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Protein function prediction

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https://www.readbyqxmd.com/read/27920762/artificial-intelligence-vs-statistical-modeling-and-optimization-of-continuous-bead-milling-process-for-bacterial-cell-lysis
#1
Shafiul Haque, Saif Khan, Mohd Wahid, Sajad A Dar, Nipunjot Soni, Raju K Mandal, Vineeta Singh, Dileep Tiwari, Mohtashim Lohani, Mohammed Y Areeshi, Thavendran Govender, Hendrik G Kruger, Arshad Jawed
For a commercially viable recombinant intracellular protein production process, efficient cell lysis and protein release is a major bottleneck. The recovery of recombinant protein, cholesterol oxidase (COD) was studied in a continuous bead milling process. A full factorial response surface methodology (RSM) design was employed and compared to artificial neural networks coupled with genetic algorithm (ANN-GA). Significant process variables, cell slurry feed rate (A), bead load (B), cell load (C), and run time (D), were investigated and optimized for maximizing COD recovery...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27920567/evaluation-of-bode-index-and-its-relationship-with-systemic-inflammation-mediated-by-proinflammatory-biomarkers-in-patients-with-copd
#2
Naushad Ahmad Khan, Mradul Kumar Daga, Istaq Ahmad, Govind Mawari, Suman Kumar, Naresh Kumar, Syed Akhter Husain
INTRODUCTION: BODE index, a multidimensional grading system which is based on Body mass index, airway Obstruction, Dyspnea scale, and Exercise capacity, has been increasingly used for the evaluation of chronic obstructive pulmonary disease (COPD). Many of the systemic manifestations of COPD are shown to be mediated by elevated levels of proinflammatory biomarkers. OBJECTIVE: We aimed to investigate the relationship between the BODE index, its components, disease severity, and proinflammatory biomarkers like C-reactive protein (CRP), tumor necrosis factor (TNF)-α, and interleukin (IL)-6...
2016: Journal of Inflammation Research
https://www.readbyqxmd.com/read/27920298/malate-synthase-and-%C3%AE-methylmalyl-coa-lyase-reactions-in-the-methylaspartate-cycle-in-haloarcula-hispanica
#3
Farshad Borjian, Jing Han, Jing Hou, Hua Xiang, Jan Zarzycki, Ivan A Berg
: Haloarchaea are extremely halophilic heterotrophic microorganisms belonging to the class Halobacteria (Euryarchaeota). Almost half of the haloarchaea possesses the genes coding for enzymes of the methylaspartate cycle, a recently discovered anaplerotic acetate assimilation pathway. In this cycle, the enzymes of the tricarboxylic acid cycle together with the dedicated enzymes of the methylaspartate cycle convert two acetyl-CoA molecules to malate. The methylaspartate cycle involves two reactions catalyzed by homologous enzymes belonging to the CitE-like enzyme superfamily, the malyl-CoA lyase/thioesterase (haloarchaeal malate synthase, hMS, Hah_2476 in Haloarcula hispanica) and the β-methylmalyl-CoA lyase (hMCL, Hah_1341)...
December 5, 2016: Journal of Bacteriology
https://www.readbyqxmd.com/read/27920204/studies-on-the-detection-expression-glycosylation-dimerization-and-ligand-binding-properties-of-mouse-siglec-e
#4
Shoib Siddiqui, Flavio Schwarz, Stevan Springer, Zahra Khedri, Hai Yu, Lingquan Deng, Andrea Verhagen, Yuko Naito-Matsui, Weiping Jiang, Daniel Kim, Jie Zhou, Beibei Ding, Xi Chen, Nissi Varki, Ajit Varki
CD33-related Siglecs are a family of proteins widely expressed on innate immune cells. Binding of sialylated glycans or other ligands triggers signals that inhibit or activate inflammation. Immunomodulation by Siglecs has been extensively studied, but relationships between structure and functions are poorly explored. Here we present new data relating the structure and function of Siglec-E, the major CD33-related Siglec expressed on mouse neutrophils, monocytes, macrophages, and dendritic cells. We generated nine new rat monoclonal antibodies specific to mouse Siglec-E, with no cross-reactivity to Siglec-F...
December 5, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27919619/microsatellite-polymorphism-located-immediately-upstream-of-the-phosphatidylinositol-glycan-class-k-gene-pigk-affects-its-expression-which-correlates-with-tyrosinase-activity-in-human-melanocytes
#5
Ken Okamura, Masahiro Hayashi, Yuko Abe, Yuta Araki, Yutaka Hozumi, Tamio Suzuki
BACKGROUND: Glycosylphosphatidylinositol (GPI) acts as a membrane anchor and a post-translational modifier for more than 150 proteins (called GPI-anchored proteins: GPI-APs). However, little study has been done to explore the role of GPI-APs in melanocytes. METHODS: The relationship between the mRNA expression of the genes which play essential roles in GPI anchoring system [phosphatidylinositol glycan, class A, and class K gene (PIGA, PIGK)] and melanogenesis-related genes (MITF, TYRP1, TYRP2, and TYR) as well as DOPA oxidase activities were evaluated in 13 different normal human epidermal melanocytes (NHEMs)...
November 27, 2016: Journal of Dermatological Science
https://www.readbyqxmd.com/read/27919260/a-frameshift-mutation-in-mocos-is-associated-with-familial-renal-syndrome-xanthinuria-in-tyrolean-grey-cattle
#6
Leonardo Murgiano, Vidhya Jagannathan, Christian Piffer, Inmaculada Diez-Prieto, Marilena Bolcato, Arcangelo Gentile, Cord Drögemüller
BACKGROUND: Renal syndromes are occasionally reported in domestic animals. Two identical twin Tyrolean Grey calves exhibited weight loss, skeletal abnormalities and delayed development associated with kidney abnormalities and formation of uroliths. These signs resembled inherited renal tubular dysplasia found in Japanese Black cattle which is associated with mutations in the claudin 16 gene. Despite demonstrating striking phenotypic similarities, no obvious presence of pathogenic variants of this candidate gene were found...
December 5, 2016: BMC Veterinary Research
https://www.readbyqxmd.com/read/27918592/microrna-497-induces-apoptosis-and-suppresses-proliferation-via-the-bcl-2-bax-caspase9-caspase3-pathway-and-cyclin-d2-protein-in-huvecs
#7
Ridong Wu, Shi Tang, Mian Wang, Xiangdong Xu, Chen Yao, Shenming Wang
INTRODUCTION: MicroRNAs play crucial roles in various types of diseases. However, to date, no information about the role of miR-497 in the development of atherosclerosis has been reported. This study investigated the possible role of miR-497 in vascular endothelial cell injury during the early stage of atherosclerosis. MATERIALS AND METHODS: The expression level of miR-497 in human umbilical vein endothelial cells (HUVECs) exposed to ox-LDL was detected using qRT-PCR...
2016: PloS One
https://www.readbyqxmd.com/read/27918494/associations-between-neutrophil-gelatinase-associated-lipocalin-neutrophil-to-lymphocyte-ratio-atrial-fibrillation-and-renal-dysfunction-in-chronic-heart-failure
#8
Onur Argan, Dilek Ural, Guliz Kozdag, Tayfun Sahin, Serdar Bozyel, Mujdat Aktas, Kurtulus Karauzum, Irem Yilmaz, Emir Dervis, Aysen Agir
BACKGROUND Atrial fibrillation (AF) and renal dysfunction are two common comorbidities in patients with chronic heart failure with reduced ejection fraction (HFrEF). This study evaluated the effect of permanent AF on renal function in HFrEF and investigated the associations of atrial fibrillation, neutrophil gelatinase-associated lipocalin (NGAL), and neutrophil-to-lymphocyte ratio (NLR) with adverse clinical outcome. MATERIAL AND METHODS Serum NGAL levels measured by ELISA and NLR were compared between patients with sinus rhythm (HFrEF-SR, n=68), with permanent AF (HFrEF-AF, n=62), and a healthy control group (n=50)...
December 5, 2016: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/27917857/relocation-of-active-site-carboxylates-in-major-facilitator-superfamily-multidrug-transporter-lmrp-reveals-plasticity-in-proton-interactions
#9
Asha V Nair, Himansha Singh, Sagar Raturi, Arthur Neuberger, Zhen Tong, Ning Ding, Kelvin Agboh, Hendrik W van Veen
The expression of polyspecific membrane transporters is one important mechanism by which cells can obtain resistance to structurally different antibiotics and cytotoxic agents. These transporters reduce intracellular drug concentrations to subtoxic levels by mediating drug efflux across the cell envelope. The major facilitator superfamily multidrug transporter LmrP from Lactococcus lactis catalyses drug efflux in a membrane potential and chemical proton gradient-dependent fashion. To enable the interaction with protons and cationic substrates, LmrP contains catalytic carboxyl residues on the surface of a large interior chamber that is formed by transmembrane helices...
December 5, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27917833/crystal-structure-of-the-toxin-msmeg_6760-the-structural-homolog-of-mycobacterium-tuberculosis-rv2035-a-novel-type-ii-toxin-involved-in-the-hypoxic-response
#10
R Alexandra Bajaj, Mark A Arbing, Annie Shin, Duilio Cascio, Linda Miallau
The structure of Msmeg_6760, a protein of unknown function, has been determined. Biochemical and bioinformatics analyses determined that Msmeg_6760 interacts with a protein encoded in the same operon, Msmeg_6762, and predicted that the operon is a toxin-antitoxin (TA) system. Structural comparison of Msmeg_6760 with proteins of known function suggests that Msmeg_6760 binds a hydrophobic ligand in a buried cavity lined by large hydrophobic residues. Access to this cavity could be controlled by a gate-latch mechanism...
December 1, 2016: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/27917155/aerobic-lineage-of-the-oxidative-stress-response-protein-rubrerythrin-emerged-in-an-ancient-microaerobic-hyper-thermophilic-environment
#11
Juan P Cardenas, Raquel Quatrini, David S Holmes
Rubrerythrins (RBRs) are non-heme di-iron proteins belonging to the ferritin-like superfamily. They are involved in oxidative stress defense as peroxide scavengers in a wide range of organisms. The vast majority of RBRs, including classical forms of this protein, contain a C-terminal rubredoxin-like domain involved in electron transport that is used during catalysis in anaerobic conditions. Rubredoxin is an ancient and large protein family of short length (<100 residues) that contains a Fe-S center involved in electron transfer...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27916780/mir-15a-5p-regulates-viability-and-matrix-degradation-of-human-osteoarthritis-chondrocytes-via-targeting-vegfa
#12
Hongwei Chen, Yun Tian
Previous studies demonstrated that miR-15a-5p was probably associated with human hepatocellular carcinoma, while the function of miR-15a-5p in OA (Osteoarthritis) still remains unknown. Here, we uncovered the potential role of miR-15a-5p on OA pathogenesis and confirmed its predicted target VEGFA (Vascular Endothelial Growth Factor A). Measured by RT-PCR, miR-15a-5p expression increased remarkably while VEGFA expression was significantly decreased in OA chondrocytes compared with normal conditions. According to Luciferase activity assay, miR-15a-5p directly targeted the 3'-UTR of VEGFA to inhibit its expression...
December 3, 2016: Bioscience Trends
https://www.readbyqxmd.com/read/27916541/the-orphan-g-protein-coupled-receptor-gpr139-is-activated-by-the-peptides-adrenocorticotropic-hormone-acth-%C3%AE-and-%C3%AE-melanocyte-stimulating-hormone-%C3%AE-msh-and-%C3%AE-msh-and-the-conserved-core-motif-hfrw
#13
Anne Cathrine Nøhr, Mohamed A Shehata, Alexander S Hauser, Vignir Isberg, Jacek Mokrosinski, I Sadaf Farooqi, Daniel Sejer Pedersen, David E Gloriam, Hans Bräuner-Osborne
GPR139 is an orphan G protein-coupled receptor that is expressed primarily in the brain. Not much is known regarding the function of GPR139. Recently we have shown that GPR139 is activated by the amino acids l-tryptophan and l-phenylalanine (EC50 values of 220 μM and 320 μM, respectively), as well as di-peptides comprised of aromatic amino acids. This led us to hypothesize that GPR139 may be activated by peptides. Sequence alignment of the binding cavities of all class A GPCRs, revealed that the binding pocket of the melanocortin 4 receptor is similar to that of GPR139...
December 1, 2016: Neurochemistry International
https://www.readbyqxmd.com/read/27915971/the-iap-protein-family-smac-mimetics-and-cancer-treatment
#14
Alex Philchenkov, Koh Miura
Since the acquired resistance of cells to apoptosis is one of the major hallmarks of cancer, the endogenous inhibitors of apoptosis can be regarded as promising targets in the design of anticancer therapeutics. In addition to their antiapoptotic activity, inhibitor of apoptosis proteins (IAPs) are able to regulate numerous other cell functions, including proliferation, differentiation, and migration, as well as proinflammatory and immune responses. Study of the IAP family as target molecules in targeted therapies has recently focused on SMAC mimetics as synthetic IAP antagonists that have been under development as promising therapeutics...
2016: Critical Reviews in Oncogenesis
https://www.readbyqxmd.com/read/27914524/the-phenylalanine-ammonia-lyase-gene-family-in-isatis-indigotica-fort-molecular-cloning-characterization-and-expression-analysis
#15
Rui-Fang Ma, Qian-Zi Liu, Ying Xiao, Lei Zhang, Qing Li, Jun Yin, Wan-Sheng Chen
Phenolic compounds, metabolites of the phenylpropanoid pathway, play an important role in the growth and environmental adaptation of many plants. Phenylalanine ammonia-lyase (PAL) is the first key enzyme of the phenylpropanoid pathway. The present study was designed to investigate whether there is a multi-gene family in I. Indigotic and, if so, to characterize their properties. We conducted a comprehensive survey on the transcription profiling database by using tBLASTn analysis. Several bioinformatics methods were employed to perform the prediction of composition and physicochemical characters...
November 2016: Chinese Journal of Natural Medicines
https://www.readbyqxmd.com/read/27914282/fam3c-modulates-osteogenic-differentiation-by-down-regulating-runx2
#16
Ameya Bendre, Kalman G Büki, Jorma A Määttä
Fam3c, a cytokine-like protein, is a member of the Fam3 family (family with sequence similarity 3) and has been implicated to play a crucial role in Epithelial-to- mesenchymal transition (EMT) and subsequent metastasis during cancer progression. A few independent genome-wide association studies on different population cohorts predicted the gene locus of Fam3c to be associated with bone mineral density and fractures. In this study, we examined the role of Fam3c during osteoblast differentiation. Fam3c was found to be expressed during osteogenic differentiation of both primary bone marrow stromal cells and MC3T3-E1 pre-osteoblasts...
November 30, 2016: Differentiation; Research in Biological Diversity
https://www.readbyqxmd.com/read/27914200/assembling-the-tat-protein-translocase
#17
Felicity Alcock, Phillip J Stansfeld, Hajra Basit, Johann Habersetzer, Matthew Ab Baker, Tracy Palmer, Mark I Wallace, Ben C Berks
The twin-arginine protein translocation system (Tat) transports folded proteins across the bacterial cytoplasmic membrane and the thylakoid membranes of plant chloroplasts. The Tat transporter is assembled from multiple copies of the membrane proteins TatA, TatB, and TatC. We combine sequence co-evolution analysis, molecular simulations, and experimentation to define the interactions between the Tat proteins of Escherichia coli at molecular-level resolution. In the TatBC receptor complex the transmembrane helix of each TatB molecule is sandwiched between two TatC molecules, with one of the inter-subunit interfaces incorporating a functionally important cluster of interacting polar residues...
December 3, 2016: ELife
https://www.readbyqxmd.com/read/27914072/identifying-bacterial-immune-evasion-proteins-using-phage-display
#18
Cindy Fevre, Lisette Scheepmaker, Pieter-Jan Haas
Methods aimed at identification of immune evasion proteins are mainly rely on in silico prediction of sequence, structural homology to known evasion proteins or use a proteomics driven approach. Although proven successful these methods are limited by a low efficiency and or lack of functional identification. Here we describe a high-throughput genomic strategy to functionally identify bacterial immune evasion proteins using phage display technology. Genomic bacterial DNA is randomly fragmented and ligated into a phage display vector that is used to create a phage display library expressing bacterial secreted and membrane bound proteins...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914063/episweep-computationally-driven-reengineering-of-therapeutic-proteins-to-reduce-immunogenicity-while-maintaining-function
#19
Yoonjoo Choi, Deeptak Verma, Karl E Griswold, Chris Bailey-Kellogg
Therapeutic proteins are yielding ever more advanced and efficacious new drugs, but the biological origins of these highly effective therapeutics render them subject to immune surveillance within the patient's body. When recognized by the immune system as a foreign agent, protein drugs elicit a coordinated response that can manifest a range of clinical complications including rapid drug clearance, loss of functionality and efficacy, delayed infusion-like allergic reactions, more serious anaphylactic shock, and even induced auto-immunity...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914061/probing-oligomerized-conformations-of-defensin-in-the-membrane
#20
Wenxun Gan, Dina Schneidman, Ning Zhang, Buyong Ma, Ruth Nussinov
Computational prediction and design of membrane protein-protein interactions facilitate biomedical engineering and biotechnological applications. Due to their antimicrobial activity, human defensins play an important role in the innate immune system. Human defensins are attractive pharmaceutical targets due to their small size, broad activity spectrum, reduced immunogenicity, and resistance to proteolysis. Protein engineering based modification of defensins can improve their pharmaceutical properties. Here we present an approach to computationally probe defensins' oligomerization states in the membrane...
2017: Methods in Molecular Biology
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