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https://www.readbyqxmd.com/read/28087697/development-of-high-affinity-and-high-specificity-inhibitors-of-metalloproteinase-14-through-computational-design-and-directed-evolution
#1
Valeria Arkadash, Gal Yosef, Jason Shirian, Itay Cohen, Yuval Horev, Moran Grossman, Irit Sagi, Evette S Radisky, Julia M Shifman, Niv Papo
Degradation of the extracellular matrices in the human body is controlled by matrix metalloproteinases (MMPs), a family of more than 20 homologous enzymes. Imbalance in MMP activity can result in many diseases, such as arthritis, cardiovascular diseases, neurological disorders, fibrosis, and cancers. Thus, MMPs present attractive targets for drug design and have been a focus for inhibitor design for as long as three decades. Yet, to date, all MMP inhibitors have failed in clinical trials because of their broad activity against numerous MMP family members and the serious side effects of the proposed treatment...
January 13, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28087672/elimination-of-sucrose-transport-and-hydrolysis-in-saccharomyces-cerevisiae-a-platform-strain-for-engineering-sucrose-metabolism
#2
Wesley Leoricy Marques, Robert Mans, Eko Roy Marella, Rosa Lorizolla Cordeiro, Marcel van den Broek, Jean-Marc G Daran, Jack T Pronk, Andreas K Gombert, Antonius J A van Maris
Many relevant options to improve efficacy and kinetics of sucrose metabolism in Saccharomyces cerevisiae and, thereby, the economics of sucrose-based processes, remain to be investigated. An essential first step is to identify all native sucrose-hydrolysing enzymes and sucrose transporters in this yeast, including those that can be activated by suppressor mutations in sucrose-negative strains. A strain in which all known sucrose-transporter genes (MAL11, MAL21, MAL31, MPH2, MPH3) were deleted did not grow on sucrose after 2 months of incubation...
January 12, 2017: FEMS Yeast Research
https://www.readbyqxmd.com/read/28087528/engineering-mycobacteria-for-the-production-of-self-assembling-biopolyesters-displaying-mycobacterial-antigens-for-use-as-tuberculosis-vaccine
#3
Jason W Lee, Natalie A Parlane, Bernd H A Rehm, Bryce M Buddle, Axel Heiser
: Tuberculosis (TB) is a disease caused by Mycobacterium tuberculosis or Mycobacterium bovis and still remains one of the world's biggest global health burdens. Recently, engineered polyhydroxyalkanoate (PHA) biobeads produced in both E. coli and Lactococcus lactis displaying mycobacterial antigens were found to induce significant cell mediated immune responses in mice. We observed that such PHA beads contained host cell proteins as impurities which we hypothesized to have the potential to induce immunity...
January 13, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28081182/combination-of-plant-metabolic-modules-yields-synthetic-synergies
#4
Fatemeh Rajabi, Ernst Heene, Jan Maisch, Peter Nick
The great potential of pharmacologically active secondary plant metabolites is often limited by low yield and availability of the producing plant. Chemical synthesis of these complex compounds is often too expensive. Plant cell fermentation offers an alternative strategy to overcome these limitations. However, production in batch cell cultures remains often inefficient. One reason might be the fact that different cell types have to interact for metabolite maturation, which is poorly mimicked in suspension cell lines...
2017: PloS One
https://www.readbyqxmd.com/read/28080037/global-metabolic-engineering-of-glycolytic-pathway-via-multi-copy-integration-in-saccharomyces-cerevisiae
#5
Ryosuke Yamada, Kazuki Wakita, Hiroyasu Ogino
The use of renewable feedstocks for producing biofuels and bio-based chemicals by engineering metabolic pathways of yeast Saccharomyces cerevisiae has recently become an attractive option. Many researchers attempted to increase glucose consumption rate by overexpressing some glycolytic enzymes because most target bio-based chemicals are derived through glycolysis. However these attempts have met with little success. In this study, to create a S. cerevisiae strain with high glucose consumption rate, we used multi-copy integration to develop a global metabolic engineering strategy...
January 12, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28080030/chemoselective-enzymatic-c-h-bond-amination-catalyzed-by-a-cytochrome-p450-containing-an-ir-me-pix-cofactor
#6
Pawel Dydio, Hanna M Key, Hiroki Hayashi, Douglas S Clark, John F Hartwig
Cytochrome P450 enzymes have been engineered to catalyze abiological C-H bond amination reactions, but this abiological process is limited by the low chemoselectivity for the amination of C-H bonds over competing reduction of the substrate to a sulfonamide. Here we report that P450s derived from a thermophilic organism and containing an iridium porphyrin cofactor (Ir(Me)-PIX) in place of the heme catalyze C-H bond amination reactions with high chemoselectivity for intramolecular insertion of the resulting nitrenes into C-H bonds over reduction of the azide to the sulfonamide and with broader substrate scope than that of enzymes containing iron porphyrins...
January 12, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28079986/establishment-of-an-in-vitro-3-d-model-for-cartilage-damage-in-rheumatoid-arthritis-ra
#7
Yvonne Peck, Li Ting Leom, Pei Fen Patricia Low, Dong-An Wang
Rheumatoid arthritis (RA) is a chronic inflammatory disease that leads to progressive joint destruction. To further understand the process of rheumatoid cartilage damage, an in vitro model consisting of an interactive tri-culture of synovial fibroblasts (SFs), LPS-stimulated macrophages and a primary chondrocyte-based tissue engineered construct was established. The tissue engineered construct has a similar composition to human cartilage, which are rich in collagen type II and proteoglycans. Data generated from this model revealed that healthy chondrocytes were activated in the presence of SFs and macrophages...
January 12, 2017: Journal of Tissue Engineering and Regenerative Medicine
https://www.readbyqxmd.com/read/28078904/malonyl-coa-pathway-a-promising-route-for-3-hydroxypropionate-biosynthesis
#8
Changshui Liu, Yamei Ding, Mo Xian, Min Liu, Huizhou Liu, Qingjun Ma, Guang Zhao
3-Hydroxypropionate (3HP) is an attractive platform chemical, serving as a precursor to a variety of commodity chemicals like acrylate and acrylamide, as well as a monomer of a biodegradable plastic. To establish a sustainable way to produce these commercially important chemicals and materials, fermentative production of 3HP is widely investigated in recent years. It is reported that 3HP can be produced from several intermediates, such as glycerol, malonyl-CoA, and β-alanine. Among all these biosynthetic routes, the malonyl-CoA pathway has some distinct advantages, including a broad feedstock spectrum, thermodynamic feasibility, and redox neutrality...
January 12, 2017: Critical Reviews in Biotechnology
https://www.readbyqxmd.com/read/28074318/boosted-large-scale-production-and-purification-of-a-thermostable-archaeal-phosphotriesterase-like-lactonase-for-organophosphate-decontamination
#9
Odile Francesca Restaino, Maria Giovanna Borzacchiello, Ilaria Scognamiglio, Elena Porzio, Giuseppe Manco, Luigi Fedele, Cinzia Donatiello, Mario De Rosa, Chiara Schiraldi
Thermostable phosphotriesterase-like lactonases (PLLs) from extremophile archaea, like SsoPox from Sulfolobus solfataricus, are attractive biotechnological tools with industrial applications as organophosphate decontaminants, but their manufacturing still remains an unresolved issue because of the high costs and the low production yields. In this paper, for the first time, an efficient biotechnological process for the production and purification of a recombinant, engineered PLL, SsoPox W263F, expressed in E...
January 11, 2017: Journal of Industrial Microbiology & Biotechnology
https://www.readbyqxmd.com/read/28074108/cellulolytic-robolector-towards-an-automated-high-throughput-screening-platform-for-recombinant-cellulase-expression
#10
Martina Mühlmann, Martin Kunze, Joaquim Ribeiro, Bertram Geinitz, Christian Lehmann, Ulrich Schwaneberg, Ulrich Commandeur, Jochen Büchs
BACKGROUND: Cellulases are key player in the hydrolyzation of cellulose. Unfortunately, this reaction is slow and a bottleneck in the process chain from biomass to intermediates and biofuels due to low activities of the enzymes. To overcome this draw back, a lot of effort is put into the area of protein engineering, to modify these enzymes by directed evolution or rational design. Huge clone libraries are constructed and have to be screened for improved variants. High-throughput screening is the method of choice to tackle this experimental effort, but up to now only a few process steps are adapted to automated platforms and little attention has been turned to the reproducibility of clone rankings...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/28069495/surface-modification-of-copolymerized-films-from-three-armed-biodegradable-macromers-an-analytical-platform-for-modified-tissue-engineering-scaffolds
#11
Benno M Müller, Rudi Loth, Peter-Georg Hoffmeister, Friederike Zühl, Liv Kalbitzer, Michael C Hacker, Michaela Schulz-Siegmund
: The concept of macromers allows for a broad adjustment of biomaterial properties by macromer chemistry or copolymerization. Copolymerization strategies can also be used to introduce reactive sites for subsequent surface modification. Control over surface features enables adjustment of cellular reactions with regard to site and object of implantation. We designed macromer-derived polymer films which function as non-implantable analytical substrates for the investigation of surface properties of equally composed scaffolds for bone tissue engineering...
January 6, 2017: Acta Biomaterialia
https://www.readbyqxmd.com/read/28068985/enzymatic-process-optimization-for-the-in-vitro-production-of-isoprene-from-mevalonate
#12
Tao Cheng, Hui Liu, Huibin Zou, Ningning Chen, Mengxun Shi, Congxia Xie, Guang Zhao, Mo Xian
BACKGROUND: As an important bulk chemical for synthetic rubber, isoprene can be biosynthesized by robust microbes. But rational engineering and optimization are often demanded to make the in vivo process feasible due to the complexities of cellular metabolism. Alternative synthetic biochemistry strategies are in fast development to produce isoprene or isoprenoids in vitro. RESULTS: This study set up an in vitro enzyme synthetic chemistry process using 5 enzymes in the lower mevalonate pathway to produce isoprene from mevalonate...
January 9, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/28068366/overproduction-of-%C3%AE-lipoic-acid-by-gene-manipulated-escherichia-coli
#13
Yirong Sun, Wenbin Zhang, Jincheng Ma, Hongshen Pang, Haihong Wang
Alpha-lipoic acid (LA) is an important enzyme cofactor widely used by organisms and is also a natural antioxidant for the treatment of pathologies driven by low levels of endogenous antioxidants. In order to establish a safer and more efficient process for LA production, we developed a new biological method for LA synthesis based on the emerging knowledge of lipoic acid biosynthesis. We first cloned the lipD gene, which encodes the lipoyl domain of the E2 subunit of pyruvate dehydrogenase, allowing high levels of LipD production...
2017: PloS One
https://www.readbyqxmd.com/read/28068054/fabrication-of-active-surfaces-with-metastable-microgel-layers-formed-during-breath-figure-templating
#14
Yuchen Zhou, Junjie Huang, Wei Sun, Yuanlai Ju, Pinghui Yang, Lingyun Ding, Zhongren Chen, Julia A Kornfield
Patterned porous surfaces with responsive functionalities are fabricated by a thermo-responsive microgel-assisted breath figure (BF) process. When water droplets submerge into a polystyrene (PS) solution during formation of a porous surface by the bottom-up BF process, poly(N-isopropylacrylamide)-co-acrylic acid (PNIPAm-co-AA) microgels dispersed in the solution spontaneously assemble at the water-organic interfaces like "Pickering emulsions", reinforced by capillary flow. The conformal layer of PNIPAm-co-AA microgels lining the pores appears in images of scanning electron microscope (SEM) either as a smooth surface layer (L) or as an array of dome-like protrusions (D), depending on the conditions at which the sample was dried for SEM...
January 9, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28067774/distal-fes-cluster-coordination-in-nife-hydrogenase-facilitates-intermolecular-electron-transfer
#15
Alexander Petrenko, Matthias Stein
Biohydrogen is a versatile energy carrier for the generation of electric energy from renewable sources. Hydrogenases can be used in enzymatic fuel cells to oxidize dihydrogen. The rate of electron transfer (ET) at the anodic side between the [NiFe]-hydrogenase enzyme distal iron-sulfur cluster and the electrode surface can be described by the Marcus equation. All parameters for the Marcus equation are accessible from Density Functional Theory (DFT) calculations. The distal cubane FeS-cluster has a three-cysteine and one-histidine coordination [Fe₄S₄](His)(Cys)₃ first ligation sphere...
January 5, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28067165/gene-therapy-in-fanconi-anemia-a-matter-of-time-safety-and-gene-transfer-tool-efficiency
#16
Verhoeyen Els, Francisco José Román Rodríguez, François-Loïc Cosset, Camille Lévy, Paula Rio
Fanconi anemia (FA) is a rare genetic syndrome characterized by progressive marrow failure. Gene therapy by infusion of FA-corrected autologous hematopoietic stem cells (HSCs) may offer a potential cure since it is a monogenetic disease with mutations in the FANC genes, coding for DNA repair enzymes (See review[1]). However, the collection of hCD34 +-cells in FA patients implies particular challenges because of the reduced numbers of progenitor cells present in their bone marrow (BM)[2] or mobilized peripheral blood[3-5]...
January 9, 2017: Current Gene Therapy
https://www.readbyqxmd.com/read/28065867/cloning-expression-purification-and-biophysical-analysis-of-two-putative-halogenases-from-the-glycopeptide-a47-934-gene-cluster-of-streptomyces-toyocaensis
#17
Tabata P Cardoso, Larissa A de Sá, Priscila Dos S Bury, Sair M Chavez-Pacheco, Marcio V B Dias
Glycopeptides are an important class of antibiotics used in the treatment of several infections, including those caused by methicillin resistant Staphylococcus aureus. Glycopeptides are biosynthesized by a Non Ribosomal Peptide Synthase (NRPS) and the resulting peptide precursors are decorated by several tailoring enzymes, such as halogenases and glycosyltransferases. These enzymes are important targets of protein engineering to produce new derivatives of known antibiotics. Herein we show the production of two putative halogenases, denominated StaI and StaK, involved in the biosynthesis of the glycopeptide A47,934 in Streptomyces toyocaensis NRRL 15,009...
January 5, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28063825/impact-of-mutations-on-the-higher-order-structure-and-activity-of-a-recombinant-uricase
#18
Flaviu Gruia, Arun Parupudi, Manuel Baca, Chris Ward, Andrew Nyborg, Richard L Remmele, Jared S Bee
This study explores the structural and functional changes associated with a low temperature thermal transition of two engineered bacterial uricase mutants. Uricase has a non-covalent homo-tetrameric structure, with four active sites located at the interface of subunits. Using differential scanning calorimetry, a low temperature transition was identified at 42ºC for mutant A and at 33°C for mutant B. This transition was stabilized by the uricase inhibitor, oxonic acid, suggesting a strong structural relationship to the active site...
January 4, 2017: Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/28063314/construction-of-pah-degrading-mixed-microbial-consortia-by-induced-selection-in-soil
#19
German Zafra, Ángel E Absalón, Miguel Ángel Anducho-Reyes, Francisco J Fernandez, Diana V Cortés-Espinosa
Bioremediation of polycyclic aromatic hydrocarbons (PAHs)-contaminated soils through the biostimulation and bioaugmentation processes can be a strategy for the clean-up of oil spills and environmental accidents. In this work, an induced microbial selection method using PAH-polluted soils was successfully used to construct two microbial consortia exhibiting high degradation levels of low and high molecular weight PAHs. Six fungal and seven bacterial native strains were used to construct mixed consortia with the ability to tolerate high amounts of phenanthrene (Phe), pyrene (Pyr) and benzo(a)pyrene (BaP) and utilize these compounds as a sole carbon source...
December 21, 2016: Chemosphere
https://www.readbyqxmd.com/read/28062043/subangstrom-measurements-of-enzyme-function-using-a-biological-nanopore-sprnt
#20
A H Laszlo, I M Derrrington, J H Gundlach
Nanopores are emerging as new single-molecule tools in the study of enzymes. Based on the progress in nanopore sequencing of DNA, a tool called Single-molecule Picometer Resolution Nanopore Tweezers (SPRNT) was developed to measure the movement of enzymes along DNA in real time. In this new method, an enzyme is loaded onto a DNA (or RNA) molecule. A single-stranded DNA end of this complex is drawn into a nanopore by an electrostatic potential that is applied across the pore. The single-stranded DNA passes through the pore's constriction until the enzyme comes into contact with the pore...
2017: Methods in Enzymology
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