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https://www.readbyqxmd.com/read/28813686/genetic-and-functional-characterization-of-a-novel-gh10-endo-%C3%AE-1-4-xylanase-with-a-ricin-type-%C3%AE-trefoil-domain-like-domain-from-luteimicrobium-xylanilyticum-hy-24
#1
Do Young Kim, Sun Hwa Lee, Min Ji Lee, Han-Young Cho, Jong Suk Lee, Young Ha Rhee, Dong-Ha Shin, Kwang-Hee Son, Ho-Yong Park
The gene (1488-bp) encoding a novel GH10 endo-β-1,4-xylanase (XylM) consisting of an N-terminal catalytic GH10 domain and a C-terminal ricin-type β-trefoil lectin domain-like (RICIN) domain was identified from Luteimicrobium xylanilyticum HY-24. The GH10 domain of XylM was 72% identical to that of Micromonospora lupini endo-β-1,4-xylanase and the RICIN domain was 67% identical to that of Actinospica robiniae hypothetical protein. The recombinant enzyme (rXylM: 49kDa) exhibited maximum activity toward beechwood xylan at 65°C and pH 6...
August 13, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28813517/prmepred-a-protein-arginine-methylation-prediction-tool
#2
Pawan Kumar, Joseph Joy, Ashutosh Pandey, Dinesh Gupta
Protein methylation is an important Post-Translational Modification (PTMs) of proteins. Arginine methylation carries out and regulates several important biological functions, including gene regulation and signal transduction. Experimental identification of arginine methylation site is a daunting task as it is costly as well as time and labour intensive. Hence reliable prediction tools play an important task in rapid screening and identification of possible methylation sites in proteomes. Our preliminary assessment using the available prediction methods on collected data yielded unimpressive results...
2017: PloS One
https://www.readbyqxmd.com/read/28813514/the-helicobacter-pylori-type-iv-secretion-system-promotes-il-8-synthesis-in-a-model-of-pediatric-airway-epithelium-via-p38-map-kinase
#3
Myra G Dela Pena-Ponce, Monica T Jimenez, Lori M Hansen, Jay V Solnick, Lisa A Miller
Epidemiologic studies have reported an inverse relationship between childhood Helicobacter pylori infection and development of allergic asthma. Because lung epithelium plays an important role in allergic asthma pathogenesis, we hypothesized that H. pylori may directly influence airway epithelial cell innate immune function, particularly in early childhood. To test our hypothesis, we established an in vitro H. pylori infection model using primary tracheobronchial epithelial cell cultures derived from infant, juvenile and adult rhesus monkeys...
2017: PloS One
https://www.readbyqxmd.com/read/28813493/mpp10-represents-a-platform-for-the-interaction-of-multiple-factors-within-the-90s-pre-ribosome
#4
Bebiana Sá-Moura, Markus Kornprobst, Satyavati Kharde, Yasar Luqman Ahmed, Gunter Stier, Ruth Kunze, Irmgard Sinning, Ed Hurt
In eukaryotes, ribosome assembly is a highly complex process that involves more than 200 assembly factors that ensure the folding, modification and processing of the different rRNA species as well as the timely association of ribosomal proteins. One of these factors, Mpp10 associates with Imp3 and Imp4 to form a complex that is essential for the normal production of the 18S rRNA. Here we report the crystal structure of a complex between Imp4 and a short helical element of Mpp10 to a resolution of 1.88 Å. Furthermore, we extend the interaction network of Mpp10 and characterize two novel interactions...
2017: PloS One
https://www.readbyqxmd.com/read/28813471/mitochondrial-genome-evolution-in-the-saccharomyces-sensu-stricto-complex
#5
Jiangxing Ruan, Jian Cheng, Tongcun Zhang, Huifeng Jiang
Exploring the evolutionary patterns of mitochondrial genomes is important for our understanding of the Saccharomyces sensu stricto (SSS) group, which is a model system for genomic evolution and ecological analysis. In this study, we first obtained the complete mitochondrial sequences of two important species, Saccharomyces mikatae and Saccharomyces kudriavzevii. We then compared the mitochondrial genomes in the SSS group with those of close relatives, and found that the non-coding regions evolved rapidly, including dramatic expansion of intergenic regions, fast evolution of introns and almost 20-fold higher rearrangement rates than those of the nuclear genomes...
2017: PloS One
https://www.readbyqxmd.com/read/28813459/%C3%AE-2-microglobulin-gene-duplication-in-cetartiodactyla-remains-intact-only-in-pigs-and-possibly-confers-selective-advantage-to-the-species
#6
Thong Minh Le, Quy Van Chanh Le, Dung Minh Truong, Hye-Jeong Lee, Min-Kyeung Choi, Hyesun Cho, Hak-Jae Chung, Jin-Hoi Kim, Jeong-Tae Do, Hyuk Song, Chankyu Park
Several β2-microglobulin (B2M) -bound protein complexes undertake key roles in various immune system pathways, including the neonatal Fc receptor (FcRn), cluster of differentiation 1 (CD1) protein, non-classical major histocompatibility complex (MHC), and well-known MHC class I molecules. Therefore, the duplication of B2M may lead to an increase in the biological competence of organisms to the environment. Based on the pig genome assembly SSC10.2, a segmental duplication of ~45.5 kb, encoding the entire B2M protein, was identified in pig chromosome 1...
2017: PloS One
https://www.readbyqxmd.com/read/28813159/enhancing-enzyme-activity-and-immobilization-in-nanostructured-inorganic-enzyme-complexes
#7
Xuye Lang, Lingling Zhu, Yingning Gao, Ian Wheeldon
Understanding the chemical and physical interactions at the interface of protein surfaces and inorganic crystals has important implications in the advancement of immobilized enzyme catalysis. Recently, enzyme-inorganic hybrid complexes have been demonstrated as effective materials for enzyme-immobilization. The precipitation of phosphate nanocrystals in the presence of enzymes creates enzyme-Cu3(PO4)2-3H2O particles with high surface-to-volume ratios, enhanced activity, and increased stability. Here, we begin to develop a mechanistic understanding of enzyme loading in such complexes...
August 16, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28813018/biophysical-and-computational-studies-of-the-vcci-vmip-ii-complex
#8
Anna F Nguyen, Nai-Wei Kuo, Laura J Showalter, Ricardo Ramos, Cynthia M Dupureur, Michael E Colvin, Patricia J LiWang
Certain viruses have the ability to subvert the mammalian immune response, including interference in the chemokine system. Poxviruses produce the chemokine binding protein vCCI (viral CC chemokine inhibitor; also called 35K), which tightly binds to CC chemokines. To facilitate the study of vCCI, we first provide a protocol to produce folded vCCI from Escherichia coli (E. coli.) It is shown here that vCCI binds with unusually high affinity to viral Macrophage Inflammatory Protein-II (vMIP-II), a chemokine analog produced by the virus, human herpesvirus 8 (HHV-8)...
August 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28812992/endolysosomal-degradation-of-allergenic-ole-e-1-like-proteins-analysis-of-proteolytic-cleavage-sites-revealing-t-cell-epitope-containing-peptides
#9
Sabrina Wildner, Brigitta Elsässer, Teresa Stemeseder, Peter Briza, Wai Tuck Soh, Mayte Villalba, Jonas Lidholm, Hans Brandstetter, Gabriele Gadermaier
Knowledge of the susceptibility of proteins to endolysosomal proteases provides valuable information on immunogenicity. Though Ole e 1-like proteins are considered relevant allergens, little is known about their immunogenic properties and T cell epitopes. Thus, six representative molecules, i.e., Ole e 1, Fra e 1, Sal k 5, Che a 1, Phl p 11 and Pla l 1, were investigated. Endolysosomal degradation and peptide generation were simulated using microsomal fractions of JAWS II dendritic cells. Kinetics and peptide patterns were evaluated by gel electrophoresis and mass spectrometry...
August 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28812356/single-molecule-nanopore-spectrometry-for-peptide-detection
#10
Amy E Chavis, Kyle T Brady, Grace A Hatmaker, Christopher E Angevine, Nuwan Kothalawala, Amala Dass, Joseph W F Robertson, Joseph E Reiner
Sensing and characterization of water-soluble peptides is of critical importance in a wide variety of bioapplications. Single molecule nanopore spectrometry (SMNS) is based on the idea that one can use biological protein nanopores to resolve different sized molecules down to limits set by the blockade duration and noise. Previous work has shown that this enables discrimination between polyethylene glycol (PEG) molecules that differ by a single monomer unit. This paper describes efforts to extend SMNS to a variety of biologically relevant, water-soluble peptides...
August 16, 2017: ACS Sensors
https://www.readbyqxmd.com/read/28812069/the-sensitivity-of-folding-free-energy-landscapes-of-trpzips-to-mutations-in-the-hydrophobic-core
#11
Madhulika Gupta, Prabir Khatua, Charusita Chakravarty, Sanjoy Bandyopadhyay
The sensitivity of the stability of folded states and free energy landscapes to the differences in the hydrophobic content of the core residues has been studied for the set of 16-residue trpzips, namely, Trpzip4, Trpzip5 and Trpzip6. The combination of principal component analysis and different secondary structure order metrics as reaction coordinates has been used to characterize and identify all the underlying attractive basins corresponding to the folded and the unfolded states for each trpzip at 300 K. Our results reveal that even a single mutation in the hydrophobic core perturbs the stability of the folded peptide and the conformational preferences for the partially folded and unfolded states significantly, leading to concomitant alterations in the free energy landscape of trpzips...
August 16, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28811596/complete-alanine-scanning-of-the-escherichia-coli-rbsb-ribose-binding-protein-reveals-residues-important-for-chemoreceptor-signaling-and-periplasmic-abundance
#12
Artur Reimer, Vitali Maffenbeier, Manupriyam Dubey, Vladimir Sentchilo, Diogo Tavares, Manuel Hernandez Gil, Siham Beggah, Jan Roelof van der Meer
The Escherichia coli RbsB ribose binding protein has been used as a scaffold for predicting new ligand binding functions through in silico modeling, yet with limited success and reproducibility. In order to possibly improve the success of predictive modeling on RbsB, we study here the influence of individual residues on RbsB-mediated signaling in a near complete library of alanine-substituted RbsB mutants. Among a total of 232 tested mutants, we found 10 which no longer activated GFPmut2 reporter expression in E...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811385/circulating-mir-200c-is-up-regulated-in-paediatric-patients-with-familial-hypercholesterolaemia-and-correlates-with-mir-33a-b-levels-implication-of-a-zeb1-dependent-mechanism
#13
Marco D'Agostino, Francesco Martino, Sara Sileno, Francesco Barilla, Sara Beji, Lorenza Marchetti, Fabio Maria Gangi, Luca Persico, Mario Picozza, Anna Montali, Eliana Martino, Cristina Zanoni, Daniele Avitabile, Sandro Parrotto, Maurizio C Capogrossi, Alessandra Magenta
Hypercholesterolaemia provokes reactive oxygen species (ROS) increase and is a major risk factor for cardiovascular diseases (CVD) development. We previously showed that circulating microRNA(miR)-33a/b expression levels were up-regulated in children with familial hypercholesterolaemia (FH). miR-33a/b control cholesterol homoeostasis and recently miR-33b has been demonstrated to directly target the transcription factor ZEB1. The latter acts in a negative feedback-loop with miR-200 family. Our previous studies showed that the ROS-dependent miR-200c up-regulation induces endothelial dysfunction and provokes a ZEB1-dependent apoptosis and senescence...
August 15, 2017: Clinical Science (1979-)
https://www.readbyqxmd.com/read/28811318/the-%C3%AE-cell-assassin-iapp-cytotoxicity
#14
Daniel Raleigh, Xiaoxue Zhang, Benoit Hastoy, Anne Clark
Islet amyloid polypeptide (IAPP) forms cytotoxic oligomers and amyloid fibrils in islets in Type 2 diabetes (T2DM). The causal factors for amyloid formation are largely unknown. Mechanisms of molecular folding and assembly of human IAPP (hIAPP) into β-sheets, oligomers and fibrils have been assessed by detailed biophysical studies of hIAPP and non-fibrillogenic, rodent IAPP (rIAPP); cytotoxicity is associated with the early phases (oligomers/multimers) of fibrillogenesis. Interaction with synthetic membranes promotes β-sheet assembly possibly via a transient α-helical molecular conformation...
August 15, 2017: Journal of Molecular Endocrinology
https://www.readbyqxmd.com/read/28811265/molecular-cloning-heterologous-expression-and-functional-characterization-of-gamma-tocopherol-methyl-transferase-%C3%AE-tmt-from-glycine-max
#15
Kalpana Tewari, Anil Dahuja, Archana Sachdev, Kishwar Ali, Vaibhav Kumar, Amresh Kumar, Sweta Kumari
γ-Tocopherol methyltransferase (γ-TMT) (EC 2.1.1.95) is the last enzyme in the tocopherol biosynthetic pathway and it catalyzes the conversion of γ-tocopherol into α-tocopherol, the nutritionally significant and most bioactive form of vitamin E. Although the γ-TMT gene has been successfully overexpressed in many crops to enhance their α-tocopherol content but still only few attempts have been made to uncover its structural, functional and regulation aspects at protein level. In this study, we have cloned the complete 909bp coding sequence of Glycine max γ-TMT (Gm γ-TMT) gene that encodes the corresponding protein comprising of 302 amino acid residues...
August 12, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28811130/comparative-study-on-stabilizing-ability-of-food-protein-non-ionic-surfactant-and-anionic-surfactant-on-bcs-type-ii-drug-carvedilol-loaded-nanosuspension-physicochemical-and-pharmacokinetic-investigation
#16
Tianjiao Geng, Parikshit Banerjee, Zhangdi Lu, Abdelmoumin Zoghbi, Tiantian Li, Bo Wang
Carvedilol (CAR) in its pure state has low aqueous solubility and extremely poor bioavailability which largely limit its clinical application. The aim of the study is to improve the dissolution rate and the bioavailability of CAR via preparing nanosuspensions with different stabilizers. Antisolvent precipitation-ultrasonication technique was used here. Attempts have been made to use food protein- Whey protein isolate (WPI) as a stabilizer in CAR loaded nanosuspension and also to compare its stabilizing potential with conventional nanosuspension stabilizers such as non-ionic linear copolymer-poloxamer 188 (PLX188) and anionic surfactant-sodium dodecyl sulfate (SDS)...
August 12, 2017: European Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/28811070/evaluation-of-sequence-variability-in-hiv-1-gp41-c-peptide-helix-grafted-proteins
#17
Rachel L Tennyson, Susanne N Walker, Terumasa Ikeda, Reuben S Harris, Brian R McNaughton
Many therapeutically-relevant protein-protein interactions (PPIs) have been reported that feature a helix and helix-binding cleft at the interface. Given this, different approaches to disrupting such PPIs have been developed. While short peptides (<15 amino acids) typically do not fold into a stable helix, researchers have reported chemical approaches to constraining helix structure. However, these approaches rely on laborious, and often expensive, chemical synthesis and purification. Our premise is that protein-based solutions that stabilize a therapeutically-relevant helix offer a number of advantages...
August 1, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28811027/design-of-carbohydrate-electron-transfer-peptides-for-human-histocytic-lymphoma-cell-sensing
#18
Kazuharu Sugawara, Toshihiko Kadoya, Hideki Kuramitz, Yoshihiro Mihara
A carbohydrate/electro-transfer peptide probe was fabricated to perform cell sensing. The probe consisted of a cello-oligosaccharide that was created by the conjugation of an electron-transfer peptide (Y5C) and a carbohydrate via a Schiff base. An oxidation wave due to a phenolic hydroxyl group was obtained by scanning with a glassy carbon electrode. This cell-sensing system was based on a competitive reaction between carbohydrates on a cell surface and the probe as each reacted to a protein that recognized the carbohydrate...
August 29, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28810831/application-of-a-bayesian-non-linear-model-hybrid-scheme-to-sequence-data-for-genomic-prediction-and-qtl-mapping
#19
Tingting Wang, Yi-Ping Phoebe Chen, Iona M MacLeod, Jennie E Pryce, Michael E Goddard, Ben J Hayes
BACKGROUND: Using whole genome sequence data might improve genomic prediction accuracy, when compared with high-density SNP arrays, and could lead to identification of casual mutations affecting complex traits. For some traits, the most accurate genomic predictions are achieved with non-linear Bayesian methods. However, as the number of variants and the size of the reference population increase, the computational time required to implement these Bayesian methods (typically with Monte Carlo Markov Chain sampling) becomes unfeasibly long...
August 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28810783/self-consistent-calculation-of-protein-folding-pathways
#20
S Orioli, S A Beccara, P Faccioli
We introduce an iterative algorithm to efficiently simulate protein folding and other conformational transitions, using state-of-the-art all-atom force fields. Starting from the Langevin equation, we obtain a self-consistent stochastic equation of motion, which directly yields the reaction pathways. From the solution of this set of equations we derive a stochastic estimate of the reaction coordinate. We validate this approach against the results of plain MD simulations of the folding of a small protein, which were performed on the Anton supercomputer...
August 14, 2017: Journal of Chemical Physics
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