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https://www.readbyqxmd.com/read/27914364/structure-based-exploration-and-exploitation-of-the-s4-subsite-of-norovirus-3cl-protease-in-the-design-of-potent-and-permeable-inhibitors
#1
Anushka C Galasiti Kankanamalage, Yunjeong Kim, Athri D Rathnayake, Vishnu C Damalanka, Pathum M Weerawarna, Sean T Doyle, Amer F Alsoudi, D M Padmasankha Dissanayake, Gerald H Lushington, Nurjahan Mehzabeen, Kevin P Battaile, Scott Lovell, Kyeong-Ok Chang, William C Groutas
Human noroviruses are the primary cause of epidemic and sporadic acute gastroenteritis. The worldwide high morbidity and mortality associated with norovirus infections, particularly among the elderly, immunocompromised patients and children, constitute a serious public health concern. There are currently no approved human vaccines or norovirus-specific small-molecule therapeutics or prophylactics. Norovirus 3CL protease has recently emerged as a potential therapeutic target for the development of anti-norovirus agents...
November 14, 2016: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/27914345/biopolymer-matrix-for-nano-encapsulation-of-urease-a-model-protein-and-its-application-in-urea-detection
#2
Abhishek Saxena, Arpita Bhattacharya, Satish Kumar, Irving R Epstein, Rachana Sahney
Alginate microparticles and nanoparticles crosslinked with Ca(+2) ions are frequently employed in biomedical applications. Here we use microemulsion polymerization to prepare alginate nanoparticles (nanogels) using different crosslinking ions (Ca(+2), Sr(+2), Ba(+2)) to encapsulate a model protein, urease enzyme (jackbeans). With alginate concentrations of 0.2wt% in the aqueous phase, emulsion droplets showed good stability and narrow, monomodal distributions with radii ∼65±10nm. The size of the nanogel varies with the crosslinking cation and its affinity for the mannuronate and guluronate units in the linear alginate chain...
November 9, 2016: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/27914332/amyloid-graphene-oxide-as-immobilization-platform-of-au-nanocatalysts-and-enzymes-for-improved-glucose-sensing-activity
#3
Xiaochen Wu, Mingjie Li, Zehui Li, Lili Lv, Yan Zhang, Chaoxu Li
Two-dimensional GO nanosheets and one-dimensional lysozyme nanofibrils were hybridized through electrostatic interaction to get a novel amyloid-GO composite, which promised a biocompatible immobilization platform for Au nanocatalysts as well as enzymes. The immobilization platform could load a large and tunable amount of Au NPs while maintaining their high catalytic activity. The immobilized catalysts showed high electrochemical behaviors, being ideal as glucose sensing systems. Furthermore, enzymes could also be immobilized on the residual bare surfaces of amyloid-GO, and served by a colorimetric method for a sensitive and selective analytical glucose-detecting platform...
November 16, 2016: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/27914320/biochemical-precursor-effects-on-the-fatty-acid-production-in-cell-suspension-cultures-of-theobroma-cacao-l
#4
O Parra, A M Gallego, A Urrea, L F Rojas, C Correa, L Atehortúa
Cocoa butter (CB) is composed of 96% palmitic, stearic, oleic, linoleic and linolenic fatty acids that are responsible for the hardness, texture and fusion properties of chocolate. Through in vitro plant cell culture it is possible to modify CB lipid profiles and to study the fatty acid biosynthesis pathway on a subcellular level, evaluating fundamental aspects to enhance in vitro fatty acid production in a specific and controlled way. In this research, culture media was supplemented with acetate, biotin, pyruvate, bicarbonate and glycerol at three different concentrations and the effects on the biomass production (g/L), cell viability, and fatty acids profile and production was evaluated in in vitro cell suspensions culture...
November 25, 2016: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/27914308/regulation-of-t-helper-cell-differentiation-by-e3-ubiquitin-ligases-and-deubiquitinating-enzymes
#5
REVIEW
Si-Fa Gao, Bo Zhong, Dandan Lin
CD4 T cells are essential components of adaptive immunity and play a critical role in anti-pathogenic or anti-tumor responses as well as autoimmune and allergic diseases. Naive CD4 T cells differentiate into distinct subsets of T helper (Th) cells by various signals including TCR, costimulatory and cytokine signals. Accumulating evidence suggests that these signaling pathways are critically regulated by ubiquitination and deubiquitination, two reversible posttranslational modifications mediated by E3 ubiquitin ligases and deubiquitinating enzymes (DUBs), respectively...
November 30, 2016: International Immunopharmacology
https://www.readbyqxmd.com/read/27914300/structure-based-analysis-of-bacilli-and-plasmid-dihydrofolate-reductase-evolution
#6
Mona Alotaibi, Ben Delos Reyes, Tin Le, Phuong Luong, Faramarz Valafar, Robert P Metzger, Gary B Fogel, David Hecht
Dihydrofolate reductase (DHFR), a key enzyme in tetrahydrofolate-mediated biosynthetic pathways, has a structural motif known to be highly conserved over a wide range of organisms. Given its critical role in purine and amino acid synthesis, DHFR is a well established therapeutic target for treating a wide range of prokaryotic and eukaryotic infections as well as certain types of cancer. Here we present a structural-based computer analysis of bacterial (Bacilli) and plasmid DHFR evolution. We generated a structure-based sequence alignment using 7 wild-type DHFR x-ray crystal structures obtained from the RCSB Protein Data Bank and 350 chromosomal and plasmid homology models we generated from sequences obtained from the NCBI Protein Database...
November 22, 2016: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/27914299/the-effects-of-fluorine-substitution-on-the-chemical-properties-and-inhibitory-capacity-of-donepezil-anti-alzheimer-drug-density-functional-theory-and-molecular-docking-calculations
#7
Azita Khosravan, Safora Marani, Mohammad Sadegh Sadeghi Googheri
Drug fluorination has the potential to reproduce useful drugs with decreasing the side effect of them. Identifying the effect of this improvement on the chemical properties and biological interactions of drug symbolizes a meaningful progress in drug design. Here the fluorination of Donepezil as an anti-Alzheimer drug, including 7 fluorinated derivatives of it, was investigated computationally. In the first part of our calculations, the most important chemical properties of drug that affects the drug efficiency were investigated by applying the M06/6-31g (d, p) and M062X/6-31g (d, p) levels of theories...
November 25, 2016: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/27914284/applying-crispr-cas-for-genome-engineering-in-plants-the-best-is-yet-to-come
#8
REVIEW
Holger Puchta
Less than 5 years ago the CRISPR/Cas nuclease was first introduced into eukaryotes, shortly becoming the most efficient and widely used tool for genome engineering. For plants, efforts were centred on obtaining heritable changes in most transformable crop species by inducing mutations into open reading frames of interest, via non-homologous end joining. Now it is important to take the next steps and further develop the technology to reach its full potential. For breeding, besides using DNA-free editing and avoiding off target effects, it will be desirable to apply the system for the mutation of regulatory elements and for more complex genome rearrangements...
November 30, 2016: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/27914283/binding-pattern-of-intermediate-udp-4-keto-xylose-to-human-udp-xylose-synthase-synthesis-and-std-nmr-of-model-keto-saccharides
#9
Claudia Puchner, Thomas Eixelsberger, Bernd Nidetzky, Lothar Brecker
Human UDP-xylose synthase (hUXS1) exclusively converts UDP-glucuronic acid to UDP-xylose via intermediate UDP-4-keto-xylose (UDP-Xyl-4O). Synthesis of model compounds like methyl-4-keto-xylose (Me-Xyl-4O) is reported to investigate the binding pattern thereof to hUXS1. Hence, selective oxidation of the desired hydroxyl function required employment of protecting group chemistry. Solution behavior of synthesized keto-saccharides was studied without enzyme via (1)H and (13)C NMR spectroscopy with respect to existent forms in deuterated potassium phosphate buffer...
November 5, 2016: Carbohydrate Research
https://www.readbyqxmd.com/read/27914214/antithrombin-improves-the-maternal-and-neonatal-outcomes-but-not-the-angiogenic-factors-in-extremely-growth-restricted-fetuses-at-28-weeks-of-gestation
#10
Midori Fujisaki, Ken Furuta, Masanao Ohhashi, Seishi Furukawa, Yuki Kodama, Yasuyuki Kawagoe, Hiroshi Sameshima, Tsuyomu Ikenoue
AIMS: Severe preterm fetal growth restriction (FGR) remote from term is problematic. We aimed to investigate the effect of maternally-administered antithrombin on maternal and neonatal outcomes. A prospective, one-arm, pilot study was performed in 14 women with severe FGR (≤5th centile) at <28 weeks of gestation, without hypertensive disorders. Maternal plasma concentrations of soluble Feline McDonough Sarcoma (FMS)-like trypsin kinase-1 (sFlt-1) and placental growth factor (PlGF) were measured and categorized into three groups: group 1; low sFlt-1 and high PlGF, group 2; moderate sFlt-1 and low PlGF, and group 3; high sFlt-1 and low PlGF...
December 3, 2016: Journal of Perinatal Medicine
https://www.readbyqxmd.com/read/27914133/lobeglitazone-a-novel-thiazolidinedione-improves-non-alcoholic-fatty-liver-disease-in-type-2-diabetes-its-efficacy-and-predictive-factors-related-to-responsiveness
#11
Yong Ho Lee, Jae Hyeon Kim, So Ra Kim, Heung Yong Jin, Eun Jung Rhee, Young Min Cho, Byung Wan Lee
Despite the rapidly increasing prevalence of non-alcoholic fatty liver disease (NAFLD) in type 2 diabetes (T2D), few treatment modalities are currently available. We investigated the hepatic effects of the novel thiazolidinedione (TZDs), lobeglitazone (Duvie) in T2D patients with NAFLD. We recruited drug-naïve or metformin-treated T2D patients with NAFLD to conduct a multicenter, prospective, open-label, exploratory clinical trial. Transient liver elastography (Fibroscan®; Echosens, Paris, France) with controlled attenuation parameter (CAP) was used to non-invasively quantify hepatic fat contents...
January 2017: Journal of Korean Medical Science
https://www.readbyqxmd.com/read/27914128/seroprevalence-of-severe-fever-with-thrombocytopenia-syndrome-in-southeastern-korea-2015
#12
Kye Hyung Kim, Mee Kyung Ko, Namhee Kim, Hyung Hoi Kim, Jongyoun Yi
Severe fever with thrombocytopenia syndrome (SFTS) is an emerging tick-borne disease characterized by fever, thrombocytopenia and diarrhea. SFTS was firstly reported in Korea in 2013 but its seroprevalence in the country has yet to be investigated. Here, we investigate the seroprevalence of SFTS in a Korean population. A cross-sectional study was conducted on patients who had their sera tested for various reasons at a tertiary university hospital on particular days in May 2015. This study was conducted in a tertiary hospital in southeastern Korea...
January 2017: Journal of Korean Medical Science
https://www.readbyqxmd.com/read/27914120/effect-of-glycosylation-on-the-biocatalytic-properties-of-hydroxynitrile-lyase-from-the-passion-fruit-passiflora-edulis-a-comparison-of-natural-and-recombinant-enzymes
#13
Aem Nuylert, Yuko Ishida, Yasuhisa Asano
A hydroxynitrile lyase from the passion fruit, Passiflora edulis (PeHNL) was isolated from the leaves and showed high stability in biphasic co-organic solvent systems for cyanohydrin synthesis. Cyanohydrins are important building blocks for the production of fine chemicals and pharmaceuticals. Thus, to enhance production yields of PeHNL for industrial applications, we cloned and expressed recombinant PeHNL in E. coli BL21 (DE3) and P. pastoris GS115 cells without a signal peptide sequence. The aim of the present study is to determine the effect of N-glycosylation on enzyme stability and catalytic properties in microbial expression systems...
December 3, 2016: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/27914091/toward-clinical-use-of-the-igg-specific-enzymes-ides-and-endos-against-antibody-mediated-diseases
#14
Mattias Collin, Lars Björck
The endoglycosidase EndoS and the protease IdeS from the human pathogen Streptococcus pyogenes are immunomodulating enzymes hydrolyzing human IgG. IdeS cleaves IgG in the lower hinge region, while EndoS hydrolyzes the conserved N-linked glycan in the Fc region. Both enzymes are remarkably specific for human IgG that after hydrolysis loses most of its effector functions, such as binding to leukocytes and complement activation, all contributing to bacterial evasion of adaptive immunity. However, taken out of their infectious context, we and others have shown that IdeS and EndoS can alleviate autoimmune disease in a number of animal models of antibody-mediated disorders...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914090/measuring-antibody-orientation-at-the-bacterial-surface
#15
Oonagh Shannon, Pontus Nordenfelt
Many bacteria have the ability to interact with antibodies as a means to circumvent the immune response. This includes binding to the Fc portion of antibodies, effectively reversing the antibody orientation and thus decreasing the Fc-mediated immune signaling. Since antibody orientation at the bacterial surface has been shown to be important in human disease, it is valuable to be able to assess how antibodies are interacting with bacterial pathogens. Here, we describe a method to measure the proportion of human IgG that are bound via their Fc or Fabs to a bacterial surface...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914089/generating-and-purifying-fab-fragments-from-human-and-mouse-igg-using-the-bacterial-enzymes-ides-speb-and-kgp
#16
Jonathan Sjögren, Linda Andersson, Malin Mejàre, Fredrik Olsson
Fab fragments are valuable research tools in various areas of science including applications in imaging, binding studies, removal of Fc-mediated effector functions, mass spectrometry, infection biology, and many others. The enzymatic tools for the generation of Fab fragments have been discovered through basic research within the field of molecular bacterial pathogenesis. Today, these enzymes are widely applied as research tools and in this chapter, we describe methodologies based on bacterial enzymes to generate Fab fragments from both human and mouse IgG...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914058/osprey-predicts-resistance-mutations-using-positive-and-negative-computational-protein-design
#17
Adegoke Ojewole, Anna Lowegard, Pablo Gainza, Stephanie M Reeve, Ivelin Georgiev, Amy C Anderson, Bruce R Donald
Drug resistance in protein targets is an increasingly common phenomenon that reduces the efficacy of both existing and new antibiotics. However, knowledge of future resistance mutations during pre-clinical phases of drug development would enable the design of novel antibiotics that are robust against not only known resistant mutants, but also against those that have not yet been clinically observed. Computational structure-based protein design (CSPD) is a transformative field that enables the prediction of protein sequences with desired biochemical properties such as binding affinity and specificity to a target...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914045/achievements-and-challenges-in-computational-protein-design
#18
Ilan Samish
Computational protein design (CPD), a yet evolving field, includes computer-aided engineering for partial or full de novo designs of proteins of interest. Designs are defined by a requested structure, function, or working environment. This chapter describes the birth and maturation of the field by presenting 101 CPD examples in a chronological order emphasizing achievements and pending challenges. Integrating these aspects presents the plethora of CPD approaches with the hope of providing a "CPD 101". These reflect on the broader structural bioinformatics and computational biophysics field and include: (1) integration of knowledge-based and energy-based methods, (2) hierarchical designated approach towards local, regional, and global motifs and the integration of high- and low-resolution design schemes that fit each such region, (3) systematic differential approaches towards different protein regions, (4) identification of key hot-spot residues and the relative effect of remote regions, (5) assessment of shape-complementarity, electrostatics and solvation effects, (6) integration of thermal plasticity and functional dynamics, (7) negative design, (8) systematic integration of experimental approaches, (9) objective cross-assessment of methods, and (10) successful ranking of potential designs...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914022/alkaline-protease-production-from-brevibacterium-luteolum-mtcc-5982-under-solid-state-fermentation-and-its-application-for-sulfide-free-unhairing-of-cowhides
#19
R Renganath Rao, M Vimudha, N R Kamini, M K Gowthaman, B Chandrasekran, P Saravanan
Enzyme-based unhairing in replacement of conventional lime sulfide system has been attempted as an alternative for tackling pollution. The exorbitant cost of enzyme and the need for stringent process control need to be addressed yet. This study developed a mechanism for regulated release of protease from cheaper agro-wastes, which overcomes the necessity for stringent process control along with total cost reduction. The maximum protease activity of 1193.77 U/g was obtained after 96 h of incubation with 15% inoculum of the actinomycete strain Brevibacterium luteolum (MTCC 5982) under solid-state fermentation (SSF)...
December 2, 2016: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/27914020/characterization-of-xylanase-and-cellulase-produced-by-a-newly-isolated-aspergillus-fumigatus-n2-and-its-efficient-saccharification-of-barley-straw
#20
Chaoyang Lin, Zhicheng Shen, Wensheng Qin
Aspergillus fumigatus N2 was isolated from decaying wood. This strain produces extracellular xylanases and cellulases. The highest xylanase (91.9 U/mL) and CMCase (5.61 U/mL) activity was produced when 1% barley straw was used as the carbon source. The optimum pH and temperature for xylanase activity were 6.0 and 65 °C, respectively. CMCase revealed maximum activity at pH 4.0 and in the range of 65 °C. The FPase was optimally active at pH 5.0 and 60 °C. The zymograms produced by the SDS-PAGE resolution of the crude enzymes indicated that multiple enzymes were secreted into the fermentation supernatant...
December 2, 2016: Applied Biochemistry and Biotechnology
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