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https://www.readbyqxmd.com/read/28213235/preparation-and-characterization-of-a-packed-bead-immobilized-trypsin-reactor-integrated-into-a-pdms-microfluidic-chip-for-rapid-protein-digestion
#1
Adam Kecskemeti, Attila Gaspar
This paper demonstrates the design, efficiency and applicability of a simple, inexpensive and high sample throughput microchip immobilized enzymatic reactor (IMER) for rapid protein digestion. The IMER contains conventional silica particles with covalently immobilized trypsin packed inside of a poly(dimethylsiloxane) (PDMS) microchip channel (10mm×1mm×35µm). The microchip consists of 9 different channels, enabling 9 simultaneous protein digestions. Trypsin was covalently immobilized using carbodiimide activation, the ideal trypsin/silica particle ratio (i...
May 1, 2017: Talanta
https://www.readbyqxmd.com/read/28213128/quantitative-proteomic-analysis-of-human-testis-reveals-system-wide-molecular-and-cellular-pathways-associated-with-non-obstructive-azoospermia
#2
Mehdi Alikhani, Mehdi Mirzaei, Marjan Sabbaghian, Pouria Parsamatin, Razieh Karamzadeh, Samane Adib, Niloofar Sodeifi, Mohammad Ali Sadighi Gilani, Masoud Zabet-Moghaddam, Lindsay Parker, Yunqi Wo, Vivek Gupta, Paul A Haynes, Hamid Gourabi, Hossein Baharvand, Ghasem Hosseini Salekdeh
: Male infertility accounts for half of the infertility problems experienced by couples. Azoospermia, having no measurable level of sperm in seminal fluid, is one of the known conditions resulting in male infertility. In order to elucidate the complex molecular mechanisms causing male azoospermia, label-free quantitative shotgun proteomics was carried out on testicular tissue specimens from patients with obstructive azoospermia and non-obstructive azoospermia, including maturation arrest (MA) and Sertoli cell only syndrome (SCOS)...
February 14, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28211870/non-apoptotic-functions-of-caspases-in-myeloid-cell-differentiation
#3
REVIEW
Stéphanie Solier, Michaela Fontenay, William Vainchenker, Nathalie Droin, Eric Solary
Subtle caspase activation is associated with the differentiation of several myeloid lineages. A tightly orchestrated dance between caspase-3 activation and the chaperone HSP70 that migrates to the nucleus to protect the master regulator GATA-1 from cleavage transiently occurs in basophilic erythroblasts and may prepare nucleus and organelle expel that occurs at the terminal phase of erythroid differentiation. A spatially restricted activation of caspase-3 occurs in maturing megakaryocytes to promote proplatelet maturation and platelet shedding in the bloodstream...
February 17, 2017: Cell Death and Differentiation
https://www.readbyqxmd.com/read/28211472/proteolysis-regulates-cardiomyocyte-maturation-and-tissue-integration
#4
Ryuichi Fukuda, Felix Gunawan, Arica Beisaw, Vanesa Jimenez-Amilburu, Hans-Martin Maischein, Sawa Kostin, Koichi Kawakami, Didier Y R Stainier
Tissue integrity is critical for organ formation and function. During heart development, cardiomyocytes differentiate and integrate to form a coherent tissue that contracts synchronously. However, the molecular mechanisms regulating cardiac tissue integrity are poorly understood. Here we show that proteolysis, via the E3 ubiquitin ligase ASB2, regulates cardiomyocyte maturation and tissue integrity. Cardiomyocytes in asb2b zebrafish mutants fail to terminally differentiate, resulting in reduced cardiac contractility and output...
February 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/28208022/protein-requirements-for-critically-ill-patients-with-renal-and-liver-failure
#5
Jayshil J Patel, Craig J McClain, Menaka Sarav, Jill Hamilton-Reeves, Ryan T Hurt
Diseases leading to critical illness induce proteolysis resulting in muscle wasting and negative nitrogen balance. Muscle wasting has been associated with poor intensive care unit (ICU)-related outcomes, including an increased risk for mortality. Acute kidney injury (AKI) represents a common organ dysfunction associated with ICU-related disorders, such as sepsis, trauma, and respiratory failure. AKI and renal replacement therapy lead to amino acid loss. Decompensated liver cirrhosis (DLC) and acute liver failure (ALF) represent more severe forms of liver dysfunction leading to ICU admission...
February 1, 2017: Nutrition in Clinical Practice
https://www.readbyqxmd.com/read/28207895/the-metastasis-suppressor-kiss1-is-an-intrinsically-disordered-protein-slightly-more-extended-than-a-random-coil
#6
Alain Ibáñez de Opakua, Nekane Merino, Maider Villate, Tiago N Cordeiro, Georgina Ormaza, Marta Sánchez-Carbayo, Tammo Diercks, Pau Bernadó, Francisco J Blanco
The metastasis suppressor KISS1 is reported to be involved in the progression of several solid neoplasias, making it a promising molecular target for controlling their metastasis. The KISS1 sequence contains an N-terminal secretion signal and several dibasic sequences that are proposed to be the proteolytic cleavage sites. We present the first structural characterization of KISS1 by circular dichroism, multi-angle light scattering, small angle X-Ray scattering and NMR spectroscopy. An analysis of the KISS1 backbone NMR chemical shifts does not reveal any preferential conformation and deviation from a random coil ensemble...
2017: PloS One
https://www.readbyqxmd.com/read/28205580/accelerated-biodegradation-of-silk-sutures-through-matrix-metalloproteinase-activation-by-incorporating-4-hexylresorcinol
#7
You-Young Jo, HaeYong Kweon, Dae-Won Kim, Min-Keun Kim, Seong-Gon Kim, Jwa-Young Kim, Weon-Sik Chae, Sam-Pyo Hong, Young-Hwan Park, Si Young Lee, Je-Yong Choi
Silk suture material is primarily composed of silk fibroin and regarded as a non-resorbable material. It is slowly degraded by proteolysis when it is implanted into the body. 4-Hexylresorcinol (4HR) is a well-known antiseptic. In this study, the biodegradability of 4HR-incorporated silk sutures were compared to that of untreated silk sutures and polyglactin 910 sutures, a commercially available resorbable suture. 4HR-incorporated silk sutures exhibited anti-microbial properties. Matrix metalloproteinase (MMP) can digest a wide spectrum of proteins...
February 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28197071/chemosensitivity-of-u251-cells-to-the-co-treatment-of-d-penicillamine-and-copper-possible-implications-on-wilson-disease-patients
#8
Meghri Katerji, Kassem Barada, Mustapha Jomaa, Firas Kobeissy, Ahmad-Kareem Makkawi, Wassim Abou-Kheir, Julnar Usta
D-Penicillamine (PA), a copper chelator, and one of the recommended drugs for treatment of Wilson disease (WD) has been reported to worsen the symptoms of patients with neurologic presentations. However, the cause of this paradoxical response has not been fully elucidated and requires further investigations. Accordingly, we have studied the in vitro effect of Copper (Cu) and/or PA treatment on human glioblastoma U251 cells as an in vitro model of Cu cytotoxicity. Treatment of U251 cells with either Cu or PA exerted no significant effect on their morphology, viability or ROS level...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28196883/evidence-for-the-principle-of-minimal-frustration-in-the-evolution-of-protein-folding-landscapes
#9
Franco O Tzul, Daniel Vasilchuk, George I Makhatadze
Theoretical and experimental studies have firmly established that protein folding can be described by a funneled energy landscape. This funneled energy landscape is the result of foldable protein sequences evolving following the principle of minimal frustration, which allows proteins to rapidly fold to their native biologically functional conformations. For a protein family with a given functional fold, the principle of minimal frustration suggests that, independent of sequence, all proteins within this family should fold with similar rates...
February 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28195700/discovery-and-characterization-of-a-potent-and-specific-peptide-ligand-targeting-endothelial-progenitor-cells-and-endothelial-cells-for-tissue-regeneration
#10
Dake Hao, Wenwu Xiao, Ruiwu Liu, Priyadarsini Kumar, YuanPei Li, Ping Zhou, Fuzheng Guo, Diana L Farmer, Kit S Lam, Fengshan Wang, Aijun Wang
Endothelial progenitor cells (EPCs) and endothelial cells (ECs) play a vital role in endothelialization and vascularization for tissue regeneration. Various EPC/EC targeting biomolecules have been investigated to improve tissue regeneration with limited success often due to their limited functional specificity and structural stability. One-Bead-One-Compound (OBOC) combinatorial technology is an ultra-high throughput chemical library synthesis and screening method suitable for ligand discovery against a wide range of biological targets, such as integrins...
February 14, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28193899/structure-of-a-lipid-a-phosphoethanolamine-transferase-suggests-how-conformational-changes-govern-substrate-binding
#11
Anandhi Anandan, Genevieve L Evans, Karmen Condic-Jurkic, Megan L O'Mara, Constance M John, Nancy J Phillips, Gary A Jarvis, Siobhan S Wills, Keith A Stubbs, Isabel Moraes, Charlene M Kahler, Alice Vrielink
Multidrug-resistant (MDR) gram-negative bacteria have increased the prevalence of fatal sepsis in modern times. Colistin is a cationic antimicrobial peptide (CAMP) antibiotic that permeabilizes the bacterial outer membrane (OM) and has been used to treat these infections. The OM outer leaflet is comprised of endotoxin containing lipid A, which can be modified to increase resistance to CAMPs and prevent clearance by the innate immune response. One type of lipid A modification involves the addition of phosphoethanolamine to the 1 and 4' headgroup positions by phosphoethanolamine transferases...
February 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28193551/a-gibbs-sampling-method-to-determine-biomarkers-for-asthma
#12
Zhi-Jian Huang, Qin-Hai Shen, Yan-Sheng Wu, Ya-Li Huang
PURPOSE: To identify potential biomarkers and to uncover the mechanisms underlying asthma based on Gibbs sampling. METHODS: The molecular functions (MFs) with genes greater than 5 were determined using AnnotationMFGO of BAGS package, and the obtained MFs were then transformed to Markov chain (MC). Gibbs sampling was conducted to obtain a new MC. Meanwhile, the average probabilities of MFs were computed via MC Monte Carlo (MCMC) algorithm, followed by identification of differentially expressed MFs based on the probabilities of MF more than 0...
January 22, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28193432/biochemical-and-milk-clotting-properties-and-mapping-of-catalytic-subsites-of-an-extracellular-aspartic-peptidase-from-basidiomycete-fungus-phanerochaete-chrysosporium
#13
Ronivaldo Rodrigues da Silva, Lilian Caroline Gonçalves de Oliveira, Maria Aparecida Juliano, Luiz Juliano, Arthur H C de Oliveira, Jose C Rosa, Hamilton Cabral
For a long time, proteolytic enzymes have been employed as key tools of industrial processes, especially in the dairy industry. In the present work, we used Phanerochaete chrysosporium for biochemical characterization and analysis of catalytic specificity of an aspartic peptidase. Our results revealed an aspartic peptidase with molecular mass ∼38kDa, maximal activity at pH 4.5 and 50°C, and stability above 80% in the pH range of 3-8 and temperature up to 55°C for 1h. In a milk-clotting assay, this peptidase showed maximal milk clotting activity at 60-65°C and maintenance of enzymatic activity above 80% in the presence of 20mM CaCl2...
June 15, 2017: Food Chemistry
https://www.readbyqxmd.com/read/28192749/ascorbic-acid-ameliorates-behavioural-deficits-and-neuropathological-alterations-in-rat-model-of-alzheimer-s-disease
#14
Olayemi Joseph Olajide, Emmanuel Olusola Yawson, Ismail Temitayo Gbadamosi, Tolulope Timothy Arogundade, Ezra Lambe, Kosisochukwu Obasi, Ismail Tayo Lawal, Abdulmumin Ibrahim, Kehinde Yomi Ogunrinola
Exploring the links between neural pathobiology and behavioural deficits in Alzheimer's disease (AD), and investigating substances with known therapeutic advantages over subcellular mechanisms underlying these dysfunctions could advance the development of potent therapeutic molecules for AD treatment. Here we investigated the efficacy of ascorbic acid (AA) in reversing aluminium chloride (AlCl3)-induced behavioural deficits and neurotoxic cascades within prefrontal cortex (PFC) and hippocampus of rats. A group of rats administered oral AlCl3 (100mg/kg) daily for 15days showed degenerative changes characterised by significant weight loss, reduced exploratory/working memory, frontal-dependent motor deficits, cognitive decline, memory dysfunction and anxiety during behavioural assessments compared to control...
February 6, 2017: Environmental Toxicology and Pharmacology
https://www.readbyqxmd.com/read/28186774/quantitative-map-of-%C3%AE-lactone-induced-virulence-regulation
#15
Joanna Krysiak, Matthias Stahl, Jan Vomacka, Christian Fetzer, Markus Lakemeyer, Anja Fux, Stephan A Sieber
β-Lactones have recently been introduced as the first selective ClpP inhibitors that attenuate virulence of both sensitive Staphylococcus aureus and multiresistant strains (MRSA). Although previous knockout studies showed that ClpP is essential for S. aureus alpha-toxin production, a link between β-lactone inhibition and molecular virulence mechanisms has been lacking so far. We here perform a chemical-proteomic approach to elucidate antivirulence pathways. First, we demonstrate by gel-free activity-based protein profiling that ClpP is the predominant target of β-lactones...
February 10, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28186401/chemoproteomic-screening-of-covalent-ligands-reveals-uba5-as-a-novel-pancreatic-cancer-target
#16
Allison M Roberts, David K Miyamoto, Tucker R Huffman, Leslie A Bateman, Ashley N Ives, David Akopian, Martin J Heslin, Carlo M Contreras, Michael Rape, Christine F Skibola, Daniel K Nomura
Chemical genetic screening of small-molecule libraries has been a promising strategy for discovering unique and novel therapeutic compounds. However, identifying the targets of lead molecules that arise from these screens has remained a major bottleneck in understanding the mechanism of action of these compounds. Here, we have coupled the screening of a cysteine-reactive fragment-based covalent ligand library with an isotopic tandem orthogonal proteolysis-enabled activity-based protein profiling (isoTOP-ABPP) chemoproteomic platform to rapidly couple the discovery of lead small molecules that impair pancreatic cancer pathogenicity with the identification of druggable hotspots for potential cancer therapy...
February 15, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28186169/functionalized-graphene-oxide-with-chitosan-for-protein-nanocarriers-to-protect-against-enzymatic-cleavage-and-retain-collagenase-activity
#17
Fatemeh Emadi, Abbas Amini, Ahmad Gholami, Younes Ghasemi
Proteins have short half-life because of enzymatic cleavage. Here, a new protein nanocarrier made of graphene oxide (GO) + Chitosan (CS) is proposed to successfully prevent proteolysis in protein and simultaneously retain its activity. Bovine serum albumin (BSA) and collagenase were loaded on GO and GO-CS to explore the stability and activity of proteins. SEM, AFM, TEM, DSC, UV-Vis, FT-IR, RBS, Raman, SDS-PAGE and zymography were utilized as characterization techniques. The protecting role of GO and GO-CS against enzymatic cleavage was probed by protease digestion analysis on BSA, where the protease solution was introduced to GO-BSA and GO-CS-BSA at 37 °C for 0...
February 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28185716/mitochondrial-complex-ii-at-the-crossroads
#18
REVIEW
Ayenachew Bezawork-Geleta, Jakub Rohlena, Lanfeng Dong, Karel Pacak, Jiri Neuzil
Mitochondrial complex II (CII), also called succinate dehydrogenase (SDH), is a central purveyor of the reprogramming of metabolic and respiratory adaptation in response to various intrinsic and extrinsic stimuli and abnormalities. In this review we discuss recent findings regarding SDH biogenesis, which requires four known assembly factors, and modulation of its enzymatic activity by acetylation, succinylation, phosphorylation, and proteolysis. We further focus on the emerging role of both genetic and epigenetic aberrations leading to SDH dysfunction associated with various clinical manifestations...
February 6, 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28181499/involvement-of-%C3%AE-defensin-130-defb130-in-the-macrophage-microbicidal-mechanisms-for-killing-plasmodium-falciparum
#19
Mohamad Alaa Terkawi, Ryo Takano, Atsushi Furukawa, Fumi Murakoshi, Kentaro Kato
Understanding the molecular defense mechanism of macrophages and identifying their effector molecules against malarial parasites may provide important clues for the discovery of new therapies. To analyze the immunological responses of malarial parasite-induced macrophages, we used DNA microarray technology to examine the gene profile of differentiated macrophages phagocytizing Plasmodium falciparum-parasitized erythrocytes (iRBC). The transcriptional gene profile of macrophages in response to iRBCs represented 168 down-regulated genes, which were mainly involved in the cellular immune response, and 216 upregulated genes, which were involved in cellular proteolysis, growth, and adhesion...
February 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28179995/caspase-mediated-proteolysis-of-the-sorting-nexin-2-disrupts-retromer-assembly-and-potentiates-met-hepatocyte-growth-factor-receptor-signaling
#20
Catherine M Duclos, Audrey Champagne, Julie C Carrier, Caroline Saucier, Christine L Lavoie, Jean-Bernard Denault
The unfolding of apoptosis involves the cleavage of hundreds of proteins by the caspase family of cysteinyl peptidases. Among those substrates are proteins involved in intracellular vesicle trafficking with a net outcome of shutting down the crucial processes governing protein transport to organelles and to the plasma membrane. However, because of the intertwining of receptor trafficking and signaling, cleavage of specific proteins may lead to unintended consequences. Here we show that in apoptosis, sorting nexin 1 and 2 (SNX1 and SNX2), two proteins involved in endosomal sorting, are cleaved by initiator caspases and also by executioner caspase-6 in the case of SNX2...
2017: Cell Death Discovery
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