-binds-glutamyl-prolyl-trna-synthetase-and-scaffold-protein-aminoacyl-trna-synthetase-complex-interacting-multifunctional-protein-3-of-the-multi-trna-synthetase-complex
#2
Margaret A Schwarz, Daniel D Lee, Seamus Bartlett
Higher eukaryotes have developed extensive compartmentalization of amino acid (aa) - tRNA coupling through the formation of a multi-synthetase complex (MSC) that is composed of eight aa-tRNA synthetases (ARS) and three scaffold proteins: aminoacyl tRNA synthetase complex interacting multifunctional proteins (AIMP1, 2 and 3). Lower eukaryotes have a much smaller complex while yeast MSC consists of only two ARS (MetRS and GluRS) and one ARS cofactor 1 protein, Arc1p (Simos et al., 1996), the homolog of the mammalian AIMP1...
April 18, 2018: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/29679756/myh9-structure-functions-and-role-of-non-muscle-myosin-iia-in-human-disease
#3
REVIEW
Alessandro Pecci, Xuefei Ma, Anna Savoia, Robert S Adelstein
The MYH9 gene encodes the heavy chain of non-muscle myosin IIA, a widely expressed cytoplasmic myosin that participates in a variety of processes requiring the generation of intracellular chemomechanical force and translocation of the actin cytoskeleton. Non-muscle myosin IIA functions are regulated by phosphorylation of its 20 kDa light chain, of the heavy chain, and by interactions with other proteins. Variants of MYH9 cause an autosomal-dominant disorder, termed MYH9-related disease, and may be involved in other conditions, such as chronic kidney disease, non-syndromic deafness, and cancer...
April 18, 2018: Gene
https://www.readbyqxmd.com/read/29679745/integrated-genomic-and-metabolomic-profiling-of-isc1-an-emerging-leishmania-donovani-population-in-the-indian-subcontinent
#4
Bart Cuypers, Maya Berg, Hideo Imamura, Franck Dumetz, Géraldine De Muylder, Malgorzata A Domagalska, Suman Rijal, Narayan Raj Bhattarai, Ilse Maes, Mandy Sanders, James A Cotton, Pieter Meysman, Kris Laukens, Jean-Claude Dujardin
Leishmania donovani is the responsible agent for visceral leishmaniasis (VL) in the Indian subcontinent (ISC). The disease is lethal without treatment and causes 0.2 to 0.4 million cases each year. Recently, reports of VL in Nepalese hilly districts have increased as well as VL cases caused by L. donovani from the ISC1 genetic group, a new and emerging genotype. In this study, we perform for the first time an integrated, untargeted genomics and metabolomics approach to characterize ISC1, in comparison with the Core Group (CG), main population that drove the last outbreak of VL in the ISC...
April 18, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29679701/the-role-of-%C3%AE-2-integrin-associated-heparin-binding-protein-release-in-ards
#5
Yang Liu, Shaolin Ma, Xuebin Wang, Yajing Feng, Shouqin Zhang, Sheng Wang, Xiangyu Zhang
AIMS: PMNs (polymorphonuclear neutrophil) play important roles in early stage of inflammation induced ARDS (Acute Respiratory Distress Syndrome). Both HBP (Heparin-Binding Protein) released from active PMNs and β2 integrins on the surface of PMNs are involved in vascular leakage. The role and relationship of HBP and β2 integrins on ARDS still requires study. MATERIALS AND METHODS: We established ARDS model using C57BL/6 mice with cecal ligation and puncture and eliminating HBP and β2 integrin with respective antibodies...
April 18, 2018: Life Sciences
https://www.readbyqxmd.com/read/29679567/hdac-mediated-deacetylation-of-klf5-associates-with-its-proteasomal-degradation
#6
Ran Tao, Baotong Zhang, Yixiang Li, Jamie L King, Ruoyu Tian, Siyuan Xia, Cara Rae Schiavon, Jin-Tang Dong
Krüppel-like factor 5 (KLF5) is a basic transcription factor that regulates diverse cellular processes during tumor development. Acetylation of KLF5 at lysine 369 (K369) reverses its function from promoting to suppressing cell proliferation and tumor growth. In this study, we examined the regulation of KLF5 by histone deacetylases in the prostate cancer cell line DU 145. While confirming the functions of HDAC1/2 in KLF5 deacetylation and the promotion of cell proliferation, we found that the knockdown of HDAC1/2 upregulated KLF5 protein but not KLF5 mRNA, and the increase in KLF5 protein level by silencing HDAC1/2 was at least in part due to decreased proteasomal degradation...
April 18, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29679564/frequencies-and-expression-levels-of-programmed-death-ligand-1-pd-l1-in-circulating-tumor-rna-ctrna-in-various-cancer-types
#7
Toshiyuki Ishiba, Andreas-Claudius Hoffmann, Joshua Usher, Yahya Elshimali, Todd Sturdevant, Mai Dang, Yolanda Jaimes, Rama Tyagi, Ronald Gonzalez, Mary Grino, Jacek K Pinski, Afsaneh Barzi, Luis E Raez, Wilfried E Eberhardt, Dirk Theegarten, Heinz-Josef Lenz, Hiroyuki Uetake, Peter V Danenberg, Kathleen Danenberg
BACKGROUND: Precision medicine and prediction of therapeutic response requires monitoring potential biomarkers before and after treatment. Liquid biopsies provide noninvasive prognostic markers such as circulating tumor DNA and RNA. Circulating tumor RNA (ctRNA) in blood is also used to identify mutations in genes of interest, but additionally, provides information about relative expression levels of important genes. In this study, we analyzed PD-L1 expression in ctRNA isolated from various cancer types...
April 18, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29679325/biofunctionalization-of-poly-acrylamide-gels
#8
Julieta I Paez, Aleeza Farrukh, Oya Ustahüseyin, Aránzazu Del Campo
Engineering novel biomaterials that mimic closer in vivo scenarios requires the simple and quantitative incorporation of multiple instructive signals to gain a higher level of control and complexity at the cell-matrix interface. Poly(acrylamide) (PAAm) gels are very popular among biology labs as 2D model substrates with defined biochemical and mechanical properties. These gels are cost effective, easy to prepare, reproducible, and available in a wide range of stiffness. However, their functionalization with bioactive ligands (cell adhesive proteins or peptides, growth factors, etc...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29679324/controlling-fibrin-network-morphology-polymerization-and-degradation-dynamics-in-fibrin-gels-for-promoting-tissue-repair
#9
Erin P Sproul, Riley T Hannan, Ashley C Brown
Fibrin is an integral part of the clotting cascade and is formed by polymerization of the soluble plasma protein fibrinogen. Following stimulation of the coagulation cascade, thrombin activates fibrinogen, which binds to adjacent fibrin(ogen) molecules resulting in the formation of an insoluble fibrin matrix. This fibrin network is the primary protein component in clots and subsequently provides a scaffold for infiltrating cells during tissue repair. Due to its role in hemostasis and tissue repair, fibrin has been used extensively as a tissue sealant...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29679217/spatiotemporal-imaging-of-cellular-energy-metabolism-with-genetically-encoded-fluorescent-sensors-in-brain
#10
REVIEW
Zhuo Zhang, Weicai Chen, Yuzheng Zhao, Yi Yang
The brain has very high energy requirements and consumes 20% of the oxygen and 25% of the glucose in the human body. Therefore, the molecular mechanism underlying how the brain metabolizes substances to support neural activity is a fundamental issue for neuroscience studies. A well-known model in the brain, the astrocyte-neuron lactate shuttle, postulates that glucose uptake and glycolytic activity are enhanced in astrocytes upon neuronal activation and that astrocytes transport lactate into neurons to fulfill their energy requirements...
April 20, 2018: Neuroscience Bulletin
https://www.readbyqxmd.com/read/29679095/implication-of-the-vrk1-chromatin-kinase-in-the-signaling-responses-to-dna-damage-a-therapeutic-target
#11
REVIEW
Ignacio Campillo-Marcos, Pedro A Lazo
DNA damage causes a local distortion of chromatin that triggers the sequential processes that participate in specific DNA repair mechanisms. This initiation of the repair response requires the involvement of a protein whose activity can be regulated by histones. Kinases are candidates to regulate and coordinate the connection between a locally altered chromatin and the response initiating signals that lead to identification of the type of lesion and the sequential steps required in specific DNA damage responses (DDR)...
April 20, 2018: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/29679079/a-molecular-dynamics-simulation-study-decodes-the-zika-virus-ns5-methyltransferase-bound-to-sah-and-rna-analogue
#12
Chih-Hung Chuang, Shean-Jaw Chiou, Tian-Lu Cheng, Yeng-Tseng Wang
Since 2015, widespread Zika virus outbreaks in Central and South America have caused increases in microcephaly cases, and this acute problem requires urgent attention. We employed molecular dynamics and Gaussian accelerated molecular dynamics techniques to investigate the structure of Zika NS5 protein with S-adenosyl-L-homocysteine (SAH) and an RNA analogue, namely 7-methylguanosine 5'-triphosphate (m7GTP). For the binding motif of Zika virus NS5 protein and SAH, we suggest that the four Zika NS5 substructures (residue orders: 101-112, 54-86, 127-136 and 146-161) and the residues (Ser56, Gly81, Arg84, Trp87, Thr104, Gly106, Gly107, His110, Asp146, Ile147, and Gly148) might be responsible for the selectivity of the new Zika virus drugs...
April 20, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29679077/proteome-wide-analysis-of-cysteine-oxidation-reveals-metabolic-sensitivity-to-redox-stress
#13
Jiska van der Reest, Sergio Lilla, Liang Zheng, Sara Zanivan, Eyal Gottlieb
Reactive oxygen species (ROS) are increasingly recognised as important signalling molecules through oxidation of protein cysteine residues. Comprehensive identification of redox-regulated proteins and pathways is crucial to understand ROS-mediated events. Here, we present stable isotope cysteine labelling with iodoacetamide (SICyLIA), a mass spectrometry-based workflow to assess proteome-scale cysteine oxidation. SICyLIA does not require enrichment steps and achieves unbiased proteome-wide sensitivity. Applying SICyLIA to diverse cellular models and primary tissues provides detailed insights into thiol oxidation proteomes...
April 20, 2018: Nature Communications
https://www.readbyqxmd.com/read/29679022/biological-recognition-of-graphene-nanoflakes
#14
V Castagnola, W Zhao, L Boselli, M C Lo Giudice, F Meder, E Polo, K R Paton, C Backes, J N Coleman, K A Dawson
The systematic study of nanoparticle-biological interactions requires particles to be reproducibly dispersed in relevant fluids along with further development in the identification of biologically relevant structural details at the materials-biology interface. Here, we develop a biocompatible long-term colloidally stable water dispersion of few-layered graphene nanoflakes in the biological exposure medium in which it will be studied. We also report the study of the orientation and functionality of key proteins of interest in the biolayer (corona) that are believed to mediate most of the early biological interactions...
April 20, 2018: Nature Communications
https://www.readbyqxmd.com/read/29679011/human-kallikrein-related-peptidase-12-stimulates-endothelial-cell-migration-by-remodeling-the-fibronectin-matrix
#15
T Kryza, C Parent, J Pardessus, A Petit, J Burlaud-Gaillard, P Reverdiau, S Iochmann, V Labas, Y Courty, N Heuzé-Vourc'h
Kallikrein-related peptidase 12 (KLK12) is a kallikrein family peptidase involved in angiogenesis - a complex biological process in which the sprouting, migration and stabilization of endothelial cells requires extracellular matrix remodeling. To characterize the molecular mechanisms associated with KLK12's proangiogenic activity, we evaluated its ability to hydrolyze various matrix proteins. Our results show that KLK12 efficiently cleaved the human extracellular matrix proteins fibronectin and tenascin, both of which are involved in the regulation of endothelial cell adhesion and migration...
April 20, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29678998/acid-stimulation-of-the-citrate-transporter-nadc-1-requires-pyk2-and-erk1-2-signaling-pathways
#16
Miriam Zacchia, Xuefei Tian, Enrica Zona, Robert J Alpern, Patricia A Preisig
Background Urine citrate is reabsorbed exclusively along the renal proximal tubule via the apical Na+ -dicarboxylate cotransporter NaDC-1. We previously showed that an acid load in vivo and media acidification in vitro increase NaDC-1 activity through endothelin-1 (ET-1)/endothelin B (ETB ) signaling. Here, we further examined the signaling pathway mediating acid-induced NaDC-1 activity. Methods We transiently transfected cultured opossum kidney cells, a model of the proximal tubule, with NaDC-1 and ETB and measured [14 C]-citrate uptake after media acidification under various experimental conditions, including inactivation of Pyk2 and c-Src, which were previously shown to be activated by media acidification...
April 20, 2018: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/29678960/toxoplasma-gondii-acetyl-coa-synthetase-is-involved-in-fatty-acid-elongation-of-long-fatty-acid-chains-during-tachyzoite-life-stages
#17
David Dubois, Stella Fernandes, Souad Amiar, Sheena Dass, Nicholas J Katris, Cyrille Y Botte, Yoshiki Yamaryo-Botte
Apicomplexan parasites are pathogens responsible for major human diseases such as toxoplasmosis caused by Toxoplasma gondii and malaria caused by Plasmodium spp.. Throughout their intracellular division cycle, the parasites require vast and specific amounts of lipids to divide and survive. This demand for lipids relies on a fine balance between de novo synthesized lipids and scavenged lipids from the host. Acetyl-CoA is a major and central precursor for many metabolic pathways especially for lipid biosynthesis...
April 20, 2018: Journal of Lipid Research
https://www.readbyqxmd.com/read/29678904/lipid-droplet-consumption-is-functionally-coupled-to-vacuole-homeostasis-independent-of-lipophagy
#18
S Ouahoud, M D Fiet, F Martínez-Montañés, C S Ejsing, O Kuss, M Roden, D F Markgraf
Lipid droplets (LDs) store neutral lipids and are integrated into a cellular metabolic network that relies on functional coupling with various organelles. Factors mediating efficient coupling and mechanisms regulating them remain unknown. Here, we conducted a global screen in S. cerevisiae to identify genes required for the functional coupling of LDs and other organelles during LD consumption. We show that LD utilization during growth resumption is coupled to vacuole homeostasis. ESCRT-, V-ATPase- and vacuole protein sorting-mutants negatively affect LD consumption, independent of lipophagy...
April 20, 2018: Journal of Cell Science
https://www.readbyqxmd.com/read/29678883/ribosome-maturation-by-the-endoribonuclease-ybey-stabilises-a-type-iii-secretion-system-transcript-required-for-virulence-of-enterohemorrhagic-escherichia-coli
#19
Sean P McAteer, Brandon M Sy, Julia L Wong, David Tollervey, David L Gally, Jai J Tree
Enterohemorrhagic Escherichia coli (EHEC) is a significant human pathogen that colonizes humans and its reservoir host, cattle. Colonization requires the expression of a type III secretion (T3S) system that injects a cocktail of effector proteins into host cells, to promote bacterial attachment and disease progression. The T3S system is tightly regulated by a complex network of transcriptional and post-transcriptional regulators. Using transposon mutagenesis, here we identified the ybeZYX-int operon as being required for normal T3S levels...
April 20, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29678879/potassium-is-a-trigger-for-conformational-change-in-the-fusion-spike-of-an-enveloped-rna-virus
#20
Emma K Punch, Samantha Hover, Henry Tw Blest, Jack Fuller, Roger Hewson, Juan Fontana, Jamel Mankouri, John N Barr
Many enveloped viruses enter cells through the endocytic network, from which they must subsequently escape through fusion of viral and endosomal membranes. This membrane fusion is mediated by virus-encoded spikes that respond to the changing endosomal environment, which triggers conformational change in the spike that initiate the fusion process. Several fusion triggers have been identified and include pH, membrane composition and endosome-resident proteins and these cues dictate when and where viral fusion occurs...
April 20, 2018: Journal of Biological Chemistry
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